bluuebunny/crossref_metadata_2025_split huggingface dataset:
Murein (Peptidoglycan) Binding Property of the Essential Cell Division Protein FtsN from
Escherichia coli
Authors: Ursinus Astrid , van den Ent Fusinita , Brechtel Sonja , de Pedro Miguel , Höltje Joachim-Volker , Löwe Jan , Vollmer Waldemar 
Published: October 2004

ABSTRACT

The binding of the essential cell division protein FtsN of
Escherichia coli
to the murein (peptidoglycan) sacculus was studied. Soluble truncated variants of FtsN, including the complete periplasmic part of the protein as well as a variant containing only the C-terminal 77 amino acids, did bind to purified murein sacculi isolated from wild-type cells. FtsN variants lacking this C-terminal region showed reduced or no binding to murein. Binding of FtsN was severely reduced when tested against sacculi isolated either from filamentous cells with blocked cell division or from chain-forming cells of a triple amidase mutant. Binding experiments with radioactively labeled murein digestion products revealed that the longer murein glycan strands (>25 disaccharide units) showed a specific affinity to FtsN, but neither muropeptides, peptides, nor short glycan fragments bound to FtsN. In vivo FtsN could be cross-linked to murein with the soluble disulfide bridge containing cross-linker DTSSP. Less FtsN, but similar amounts of OmpA, was cross-linked to murein of filamentous or of chain-forming cells compared to levels in wild-type cells. Expression of truncated FtsN variants in cells depleted in full-length FtsN revealed that the presence of the C-terminal murein-binding domain was not required for cell division under laboratory conditions. FtsN was present in 3,000 to 6,000 copies per cell in exponentially growing wild-type
E. coli
MC1061. We discuss the possibilities that the binding of FtsN to murein during cell division might either stabilize the septal region or might have a function unrelated to cell division.
Concerted Effects of Amino Acid Substitutions in Conserved Charged Residues and Other Residues in the Cytoplasmic Domain of PomA, a Stator Component of Na
+
-Driven Flagella
Authors: Fukuoka Hajime , Yakushi Toshiharu , Homma Michio 
Published: October 2004

ABSTRACT

PomA is a membrane protein that is one of the essential components of the sodium-driven flagellar motor in
Vibrio
species. The cytoplasmic charged residues of
Escherichia coli
MotA, which is a PomA homolog, are believed to be required for the interaction of MotA with the C-terminal region of FliG. It was previously shown that a PomA variant with neutral substitutions in the conserved charged residues (R88A, K89A, E96Q, E97Q, and E99Q; AAQQQ) was functional. In the present study, five other conserved charged residues were replaced with neutral amino acids in the AAQQQ PomA protein. These additional substitutions did not affect the function of PomA. However, strains expressing the AAQQQ PomA variant with either an L131F or a T132M substitution, neither of which affected motor function alone, exhibited a temperature-sensitive (TS) motility phenotype. The double substitutions R88A or E96Q together with L131F were sufficient for the TS phenotype. The motility of the PomA TS mutants immediately ceased upon a temperature shift from 20 to 42°C and was restored to the original level approximately 10 min after the temperature was returned to 20°C. It is believed that PomA forms a channel complex with PomB. The complex formation of TS PomA and PomB did not seem to be affected by temperature. Suppressor mutations of the TS phenotype were mapped in the cytoplasmic boundaries of the transmembrane segments of PomA. We suggest that the cytoplasmic surface of PomA is changed by the amino acid substitutions and that the interaction of this surface with the FliG C-terminal region is temperature sensitive.
FtsZ Collaborates with Penicillin Binding Proteins To Generate Bacterial Cell Shape inEscherichia coli
Authors: Varma Archana , Young Kevin D. 
Published: October 2004

ABSTRACTThe mechanisms by which bacteria adopt and maintain individual shapes remain enigmatic. Outstanding questions include why cells are a certain size, length, and width; why they are uniform or irregular; and why some branch while others do not. Previously, we showed thatEscherichia colimutants lacking multiple penicillin binding proteins (PBPs) display extensive morphological diversity. Because defective sites in these cells exhibit the structural and functional characteristics of improperly localized poles, we investigated the connection between cell division and shape. Here we show that under semipermissive conditions the temperature-sensitive FtsZ84 protein produces branched and aberrant cells at a high frequency in mutants lacking PBP 5, and this phenotype is exacerbated by the loss of additional peptidoglycan endopeptidases. Surprisingly, certainftsZ84strains lyse at the nonpermissive temperature instead of filamenting, and inhibition of wild-type FtsZ forces some mutants into tightly wound spirillum-like morphologies. The results demonstrate that significant aspects of bacterial shape are dictated by a previously unrecognized relationship between the septation machinery and ostensibly minor peptidoglycan-modifying enzymes and that under certain circumstances improper FtsZ function can destroy the structural integrity of the cell.
PAS Domain of the Aer Redox Sensor Requires C-Terminal Residues for Native-Fold Formation and Flavin Adenine Dinucleotide Binding
Authors: Herrmann Sarah , Ma Qinhong , Johnson Mark S. , Repik Alexandre V. , Taylor Barry L. 
Published: October 2004

