| rnase h2 roles in genome integrity revealed by unlinking its activities. | ribonuclease h2 (rnase h2) protects genome integrity by its dual roles of resolving transcription-related r-loops and ribonucleotides incorporated in dna during replication. to unlink these two functions, we generated a saccharomyces cerevisiae rnase h2 mutant that can resolve r-loops but cannot cleave single ribonucleotides in dna. this mutant definitively correlates the 2-5 bp deletions observed in rnh201δ strains with single rnmps in dna. it also establishes a connection between r-loops and s ... | 2013 | 23355612 |
| molecular paleontology: a biochemical model of the ancestral ribosome. | ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro and in vivo. the resulting model of the ancestral ribosome presented here incorporates ∼20% of the extant 23s rrna and fragments of five ribosomal proteins. we test hypotheses that ancestral rrna can: (i) assume canonical 23s rrna-like secondary structure, (ii) assume canonical tertiary structure and (iii) form native complexes with ribosomal protein fragments. footprinting experi ... | 2013 | 23355613 |
| systematic functional comparative analysis of four single-stranded dna-binding proteins and their affection on viral rna metabolism. | the accumulation of single-stranded dna-binding (ssb) proteins is essential for organisms and has various applications. however, no study has simultaneously and systematically compared the characteristics of ssb proteins. in addition, ssb proteins may bind rna and play an unknown biological role in rna metabolism. here, we expressed a novel species of ssb protein derived from thermococcus kodakarensis kod1 (kod), as well as ssb proteins from thermus thermophilus (tth), escherichia coli, and sulf ... | 2013 | 23365690 |
| propylisopropylacetic acid (pia), a constitutional isomer of valproic acid, uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: a potential drug for bipolar disorder. | mood stabilizers used for treating bipolar disorder (bd) selectively downregulate arachidonic acid (aa) turnover (deacylation-reacylation) in brain phospholipids, when given chronically to rats. in vitro studies suggest that one of these, valproic acid (vpa), which is teratogenic, reduces aa turnover by inhibiting the brain long-chain acyl-coa synthetase (acsl)4 mediated acylation of aa to aa-coa. we tested whether non-teratogenic vpa analogues might also inhibit acsl4 catalyzed acylation, and t ... | 2013 | 23354024 |
| the molecular mechanism of hsp100 chaperone inhibition by the prion curing agent guanidinium chloride. | the hsp100 chaperones clpb and hsp104 utilize the energy from atp hydrolysis to reactivate aggregated proteins in concert with the dnak/hsp70 chaperone system, thereby playing an important role in protein quality control. they belong to the family of aaa+ proteins (atpases associated with various cellular activities), possess two nucleotide binding domains per monomer (nbd1 and nbd2), and oligomerize into hexameric ring complexes. furthermore, hsp104 is involved in yeast prion propagation and in ... | 2013 | 23341453 |
| distinct conformation of atp molecule in solution and on protein. | adenosine triphosphate (atp) is a versatile molecule used mainly for energy and a phosphate source. the hydrolysis of γ phosphate initiates the reactions and these reactions almost always start when atp binds to protein. therefore, there should be a mechanism to prevent spontaneous hydrolysis reaction and a mechanism to lead atp to a pure energy source or to a phosphate source. to address these questions, we extensively analyzed the effect of protein to atp conformation based on the sampling of ... | 2013 | 27493535 |
| investigation of stable and transient protein-protein interactions: past, present, and future. | this article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (ppis) with a focus on their function within cells, organs, and organisms. the significance of ptms within the ppis is also discussed. we focus on methods to study ppis and methods of detecting ppis, with particular emphasis on electrophoresis-based and ms-based investigation of ppis, including specific examples. the validation of ppis is emphas ... | 2013 | 23193082 |
| in vitro reconstitution of cascade-mediated crispr immunity in streptococcus thermophilus. | clustered regularly interspaced short palindromic repeats (crispr)-encoded immunity in type i systems relies on the cascade (crispr-associated complex for antiviral defence) ribonucleoprotein complex, which triggers foreign dna degradation by an accessory cas3 protein. to establish the mechanism for adaptive immunity provided by the streptococcus thermophilus crispr4-cas (crispr-associated) system (st-crispr4-cas), we isolated an effector complex (st-cascade) containing 61-nucleotide crispr rna ... | 2013 | 23334296 |
| regulation of argonaute slicer activity by guide rna 3' end interactions with the n-terminal lobe. | structural studies indicate that binding of both the guide rna (sirna and mirna) and the target mrna trigger substantial conformational changes in the argonaute proteins. here we explore the role of the n-terminal lobe (and its paz domain) in these conformational changes using biochemical and cell culture-based approaches. in vitro, whereas deletion (or mutation) of the n-terminal lobe of dmago1 and dmago2 had no effect on binding affinity to guide rnas, we observed a loss of protection of the 3 ... | 2013 | 23329841 |
| deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid alvinella pompejana identifies the cvp-bias as a robust measure of eukaryotic thermostability. | alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the pacific ocean. living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions, including high temperature and pressure as well as high levels of sulfide and heavy metals. a. pompejana is one of the most thermotolerant metazoans, making this animal a subject of great interest for studies of eukaryotic thermoadaptation. | 2013 | 23324115 |
| snapshots of a protein folding intermediate. | we have investigated the folding dynamics of thermus thermophilus cytochrome c(552) by time-resolved fluorescence energy transfer between the heme and each of seven site-specific fluorescent probes. we have found both an equilibrium unfolding intermediate and a distinct refolding intermediate from kinetics studies. depending on the protein region monitored, we observed either two-state or three-state denaturation transitions. the unfolding intermediate associated with three-state folding exhibit ... | 2013 | 23319660 |
| structural characterization of a mouse ortholog of human neil3 with a marked preference for single-stranded dna. | endonuclease viii-like 3 (neil3) is a dna glycosylase of the base excision repair pathway that protects cells from oxidative dna damage by excising a broad spectrum of cytotoxic and mutagenic base lesions. interestingly, neil3 exhibits an unusual preference for dna with single-stranded regions. here, we report the 2.0 å crystal structure of a neil3 enzyme. although the glycosylase region of mouse neil3 (mmuneil3δ324) exhibits the same overall fold as that of other fpg/nei proteins, it presents d ... | 2013 | 23313161 |
