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PubMed1985

Modification of subunit b of the F0 complex from Escherichia coli ATP synthase by a hydrophobic maleimide and its effects on F0 functions.

Purified F0 from Escherichia coli ATP synthase was labelled with N-(7-dimethylamino-4-methyl-coumarinyl)-maleimide (DACM), a hydrophobic reagent which forms a stable, strongly fluorescent adduct with SH groups. Sodium dodecyl sulfate gel electrophoresis clearly demonstrated that subunit b was exclusively labelled, most likely at Cys-21, the only cysteine residue in E. coli F0. The amount of two molecules of DACM bound per F0, which was calculated from the absorption spectrum at 380 nm, is in full agreement with the postulated stoichiometry of two copies of subunit b/F0 complex. Thus the label provides a useful tool for simply detecting subunit b in protein chemical studies. DACM-labelled F0 was incorporated into liposomes and assayed for H+ translocating activity and its capacity to bind purified F1. Whereas the initial rate of H+ uptake was inhibited about 40% the reconstitution of a dicyclohexylcarbodiimide-sensitive F1F0 ATPase activity was completely unaffected. In a second set of experiments we reconstituted an F0 complex from DACM-labelled purified subunit b and an ac complex. In contrast to the results obtained with intact, DACM-labelled F0, both H+ translocating activity and F1 binding capacity were greatly reduced. Our data indicate that cysteine-21, probably together with other amino acids, is involved in maintaining a proper interaction of the hydrophobic N-terminal region of subunit b with the ac complex. This interplay seems to be a prerequisite for at least the in vitro assembly of a functional F0 complex.

Amino Acids↗

PubMed1999

The C-terminal domain of the Pseudomonas secretin XcpQ forms oligomeric rings with pore activity.

The Pseudomonas secretin XcpQ forms an oligomeric complex, which is involved in the translocation of proteins across the outer membrane via the type II secretion pathway. Pseudomonas aeruginosa produces only small amounts of this complex, 50 to 100 copies per bacterium, and overexpression is lethal to these cells. However, overexpression of Pseudomonas alcaligenes XcpQ could be achieved in the P. alcaligenes mutant strain 537. Protease protection experiments with P. alcaligenes XcpQ showed that the C-terminal domain of XcpQ, which is conserved in all the different members of the secretin family, is largely resistant to proteinase K. This protease-resistant fragment is embedded in the membrane and remains a stable complex, indicating that this domain is involved in complex formation. Both the intact and the protease-protected XcpQ complex showed a tendency to form two-dimensional crystal-like structures. Electron microscopic analysis of these structures showed that the overall oligomeric rings of the intact and of the protease-resistant complex are highly similar. The central cavity of the intact XcpQ complex contains structured mass. Both the intact and the protease-protected XcpQ complex showed pore-forming activity in planar lipid bilayers, consistent with their role as a translocation channel. However, the single-channel conductances observed were not uniform. Together, these results demonstrate that the C-terminal secretin homology domain of XcpQ is the structural domain that forms the channel through which macromolecules are being transported.

Bacterial Proteins↗

PubMed2005

ATP induces conformational changes of periplasmic loop regions of the maltose ATP-binding cassette transporter.