ABSTRACTThe Aer protein inEscherichia coliis a membrane-bound, FAD-containing aerotaxis and energy sensor that putatively monitors the redox state of the electron transport system. Binding of FAD to Aer requires the N-terminal PAS domain and residues in the F1 region and C-terminal HAMP domain. The PAS domains of other PAS proteins are soluble in water. To investigate properties of the PAS domain, we subcloned segments of theaergene fromE. colithat encode the PAS domain with and without His6tags and expressed the PAS peptides inE. coli. The 20-kDa His6-Aer2-166PAS-F1 fragment was purified as an 800-kDa complex by gel filtration chromatography, and the associating protein was identified by N-terminal sequencing as the chaperone protein GroEL. None of the N-terminal fragments of Aer found in the soluble fraction was released from GroEL, suggesting that these peptides do not fold correctly in an aqueous environment and require a motif external to the PAS domain for proper folding. Consistent with this model, peptide fragments that included the membrane binding region and part (Aer2-231) or all (Aer2-285) of the HAMP domain inserted into the membrane, indicating that they were released by GroEL. Aer2-285, but not Aer2-231, bound FAD, confirming the requirement for the HAMP domain in stabilizing FAD binding. The results raise an interesting possibility that residues outside the PAS domain that are required for FAD binding are essential for formation of the PAS native fold.
Methylation of GPLs inMycobacterium smegmatisandMycobacterium avium
Authors: Jeevarajah Dharshini , Patterson John H. , Taig Ellen , Sargeant Tobias , McConville Malcolm J. , Billman-Jacobe Helen 
Published: October 2004

ABSTRACTSeveral species of mycobacteria express abundant glycopeptidolipids (GPLs) on the surfaces of their cells. The GPLs are glycolipids that contain modified sugars including acetylated 6-deoxy-talose and methylated rhamnose. Four methyltransferases have been implicated in the synthesis of the GPLs ofMycobacterium smegmatisandMycobacterium avium.A rhamnosyl 3-O-methytransferase and a fatty acid methyltransferase ofM. smegmatishave been previously characterized. In this paper, we characterize the methyltransferases that are responsible for modifying the hydroxyl groups at positions 2 and 4 of rhamnose and propose the biosynthetic sequence of GPL trimethylrhamnose formation. The analysis ofM. aviumgenes through the creation of specific mutants is technically difficult; therefore, an alternative approach to determine the function of putative methyltransferases ofM. aviumwas undertaken. Complementation ofM. smegmatismethyltransferase mutants withM. aviumgenes revealed that MtfC and MtfB of the latter species have 4-O-methyltransferase activity and that MtfD is a 3-O-methyltransferase which can modify rhamnose of GPLs inM. smegmatis.
The Transcriptional Regulator AlgR Controls Cyanide Production in
Pseudomonas aeruginosa
Authors: Carterson Alexander J. , Morici Lisa A. , Jackson Debra W. , Frisk Anders , Lizewski Stephen E. , Jupiter Ryan , Simpson Kendra , Kunz Daniel A. , Davis Scott H. , Schurr Jill R. , Hassett Daniel J. , Schurr Michael J. 
Published: October 2004