| the remorin c-terminal anchor was shaped by convergent evolution among membrane binding domains. | strem1.3 remorin is a well-established plant raftophilic protein, predominantly associated with sterol- and sphingolipid-rich membrane rafts. we recently identified a c-terminal domain (remca) required and sufficient for strem1.3 anchoring to the plasma membrane. here, we report a search for homologs and analogs of remca domain in publicly available protein sequence and structure databases. we could not identify remca homologous domains outside the remorin family but we identified domains sharin ... | 2013 | 23299327 |
| characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium cupriavidus basilensis b-8. | | 2013 | 23298573 |
| the n termini of a-subunit isoforms are involved in signaling between vacuolar h+-atpase (v-atpase) and cytohesin-2. | previously, we reported an acidification-dependent interaction of the endosomal vacuolar h(+)-atpase (v-atpase) with cytohesin-2, a gdp/gtp exchange factor (gef), suggesting that it functions as a ph-sensing receptor. here, we have studied the molecular mechanism of signaling between the v-atpase, cytohesin-2, and arf gtp-binding proteins. we found that part of the n-terminal cytosolic tail of the v-atpase a2-subunit (a2n), corresponding to its first 17 amino acids (a2n(1-17)), potently modulate ... | 2013 | 23288846 |
| methylerythritol phosphate pathway of isoprenoid biosynthesis. | isoprenoids are a class of natural products with more than 55,000 members. all isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (mep) pathway] and a modified mevalonic acid (mva) pathway. in this review, we summarize mechanistic insights on the mep ... | 2013 | 23746261 |
| coaggregation occurs amongst bacteria within and between biofilms in domestic showerheads. | showerheads support the development of multi-species biofilms that can be unsightly, produce malodor, and may harbor pathogens. the outer-surface spray-plates of many showerheads support visible biofilms that likely contain a mixture of bacteria from freshwater and potentially from human users. coaggregation, a mechanism by which genetically distinct bacteria specifically recognize one another, may contribute to the retention and enrichment of different species within these biofilms. the aim of ... | 2013 | 23194413 |
| lack of discrimination against non-proteinogenic amino acid norvaline by elongation factor tu from escherichia coli. | the gtp-bound form of elongation factor tu (ef-tu) brings aminoacylated trnas (aa-trna) to the a-site of the ribosome. ef-tu binds all cognate elongator aa-trnas with highly similar affinities, and its weaker or tighter binding of misacylated trnas may discourage their participation in translation. norvaline (nva) is a non-proteinogenic amino acid that is activated and transferred to trna(leu) by leucyl-trna synthetase (leurs). no notable accumulation of nva-trna(leu) has been observed in vitro, ... | 2013 | 23750044 |
| rotary atpases: models, machine elements and technical specifications. | rotary atpases are molecular rotary motors involved in biological energy conversion. they either synthesize or hydrolyze the universal biological energy carrier adenosine triphosphate. recent work has elucidated the general architecture and subunit compositions of all three sub-types of rotary atpases. composite models of the intact f-, v- and a-type atpases have been constructed by fitting high-resolution x-ray structures of individual subunits or sub-complexes into low-resolution electron dens ... | 2013 | 23369889 |
| morphological development and cytochrome c oxidase activity in streptomyces lividans are dependent on the action of a copper bound sco protein. | copper has an important role in the life cycle of many streptomycetes, stimulating the developmental switch between vegetative mycelium and aerial hyphae concomitant with the production of antibiotics. in streptomycetes, a gene encoding for a putative sco-like protein has been identified and is part of an operon that contains two other genes predicted to handle cellular copper. we report on the sco-like protein from streptomyces lividans (sco(sl)) and present a series of experiments that firmly ... | 2013 | 23345541 |
| dna repair by reversal of dna damage. | endogenous and exogenous factors constantly challenge cellular dna, generating cytotoxic and/or mutagenic dna adducts. as a result, organisms have evolved different mechanisms to defend against the deleterious effects of dna damage. among these diverse repair pathways, direct dna-repair systems provide cells with simple yet efficient solutions to reverse covalent dna adducts. in this review, we focus on recent advances in the field of direct dna repair, namely, photolyase-, alkyltransferase-, an ... | 2013 | 23284047 |
| a structural basis for streptomycin-induced misreading of the genetic code. | during protein synthesis, the ribosome selects aminoacyl-transfer rnas with anticodons matching the messenger rna codon present in the a site of the small ribosomal subunit. the aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. here we use x-ray crystallography to define the impact of streptomycin on the decoding site of the thermus thermophilus 30s ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogues ... | 2013 | 23322043 |
| a mutation of the rna polymerase β' subunit (rpoc) confers cephalosporin resistance in bacillus subtilis. | in bacteria, mutations affecting the major catalytic subunits of rna polymerase (encoded by rpob and rpoc) emerge in response to a variety of selective pressures. here we isolated a bacillus subtilis strain with high-level resistance to cefuroxime (cef). whole-genome resequencing revealed only one missense mutation affecting an invariant residue in close proximity to the c-terminal dna-binding domain of rpoc (g1122d). genetic reconstruction experiments demonstrate that this substitution is suffi ... | 2013 | 23070162 |
| characterization of recombinant fluoroquinolone-resistant pneumococcus-like isolates. | fourteen fluoroquinolone-resistant streptococcal isolates with recombinant dna topoisomerase genes, preliminarily identified as pneumococci, were further characterized using phenotypic and genotypic approaches. phenotypic tests classified them as atypical pneumococci. phylogenetic relationships were analyzed by using the sequences of seven housekeeping alleles from these isolates and from isolates of streptococcus pneumoniae, streptococcus mitis, streptococcus oralis, and streptococcus pseudopne ... | 2013 | 23114769 |
| convergent evolution of aua decoding in bacteria and archaea. | deciphering aua codons is a difficult task for organisms, because aua and aug specify isoleucine (ile) and methionine (met), separately. each of the other purine-ending sense co-don sets (nnr) specifies a single amino acid in the universal genetic code. in bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (l or lysidine) and 2-agmatinylcytidine (agm(2)c or agmatidine), respectively, are found at the first letter of the anticodon of trna(ile) responsible for aua codons. these modifi ... | 2014 | 25629511 |