We have studied cofactor-induced conformational changes of the maltose ATP-binding cassette transporter by employing limited proteolysis in detergent solution. The transport complex consists of one copy each of the transmembrane subunits, MalF and MalG, and of two copies of the nucleotide-binding subunit, MalK. Transport activity further requires the periplasmic maltose-binding protein, MalE. Binding of ATP to the MalK subunits increased the susceptibility of two tryptic cleavage sites in the periplasmic loops P2 of MalF and P1 of MalG, respectively. Lys(262) of MalF and Arg(73) of MalG were identified as probable cleavage sites, resulting in two N-terminal peptide fragments of 29 and 8 kDa, respectively. Trapping the complex in the transition state by vanadate further stabilized the fragments. In contrast, the tryptic cleavage profile of MalK remained largely unchanged. ATP-induced conformational changes of MalF-P2 and MalG-P1 were supported by fluorescence spectroscopy of complex variants labeled with 2-(4'-maleimidoanilino)naphthalene-6-sulfonic acid. Limited proteolysis was subsequently used as a tool to study the consequences of mutations on the transport cycle. The results suggest that complex variants exhibiting a binding protein-independent phenotype (MalF500) or containing a mutation that affects the "catalytic carboxylate" (MalKE159Q) reside in a transition state-like conformation. A similar conclusion was drawn for a complex containing a replacement of MalKQ140 in the signature sequence by leucine, whereas substitution of lysine for Gln(140) appears to lock the transport complex in the ground state. Together, our data provide the first evidence for conformational changes of the transmembrane subunits of an ATP-binding cassette import system upon binding of ATP.

ATP-Binding Cassette Transporters↗

PubMed2004

Trigonal DnaK-DnaJ complex versus free DnaK and DnaJ: heat stress converts the former to the latter, and only the latter can do disaggregation in cooperation with ClpB.

DnaK from Thermus thermophilus (TDnaK) is unique because significant fractions of cellular TDnaK exist as a trigonal K.J complex that consists of three copies each of TDnaK, TDnaJ, and an assembly factor TDafA. Here, chaperone functions of the K.J complex and free TDnaK plus free TDnaJ (K+J) were compared. Substrate proteins were completely denatured at 72-73 degrees C or 89 degrees C in the absence or the presence of K.J complex or K+J and were subsequently incubated at a moderate temperature of 55 degrees C. TGrpE and ATP were always included in the K.J complex and K+J, and TClpB was supplemented at 55 degrees C. At 72-73 degrees C, both the K.J complex and K+J suppressed heat aggregation of substrate proteins. During the next incubation at 55 degrees C, K+J, assisted by TClpB, was able to disaggregate the heat aggregates and efficiently reactivate activities of the proteins, whereas the K.J complex was not; it reactivated only the soluble inactivated proteins. When substrate proteins were heated to 89 degrees C, both the K.J complex and K+J were no longer able to prevent heat aggregation, and because of selective, irreversible denaturation of TDafA the K.J complex dissociated into K+J, which then exhibited disaggregation activity during the next incubation at 55 degrees C. Thus, TClpB-assisted disaggregation activity belongs only to K+J, and TDafA is a potential thermosensor for converting the K.J complex to K+J in response to heat stress.

Bacterial Proteins↗

PubMed2004

Associations between Bacillus subtilis sigmaB regulators in cell extracts.

The general stress regulon of Bacillus subtilis is induced by the activation of the sigma(B) transcription factor. Activation of sigma(B) occurs as a consequence of the dephosphorylation of its positive regulator RsbV by one of two phosphatases that respond to either physical or nutritional stress. The physical stress phosphatase (RsbU) requires a second protein (RsbT) for activity. Stress is thought to initiate a process that triggers the release of RsbT from a large inhibitory complex composed of multiple copies of two protein species, RsbR (and/or its paralogues) and RsbS. The stress-derived signal driving RsbT release is unknown, but it fails to develop in B. subtilis lacking either ribosome protein L11 or the ribosome-associated protein Obg. RsbR, RsbS, RsbT, Obg and ribosomes elute in common high-molecular-mass fractions during gel-filtration chromatography of crude B. subtilis extracts. This paper reports the investigation of the basis of this coelution by the examining of associations between these proteins in extracts prepared from wild-type and mutant B. subtilis, and Escherichia coli engineered to express RsbR, RsbS and RsbT. Large RsbR/RsbS complexes, distinct from ribosomes, were detected in extracts of both B. subtilis and E. coli. In E. coli, high-molecular-mass forms of RsbS were less abundant when RsbR was absent, but in B. subtilis, only when both RsbR and its principal paralogues were missing from the extract was this form less abundant. This finding is consistent with the notion that the RsbR paralogues, present in B. subtilis but not E. coli, can substitute for RsbR in such complexes. RsbT was not bound to RsbR/RsbS in any extract that was examined, including one prepared from a B. subtilis strain with an RsbS variant (RsbS59SA) that is believed to continuously associate with RsbT. The high-molecular-mass forms of RsbT were found to be Triton-sensitive and independent of any other B. subtilis protein for their formation. These probably represent RsbT aggregates. The data suggest that the contribution of ribosomes/Obg to sigma(B) activation does not involve formation of a stable association between these proteins and the Rsb complex. In addition, the binding of RsbT to RsbS/RsbR appears to be more labile than the binding between the previously analysed Rsb proteins which form inhibitory complexes. This, and the apparent proclivity of RsbT to aggregate, suggests an inherent instability in RsbT which may play a role in its regulation.

