bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interrelations between Glycine Betaine Catabolism and Methionine Biosynthesis in
Sinorhizobium meliloti
Strain 102F34
Authors: Barra Lise , Fontenelle Catherine , Ermel Gwennola , Trautwetter Annie , Walker Graham C. , Blanco Carlos 
Published: October 2006

ABSTRACT

Methionine is produced by methylation of homocysteine.
Sinorhizobium
meliloti
102F34 possesses only one methionine synthase, which catalyzes the transfer of a methyl group from methyl tetrahydrofolate to homocysteine. This vitamin B
12
-dependent enzyme is encoded by the
metH
gene. Glycine betaine can also serve as an alternative methyl donor for homocysteine. This reaction is catalyzed
by betaine-homocysteine methyl transferase (BHMT), an enzyme that has been characterized in humans and rats. An
S. meliloti
gene whose product is related to the human BHMT enzyme has been identified and named
bmt
. This enzyme is closely related to mammalian BHMTs but has no homology with previously described bacterial betaine
methyl transferases. Glycine betaine inhibits the growth of an
S. meliloti bmt
mutant in low- and high-osmotic strength media, an effect that correlates with a decrease in the catabolism of glycine betaine. This inhibition was not observed with other betaines, like homobetaine, dimethylsulfoniopropionate, and trigonelline. The addition
of methionine to the growth medium allowed a
bmt
mutant to recover growth despite the presence of glycine betaine. Methionine also stimulated glycine betaine catabolism in a
bmt
strain, suggesting the existence of another catabolic pathway. Inactivation of
metH
or
bmt
did not affect the nodulation efficiency
of the mutants in the 102F34 strain background. Nevertheless, a
metH
strain was severely defective in competing with the
wild-type strain in a coinoculation
experiment.
Time-Dependent Proteome Alterations under Osmotic Stress during Aerobic and Anaerobic Growth in
Escherichia coli
Authors: Weber Arnim , Kögl Stephanie A. , Jung Kirsten 
Published: October 2006

ABSTRACT

Escherichia coli
lives in the mammalian gastrointestinal tract anaerobically at high osmolarity as well as in the soil aerobically at varying osmolarities. Adaptation to these varying environmental conditions is crucial for growth and survival of
E. coli
. Two-dimensional protein gels were used to visualize global time-dependent changes (10 to 60 min) in the proteome of cells responding to osmotic stress (0.4 M NaCl or 0.7 M sorbitol) under aerobic or anaerobic conditions. The protein profiles revealed an induction of 12 proteins (Dps, HchA, HdhA, InfB, OsmC, OsmY, ProX, KatE, PspA, TalA, TktB, and TreF) under osmotic stress in an aerobic milieu. Eleven additional proteins (OtsB, YceI, YciE, YciF, YgaU, YjbJ, AcnA, MetL, PoxB, Ssb, and YhbO) were induced by osmotic stress imposed by NaCl. Most of the accumulated proteins were cross-protecting proteins (e.g., OsmY, OsmC, Dps, and KatE) which are regulated at the transcriptional level predominantly by RpoS and other regulators (e.g., integration host factor, OxyR, H-NS, LRP, and FIS). Comparative analysis of the proteome of
E. coli
grown under aerobic or anaerobic conditions under osmotic stress (NaCl) revealed an overlap of the up-regulated proteins of more than 50%. Ten proteins (PoxB, AcnA, TalA, TktB, KatE, PspA, Ssb, TreF, MetL, and YhbO) were detectable only under aerobic, high-osmolality conditions. Time-dependent alterations of the proteome were monitored, allowing classification of the up-regulated proteins into early, middle, and long-term phases of adaptation. Only a few proteins were found to be down-regulated upon osmotic stress.
FtsZ from Divergent Foreign Bacteria Can Function for Cell Division inEscherichia coli
Authors: Osawa Masaki , Erickson Harold P. 
Published: October 2006