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen that causes chronic lung infections in cystic fibrosis (CF) patients. One characteristic of
P. aeruginosa
CF isolates is the overproduction of the exopolysaccharide alginate, controlled by AlgR. Transcriptional profiling analyses comparing mucoid
P. aeruginosa
strains to their isogenic
algR
deletion strains showed that the transcription of cyanide-synthesizing genes (
hcnAB
) was ∼3-fold lower in the
algR
mutants. S1 nuclease protection assays corroborated these findings, indicating that AlgR activates
hcnA
transcription in mucoid
P. aeruginosa
. Quantification of hydrogen cyanide (HCN) production from laboratory isolates revealed that mucoid laboratory strains made sevenfold more HCN than their nonmucoid parental strains. In addition, comparison of laboratory and clinically derived nonmucoid strains revealed that HCN was fivefold higher in the nonmucoid CF isolates. Moreover, the average amount of cyanide produced by mucoid clinical isolates was 4.7 ± 0.85 μmol of HCN/mg of protein versus 2.4 ± 0.40 μmol of HCN/mg of protein for nonmucoid strains from a survey conducted with 41
P. aeruginosa
CF isolates from 24 patients. Our data indicate that (i) mucoid
P. aeruginosa
regardless of their origin (laboratory or clinically derived) produce more cyanide than their nonmucoid counterparts, (ii) AlgR regulates HCN production in
P. aeruginosa
, and (iii)
P. aeruginosa
CF isolates are more hypercyanogenic than nonmucoid laboratory strains. Taken together, cyanide production may be a relevant virulence factor in CF lung disease, the production of which is regulated, in part, by AlgR.
Identification of a Reactivating Factor for Adenosylcobalamin-Dependent Ethanolamine Ammonia Lyase
Authors: Mori Koichi , Bando Reiko , Hieda Naoki , Toraya Tetsuo 
Published: October 2004

ABSTRACT

The holoenzyme of adenosylcobalamin-dependent ethanolamine ammonia lyase undergoes suicidal inactivation during catalysis as well as inactivation in the absence of substrate. The inactivation involves the irreversible cleavage of the Co-C bond of the coenzyme. We found that the inactivated holoenzyme undergoes rapid and continuous reactivation in the presence of ATP, Mg
2+
, and free adenosylcobalamin in permeabilized cells (in situ), homogenate, and cell extracts of
Escherichia coli
. The reactivation was observed in the permeabilized
E. coli
cells carrying a plasmid containing the
E. coli eut
operon as well. From coexpression experiments, it was demonstrated that the
eutA
gene, adjacent to the 5′ end of ethanolamine ammonia lyase genes (
eutBC
), is essential for reactivation. It encodes a polypeptide consisting of 467 amino acid residues with predicted molecular weight of 49,599. No evidence was obtained that shows the presence of the auxiliary protein(s) potentiating the reactivation or associating with EutA. It was demonstrated with purified recombinant EutA that both the suicidally inactivated and O
2
-inactivated holoethanolamine ammonia lyase underwent rapid reactivation in vitro by EutA in the presence of adenosylcobalamin, ATP, and Mg
2+
. The inactive enzyme-cyanocobalamin complex was also activated in situ and in vitro by EutA under the same conditions. Thus, it was concluded that EutA is the only component of the reactivating factor for ethanolamine ammonia lyase and that reactivation and activation occur through the exchange of modified coenzyme for free intact adenosylcobalamin.
Isolation and Characterization of Ribosomes and Translation Initiation Factors from the Gram-Positive Soil Bacterium
Streptomyces lividans
Authors: Day J. Michael , Janssen Gary R. 
Published: October 2004

ABSTRACT

A primer extension inhibition (toeprint) assay was developed using ribosomes and ribosomal subunits from
Streptomyces lividans
. This assay allowed the study of ribosome binding to streptomycete leaderless and leadered mRNA. Purified 30S subunits were unable to form a ternary complex on
aph
leaderless mRNA, whereas 70S ribosomes could form ternary complexes on this mRNA. 30S subunits formed ternary complexes on leadered
aph
and
malE
mRNA. The translation initiation factors (IF1, IF2, and IF3) from
S. lividans
were isolated and included in toeprint and filter binding assays with leadered and leaderless mRNA. Generally, the IFs reduced the toeprint signal on leadered mRNA; however, incubation of IF1 and IF2 with 30S subunits that had been washed under high-salt conditions promoted the formation of a ternary complex on
aph
leaderless mRNA. Our data suggest that, as reported for
Escherichia coli
, initiation complexes with leaderless mRNAs might use a novel pathway involving 70S ribosomes or 30S subunits bound by IF1 and IF2 but not IF3. Some mRNA-ribosome-initiator tRNA reactions that yielded weak or no toeprint signals still formed complexes in filter binding assays, suggesting the occurrence of interactions that are not stable in the toeprint assay.
Isolation, Free-Living Capacities, and Genome Structure of “
Candidatus
Glomeribacter gigasporarum,” the Endocellular Bacterium of the Mycorrhizal Fungus
Gigaspora margarita
Authors: Jargeat P. , Cosseau C. , Ola'h B. , Jauneau A. , Bonfante P. , Batut J. , Bécard G. 
Published: October 2004

