bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel scaffold protein, TANC, possibly a rat homolog of Drosophila rolling pebbles (rols), forms a multiprotein complex with various postsynaptic density proteins
Authors: Suzuki Tatsuo , Li Weidong , Zhang Jing‐Ping , Tian Qing‐Bao , Sakagami Hiroyuki , Usada Nobuteru , Kondo Hisatake , Fujii Toshihiro , Endo Shogo 
Published: January 2005

AbstractWe cloned from the rat brain a novel gene, tanc (GenBankTM Accession No. AB098072), which encoded a protein containing three tetratricopeptide repeats (TPRs), ten ankyrin repeats and a coiled‐coil region, and is possibly a rat homolog of Drosophila rolling pebbles (rols). The tanc gene was expressed widely in the adult rat brain. Subcellular distribution, immunohistochemical study of the brain and immunocytochemical studies of cultured neuronal cells indicated the postsynaptic localization of TANC protein of 200 kDa. Pull‐down experiments showed that TANC protein bound PSD‐95, SAP97, and Homer via its C‐terminal PDZ‐binding motif, ‐ESNV, and fodrin via both its ankyrin repeats and the TPRs together with the coiled‐coil domain. TANC also bound the α subunit of Ca2+/calmodulin‐dependent protein kinase II. An immunoprecipitation study showed TANC association with various postsynaptic proteins, including guanylate kinase‐associated protein (GKAP), α‐internexin, and N‐methyl‐d‐aspartate (NMDA)‐type glutamate receptor 2B and AMPA‐type glutamate receptor (GluR1) subunits. These results suggest that TANC protein may work as a postsynaptic scaffold component by forming a multiprotein complex with various postsynaptic density proteins.
Centre‐surround interactions in response to natural scene stimulation in the primary visual cortex
Authors: Guo Kun , Robertson Robert G. , Mahmoodi Sasan , Young Malcolm P. 
Published: January 2005

AbstractCentre–surround interaction in the primary visual cortex (area V1) has been studied extensively using artificial, abstract stimulus patterns, such as bars, gratings and simple texture patterns. In this experiment, we extend the study of centre–surround interaction by using natural scene images. We systematically varied the contrast of natural image surrounds presented outside the classical receptive field (CRF), and recorded neuronal response to a natural image patch presented within the CRF in area V1 of awake, fixating macaques. For the majority of neurons (67 out of 111), the natural image surrounds profoundly modulated, mainly by suppressing, neuronal responses to CRF images. These modulatory effects started at the earliest stage of neuronal responses, and often depended on the contrast and higher‐order structures of the surrounds. For 47 out of 67 neurons, randomising the phases of the Fourier spectrum of the natural image surround diminished the centre–surround interaction. Our results suggest that the centre–surround interaction in area V1 can be extended to natural vision, and is sensitive to the higher‐order structures of natural scene images, such as image contours.
Differential expression of two NMDA receptor interacting proteins, PSD‐95 and SynGAP during mouse development
Authors: Porter Karen , Komiyama Noboru H. , Vitalis Tania , Kind Peter C. , Grant Seth G. N. 
Published: January 2005