ABSTRACTFtsZs fromMycoplasma pulmonis(MpuFtsZ) andBacillus subtilis(BsFtsZ) are only 46% and 53% identical in amino acid sequence to FtsZ fromEscherichia coli(EcFtsZ). In the present study we show that MpuFtsZ and BsFtsZ can function for cell division inE. coliprovided we make two modifications. First, we replaced their C-terminal tails with that fromE. coli, giving the foreign FtsZ the binding site forE. coliFtsA and ZipA. Second, we selected for mutations in theE. coligenome that facilitated division by the foreign FtsZs. These suppressor strains arose at a relatively high frequency of 10−3to 10−5, suggesting that they involve loss-of-function mutations in multigene pathways. These pathways may be negative regulators of FtsZ or structural pathways that facilitate division by slightly defective FtsZ. Related suppressor strains were obtained for EcFtsZ containing certain point mutations or insertions of yellow fluorescent protein. The ability of highly divergent FtsZs to function for division inE. coliis consistent with a two-part mechanism. FtsZ assembles the Z ring, and perhaps generates the constriction force, through self interactions; the downstream division proteins remodel the peptidoglycan wall by interacting with each other and the wall. The C-terminal peptide of FtsZ, which binds FtsA, provides the link between FtsZ assembly and peptidoglycan remodeling.
Comparative Phylogenomics of
Clostridium difficile
Reveals Clade Specificity and Microevolution of Hypervirulent Strains
Authors: Stabler R. A. , Gerding D. N. , Songer J. G. , Drudy D. , Brazier J. S. , Trinh H. T. , Witney A. A. , Hinds J. , Wren B. W. 
Published: October 2006

ABSTRACT

Clostridium difficile
is the most frequent cause of nosocomial diarrhea worldwide, and recent reports suggested the emergence of a hypervirulent strain in North America and Europe. In this study, we applied comparative phylogenomics (whole-genome comparisons using DNA microarrays combined with Bayesian phylogenies) to model the phylogeny of
C. difficile
, including 75 diverse isolates comprising hypervirulent, toxin-variable, and animal strains. The analysis identified four distinct statistically supported clusters comprising a hypervirulent clade, a toxin A
−
B
+
clade, and two clades with human and animal isolates. Genetic differences among clades revealed several genetic islands relating to virulence and niche adaptation, including antibiotic resistance, motility, adhesion, and enteric metabolism. Only 19.7% of genes were shared by all strains, confirming that this enteric species readily undergoes genetic exchange. This study has provided insight into the possible origins of
C. difficile
and its evolution that may have implications in disease control strategies.
Threonine-978 in the Transmembrane Segment of the Multidrug Efflux Pump AcrB of
Escherichia coli
Is Crucial for Drug Transport as a Probable Component of the Proton Relay Network
Authors: Takatsuka Yumiko , Nikaido Hiroshi 
Published: October 2006

ABSTRACT

Escherichia coli
AcrB is a multidrug efflux transporter that recognizes multiple toxic chemicals and expels them from cells. It is a proton antiporter belonging to the resistance-nodulation-division (RND) superfamily. Asp407, Asp408, Lys940, and Arg971 in transmembrane (TM) helices of this transporter have been identified as essential amino acid residues that probably function as components of the proton relay system. In this study, we identified a novel residue in TM helix 11, Thr978, as an essential residue by alanine scanning mutagenesis. Its location close to Asp407 suggests that it is also a component of the proton translocation pathway, a prediction confirmed by the similar conformations adopted by T978A, D407A, D408A, and K940A mutant proteins (see the accompanying paper). Sequence alignment of 566 RND transporters showed that this threonine residue is conserved in about 96% of cases. Our results suggest the hypotheses that Thr978 functions through hydrogen bonding with Asp407 and that protonation of the latter alters the salt bridging and hydrogen bonding pattern in the proton relay network, thus initiating a series of conformational changes that ultimately result in drug extrusion.
Identification and Sequence of a
tet
(M) Tetracycline Resistance Determinant Homologue in Clinical Isolates of
Escherichia coli
Authors: Jones C. Hal , Tuckman Margareta , Murphy Ellen , Bradford Patricia A. 
Published: October 2006