ABSTRACT

“
Candidatus
Glomeribacter gigasporarum” is an endocellular β-proteobacterium present in the arbuscular mycorrhizal (AM) fungus
Gigaspora margarita
. We established a protocol to isolate “
Ca
. Glomeribacter gigasporarum” from its host which allowed us to carry out morphological, physiological, and genomic investigations on purified bacteria. They are rod shaped, with a cell wall typical of gram-negative bacteria and a cytoplasm rich in ribosomes, and they present no flagella or pili. Isolated bacteria could not be grown in any of the 19 culture media tested, but they could be kept alive for up to 4 weeks. PCR-based investigations of purified DNA from isolated bacteria did not confirm the presence of all genes previously assigned to “
Ca
. Glomeribacter gigasporarum.” In particular, the presence of
nif
genes could not be detected. Pulsed-field gel electrophoresis analyses allowed us to estimate the genome size of “
Ca
. Glomeribacter gigasporarum” to approximately 1.4 Mb with a ca. 750-kb chromosome and a 600- to 650-kb plasmid. This is the smallest genome known for a β-proteobacterium. Such small genome sizes are typically found in endocellular bacteria living permanently in their host. Altogether, our data suggest that “
Ca
. Glomeribacter gigasporarum” is an ancient obligate endocellular bacterium of the AM fungus
G. margarita
.
MODELLING LIVING FLUIDS WITH THE SUBDIVISION INTO THE COMPONENTS IN TERMS OF PROBABILITY DISTRIBUTIONS
Authors: WILLANDER M. , MAMONTOV E. , CHIRAGWANDI Z. 
Published: October 2004

As it follows from the results of C. H. Waddigton, F. E. Yates, A. S. Iberall, and other well-known bio-physicists, living fluids cannot be modelled within the frames of the fundamental assumptions of the statistical-mechanics formalism. One has to go beyond them. The present work does it by means of the generalized kinetics (GK), the theory enabling one to allow for the complex stochasticity of internal properties and parameters of the fluid particles. This is one of the key features which distinguish living fluids from the nonliving ones. It creates the disparity of the particles and hence breaks the each-fluid-component-uniformity requirement underlying statistical mechanics. The work deals with the corresponding modification of common kinetic equations which is in line with the GK theory and is the complement to the latter. This complement allows a subdivision of a fluid into the fluid components in terms of nondiscrete probability distributions. The treatment leads to one more equation that describes the above internal parameters. The resulting model is the system of these two equations. It appears to be always nonlinear in case of living fluids. In case of nonliving fluids, the model can be linear. Moreover, the living-fluid model, as a whole, cannot have the thermodynamic equilibrium, only partial equilibriums (such as the motional one) are possible. In contrast to this, in case of nonliving fluids, the thermodynamic equilibrium is, of course, possible. The number of the fluid components is treated as the number of the modes of the particle-characteristic probability density. In so doing, a fairly general extension of the notion of the mode from the one-dimensional case to the multidimensional case is proposed. The work also discusses the variety of the time-scales in a living fluid, the simplest quantum-mechanical equation relevant to living fluids, and the non-equilibrium nonlinear stochastic hydrodynamics option. The latter is simpler than, but conceptually comparable to, stochastic kinetic equations. A few directions for future research are suggested. The work notes a cohesion of mathematical physics and fluid mechanics with the living-fluid-related fields as a complex interdisciplinary problem.
Acute hypoxia and pulmonary vasoconstriction in humans: uncovering the mechanism of the pressor response
Authors: Fishman Alfred P. 
Published: October 2004

This essay looks at the historical significance of an APS classic paper that is freely available online:Motley HL, Cournand A, Werko L, Himmelstein A, and Dresdale D. The influence of short periods of induced acute anoxia upon pulmonary artery pressures in man. Am J Physiol 150: 315–320, 1947 ( http://ajplegacy.physiology.org/cgi/reprint/150/2/315 ).
Discovery of the luteinizing hormone of the anterior pituitary gland
Authors: Goodman H. Maurice 
Published: October 2004

This essay looks at the historical significance of an APS classic paper that is freely available online: Fevold HL, Hisaw FL, Leonard SL. The gonad stimulating and the luteinizing hormones of the anterior lobe of the hypophesis. Am J Physiol 97: 291—301, 1931 ( http://ajplegacy.physiology.org/cgi/reprint/97/2/291 ).
The pioneering use of systems analysis to study cardiac output regulation
Authors: Hall John E. 
Published: October 2004