AbstractPatterns of neural activity mediated by N‐methyl‐d‐aspartate (NMDA) receptors are known to play important roles in development of the central nervous system. However, the signalling pathways downstream from NMDA receptors that are critical for normal neuronal development are not yet clearly understood. NMDA receptors interact with various signalling proteins via scaffolding proteins, which are important in adult neuronal and behavioural plasticity. For example, the NR2B subunits of the NMDA receptor interact with postsynaptic density 95 (PSD‐95), which in turn binds to synaptic ras GTPase‐activating protein (SynGAP). Interestingly, the developmental phenotype of mice carrying null mutations in these genes differ. NR2B and SynGAP homozygote mice die within the first week of birth whereas PSD‐95 homozygote mice survive to adulthood. We therefore examined the expression patterns of PSD‐95 and SynGAP genes from embryonic stages to adult using lacZ (β‐galactosidase) marker gene knock‐in mice. Dramatic changes of expression were observed throughout development in brain and other tissues. Although SynGAP binds PSD‐95, both genes had distinct, as well as overlapping expression. SynGAP expression peaked at times of synaptogenesis and developmental plasticity in contrast to PSD‐95, which was expressed throughout the brain from early embryonic stages. Furthermore, SynGAP showed a more spatially restricted pattern as illustrated by its restriction to forebrain in contrast to PSD‐95, which was also found in mid‐ and hindbrain. These data support the model that synaptic signalling complexes are heterogeneous and individual components show temporal and spatial specificity during development.
Duration of α1‐antichymotrypsin gene activation by interleukin‐1 is determined by efficiency of inhibitor of nuclear factor κBα resynthesis in primary human astrocytes
Authors: Kiss Daniel L. , Xu Weili , Gopalan Sunita , Buzanowska Katarzyna , Wilczynska Katarzyna M. , Rydel Russell E. , Kordula Tomasz 
Published: February 2005

AbstractExpression of α1antichymotrypsin (ACT) is significantly activated by interleukin‐1 (IL‐1) in human astrocytes; however, it is barely affected by IL‐1 in hepatocytes. This tissue‐specific regulation depends upon an enhancer that contains both nuclear factor κB (NF‐κB) and activating protein 1 (AP‐1) elements, and is also observed for an NF‐κB reporter but not for an AP‐1 reporter. We found efficient activation of NF‐κB binding in both cell types; however, this binding was persistent in glial cells and only transient in hepatocytes. IL‐1‐activated NF‐κB complexes consisted of p65 and p50, with p65 transiently phosphorylated on serine 536 in glial cells whereas more persistently in hepatic cells. Overexpression of p65 or constitutively active IKKβ (inhibitor of NF‐κB kinase β) resulted in an efficient activation of the ACT reporter in hepatic cells, indicating that a specific mechanism exists in these cells terminating IL‐1 signaling. IL‐1 effectively induced the degradation of inhibitor of NF‐κBα (IkBα) and IkBε in both cell types but IkBβ was not affected. However, IkBα was resynthesized much more rapidly in hepatic cells in comparison to glial cells. In addition, the initial levels of IkBα were much lower in glial cells. We propose that the tissue‐specific regulation of the ACT gene expression by IL‐1 is determined by different efficiencies of IkBα resynthesis in glial and hepatic cells.
Alteration of cytosolic free calcium homeostasis by SIN‐1: high sensitivity of L‐type Ca2+ channels to extracellular oxidative/nitrosative stress in cerebellar granule cells
Authors: Gutiérrez‐Martín Yolanda , Martín‐Romero Francisco Javier , Henao Fernando , Gutiérrez‐Merino Carlos 
Published: February 2005