ABSTRACT

The presence of the tetracycline resistance determinant
tet
(M) in human clinical isolates of
Escherichia coli
is described for the first time in this report. The homologue was >99% identical to the
tet
(M) genes reported to occur in
Lactobacillus plantarum
,
Neisseria meningitidis
, and
Streptococcus agalactiae
, and 3% of the residues in its deduced amino acid sequence diverge from
tet
(M) of
Staphylococcus aureus
. Sequence analysis of the regions immediately flanking the gene revealed that sequences upstream of
tet
(M) in
E. coli
have homology to Tn
916
; however, a complete IS
26
insertion element was present immediately upstream of the promoter element. Downstream from the termination codon is an insertion sequence that was homologous to the IS
Vs1
element reported to occur in a plasmid from
Vibrio salmonicida
that has been associated with another tetracycline resistance determinant,
tet
(E). Results of mating experiments demonstrated that the
E. coli tet
(M) gene was on a mobile element so that resistance to tetracycline and minocycline could be transferred to a susceptible strain by conjugation. Expression of the cloned
tet
(M) gene, under the control of its own promoter, provided tetracycline and minocycline resistance to the
E. coli
host.
Molecular and Biochemical Characterization of α-Glucosidase and α-Mannosidase and Their Clustered Genes from the Thermoacidophilic Archaeon
Picrophilus torridus
Authors: Angelov Angel , Putyrski Mateusz , Liebl Wolfgang 
Published: October 2006

ABSTRACT

The genes encoding a putative α-glucosidase (
aglA
) and an α-mannosidase (
manA
) appear to be physically clustered in the genome of the extreme acidophile
Picrophilus torridus
, a situation not found previously in any other organism possessing
aglA
or
manA
homologs. While archaeal α-glucosidases have been described, no α-mannosidase enzymes from the archaeal kingdom have been reported previously. Transcription start site mapping and Northern blot analysis revealed that despite their colinear orientation and the small intergenic space, the genes are independently transcribed, both producing leaderless mRNA.
aglA
and
manA
were cloned and overexpressed in
Escherichia coli
, and the purified recombinant enzymes were characterized with respect to their physicochemical and biochemical properties. AglA displayed strict substrate specificity and hydrolyzed maltose, as well as longer α-1,4-linked maltooligosaccharides. ManA, on the other hand, hydrolyzed all possible linkage types of α-glycosidically linked mannose disaccharides and was able to hydrolyze α3,α6-mannopentaose, which represents the core structure of many triantennary N-linked carbohydrates in glycoproteins. The probable physiological role of the two enzymes in the utilization of exogenous glycoproteins and/or in the turnover of the organism's own glycoproteins is discussed.
Defining the
Pseudomonas aeruginosa
SOS Response and Its Role in the Global Response to the Antibiotic Ciprofloxacin
Authors: Cirz Ryan T. , O'Neill Bryan M. , Hammond Jennifer A. , Head Steven R. , Romesberg Floyd E. 
Published: October 2006

ABSTRACT

Pseudomonas aeruginosa
infections can be virtually impossible to eradicate, and the evolution of resistance during antibiotic therapy is a significant concern. In this study, we use DNA microarrays to characterize the global transcriptional response of
P. aeruginosa
to clinical-like doses of the antibiotic ciprofloxacin and also to determine the component that is regulated by LexA cleavage and the SOS response. We find that genes involved in virtually every facet of metabolism are down-regulated in response to ciprofloxacin. The LexA-controlled SOS regulon identified by microarray analysis includes only 15 genes but does include several genes that encode proteins involved in recombination and replication, including two inducible polymerases known to play a role in mutation and the evolution of antibiotic resistance in other organisms. The data suggest that the inhibition of LexA cleavage during therapy might help combat this pathogen by decreasing its ability to adapt and evolve resistance.
The σ
E
Cell Envelope Stress Response of
Streptomyces coelicolor
Is Influenced by a Novel Lipoprotein, CseA
Authors: Hutchings Matthew I. , Hong Hee-Jeon , Leibovitz Emmanuelle , Sutcliffe Iain C. , Buttner Mark J. 
Published: October 2006