| convergent evolution of aua decoding in bacteria and archaea. | deciphering aua codons is a difficult task for organisms, because aua and aug specify isoleucine (ile) and methionine (met), separately. each of the other purine-ending sense co-don sets (nnr) specifies a single amino acid in the universal genetic code. in bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (l or lysidine) and 2-agmatinylcytidine (agm(2)c or agmatidine), respectively, are found at the first letter of the anticodon of trna(ile) responsible for aua codons. these modifi ... | 2014 | 25629511 |
| two-subunit enzymes involved in eukaryotic post-transcriptional trna modification. | trna modifications are crucial for efficient and accurate protein translation, with defects often linked to disease. there are 7 cytoplasmic trna modifications in the yeast saccharomyces cerevisiae that are formed by an enzyme consisting of a catalytic subunit and an auxiliary protein, 5 of which require only a single subunit in bacteria, and 2 of which are not found in bacteria. these enzymes include the deaminase tad2-tad3, and the methyltransferases trm6-trm61, trm8-trm82, trm7-trm732, and tr ... | 2014 | 25625329 |
| two-subunit enzymes involved in eukaryotic post-transcriptional trna modification. | trna modifications are crucial for efficient and accurate protein translation, with defects often linked to disease. there are 7 cytoplasmic trna modifications in the yeast saccharomyces cerevisiae that are formed by an enzyme consisting of a catalytic subunit and an auxiliary protein, 5 of which require only a single subunit in bacteria, and 2 of which are not found in bacteria. these enzymes include the deaminase tad2-tad3, and the methyltransferases trm6-trm61, trm8-trm82, trm7-trm732, and tr ... | 2014 | 25625329 |
| the identification and characterization of non-coding and coding rnas and their modified nucleosides by mass spectrometry. | the analysis of ribonucleic acids (rna) by mass spectrometry has been a valuable analytical approach for more than 25 years. in fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from rna isolated out of biological samples. this review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. applications of mass spectrometry in the identification, characterization and quantification of modified nucleo ... | 2014 | 25616408 |
| the identification and characterization of non-coding and coding rnas and their modified nucleosides by mass spectrometry. | the analysis of ribonucleic acids (rna) by mass spectrometry has been a valuable analytical approach for more than 25 years. in fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from rna isolated out of biological samples. this review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. applications of mass spectrometry in the identification, characterization and quantification of modified nucleo ... | 2014 | 25616408 |
| pseudomonas aeruginosa isolates from dental unit waterlines can be divided in two distinct groups, including one displaying phenotypes similar to isolates from cystic fibrosis patients. | pseudomonas aeruginosa displays broad genetic diversity, giving it an astonishing capacity to adapt to a variety of environments and to infect a wide range of hosts. while many p. aeruginosa isolates of various origins have been analyzed, isolates from cystic fibrosis (cf) patients have received the most attention. less is known about the genetic and phenotypic diversity of p. aeruginosa isolates that colonize other environments where flourishing biofilms can be found. in the present study, 29 p ... | 2014 | 25653647 |
| pseudomonas aeruginosa isolates from dental unit waterlines can be divided in two distinct groups, including one displaying phenotypes similar to isolates from cystic fibrosis patients. | pseudomonas aeruginosa displays broad genetic diversity, giving it an astonishing capacity to adapt to a variety of environments and to infect a wide range of hosts. while many p. aeruginosa isolates of various origins have been analyzed, isolates from cystic fibrosis (cf) patients have received the most attention. less is known about the genetic and phenotypic diversity of p. aeruginosa isolates that colonize other environments where flourishing biofilms can be found. in the present study, 29 p ... | 2014 | 25653647 |
| an mrps12 mutation modifies aminoglycoside sensitivity caused by 12s rrna mutations. | several homoplasmic pathologic mutations in mitochondrial dna, such as those causing leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. therefore, other elements must modify their pathogenicity. discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasm ... | 2014 | 25642242 |
| an mrps12 mutation modifies aminoglycoside sensitivity caused by 12s rrna mutations. | several homoplasmic pathologic mutations in mitochondrial dna, such as those causing leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. therefore, other elements must modify their pathogenicity. discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasm ... | 2014 | 25642242 |
| trigger loop folding determines transcription rate of escherichia coli's rna polymerase. | two components of the rna polymerase (rnap) catalytic center, the bridge helix and the trigger loop (tl), have been linked with changes in elongation rate and pausing. here, single molecule experiments with the wt and two tl-tip mutants of the escherichia coli enzyme reveal that tip mutations modulate rnap's pause-free velocity, identifying tl conformational changes as one of two rate-determining steps in elongation. consistent with this observation, we find a direct correlation between helix pr ... | 2014 | 25552559 |
| trigger loop folding determines transcription rate of escherichia coli's rna polymerase. | two components of the rna polymerase (rnap) catalytic center, the bridge helix and the trigger loop (tl), have been linked with changes in elongation rate and pausing. here, single molecule experiments with the wt and two tl-tip mutants of the escherichia coli enzyme reveal that tip mutations modulate rnap's pause-free velocity, identifying tl conformational changes as one of two rate-determining steps in elongation. consistent with this observation, we find a direct correlation between helix pr ... | 2014 | 25552559 |
| a structural determinant in the uracil dna glycosylase superfamily for the removal of uracil from adenine/uracil base pairs. | the uracil dna glycosylase superfamily consists of several distinct families. family 2 mismatch-specific uracil dna glycosylase (mug) from escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, t/u, g/u and c/u. family 1 uracil n-glycosylase (ung) from e. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the a/u base pair. here, we report the identification of an important structural determinant that un ... | 2014 | 25550433 |
