bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conquering the city: The representation of Milan in Massimo Bontempelli's La vita operosa
Authors: Storchi Simona 
Published: October 2002

SummaryThe article focuses on the representation of Milan in Massimo Bontempelli's 1920 short novel La vita operosa. In this novel the protagonist-narrator, a writer and journalist returning to Milan after the end of the war, is confronted with a city which has lost all its points of reference and has turned into a place dominated by the ethics of speed and profit. In this context, the protagonist's adventures in Milan assume the features of an ironic and self-ironic journey of discovery for the letterato who finds himself having to redefine his identity and role in a society whose taste and values have profoundly changed.
Effects of Multiple Deletions of Murein Hydrolases on Viability, Septum Cleavage, and Sensitivity to Large Toxic Molecules in
Escherichia coli
Authors: Heidrich Christoph , Ursinus Astrid , Berger Jürgen , Schwarz Heinz , Höltje Joachim-Volker 
Published: October 2002

ABSTRACT

The multiplicity of murein hydrolases found in most bacteria presents an obstacle to demonstrating the necessity of these potentially autolytic enzymes. Therefore,
Escherichia coli
mutants with deletions in multiple murein hydrolases, including lytic transglycosylases, amidases, and
dd
-endopeptidases, were constructed. Even a mutant from which seven different hydrolases were deleted was viable and grew at a normal rate. However, penicillin-induced lysis was retarded. Most of the mutants were affected in septum cleavage, which resulted in the formation of chains of cells. All three enzymes were shown to be capable of splitting the septum. Failure to cleave the septum resulted in an increase in outer membrane permeability, and thus the murein hydrolase mutants did not grow on MacConkey agar plates. In addition, the hydrolase mutants not only could be lysed by lysozyme in the absence of EDTA but also were sensitive to high-molecular-weight antibiotics, such as vancomycin and bacitracin, which are normally ineffective against
E. coli.
The PrpC Serine-Threonine Phosphatase and PrkC Kinase Have Opposing Physiological Roles in Stationary-Phase
Bacillus subtilis
Cells
Authors: Gaidenko Tatiana A. , Kim Tae-Jong , Price Chester W. 
Published: October 2002

ABSTRACT

Loss of the PrpC serine-threonine phosphatase and the associated PrkC kinase of
Bacillus subtilis
were shown to have opposite effects on stationary-phase physiology by differentially affecting cell density, cell viability, and accumulation of β-galactosidase from a general stress reporter fusion. These pleiotropic effects suggest that PrpC and PrkC have important regulatory roles in stationary-phase cells. Elongation factor G (EF-G) was identified as one possible target of the PrpC and PrkC pair in vivo, and purified PrpC and PrkC manifested the predicted phosphatase and kinase activities against EF-G in vitro.
Expression, Purification, and Characterization of AknX Anthrone Oxygenase, Which Is Involved in Aklavinone Biosynthesis in
Streptomyces galilaeus
Authors: Chung Jin-young , Fujii Isao , Harada Shigeharu , Sankawa Ushio , Ebizuka Yutaka 
Published: October 2002

ABSTRACT

In streptomycete anthracycline biosynthetic gene clusters, small open reading frames are located just upstream of minimal polyketide synthase genes.
aknX
is such a gene found in the aklavinone-aclacinomycin biosynthetic gene cluster of
Streptomyces galilaeus
. In order to identify its function, the
aknX
gene was expressed in
Escherichia coli
. The cell extract prepared from
E. coli
cells overexpressing AknX protein exhibited anthrone oxygenase activity, which converted emodinanthrone to anthraquinone emodin. This indicates that AknX and related gene products such as DnrG and SnoaB are involved in the formation of aklanonic acid from its anthrone precursor, as suggested by their homology with TcmH and ActVA6. The AknX protein fused with a His
6
tag was efficiently purified to homogeneity by Ni
2+
affinity and anion-exchange column chromatography. The native molecular mass of AknX was estimated to be 42 kDa by gel filtration. Thus, native AknX is considered to have a homotrimeric subunit structure. AknX, like TcmH and ActVA6, possesses no apparent prosthetic group for oxygen activation. Site-directed mutagenesis was carried out to identify the key amino acid residue(s) involved in the oxygenation reaction. Of seven AknX mutants expressed, the W67F mutant showed significantly reduced oxygenase activity, suggesting the important role of the W67 residue in the AknX reaction. A possible mechanism for the reaction via peroxy anion intermediate is proposed.
Regulation of the
Bacillus subtilis bcrC
Bacitracin Resistance Gene by Two Extracytoplasmic Function σ Factors
Authors: Cao Min , Helmann John D. 
Published: October 2002