ABSTRACT

We have investigated the role of CseA in the σ
E
cell envelope stress response of the gram-positive bacterium
Streptomyces coelicolor
. σ
E
is an extracytoplasmic function RNA polymerase sigma factor required for normal cell envelope integrity in
S. coelicolor
. σ
E
is encoded within a four-gene operon that also encodes CseA, a protein of unknown function, CseB, a response regulator and CseC, a transmembrane sensor histidine kinase (Cse represents
c
ontrol of
s
igma
E
). Previous work has shown that transcription of the
sigE
gene is completely dependent on the CseBC two-component system and that the CseBC-σ
E
signal transduction system is induced by a wide variety of cell-wall-damaging agents. Here we address the role of CseA, a protein with no homologues outside the streptomycetes. We show that CseA is a novel lipoprotein localized to the extracytoplasmic face of the cell membrane and that loss of CseA results in upregulation of the
sigE
promoter.
The Rgg Regulator of
Streptococcus pyogenes
Influences Utilization of Nonglucose Carbohydrates, Prophage Induction, and Expression of the NAD-Glycohydrolase Virulence Operon
Authors: Dmitriev Alexander V. , McDowell Emily J. , Kappeler Kyle V. , Chaussee Michelle A. , Rieck Lindsey D. , Chaussee Michael S. 
Published: October 2006

ABSTRACT

The expression of many virulence-associated genes in
Streptococcus pyogenes
is controlled in a growth phase-dependent manner. Unlike the model organisms
Escherichia coli
and
Bacillus subtilis
, such regulation is apparently not dependent upon alternative sigma factors but appears to rely on complex interactions among several transcriptional regulators, including Rgg. The purpose of this study was to identify changes in gene expression associated with inactivation of the
rgg
gene in
S. pyogenes
strain NZ131 (serotype M49). To this end, the transcriptomes of wild-type and
rgg
mutant strains were analyzed during both the exponential and postexponential phases of growth using Affymetrix NimbleExpress gene chips. Genomewide differences in transcript levels were identified in both phases of growth. Inactivation of
rgg
disrupted coordinate expression of genes associated with the metabolism of nonglucose carbon sources, such as fructose, mannose, and sucrose. The changes were associated with an inability of the mutant strain to grow using these compounds as the primary carbon source. Bacteriophage transcript levels were also altered in the mutant strain and were associated with decreased induction of at least one prophage. Finally, transcripts encoding virulence factors involved in cytolysin-mediated translocation of NAD-glycohydrolase, including the immunity factor IFS and the cytolysin (streptolysin O [SLO]), were more abundant in the mutant strain, which correlated with the amount of NADase and SLO activities in culture supernatant fluids. The results provide further evidence that Rgg contributes to growth phase-dependent gene regulation in strain NZ131.
Replisome Localization in Vegetative and Aerial Hyphae of
Streptomyces coelicolor
Authors: Ruban-Ośmiałowska Beata , Jakimowicz Dagmara , Smulczyk-Krawczyszyn Aleksandra , Chater Keith F. , Zakrzewska-Czerwińska Jolanta 
Published: October 2006

ABSTRACT

Using a functional fusion of DnaN to enhanced green fluorescent protein, we examined the subcellular localization of the replisome machinery in the vegetative mycelium and aerial mycelium of the multinucleoid organism
Streptomyces coelicolor
. Chromosome replication took place in many compartments of both types of hypha, with the apical compartments of the aerial mycelium exhibiting the highest replication activity. Within a single compartment, the number of “current” ongoing DNA replications was lower than the expected chromosome number, and the appearance of fluorescent foci was often heterogeneous, indicating that this process is asynchronous within compartments and that only selected chromosomes undergo replication.
On the Time Course of Visual Word Recognition: An Event-related Potential Investigation using Masked Repetition Priming
Authors: Holcomb Phillip J. , Grainger Jonathan 
Published: October 2006

Abstract
The present study used event-related potentials (ERPs) to examine the time course of visual word recognition using a masked repetition priming paradigm. Participants monitored target words for occasional animal names, and ERPs were recorded to nonanimal critical items that were full repetitions, partial repetitions, or unrelated to the immediately preceding masked prime word. The results showed a strong modulation of the N400 and three earlier ERP components (P150, N250, and the P325) that we propose reflect sequential overlapping steps in the processing of printed words.
The Anatomy of Category-specific Object Naming in Neurodegenerative Diseases
Authors: Brambati S. M. , Myers D. , Wilson A. , Rankin K. P. , Allison S. C. , Rosen H. J. , Miller B. L. , Gorno-Tempini M. L. 
Published: October 2006