Bacillus subtilis↗

PubMed1994

A differential cloning procedure of complex genomic DNA fragments.

We have developed a differential cloning procedure designed for cloning of anonymous restriction DNA fragments whose molecular sizes differ between two genomic DNA preparations from higher organisms. The procedure, which was extensively revised from the original one, consists of several steps as summarized below. (i) Digestion of two DNA preparations (target and reference DNA) with the same restriction enzyme (4 base cutter). (ii) Biotinylation of target DNA and conversion of reference DNA to nonamplifiable form by terminal dephosphorylation. (iii) Electrophoresis of the two DNA preparations through a synthetic gel with a large excess of reference DNA as a competitor. (iv) In-gel alkaline dissociation of DNA, followed by reassociation (in-gel competitive reassociation). (v) Elution of DNA from the gel and PCR after adapter ligation and adsorption of DNA onto streptavidin-coated matrix. By repeating these steps, we attained substantial enrichment (approximately 10,000-fold) of DNA fragments which were originally present at one copy or less per complex mammalian genome. The details of the procedure and its unique characteristics in cloning of altered genomic DNA fragments, particularly from mammalian genome, are discussed.

Adenine Phosphoribosyltransferase↗

PubMed1993

Quantitative model of ColE1 plasmid copy number control.

Initiation of replication of the Escherichia coli plasmid ColE1 is inhibited by formation of a complex between a small plasmid RNA (RNA I) and the pre-primer for DNA synthesis (RNA II). Complex formation (and inhibition of replication) is enhanced by the plasmid-encoded Rom protein. The in vitro kinetics of complex formation were previously studied both experimentally and theoretically. The in vivo concentrations and half-lives of RNA I, RNA II and Rom protein have been measured recently. We present a dynamic model for the in vivo replication control mechanism that accounts for the measured concentration values. From the model we deduce a simple formula for the steady-state plasmid concentration. Our results agree with a previous simple steady-state analysis done by Brenner and Tomizawa, in that plasmid copy number is most strongly dependent on the per plasmid rate of RNA I synthesis. However, our model predicts other parameter dependencies that are not evident from or at variance with the previous analysis. Accordingly, we predict that plasmid copy number is greatly influenced by changes in the rate constant describing the formation of an initial unstable RNA I-RNA II complex, but is only slightly influenced by changes in the dissociation rate of this complex. Plasmid copy number per average cell volume is predicted to increase linearly with increases in the RNA II synthesis rate and with increases in the generation time of the host culture. Rom protein, which promotes conversion of the unstable RNA I-RNA II complex to a stable complex, serves to decrease copy number; however, its presence or absence does not seem to qualitatively alter the copy number control mechanism. Our model predicts the quantitative increase of plasmid copy number in rom- mutants. Several experiments are suggested to investigate the predictions of the model.

Bacterial Proteins↗

PubMed1996

MRI and nonverbal cognitive deficits in children with neurofibromatosis 1.