AbstractExposure of cerebellar granule neurones in 25 mm KCl HEPES‐containing Locke's buffer (pH 7.4) to 50–100 µm SIN‐1 during 2 h decreased the steady‐state free cytosolic Ca2+ concentration ([Ca2+]i) from 168 ± 33 nm to 60 ± 10 nm, whereas exposure to ≥ 0.3 mm SIN‐1 produced biphasic kinetics: (i) decrease of [Ca2+]i during the first 30 min, reaching a limiting value of 75 ± 10 nm (due to inactivation of L‐type Ca2+ channels) and (ii) a delayed increase of [Ca2+]i at longer exposures, which correlated with SIN‐1‐induced necrotic cell death. Both effects of SIN‐1 on [Ca2+]i are blocked by superoxide dismutase plus catalase and by Mn(III)tetrakis(4‐benzoic acid)porphyrin chloride. Supplementation of Locke's buffer with catalase before addition of 0.5–1 mm SIN‐1 had no effect on the decrease of [Ca2+]i but further delayed and attenuated the increase of [Ca2+]i observed after 60–120 min exposure to SIN‐1 and also protected against SIN‐1‐induced necrotic cell death. α‐Tocopherol, the potent NMDA receptor antagonist (+)‐MK‐801 and the N‐ and P‐type Ca2+ channels blocker ω‐conotoxin MVIIC had no effect on the alterations of [Ca2+]i upon exposure to SIN‐1. However, inhibition of the plasma membrane Ca2+ ATPase can account for the increase of [Ca2+]i observed after 60–120 min exposure to 0.5–1 mm SIN‐1. It is concluded that L‐type Ca2+ channels are a primary target of SIN‐1‐induced extracellular nitrosative/oxidative stress, being inactivated by chronic exposure to fluxes of peroxynitrite of 0.5–1 μm/min, while higher concentrations of peroxynitrite and hydrogen peroxide are required for the inhibition of the plasma membrane Ca2+ ATPase and induction of necrotic cell death, respectively.
GlnD Is Essential for NifA Activation, NtrB/NtrC-Regulated Gene Expression, and Posttranslational Regulation of Nitrogenase Activity in the Photosynthetic, Nitrogen-Fixing Bacterium
Rhodospirillum rubrum
Authors: Zhang Yaoping , Pohlmann Edward L. , Roberts Gary P. 
Published: February 2005

ABSTRACT

GlnD is a bifunctional uridylyltransferase/uridylyl-removing enzyme and is thought to be the primary sensor of nitrogen status in the cell. It plays an important role in nitrogen assimilation and metabolism by reversibly regulating the modification of P
II
proteins, which in turn regulate a variety of other proteins. We report here the characterization of
glnD
mutants from the photosynthetic, nitrogen-fixing bacterium
Rhodospirillum rubrum
and the analysis of the roles of GlnD in the regulation of nitrogen fixation. Unlike
glnD
mutations in
Azotobacter vinelandii
and some other bacteria,
glnD
deletion mutations are not lethal in
R. rubrum
. Such mutants grew well in minimal medium with glutamate as the sole nitrogen source, although they grew slowly with ammonium as the sole nitrogen source (MN medium) and were unable to fix N
2
. The slow growth in MN medium is apparently due to low glutamine synthetase activity, because a Δ
glnD
strain with an altered glutamine synthetase that cannot be adenylylated can grow well in MN medium. Various mutation and complementation studies were used to show that the critical uridylyltransferase activity of GlnD is localized to the N-terminal region. Mutants with intermediate levels of uridylyltransferase activity are differentially defective in
nif
gene expression, the posttranslational regulation of nitrogenase, and NtrB/NtrC function, indicating the complexity of the physiological role of GlnD. These results have implications for the interpretation of results obtained with GlnD in many other organisms.
A Defect in the Acetyl Coenzyme A↔Acetate Pathway Poisons Recombinational Repair-Deficient Mutants ofEscherichia coli
Authors: Shi Idina Y. , Stansbury John , Kuzminov Andrei 
Published: February 2005