| a structural determinant in the uracil dna glycosylase superfamily for the removal of uracil from adenine/uracil base pairs. | the uracil dna glycosylase superfamily consists of several distinct families. family 2 mismatch-specific uracil dna glycosylase (mug) from escherichia coli is known to exhibit glycosylase activity on three mismatched base pairs, t/u, g/u and c/u. family 1 uracil n-glycosylase (ung) from e. coli is an extremely efficient enzyme that can remove uracil from any uracil-containing base pairs including the a/u base pair. here, we report the identification of an important structural determinant that un ... | 2014 | 25550433 |
| structure of the pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial trna-dependent asparagine biosynthesis. | many prokaryotes lack a trna synthetase to attach asparagine to its cognate trna(asn), and instead synthesize asparagine from trna(asn)-bound aspartate. this conversion involves two enzymes: a nondiscriminating aspartyl-trna synthetase (nd-asprs) that forms asp-trna(asn), and a heterotrimeric amidotransferase gatcab that amidates asp-trna(asn) to form asn-trna(asn) for use in protein synthesis. nd-asprs, gatcab, and trna(asn) may assemble in an ∼400-kda complex, known as the asn-transamidosome, ... | 2014 | 25548166 |
| structure of the pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial trna-dependent asparagine biosynthesis. | many prokaryotes lack a trna synthetase to attach asparagine to its cognate trna(asn), and instead synthesize asparagine from trna(asn)-bound aspartate. this conversion involves two enzymes: a nondiscriminating aspartyl-trna synthetase (nd-asprs) that forms asp-trna(asn), and a heterotrimeric amidotransferase gatcab that amidates asp-trna(asn) to form asn-trna(asn) for use in protein synthesis. nd-asprs, gatcab, and trna(asn) may assemble in an ∼400-kda complex, known as the asn-transamidosome, ... | 2014 | 25548166 |
| conformational preferences underlying reduced activity of a thermophilic ribonuclease h. | the conformational basis for reduced activity of the thermophilic ribonuclease hi enzyme from thermus thermophilus, compared to its mesophilic homolog from escherichia coli, is elucidated using a combination of nmr spectroscopy and molecular dynamics (md) simulations. explicit-solvent all-atom md simulations of the two wild-type proteins and an e. coli mutant in which a glycine residue is inserted after position 80 to mimic the t. thermophilus protein reproduce the differences in conformational ... | 2014 | 25550198 |
| conformational preferences underlying reduced activity of a thermophilic ribonuclease h. | the conformational basis for reduced activity of the thermophilic ribonuclease hi enzyme from thermus thermophilus, compared to its mesophilic homolog from escherichia coli, is elucidated using a combination of nmr spectroscopy and molecular dynamics (md) simulations. explicit-solvent all-atom md simulations of the two wild-type proteins and an e. coli mutant in which a glycine residue is inserted after position 80 to mimic the t. thermophilus protein reproduce the differences in conformational ... | 2014 | 25550198 |
| crystal structure of thermobifida fusca cse1 reveals target dna binding site. | the clustered regularly interspaced short palindromic repeats (crispr)-crispr-associated (cas) defense system is the only adaptive and inheritable immunity found in prokaryotes. the immunity is achieved through a multistep process of adaptation, expression, and interference. in the type i-e system, interference is mediated by the crispr-associated complex for antiviral defense (cascade), which recognizes invading double-stranded dna (dsdna) through the protospacer adjacent motif (pam) by one of ... | 2014 | 25420472 |
| crystal structure of thermobifida fusca cse1 reveals target dna binding site. | the clustered regularly interspaced short palindromic repeats (crispr)-crispr-associated (cas) defense system is the only adaptive and inheritable immunity found in prokaryotes. the immunity is achieved through a multistep process of adaptation, expression, and interference. in the type i-e system, interference is mediated by the crispr-associated complex for antiviral defense (cascade), which recognizes invading double-stranded dna (dsdna) through the protospacer adjacent motif (pam) by one of ... | 2014 | 25420472 |
| trnas as antibiotic targets. | transfer rnas (trnas) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. this review focuses on the role of trnas in bacterial antibiosis. we will discuss examples of antibiotics that target multiple stages in trna biology from trna biogenesis and modification, mature trnas, aminoacylation of trna as well as prevention of proper trna function by small molecules binding to the ribosome. finally, the r ... | 2014 | 25547494 |
| trnas as antibiotic targets. | transfer rnas (trnas) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. this review focuses on the role of trnas in bacterial antibiosis. we will discuss examples of antibiotics that target multiple stages in trna biology from trna biogenesis and modification, mature trnas, aminoacylation of trna as well as prevention of proper trna function by small molecules binding to the ribosome. finally, the r ... | 2014 | 25547494 |
| cmr4 is the slicer in the rna-targeting cmr crispr complex. | clustered regularly interspaced short palindromic repeat (crispr) loci and crispr-associated (cas) proteins form an adaptive immune system that protects prokaryotes against plasmids and viruses. the cmr complex, a type iii-b effector complex, uses the crispr rna (crrna) as a guide to target rna. here, we show that the cmr complex of pyrococcus furiosus cleaves rna at multiple sites that are 6 nt apart and are positioned relative to the 5'-end of the crrna. we identified cmr4 as the slicer and de ... | 2014 | 25541196 |
| cmr4 is the slicer in the rna-targeting cmr crispr complex. | clustered regularly interspaced short palindromic repeat (crispr) loci and crispr-associated (cas) proteins form an adaptive immune system that protects prokaryotes against plasmids and viruses. the cmr complex, a type iii-b effector complex, uses the crispr rna (crrna) as a guide to target rna. here, we show that the cmr complex of pyrococcus furiosus cleaves rna at multiple sites that are 6 nt apart and are positioned relative to the 5'-end of the crrna. we identified cmr4 as the slicer and de ... | 2014 | 25541196 |
| transfer rna methyltransferases from thermoplasma acidophilum, a thermoacidophilic archaeon. | we investigated trna methyltransferase activities in crude cell extracts from the thermoacidophilic archaeon thermoplasma acidophilum. we analyzed the modified nucleosides in native initiator and elongator trnamet, predicted the candidate genes for the trna methyltransferases on the basis of the trnamet and trnaleu sequences, and characterized trm5, trm1 and trm56 by purifying recombinant proteins. we found that the ta0997, ta0931, and ta0836 genes of t. acidophilum encode trm1, trm56 and trm5, ... | 2014 | 25546389 |