Magnetic resonance imaging brain scans and neuropsychological assessments of 17 children who met the NIH consensus diagnostic criteria for neurofibromatosis Type 1 were carried out in order to determine if there is a relationship between presence of high intensity signal abnormalities on MRI scans and nonverbal cognitive deficits. Cranial MRI scans in 10 patients (58.8%) demonstrated high intensity signal abnormalities, most frequently in the cerebral peduncles. Fifteen patients had nonverbal cognitive deficits (88.2%), including difficulty judging the orientation of lines, matching complex visual stimulus configurations, recalling pictures of faces, as well as copying and drawing from memory a complex geometric figure. There was not a significant association between nonverbal neuropsychological deficits and presence of high intensity signal abnormalities on MRI scans, possibly because the location of these hyperintense abnormalities was typically below the level of the basal ganglia. These findings suggest that the high intensity signal lesions seen on the MRI scans of children with neurofibromatosis Type 1 do not predict or explain their nonverbal cognitive deficits.

Adolescent↗

PubMed1995

Mutual policing and repression of competition in the evolution of cooperative groups.

Evolutionary theory has not explained how competition among lower level units is suppressed in the formation of higher-level evolutionary units. For example, the key problem of early evolution is small, individual replicators formed cooperative groups of sufficient complexity to allow accurate copying of the genetic material. The puzzle is why parasites did not subvert the formation of cells by obtaining benefits from the group without contributing to shared traits that enhance reproduction. These parasites would outcompete other replicators within the cell, disrupting reproductive fairness among subunits and destroying the functional coherence of the group. A similar problem arose at a later evolutionary stage with the orderly mendelian segregation of subunits (chromosomes) within cells, and reproductive fairness continued to be a problem in the evolution of insect and human societies. Here I present a simple model to show how reproductive fairness evolves among subunits to create functional coherence and higher-level units. Self-restraint, which evolves according to the kin-selection coefficient of relatedness, is not sufficient: mutual policing and enforcement of reproductive fairness are also required for the evolution of increasing social complexity.

Biological Evolution↗

PubMed1995

Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution.

The three-dimensional structure of the proteasome from the archaebacterium Thermoplasma acidophilum has been elucidated by x-ray crystallographic analysis by means of isomorphous replacement and cyclic averaging. The atomic model was built and refined to a crystallographic R factor of 22.1 percent. The 673-kilodalton protease complex consists of 14 copies of two different subunits, alpha and beta, forming a barrel-shaped structure of four stacked rings. The two inner rings consist of seven beta subunits each, and the two outer rings consist of seven alpha subunits each. A narrow channel controls access to the three inner compartments. The alpha 7 beta 7 beta 7 alpha 7 subunit assembly has 72-point group symmetry. The structures of the alpha and beta subunits are similar, consisting of a core of two antiparallel beta sheets that is flanked by alpha helices on both sides. The binding of a peptide aldehyde inhibitor marks the active site in the central cavity at the amino termini of the beta subunits and suggests a novel proteolytic mechanism.

Amino Acid Sequence↗

PubMed2006

Getting closer to a pre-vertebrate genome: the non-LTR retrotransposons of Branchiostoma floridae.

Non-LTR retrotransposons are common in vertebrate genomes and although present in invertebrates they appear at a much lower frequency. The cephalochordate amphioxus is the closest living relative to vertebrates and has been considered a good model for comparative analyses of genome expansions during vertebrate evolution. With the aim to assess the involvement of transposable elements in these events, we have analysed the non-LTR retrotransposons of Branchiostoma floridae. In silico searches have allowed to reconstruct non-LTR elements of six different clades (CR1, I, L1, L2, NeSL and RTE) and assess their structural features. According to the estimated copy number of these elements they account for less than 1% of the haploid genome, which reminds of the low abundance also encountered in the urochordate Ciona intestinalis. Amphioxus (B. floridae) and Ciona share a pre-vertebrate-like organization for the non-LTR retrotransposons (<150 copies, < 1% of the genome) versus the complexity associated to higher vertebrates (Homo sapiens >1.3.10(6) copies, > 20% of the genome).