ABSTRACTRecombinational repair-dependent mutants identify ways to avoid chromosomal lesions. Starting with arecBC(Ts) strain ofEscherichia coli, we looked for mutants unable to grow at 42°C in conditions that inactivate the RecBCD(Ts) enzyme. We isolated insertions inackAandpta, which comprise a two-gene operon responsible for the acetate↔acetyl coenzyme A interconversion. Using precise deletions of eitherackAorpta, we showed that either mutation makesE. colicells dependent on RecA or RecBCD enzymes at high temperature, suggesting dependence on recombinational repair rather than on the RecBCD-catalyzed linear DNA degradation. Complete inhibition of growth ofpta/ackA recmutants was observed only in the presence of nearby growing cells, indicating cross-inhibition.pta recmutants were sensitive to products of the mixed-acid fermentation of pyruvate, yet none of these substances inhibited growth of the double mutants in low-millimolar concentrations.pta, but notackA, mutants also depend on late recombinational repair functions RuvABC or RecG.pta/ackA recFmutants are viable, suggesting, together with the inviability ofpta/ackA recBCmutants, that chromosomal lesions due to thepta/ackAdefect are of the double-strand-break type. We have isolated three insertional suppressors that allow slow growth ofpta recBC(Ts) cells under nonpermissive conditions; all three are in or near genes with unknown functions. Although they do not form colonies,ackA recandpta recmutants are not killed under the nonpermissive conditions, exemplifying a case of synthetic inhibition rather than synthetic lethality.
Analysis of the Piv Recombinase-Related Gene Family of
Neisseria gonorrhoeae
Authors: Skaar Eric P. , LeCuyer Brian , Lenich Anne G. , Lazio Matthew P. , Perkins-Balding Donna , Seifert H. Steven , Karls Anna C. 
Published: February 2005

ABSTRACT

Neisseria gonorrhoeae
(the gonococcus) is an obligate human pathogen and the causative agent of the disease gonorrhea. The gonococcal pilus undergoes antigenic variation through high-frequency recombination events between unexpressed
pilS
silent copies and the pilin expression locus
pilE
. The machinery involved in pilin antigenic variation identified to date is composed primarily of genes involved in homologous recombination. However, a number of characteristics of antigenic variation suggest that one or more recombinases, in addition to the homologous recombination machinery, may be involved in mediating sequence changes at
pilE
. Previous work has identified several genes in the gonococcus with significant identity to the pilin inversion gene (
piv
) from
Moraxella
species and transposases of the IS
110
family of insertion elements. These genes were candidates for a recombinase system involved in pilin antigenic variation. We have named these genes
irg
for invertase-related gene family. In this work, we characterize these genes and demonstrate that the
irg
genes do not complement for
Moraxella lacunata
Piv invertase or IS
492
MooV transposase activities. Moreover, by inactivation of all eight gene copies and overexpression of one gene copy, we conclusively show that these recombinases are not involved in gonococcal pilin variation, DNA transformation, or DNA repair. We propose that the
irg
genes encode transposases for two different IS
110
-related elements given the names IS
Ngo2
and IS
Ngo3
. IS
Ngo2
is located at multiple loci on the chromosome of
N. gonorrhoeae
, and IS
Ngo3
is found in single and duplicate copies in the
N. gonorrhoeae
and
Neisseria meningitidis
genomes, respectively.
A Polysaccharide Deacetylase Homologue, PdaA, inBacillus subtilisActs as anN-Acetylmuramic Acid Deacetylase In Vitro
Authors: Fukushima Tatsuya , Kitajima Toshihiko , Sekiguchi Junichi 
Published: February 2005

ABSTRACTA polysaccharide deacetylase homologue, PdaA, was determined to act as anN-acetylmuramic acid deacetylase in vitro. Histidine-tagged truncated PdaA (with the putative signal sequence removed) was overexpressed inEscherichia colicells and purified. Measurement of deacetylase activity showed that PdaA could deacetylate peptidoglycan treated withN-acetylmuramoyl-l-alanine amidase CwlH but could not deacetylate peptidoglycan treated with or withoutdl-endopeptidase LytF (CwlE). Reverse-phase high-performance liquid chromatography and mass spectrometry (MS) and MS-MS analyses indicated that PdaA could deacetylate theN-acetylmuramic acid residues of purified glycan strands derived fromBacillus subtilispeptidoglycan.
Effects ofrecJ,recQ, andrecFORMutations on Recombination in Nuclease-DeficientrecB recDDouble Mutants ofEscherichia coli
Authors: Ivančić-Baće Ivana , Salaj-Šmic Erika , Brčić-Kostić Krunoslav 
Published: February 2005