| transfer rna methyltransferases from thermoplasma acidophilum, a thermoacidophilic archaeon. | we investigated trna methyltransferase activities in crude cell extracts from the thermoacidophilic archaeon thermoplasma acidophilum. we analyzed the modified nucleosides in native initiator and elongator trnamet, predicted the candidate genes for the trna methyltransferases on the basis of the trnamet and trnaleu sequences, and characterized trm5, trm1 and trm56 by purifying recombinant proteins. we found that the ta0997, ta0931, and ta0836 genes of t. acidophilum encode trm1, trm56 and trm5, ... | 2014 | 25546389 |
| a novel cytosolic nadh:quinone oxidoreductase from methanothermobacter marburgensis. | methanothermobacter marburgensis is a strictly anaerobic, thermophilic methanogenic archaeon that uses methanogenesis to convert h2 and co2 to energy. m. marburgensis is one of the best-studied methanogens, and all genes required for methanogenic metabolism have been identified. nonetheless, the present study describes a gene (gene id 9704440) coding for a putative | 2014 | 25372605 |
| ttomp85, a β-barrel assembly protein, functions by barrel augmentation. | outer membrane proteins are vital for gram-negative bacteria and organisms that inherited organelles from them. proteins from the omp85/bama family conduct the insertion of membrane proteins into the outer membrane. we show that an eight-stranded outer membrane β-barrel protein, ttoa, is inserted and folded into liposomes by an omp85 homologue. furthermore, we recorded the channel conductance of this omp85 protein in black lipid membranes, alone and in the presence of peptides comprising the seq ... | 2014 | 25537637 |
| ttomp85, a β-barrel assembly protein, functions by barrel augmentation. | outer membrane proteins are vital for gram-negative bacteria and organisms that inherited organelles from them. proteins from the omp85/bama family conduct the insertion of membrane proteins into the outer membrane. we show that an eight-stranded outer membrane β-barrel protein, ttoa, is inserted and folded into liposomes by an omp85 homologue. furthermore, we recorded the channel conductance of this omp85 protein in black lipid membranes, alone and in the presence of peptides comprising the seq ... | 2014 | 25537637 |
| enhancing allosteric inhibition in thermus thermophilus phosphofructokinase. | the coupling between the binding of the substrate fru-6-p and the inhibitor phospho(enol)pyruvate (pep) in phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus is much weaker than that seen in a pfk from bacillus stearothermophilus. from the crystal structures of bacillus stearothermophilus pfk (bspfk) the residues at positions 59, 158, and 215 in bspfk are located on the path leading from the allosteric site to the nearest active site and are part of the intricate hydroge ... | 2014 | 25531642 |
| enhancing allosteric inhibition in thermus thermophilus phosphofructokinase. | the coupling between the binding of the substrate fru-6-p and the inhibitor phospho(enol)pyruvate (pep) in phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus is much weaker than that seen in a pfk from bacillus stearothermophilus. from the crystal structures of bacillus stearothermophilus pfk (bspfk) the residues at positions 59, 158, and 215 in bspfk are located on the path leading from the allosteric site to the nearest active site and are part of the intricate hydroge ... | 2014 | 25531642 |
| the bacterial flagellar protein export apparatus processively transports flagellar proteins even with extremely infrequent atp hydrolysis. | for self-assembly of the bacterial flagellum, a specific protein export apparatus utilizes atp and proton motive force (pmf) as the energy source to transport component proteins to the distal growing end. the export apparatus consists of a transmembrane pmf-driven export gate and a cytoplasmic atpase complex composed of flih, flii and flij. the flii(6)flij complex is structurally similar to the α(3)β(3)γ complex of f(o)f(1)-atpase. flij allows the gate to efficiently utilize pmf to drive flagell ... | 2014 | 25531309 |
| molecular details of a starch utilization pathway in the human gut symbiont eubacterium rectale. | eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. starch is one of the most abundant glycans in the human diet, and e. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. here we present the results of a quantitative proteomics study in which we identify two glycoside hydr ... | 2014 | 25388295 |
| molecular details of a starch utilization pathway in the human gut symbiont eubacterium rectale. | eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. starch is one of the most abundant glycans in the human diet, and e. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. here we present the results of a quantitative proteomics study in which we identify two glycoside hydr ... | 2014 | 25388295 |
| evolution of oligomeric state through allosteric pathways that mimic ligand binding. | evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. we showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. in this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the pyrr family of pyrimidine operon attenuators. in this family, a perfectly s ... | 2014 | 25525255 |
| metatranscriptomics of n2-fixing cyanobacteria in the amazon river plume. | biological n2 fixation is an important nitrogen source for surface ocean microbial communities. however, nearly all information on the diversity and gene expression of organisms responsible for oceanic n2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from ... | 2014 | 25514535 |
| metatranscriptomics of n2-fixing cyanobacteria in the amazon river plume. | biological n2 fixation is an important nitrogen source for surface ocean microbial communities. however, nearly all information on the diversity and gene expression of organisms responsible for oceanic n2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from ... | 2014 | 25514535 |
| structural basis for the interaction of protein s1 with the escherichia coli ribosome. | in gram-negative bacteria, the multi-domain protein s1 is essential for translation initiation, as it recruits the mrna and facilitates its localization in the decoding centre. in sharp contrast to its functional importance, s1 is still lacking from the high-resolution structures available for escherichia coli and thermus thermophilus ribosomes and thus the molecular mechanism governing the s1-ribosome interaction has still remained elusive. here, we present the structure of the n-terminal s1 do ... | 2014 | 25510494 |
| structural basis for the interaction of protein s1 with the escherichia coli ribosome. | in gram-negative bacteria, the multi-domain protein s1 is essential for translation initiation, as it recruits the mrna and facilitates its localization in the decoding centre. in sharp contrast to its functional importance, s1 is still lacking from the high-resolution structures available for escherichia coli and thermus thermophilus ribosomes and thus the molecular mechanism governing the s1-ribosome interaction has still remained elusive. here, we present the structure of the n-terminal s1 do ... | 2014 | 25510494 |