This essay examines the historical significance of an APS classic paper that is freely available online: Guyton AC, Lindsey AW, and Kaufmann BN. Effect of mean circulatory filling pressure and other peripheral circulatory factors on cardiac output. Am J Physiol 180: 463-468, 1955 ( http://ajplegacy.physiology.org/cgi/reprint/180/3/463 ).
The development of clearance methods for measurement of glomerular filtration and tubular reabsorption
Authors: Hostetter T. H. , Meyer T. W. 
Published: October 2004

This essay looks at the historical significance of four APS classic papers that are freely available online: Jolliffe N, Shannon JA, and Smith HW. The excretion of urine in the dog. III. The use of non-metabolized sugars in the measurement of the glomerular filtrate. Am J Physiol 100: 301—312, 1932 ( http://ajplegacy.physiology.org/cgi/reprint/100/2/301 ). Shannon JA. The excretion of inulin by the dog. Am J Physiol 112: 405—413, 1935 ( http://ajplegacy.physiology.org/cgi/reprint/112/3/405 ). Shannon JA and Fisher S. The renal tubular reabsorption of glucose in the normal dog. Am J Physiol 122: 765—774, 1938 ( http://ajplegacy.physiology.org/cgi/reprint/122/3/765 ). Shannon JA, Farber S, and Troast L. The measurement of glucose Tm in the normal dog. Am J Physiol 133: 752—761, 1941 ( http://ajplegacy.physiology.org/cgi/reprint/133/3/752 ).
The basis for transport across epithelial cells
Authors: Montrose Marshall H. 
Published: October 2004

This essay looks at the historical significance of two APS classic papers that are freely available online: Ingraham RC and Visscher MB. Further studies on intestinal absorption with the performance of osmotic work. Am J Physiol 121: 771–785, 1938 ( http://ajplegacy.physiology.org/cgi/reprint/121/3/771 ). Visscher MB, Fetcher ES Jr, Carr CW, Gregor HP, Bushey MS, and Barker DE. Isotopic tracer studies on the movement of water and ions between intestinal lumen and blood. Am J Physiol 142: 550–575, 1944 ( http://ajplegacy.physiology.org/cgi/reprint/142/4/550 ).
Understanding pulmonary gas exchange: ventilation-perfusion relationships
Authors: West John B. 
Published: October 2004

This essay looks at the historical significance of four APS classic papers that are freely available online:Fenn WO, Rahn H, and OTIS AB. A theoretical study of the composition of the alveolar air at altitude. Am J Physiol 146: 637-653. 1946 ( http://ajplegacy.physiology.org/cgi/reprint/146/5/637 ).Rahn H. A concept of mean alveolar air and the ventilation-bloodflow relationships during pulmonary gas exchange. Am J Physiol 158: 21-30, 1949 ( http://ajplegacy.physiology.org/cgi/reprint/158/1/21) ).Riley RL. And Cournand A. "Ideal" Alveolar air and the analysis of ventilation-perfusion relationships in the lungs. J Appl Physiol 1: 825-847. 1949 ( http://jap.physiology.org/cgi/reprint/1/12/825) .Riley RL. And Cournand A. Analysis of factors affecting partial pressures of oxygen and carbon dioxide in gas and blood of lungs: theory. J Appl Physiol 4: 77-101. 1951 ( http://jap.physiology.org/cgi/reprint/4/2/77) .
Risk and the environment reporters: a four-region analysis
Authors: Sachsman David B. , Simon James , Valenti Joann Myer 
Published: October 2004

Who are the environment reporters who explain the science of the environment to the general public? Do they consider risk when writing environmental stories? How often do they say they use a risk assessment angle compared to other issues? Are they concerned that they may be exaggerating environmental risks, excessively frightening their readers and viewers?This study used a census approach to interview 354 environment reporters in four regions of the United States. The majority of environment reporters in all four regions said they used risk angles at least sometimes, many more than might have been true in the past. However, the journalists said they more frequently framed their stories using government, human-interest, business, nature, pollution, politics, science, and health angles, and some reporters, ranging from 28.3 percent in New England to 41.8 percent in the Pacific Northwest, said they rarely or never included risk assessment in their environmental stories. Although most journalists in the four regions did not believe that news reports generally sensationalized environmental risks, some reporters (16.9–25.0 percent) said that environmental journalists generally have overblown environmental risks, unduly alarming the public.