Amino Acid Sequence↗

PubMed2003

Visuomotor coordination and visuospatial working memory of children with specific reading disabilities: a study using the Rey-Osterrieth Complex Figure.

The aim of the present study was to examine the visuospatial perception, short-term working memory, and motor skills of children with special reading difficulties, using the Rey-Osterrieth Complex Figure, which can record visuomotor and memory skills, observe drawing processes, and detect deficiencies in specific skills. 306 right- and left-handed boys and girls, ages 6.6 to 9.6 yr. (102 with special reading difficulties, 102 normal readers, and 102 with general learning difficulties) comprised one experimental and two control groups, respectively. The task was to depict the Rey-Osterrieth Complex Figure under two conditions, copying and drawing it from memory. Analysis indicated that (a) difficulty of the depiction of the Rey-Osterrieth Complex Figure, especially from memory, sharply affects children's performance and (b) the experimental group's performance was significantly poorer than that of controls in both conditions. The results are discussed in view of the predictive value of certain motor and cognitive skill deficiencies of children with special reading difficulties.

Child↗

PubMed1983

Spontaneous H-2 mutants provide evidence that a copy mechanism analogous to gene conversion generates polymorphism in the major histocompatibility complex.

The analysis of H-2K products from spontaneously generated major histocompatibility complex (MHC) mutants and of the primary structure of other class I antigens suggests the genetic hypothesis that diversity in the MHC results from a copy mechanism analogous to gene conversion. The hypothesis was tested by making precise structural predictions about three partially characterized MHC mutants (bm1, bm3, and bm8). The predictions were based on consensus sequences among class I genes that differ from H-2Kb in the same region of the molecule as do the Kb mutants. In two cases (bm3 and bm8) we successfully predicted the correct amino acid substitution at positions known to be altered but for which the specific nature of the substitution had not been determined. In two additional cases (bm1 and bm8) we predicted and found both new mutation sites and the specific amino acid substitutions. The positions and identifications of the variant amino acids were determined by radiolabeled amino acid sequence analysis and DNA restriction endonuclease analysis. The interaction of MHC genes through a copy mechanism to generate diversity permits the introduction of multiple nucleotide base substitutions into class I sequences by a single genetic event. Such a mechanism may account in part for the large structural divergence among alleles of MHC loci and the high degree of MHC polymorphism among wild mice.

Amino Acid Sequence↗

PubMed2006

Impaired visual search in drivers with Parkinson's disease.

OBJECTIVE: To assess the ability for visual search and recognition of roadside targets and safety errors during a landmark and traffic sign identification task in drivers with Parkinson's disease (PD). METHODS: Seventy-nine drivers with PD and 151 neurologically normal older adults underwent a battery of visual, cognitive, and motor tests. The drivers were asked to report sightings of specific landmarks and traffic signs along a four-lane commercial strip during an experimental drive in an instrumented vehicle. RESULTS: The drivers with PD identified significantly fewer landmarks and traffic signs, and they committed more at-fault safety errors during the task than control subjects, even after adjusting for baseline errors. Within the PD group, the most important predictors of landmark and traffic sign identification rate were performances on Useful Field of View (visual speed of processing and attention) and Complex Figure Test-Copy (visuospatial abilities). Trail Making Test (B-A), a measure of cognitive flexibility independent of motor function, was the only independent predictor of at-fault safety errors in drivers with PD. INTERPRETATION: The cognitive and visual deficits associated with PD resulted in impaired visual search while driving, and the increased cognitive load during this task worsened their driving safety.

Aged↗

PubMed1995

Differential cloning using in-gel competitive reassociation.