| crystal structure of subunits d and f in complex gives insight into energy transmission of the eukaryotic v-atpase from saccharomyces cerevisiae. | eukaryotic v1vo-atpases hydrolyze atp in the v1 domain coupled to ion pumping in vo. a unique mode of regulation of v-atpases is the reversible disassembly of v1 and vo, which reduces atpase activity and causes silencing of ion conduction. the subunits d and f are proposed to be key in these enzymatic processes. here, we describe the structures of two conformations of the subunit df assembly of saccharomyces cerevisiae (scdf) v-atpase at 3.1 å resolution. subunit d (scd) consists of a long pair ... | 2014 | 25505269 |
| crystal structure of subunits d and f in complex gives insight into energy transmission of the eukaryotic v-atpase from saccharomyces cerevisiae. | eukaryotic v1vo-atpases hydrolyze atp in the v1 domain coupled to ion pumping in vo. a unique mode of regulation of v-atpases is the reversible disassembly of v1 and vo, which reduces atpase activity and causes silencing of ion conduction. the subunits d and f are proposed to be key in these enzymatic processes. here, we describe the structures of two conformations of the subunit df assembly of saccharomyces cerevisiae (scdf) v-atpase at 3.1 å resolution. subunit d (scd) consists of a long pair ... | 2014 | 25505269 |
| thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from geobacillus kaustophilus hta426. | thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. in this study, we constructed an error-prone strain of the thermophile geobacillus kaustophilus hta426 and investigated thermoadaptation-directed enzyme evolution using the strain. a mutation frequency assay using the antibiotics rifampin and streptomycin revealed that g. kaustophilus had substantially higher mutability than escherichia coli and bacill ... | 2014 | 25326311 |
| thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from geobacillus kaustophilus hta426. | thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. in this study, we constructed an error-prone strain of the thermophile geobacillus kaustophilus hta426 and investigated thermoadaptation-directed enzyme evolution using the strain. a mutation frequency assay using the antibiotics rifampin and streptomycin revealed that g. kaustophilus had substantially higher mutability than escherichia coli and bacill ... | 2014 | 25326311 |
| a mechanistic model of cor15 protein function in plant freezing tolerance: integration of structural and functional characteristics. | plants as sessile organisms are strongly challenged by environmental stresses. many plants species are able to cold-acclimate, acquiring higher freezing tolerance upon exposure to low but non-freezing temperatures. among a plethora of adaptational processes, this involves the accumulation of cold regulated (cor) proteins that are assumed to stabilize and protect cellular structures during freezing. however, their molecular functions are largely unknown. we recently reported a comprehensive study ... | 2014 | 25496049 |
| on the validation of crystallographic symmetry and the quality of structures. | in 2008, zwart and colleagues observed that the fraction of the structures deposited in the pdb alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (ncs) was about 6%, and that this percentage was rising annually. a few years later, poon and colleagues found that 2% of all the crystal structures in the pdb belonged to higher symmetry space groups than those assigned to them. here, i report an analysis of the x-ray diffraction data deposited for this class of structures, wh ... | 2014 | 25352397 |
| on the validation of crystallographic symmetry and the quality of structures. | in 2008, zwart and colleagues observed that the fraction of the structures deposited in the pdb alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (ncs) was about 6%, and that this percentage was rising annually. a few years later, poon and colleagues found that 2% of all the crystal structures in the pdb belonged to higher symmetry space groups than those assigned to them. here, i report an analysis of the x-ray diffraction data deposited for this class of structures, wh ... | 2014 | 25352397 |
| first evidence for substrate channeling between proline catabolic enzymes: a validation of domain fusion analysis for predicting protein-protein interactions. | proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate (p5c) dehydrogenase (p5cdh) catalyze the four-electron oxidation of proline to glutamate via the intermediates p5c and l-glutamate-γ-semialdehyde (gsa). in gram-negative bacteria, prodh and p5cdh are fused together in the bifunctional enzyme proline utilization a (puta) whereas in other organisms prodh and p5cdh are expressed as separate monofunctional enzymes. substrate channeling has previously been shown for bifunctional putas, bu ... | 2014 | 25492892 |
| first evidence for substrate channeling between proline catabolic enzymes: a validation of domain fusion analysis for predicting protein-protein interactions. | proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate (p5c) dehydrogenase (p5cdh) catalyze the four-electron oxidation of proline to glutamate via the intermediates p5c and l-glutamate-γ-semialdehyde (gsa). in gram-negative bacteria, prodh and p5cdh are fused together in the bifunctional enzyme proline utilization a (puta) whereas in other organisms prodh and p5cdh are expressed as separate monofunctional enzymes. substrate channeling has previously been shown for bifunctional putas, bu ... | 2014 | 25492892 |
| crispr rna binding and dna target recognition by purified cascade complexes from escherichia coli. | clustered regularly interspaced short palindromic repeats (crisprs) and their associated cas proteins comprise a prokaryotic rna-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. the type i-e crispr interference complex cascade from escherichia coli is composed of five different cas proteins and a 61-nt-long guide rna (crrna). crrnas contain a unique 32-nt spacer flanked by a repeat-derived 5' handle (8 nt) and a 3' handle (21 nt). the space ... | 2014 | 25488810 |
| crispr rna binding and dna target recognition by purified cascade complexes from escherichia coli. | clustered regularly interspaced short palindromic repeats (crisprs) and their associated cas proteins comprise a prokaryotic rna-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. the type i-e crispr interference complex cascade from escherichia coli is composed of five different cas proteins and a 61-nt-long guide rna (crrna). crrnas contain a unique 32-nt spacer flanked by a repeat-derived 5' handle (8 nt) and a 3' handle (21 nt). the space ... | 2014 | 25488810 |