Abstract
Neuropsychological studies suggest that knowledge about living and nonliving objects is processed in separate brain regions. However, lesion and functional neuroimaging studies have implicated different areas. To address this issue, we used voxel-based morphometry to correlate accuracy in naming line drawings of living and nonliving objects with gray matter volumes in 152 patients with various neurodegenerative diseases. The results showed a significant positive correlation between gray matter volumes in bilateral temporal cortices and total naming accuracy regardless of category. Naming scores for living stimuli correlated with gray matter volume in the medial portion of the right anterior temporal pole, whereas naming accuracy for familiarity-matched nonliving items correlated with the volume of the left posterior middle temporal gyrus. A previous behavioral study showed that the living stimuli used here also had in common the characteristic that they were defined by shared sensory semantic features, whereas items in the nonliving group were defined by their action-related semantic features. We propose that the anatomical segregation of living and nonliving categories is the result of their defining semantic features and the distinct neural subsystems used to process them.
It's Early: Event-related Potential Evidence for Initial Interaction of Syntax and Prosody in Speech Comprehension
Authors: Eckstein Korinna , Friederici Angela D. 
Published: October 2006

Abstract
Psycholinguistic theories assume an interaction between prosody and syntax during language processing. Based on studies using mostly off-line methods, it is unclear whether an interaction occurs at later or initial processing stages. Using event-related potentials, the present study provides neurophysiological evidence for a prosody and syntax interaction in initial processing. The sentence material contained mere prosodic and syntactic as well as combined prosodic-syntactic violations. For the syntax violation, the critical word appeared after a preposition. The suffix of the critical word either indicated a noun fulfilling the syntactic requirements of the preceding preposition or a verb causing a word category violation. For the prosodic manipulation, congruent critical words were normally intonated (signaling sentence continuation) while prosodically incongruent critical words signaled sentence end. For the mere prosodic incongruity, a broadly distributed negativity was observed at the critical word-stem (300–500 msec aligned to word onset). In response to a mere syntactic error, a left temporal negativity was elicited in an early time window (200–400 msec aligned to suffix onset), taken to reflect initial phrase structure building processes. In contrast, in response to the combined prosodic-syntactic violation, an early temporal negativity showed up bilaterally at the suffix in the same time window. Our interpretation is that the process of initial structure building as reflected in the early left anterior negativity recruits additional right hemispheric neural resources when the critical word contains both syntactic and prosodic violations. This suggests the immediate influence of phrasal prosody during the initial parsing stage in speech processing.
Local Regimes of Atmospheric Variability: A Case Study of Southern California
Authors: Conil Sebastien , Hall Alex 
Published: October 2006

Abstract
The primary regimes of local atmospheric variability are examined in a 6-km regional atmospheric model of the southern third of California, an area of significant land surface heterogeneity, intense topography, and climate diversity. The model was forced by reanalysis boundary conditions over the period 1995–2003. The region is approximately the same size as a typical grid box of the current generation of general circulation models used for global climate prediction and reanalysis product generation, and so can be thought of as a laboratory for the study of climate at spatial scales smaller than those resolved by global simulations and reanalysis products. It is found that the simulated circulation during the October–March wet season, when variability is most significant, can be understood through an objective classification technique in terms of three wind regimes. The composite surface wind patterns associated with these regimes exhibit significant spatial structure within the model domain, consistent with the complex topography of the region. These regimes also correspond nearly perfectly with the simulation’s highly structured patterns of variability in hydrology and temperature, and therefore are the main contributors to the local climate variability. The regimes are approximately equally likely to occur regardless of the phase of the classical large-scale modes of atmospheric variability prevailing in the Pacific–North American sector. The high degree of spatial structure of the local regimes and their tightly associated climate impacts, as well as their ambiguous relationship with the primary modes of large-scale variability, demonstrate that the local perspective offered by the high-resolution model is necessary to understand and predict the climate variations of the region.