ABSTRACTThe two main recombination pathways inEscherichia coli(RecBCD and RecF) have different recombination machineries that act independently in the initiation of recombination. Three essential enzymatic activities are required for early recombinational processing of double-stranded DNA ends and breaks: a helicase, a 5′→3′ exonuclease, and loading of RecA protein onto single-stranded DNA tails. The RecBCD enzyme performs all of these activities, whereas the recombination machinery of the RecF pathway consists of RecQ (helicase), RecJ (5′→3′ exonuclease), and RecFOR (RecA-single-stranded DNA filament formation). The recombination pathway operating inrecB(nuclease-deficient) mutants is a hybrid because it includes elements of both the RecBCD and RecF recombination machineries. In this study, genetic analysis of recombination in arecB(nuclease-deficient)recDdouble mutant was performed. We show that conjugational recombination and DNA repair after UV and gamma irradiation in this mutant are highly dependent onrecJ, partially dependent onrecFOR, and independent ofrecQ. These results suggest that the recombination pathway operating in a nuclease-deficientrecB recDdouble mutant is also a hybrid. We propose that the helicase and RecA loading activities belong to the RecBCD recombination machinery, while the RecJ-mediated 5′→3′ exonuclease is an element of the RecF recombination machinery.
l
-Malyl-Coenzyme A/β-Methylmalyl-Coenzyme A Lyase Is Involved in Acetate Assimilation of the Isocitrate Lyase-Negative Bacterium
Rhodobacter capsulatus
Authors: Meister Michael , Saum Stephan , Alber Birgit E. , Fuchs Georg 
Published: February 2005

ABSTRACT

Cell extracts of
Rhodobacter capsulatus
grown on acetate contained an apparent malate synthase activity but lacked isocitrate lyase activity. Therefore,
R. capsulatus
cannot use the glyoxylate cycle for acetate assimilation, and a different pathway must exist. It is shown that the apparent malate synthase activity is due to the combination of a malyl-coenzyme A (CoA) lyase and a malyl-CoA-hydrolyzing enzyme. Malyl-CoA lyase activity was 20-fold up-regulated in acetate-grown cells versus glucose-grown cells. Malyl-CoA lyase was purified 250-fold with a recovery of 6%. The enzyme catalyzed not only the reversible condensation of glyoxylate and acetyl-CoA to
l
-malyl-CoA but also the reversible condensation of glyoxylate and propionyl-CoA to β-methylmalyl-CoA. Enzyme activity was stimulated by divalent ions with preference for Mn
2+
and was inhibited by EDTA. The N-terminal amino acid sequence was determined, and a corresponding gene coding for a 34.2-kDa protein was identified and designated
mcl1
. The native molecular mass of the purified protein was 195 ± 20 kDa, indicating a homohexameric composition. A homologous
mcl1
gene was found in the genomes of the isocitrate lyase-negative bacteria
Rhodobacter sphaeroides
and
Rhodospirillum rubrum
in similar genomic environments. For
Streptomyces coelicolor
and
Methylobacterium extorquens
,
mcl1
homologs are located within gene clusters implicated in acetate metabolism. We therefore propose that
l
-malyl-CoA/β-methylmalyl-CoA lyase encoded by
mcl1
is involved in acetate assimilation by
R. capsulatus
and possibly other glyoxylate cycle-negative bacteria.
Substrate-Dependent Regulation of Anaerobic Degradation Pathways for Toluene and Ethylbenzene in a Denitrifying Bacterium, Strain EbN1
Authors: Kühner Simon , Wöhlbrand Lars , Fritz Ingo , Wruck Wasco , Hultschig Claus , Hufnagel Peter , Kube Michael , Reinhardt Richard , Rabus Ralf 
Published: February 2005