| the biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical s-adenosylmethionine enzymes. | sulfur atoms are present as thiol and thioether functional groups in amino acids, coenzymes, cofactors, and various products of secondary metabolic pathways. the biosynthetic pathways for several sulfur-containing biomolecules require the substitution of sulfur for hydrogen at unreactive aliphatic or electron-rich aromatic carbon atoms. examples discussed in this review include biotin, lipoic acid, methylthioether modifications found in some nucleic acids and proteins, and thioether cross-links ... | 2014 | 25477512 |
| the biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical s-adenosylmethionine enzymes. | sulfur atoms are present as thiol and thioether functional groups in amino acids, coenzymes, cofactors, and various products of secondary metabolic pathways. the biosynthetic pathways for several sulfur-containing biomolecules require the substitution of sulfur for hydrogen at unreactive aliphatic or electron-rich aromatic carbon atoms. examples discussed in this review include biotin, lipoic acid, methylthioether modifications found in some nucleic acids and proteins, and thioether cross-links ... | 2014 | 25477512 |
| fada5 a thiolase from mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. | with the exception of hiv, tuberculosis (tb) is the leading cause of mortality among infectious diseases. the urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant mycobacterium tuberculosis (mtb) strains. proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against tb. fada5, a thiolase from mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation ... | 2014 | 25482540 |
| fada5 a thiolase from mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. | with the exception of hiv, tuberculosis (tb) is the leading cause of mortality among infectious diseases. the urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant mycobacterium tuberculosis (mtb) strains. proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against tb. fada5, a thiolase from mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation ... | 2014 | 25482540 |
| essential structural and functional roles of the cmr4 subunit in rna cleavage by the cmr crispr-cas complex. | the cmr complex is the multisubunit effector complex of the type iii-b clustered regularly interspaced short palindromic repeats (crispr)-cas immune system. the cmr complex recognizes a target rna through base pairing with the integral crispr rna (crrna) and cleaves the target at multiple regularly spaced locations within the complementary region. to understand the molecular basis of the function of this complex, we have assembled information from electron microscopic and x-ray crystallographic ... | 2014 | 25482566 |
| a novel mechanism of protein thermostability: a unique n-terminal domain confers heat resistance to fe/mn-sods. | superoxide dismutases (sods), especially thermostable sods, are widely applied in medical treatments, cosmetics, food, agriculture, and other industries given their excellent antioxidant properties. a novel thermostable cambialistic sod from geobacillus thermodenitrificans ng80-2 exhibits maximum activity at 70 °c and high thermostability over a broad range of temperatures (20-80 °c). unlike other reported sods, this enzyme contains an extra repeat-containing n-terminal domain (ntd) of 244 resid ... | 2014 | 25445927 |
| a new window into the molecular physiology of membrane proteins. | integral membrane proteins comprise ∼25% of the human proteome. yet, our understanding of their molecular physiology is still in its infancy. this can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. new approaches are therefore required to address these challenges. recent developments in mass spectrometry have shown that it is possible to ... | 2014 | 25630257 |
| a new window into the molecular physiology of membrane proteins. | integral membrane proteins comprise ∼25% of the human proteome. yet, our understanding of their molecular physiology is still in its infancy. this can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. new approaches are therefore required to address these challenges. recent developments in mass spectrometry have shown that it is possible to ... | 2014 | 25630257 |
| interface matters: the stiffness route to stability of a thermophilic tetrameric malate dehydrogenase. | in this work we investigate by computational means the behavior of two orthologous bacterial proteins, a mesophilic and a thermophilic tetrameric malate dehydrogenase (maldh), at different temperatures. namely, we quantify how protein mechanical rigidity at different length- and time-scales correlates to protein thermophilicity as commonly believed. in particular by using a clustering analysis strategy to explore the conformational space of the folded proteins, we show that at ambient conditions ... | 2014 | 25437494 |
| substrate-specific development of thermophilic bacterial consortia by using chemically pretreated switchgrass. | microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. we exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (sg) biomass of various compositions. microbial communities were adapted to untreated, ammonium fiber expansion (afex)-pretreated, and ionic-liquid ( ... | 2014 | 25261509 |
| structural insights into translational recoding by frameshift suppressor trnasufj. | the three-nucleotide mrna reading frame is tightly regulated during translation to ensure accurate protein expression. translation errors that lead to aberrant protein production can result from the uncoupled movement of the trna in either the 5' or 3' direction on mrna. here, we report the biochemical and structural characterization of +1 frameshift suppressor trna(sufj), a trna known to decode four, instead of three, nucleotides. frameshift suppressor trna(sufj) contains an insertion 5' to its ... | 2014 | 25352689 |
| protein acetylation affects acetate metabolism, motility and acid stress response in escherichia coli. | although protein acetylation is widely observed, it has been associated with few specific regulatory functions making it poorly understood. to interrogate its functionality, we analyzed the acetylome in escherichia coli knockout mutants of cobb, the only known sirtuin-like deacetylase, and patz, the best-known protein acetyltransferase. for four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins, were identified and differentially quantified. nearly 65% of t ... | 2014 | 25518064 |
| double-sieving-defective aminoacyl-trna synthetase causes protein mistranslation and affects cellular physiology and development. | aminoacyl-trna synthetases (aarss) constitute a family of ubiquitously expressed essential enzymes that ligate amino acids to their cognate trnas for protein synthesis. recently, aars mutations have been linked to various human diseases; however, how these mutations lead to diseases has remained unclear. in order to address the importance of aminoacylation fidelity in multicellular organisms, we generated an amino-acid double-sieving model in drosophila melanogaster using phenylalanyl-trna synth ... | 2014 | 25427601 |