We describe the principle and actual processes of a differential cloning procedure designed for cloning of anonymous restriction DNA fragments whose molecular sizes differ between two genomic DNA preparations from higher organisms as a result of DNA rearrangement, polymorphism, etc. The procedure, which was extensively modified from the original one and still employs in-gel competitive reassociation (IGCR) as the basic principle, aims for cloning of DNA fragments which exist in one copy or less per mammalian genome. The modified procedure consists of dissociation and reassociation of biotinylated restriction digests of target DNA fragments (from which clones are to be isolated) in the presence of a large excess of reference (competitor) DNA in gel after electrophoresis, which is followed by absorption of the target DNA fragments to streptavidin-coated tubes and solid-phase polymerase chain reaction. After repeating these steps we attained substantial enrichment of altered DNA fragments which were originally present in one copy or less per complex mammalian genome.

Animals↗

PubMed1981

Visual cortex activation recorded by dynamic emission computed tomography of inhaled xenon 133.

Regional cerebral blood flow (CBF) was studied tomographically with 133Xe administered by inhalation over a 1-min period at a concentration of 10 mCi/l. A fast rotating ("dynamic') single-photon emission computed tomograph with four detector heads was used, an instrument that has been found to be well suited for detecting focal ischemia. In the present study its ability to detect focal hyperemia was investigated in 13 normal subjects studied during rest and during visual stimulation. A flickering light "seen' with eyes open and closed, increased blood flow in the visual cortex by 35% and 22% respectively. Looking at different pictures displayed on a screen raised regional CBF by 26%. The most complex task, reading and copying a text, increased blood flow by 45%. Averaging the different tasks resulted in a mean regional CBF increase in the visual cortex of 35%. The result is comparable with that obtained by positron emission tomography. Both forms of isotope tomography offer unique possibilities of the study of brain function in health and disease, possibilities not matched by X-ray tomography. The low cost and ready availability of appropriate single-photon radionuclides (133Xe and 127Xe) are mentioned.

Cerebrovascular Circulation↗

PubMed1991

Site-specific integration of genes into hot spots for recombination flanking aadA in Tn21 transposons.

Tn21-related transposons are widespread among bacteria and carry various resistance determinants at preferential sites, hs1 and hs2. In an in vivo integrative recombination assay it was demonstrated that these hot spots direct the integration of aminoglycoside resistance genes like aadB from Klebsiella pneumoniae and aacAI from Serratia marcescens, in a recA- background. The maximum required recognition sequence which must be present in both the donor and recipient plasmids is 5' CTAAAACAAAGTTA 3' (hs2). The double-site-specific recombination occurred with a frequency of 10(-5)-10(-6). The resulting structures include not only replicon fusion products but also more complex structures carrying two copies of the donor plasmid or simply the donor gene flanked by hs elements. hs1 and hs2 are thought to act as recognition sites for a transacting site-specific recombinase. By the use of Tn21 deletion derivatives, it has been shown that the recombinase is not encoded by Tn21. This new integrative recombination system is involved in the acquisition of new genes by Tn21-related transposons and their spread among bacterial populations.

Base Sequence↗

PubMed1990

Bean pathogenesis-related (PR) proteins deduced from elicitor-induced transcripts are members of a ubiquitous new class of conserved PR proteins including pollen allergens.

We have searched for induced transcripts in a cDNA library derived from bean cell supension cultures treated with an elicitor from Colletotrichum lindemuthianum. Six independently isolated cDNAs corresponding to rapidly induced small mRNAs have been classified by their DNA sequence and slightly different induction behaviour into two groups. 5'- and 3'-untranslated regions exhibit little similarity, but the deduced small acidic proteins designated PvPR1 and PvPR2 are 89% identical. No relationship was found with the well-characterized PR1 proteins from tobacco. However, the PvPR proteins are closely related to pI49 in pea (64% identity), pSTH2 in potato (41% identity) and PcPR1-1 in parsley (39% identity), which are also induced in response to elicitor or microbial attack. Moreover, a major pollen allergen in birch (BetvI) has a 44% identity with PvPR1 proteins. These similarities establish a ubiquitous class of conserved defense-related proteins and suggest a common yet still unknown function. Southern blot analysis indicates that PvPR protein gene organization is highly complex with an estimated copy number of more than 12 genes.

Amino Acid Sequence↗