ABSTRACT

Anaerobic biodegradation of toluene and ethylbenzene is of environmental concern and biochemical interest due to toxicity and novel reactions, respectively. The denitrifying strain EbN1 is unique in anaerobically degrading both alkylbenzenes via different pathways which converge at benzoyl coenzyme A. The organization of genes involved in both pathways was only recently determined for strain EbN1. In the present study, global expression analysis (DNA microarray and proteomics) indicated involvement of several thus-far-unknown proteins in the degradation of both alkylbenzenes. For example,
orf68
and
orf57
, framing the
ebd
operon, are implicated in ethylbenzene degradation, and the ebA1932 and ebA1936 genes, located 7.2 kb upstream of the
bbs
operon, are implicated in toluene degradation. In addition, expression studies were now possible on the level of the complete pathways. Growth experiments demonstrated that degradative capacities for toluene and ethylbenzene could be simultaneously induced, regardless of the substrate used for adaptation. Regulation was studied at the RNA (real-time reverse transcription-PCR and DNA microarray) and protein (two-dimensional-difference gel electrophoresis) level by using cells adapted to anaerobic growth with benzoate, toluene, ethylbenzene, or a mixture of toluene and ethylbenzene. Expression of the two toluene-related operons (
bss
and
bbs
) was specifically induced in toluene-adapted cells. In contrast, genes involved in anaerobic ethylbenzene degradation were induced in ethylbenzene- and toluene-adapted cells, suggesting that toluene may act as a gratuitous inducer. In agreement with the predicted sequential regulation of the ethylbenzene pathway, Ebd proteins (encoding subunits of ethylbenzene dehydrogenase) were formed in ethylbenzene- but not in acetophenone-adapted cells, while Apc proteins (subunits of predicted acetophenone carboxylase) were formed under both conditions.
Mutational Analysis of the Disulfide Catalysts DsbA and DsbB
Authors: Tan Jacqueline , Lu Ying , Bardwell James C. A. 
Published: February 2005

ABSTRACT

In prokaryotes, disulfides are generated by the DsbA-DsbB system. DsbB functions to generate disulfides by quinone reduction. These disulfides are passed to the DsbA protein and then to folding proteins. To investigate the DsbA-DsbB catalytic system, we performed an in vivo selection for chromosomal
dsbA
and
dsbB
mutants. We rediscovered many residues previously shown to be important for the activity of these proteins. In addition, we obtained one novel DsbA mutant (M153R) and four novel DsbB mutants (L43P, H91Y, R133C, and L146R). We also mutated residues that are highly conserved within the DsbB family in an effort to identify residues important for DsbB function. We found classes of mutants that specifically affect the apparent

K
m

of DsbB for either DsbA or quinones, suggesting that quinone and DsbA may interact with different regions of the DsbB protein. Our results are consistent with the interpretation that the residues Q33 and Y46 of DsbB interact with DsbA, Q95 and R48 interact with quinones, and that residue M153 of DsbA interacts with DsbB. All of these interactions could be due to direct amino acid interactions or could be indirect through, for instance, their effect on protein structure. In addition, we find that the DsbB H91Y mutant severely affects the
k
cat
of the reaction between DsbA and DsbB and that the DsbB L43P mutant is inactive, suggesting that both L43 and H91 are important for the activity of DsbB. These experiments help to better define the residues important for the function of these two protein-folding catalysts.
Expression of
Pseudomonas aeruginosa aer
-
2
, One of Two Aerotaxis Transducer Genes, Is Controlled by RpoS
Authors: Hong Chang Soo , Kuroda Akio , Takiguchi Noboru , Ohtake Hisao , Kato Junichi 
Published: February 2005

ABSTRACT

Pseudomonas aeruginosa
possesses two aerotaxis transducers, Aer and Aer-2. A deletion-insertion mutation of alternative sigma factor RpoS eliminated Aer-2-mediated aerotaxis but not Aer-mediated aerotaxis. Transcriptional analysis revealed that
cheY2
,
cheA2
,
cheW2
, and
aer
-
2
were expressed in an RpoS-dependent manner as a single transcript.