ABSTRACT

Bacitracin resistance is normally conferred by either of two major mechanisms, the BcrABC transporter, which pumps out bacitracin, or BacA, an undecaprenol kinase that provides C
55
-isoprenyl phosphate by de novo synthesis. We demonstrate that the
Bacillus subtilis bcrC
(
ywoA
) gene, encoding a putative bacitracin transport permease, is an important bacitracin resistance determinant. A
bcrC
mutant strain had an eightfold-higher sensitivity to bacitracin. Expression of
bcrC
initiated from a single promoter site that could be recognized by either of two extracytoplasmic function (ECF) σ factors, σ
X
or σ
M
. Bacitracin induced expression of
bcrC
, and this induction was dependent on σ
M
but not on σ
X
. Under inducing conditions, expression was primarily dependent on σ
M
. As a consequence, a
sigM
mutant was fourfold more sensitive to bacitracin, while the
sigX
mutant was only slightly sensitive. A
sigX sigM
double mutant was similar to a
bcrC
mutant in sensitivity. These results support the suggestion that one function of
B. subtilis
ECF σ factors is to coordinate antibiotic stress responses.
Presence of a Characteristic D-D-E Motif in IS1Transposase
Authors: Ohta Shinya , Tsuchida Ken , Choi Sunju , Sekine Yasuhiko , Shiga Yasuyuki , Ohtsubo Eiichi 
Published: October 2002

ABSTRACTTransposases encoded by various transposable DNA elements and retroviral integrases belong to a family of proteins with three conserved acidic amino acids, D, D, and E, constituting the D-D-E motif that represents the active center of the proteins. IS1, one of the smallest transposable elements in bacteria, encodes a transposase which has been thought not to belong to the family of proteins with the D-D-E motif. In this study, we found several IS1family elements that were widely distributed not only in eubacteria but also in archaebacteria. The alignment of the transposase amino acid sequences from these IS1family elements showed that out of 14 acidic amino acids present in IS1transposase, three (D, D, and E) were conserved in corresponding positions in the transposases encoded by all the elements. Comparison of the IS1transposase with other proteins with the D-D-E motif revealed that the polypeptide segments surrounding each of the three acidic amino acids were similar. Furthermore, the deduced secondary structures of the transposases encoded by IS1family elements were similar to one another and to those of proteins with the D-D-E motif. These results strongly suggest that IS1transposase has the D-D-E motif and thus belongs to the family of proteins with the D-D-E motif. In fact, mutant IS1transposases with an amino acid substitution for each of the three acidic amino acids possibly constituting the D-D-E motif were not able to promote transposition of IS1, supporting this hypothesis. The D-D-E motif identified in IS1transposase differs from those in the other proteins in that the polypeptide segment between the second D and third E in IS1transposase is the shortest, 24 amino acids in length. Because of this difference, the presence of the D-D-E motif in IS1transposase has not been discovered for some time.
Genome Analysis and Strain Comparison of Correia Repeats and Correia Repeat-Enclosed Elements in Pathogenic
Neisseria
Authors: Liu Shi V. , Saunders Nigel J. , Jeffries Alex , Rest Richard F. 
Published: October 2002

ABSTRACT

Whole genome sequences of
Neisseria meningitidis
strains Z2491 and MC58 and
Neisseria gonorrhoeae
FA1090 were analyzed for Correia repeats (CR) and CR-enclosed elements (CREE). A total of 533, 516, and 256 copies of CR and 270, 261, and 102 copies of CREE were found in these three genomes, respectively. The lengths of CREE range from 28 to 348 bp, and the lengths of multicopy CREE appear mainly in the ranges of 154 to 156 bp and 105 to 107 bp. The distribution of CREE lengths is similar between the two
N. meningitidis
genomes, with a greater number of 154- to 156-bp CREE (163 and 152 copies in
N. meningitidis
strain Z2491 and
N. meningitidis
strain MC58, respectively) than 105- to 107-bp CREE (72 and 77 copies). In the
N. gonorrhoeae
strain FA1090 genome there are relatively more 105- to 107-bp CREE (51 copies) than 154- to 156-bp CREE (36 copies). The genomic distribution of 107-bp CREE also shows similarity between the two
N. meningitidis
strains (15 copies share the same loci) and differences between
N. meningitidis
strains and
N. gonorrhoeae
FA1090 (only one copy is located in the same locus). Detailed sequence analysis showed that both the terminal inverted repeats and the core regions of CREE are composed of distinct basic sequence blocks. Direct TA dinucleotide repeats exist at the termini of all CREE. A survey of DNA sequence upstream of the sialyltransferase gene,
lst
, in several
Neisseria
isolates showed that 5
N. meningitidis
strains contain a 107-bp CREE in this region but 25
N. gonorrhoeae
strains show an exact absence of a 105-bp sequence block (i.e., the 107-bp CREE without a 5′ TA dinucleotide) in the same region. Whole-genome sequence analysis confirmed that this 105-bp indel exists in many homologous 107-bp CREE loci. Thus, we postulate that all CREE are made of target TA with indels of various lengths. Analysis of 107-bp CREE revealed that they exist predominantly in intergenic regions and are often near virulence, metabolic, and transporter genes. The abundance of CREE in
Neisseria
genomes suggests that they may have played a role in genome organization, function, and evolution. Their differential distribution in different pathogenic
Neisseria
strains may contribute to the distinct behaviors of each
Neisseria
species.
Poly-β-Hydroxybutyrate Biosynthesis in the Facultative Methylotroph
Methylobacterium extorquens
AM1: Identification and Mutation of
gap11
,
gap20
, and
phaR
Authors: Korotkova Natalia , Chistoserdova Ludmila , Lidstrom Mary E. 
Published: October 2002