| structure and transport mechanism of the sodium/proton antiporter mjnhap1. | sodium/proton antiporters are essential for sodium and ph homeostasis and play a major role in human health and disease. we determined the structures of the archaeal sodium/proton antiporter mjnhap1 in two complementary states. the inward-open state was obtained by x-ray crystallography in the presence of sodium at ph 8, where the transporter is highly active. the outward-open state was obtained by electron crystallography without sodium at ph 4, where mjnhap1 is inactive. comparison of both str ... | 2014 | 25426803 |
| structure and substrate ion binding in the sodium/proton antiporter panhap. | sodium/proton antiporters maintain intracellular ph and sodium levels. detailed structures of antiporters with bound substrate ions are essential for understanding how they work. we have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter panhap from pyrococcus abyssi at 3.2 å, and have determined its structure in two different conformations at ph 8 and ph 4. the ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in ... | 2014 | 25426802 |
| structural principles of crispr rna processing. | the cas6 superfamily, the cas5d subclass, and the host rnase iii endoribonucleases are responsible for producing small rnas (crrna) that function in the crispr-cas immunity. the three enzymes may also interact with the crrna-associated nucleic acid interference complexes. recent development in structural biology of cas6 and cas5d and their complexes with rna substrates has lent new insights on principles of crrna processing and the structural basis for linking crrna processing to interference. b ... | 2014 | 25435327 |
| structural principles of crispr rna processing. | the cas6 superfamily, the cas5d subclass, and the host rnase iii endoribonucleases are responsible for producing small rnas (crrna) that function in the crispr-cas immunity. the three enzymes may also interact with the crrna-associated nucleic acid interference complexes. recent development in structural biology of cas6 and cas5d and their complexes with rna substrates has lent new insights on principles of crrna processing and the structural basis for linking crrna processing to interference. b ... | 2014 | 25435327 |
| structure of putrescine aminotransferase from escherichia coli provides insights into the substrate specificity among class iii aminotransferases. | ygjg is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5'-phosphate (plp) as a cofactor. previous biochemical data show that the enzyme prefers primary diamines, such as putrescine, over ornithine as a substrate. to better understand the enzyme's substrate specificity, crystal structures of ygjg from escherichia coli were determined at 2.3 and 2.1 å resolutions for the free and putre ... | 2014 | 25423189 |
| tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by nmr, saxs, chemical crosslinking, and functional studies. | proteins containing iron-sulfur (fe-s) clusters arose early in evolution and are essential to life. organisms have evolved machinery consisting of specialized proteins that operate together to assemble fe-s clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. to date, the best studied system is the iron-sulfur cluster (isc) operon of escherichia coli, and the eight isc proteins it encodes. our investigations over the past five years have id ... | 2014 | 25450980 |
| tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by nmr, saxs, chemical crosslinking, and functional studies. | proteins containing iron-sulfur (fe-s) clusters arose early in evolution and are essential to life. organisms have evolved machinery consisting of specialized proteins that operate together to assemble fe-s clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. to date, the best studied system is the iron-sulfur cluster (isc) operon of escherichia coli, and the eight isc proteins it encodes. our investigations over the past five years have id ... | 2014 | 25450980 |
| recq helicase and recj nuclease provide complementary functions to resect dna for homologous recombination. | recombinational dna repair by the recf pathway of escherichia coli requires the coordinated activities of reca, recfor, recq, recj, and single-strand dna binding (ssb) proteins. these proteins facilitate formation of homologously paired joint molecules between linear double-stranded (dsdna) and supercoiled dna. repair starts with resection of the broken dsdna by recq, a 3'→5' helicase, recj, a 5'→3' exonuclease, and ssb protein. the ends of a dsdna break can be blunt-ended, or they may possess e ... | 2014 | 25411316 |
| argonaute piwi domain and microrna duplex structure regulate small rna sorting in arabidopsis. | small rnas (srnas) are loaded into argonaute (ago) proteins to induce gene silencing. in plants, the 5'-terminal nucleotide is important for srna sorting into different agos. here we show that microrna (mirna) duplex structure also contributes to mirna sorting. base pairing at the 15th nucleotide of a mirna duplex is important for mirna sorting in both arabidopsis ago1 and ago2. ago2 favours mirna duplexes with no middle mismatches, whereas ago1 tolerates, or prefers, duplexes with central misma ... | 2014 | 25406978 |
| structural and functional characterization of a ketosteroid transcriptional regulator of mycobacterium tuberculosis. | catabolism of host cholesterol is critical to the virulence of mycobacterium tuberculosis and is a potential target for novel therapeutics. kstr2, a tetr family repressor (tfr), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-h-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (hip). binding of kstr2 to its operator sequences is relieved upon binding of hip-coa. a 1.6-å resolution crystal structure of the ks ... | 2014 | 25406313 |
| structural and functional characterization of a ketosteroid transcriptional regulator of mycobacterium tuberculosis. | catabolism of host cholesterol is critical to the virulence of mycobacterium tuberculosis and is a potential target for novel therapeutics. kstr2, a tetr family repressor (tfr), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-h-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (hip). binding of kstr2 to its operator sequences is relieved upon binding of hip-coa. a 1.6-å resolution crystal structure of the ks ... | 2014 | 25406313 |
| movement of elongation factor g between compact and extended conformations. | previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor g (ef-g). here, we follow the movement of domain iv of ef-g relative to domain ii of ef-g using ensemble and single-molecule förster resonance energy transfer. our results indicate that ribosome-free ef-g predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain iv moves away f ... | 2014 | 25463439 |
| movement of elongation factor g between compact and extended conformations. | previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor g (ef-g). here, we follow the movement of domain iv of ef-g relative to domain ii of ef-g using ensemble and single-molecule förster resonance energy transfer. our results indicate that ribosome-free ef-g predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain iv moves away f ... | 2014 | 25463439 |