ABSTRACT

Methylobacterium extorquens
AM1, a serine cycle facultative methylotroph, accumulates poly-β-hydroxybutyrate (PHB) as a carbon and energy reserve material during growth on both multicarbon- and single-carbon substrates. Recently, the identification and mutation of the genes involved in the biosynthesis and degradation of PHB have been described for this bacterium, demonstrating that two of the genes of the PHB cycle (
phaA
and
phaB
) are also involved in C
1
and C
2
metabolism, as part of a novel pathway for glyoxylate regeneration in the serine cycle (N. Korotkova and M. E. Lidstrom, J. Bacteriol. 183:1038-1046, 2001; N. Korotkova, L. Chistoserdova, V. Kuksa, and M. E. Lidstrom, J. Bacteriol. 184:1750-1758, 2002). In this work, three new genes involved in PHB biosynthesis in this bacterium have been investigated via mutation and phenotypic analysis:
gap11
,
gap20
, and
phaR
. We demonstrate that
gap11
and
gap20
encode two major granule-associated proteins (phasins) and that mutants with mutations in these genes are defective in PHB production and also in growth on C
2
compounds, while they show wild-type growth characteristics on C
1
or multicarbon compounds. The
phaR
mutant shows defects in both PHB accumulation and growth characteristics when grown on C
1
compounds and has defects in PHB accumulation but grows normally on C
3
and C
4
compounds, while both PHB accumulation and growth rate are at wild-type levels during growth on C
2
compounds. Our results suggest that this phenotype is due to altered fluxes of acetyl coenzyme A (CoA), a major intermediate in C
1
, C
2
, and heterotrophic metabolism in
M. extorquens
AM1, as well as the entry metabolite for the PHB cycle. Therefore, it seems likely that PhaR acts to control acetyl-CoA flux to PHB in this methylotrophic bacterium.
Chloride, a New Environmental Signal Molecule Involved in Gene Regulation in a Moderately Halophilic Bacterium,Halobacillus halophilus
Authors: Roeβler Markus , Müller Volker 
Published: October 2002

ABSTRACTThe gram-positive, aerobic, moderately halophilic bacteriumHalobacillus halophilusis challenged in its environment by frequently changing salt (NaCl) concentrations. Recently,H. halophiluswas shown to be the first prokaryote that is dependent on Cl−for growth. In a search for the biological function of Cl−in this prokaryote, we identified different Cl−-dependent processes, which suggests a more general role for Cl−in the metabolism ofH. halophilus. To analyze the effect of Cl−in more detail, we concentrated on one model system, the Cl−-dependent production of flagella, and aimed to identify the molecular basis for the Cl−dependence of flagellum production. Here, we report that synthesis of the major subunit of the flagellum, FliC, is dependent on the Cl−concentration of the medium, as determined by Western blot analyses. The gene encoding FliC was cloned and sequenced, and Northern blot as well as reverse transcriptase PCR analyses revealed that expression offliCis Cl−dependent. FliC is the first protein of known function demonstrated to be synthesized in a Cl−-dependent manner in a prokaryote. Two-dimensional gel electrophoresis of cells grown under different conditions revealed five more Cl−-induced proteins; these were identified by N-terminal sequencing and database searches to be orthologs of proteins involved in stress response inBacillus subtilis. The data indicate that Cl−is an important environmental signal in this moderate halophile and regulates protein synthesis and gene expression. Furthermore, the data may suggest that Cl−plays a role in the signal transduction involved in salt perception by this bacterium.
Escherichia coli
Gene Expression Responsive to Levels of the Response Regulator EvgA
Authors: Masuda Nobuhisa , Church George M. 
Published: October 2002

ABSTRACT

To investigate the function of the EvgA response regulator, we compared the genome-wide transcription profile of EvgA-overexpressing and EvgA-lacking
Escherichia coli
strains by oligonucleotide microarrays. The microarray measurements allowed the identification of at least 37 EvgA-activated genes, including acid resistance-related genes
gadABC
and
hdeAB
, efflux pump genes
yhiUV
and
emrK
, and 21 genes with unknown function. EvgA overexpression conferred acid resistance to exponentially growing cells. This acid resistance was abolished by deletion of
ydeP
,
ydeO
, or
yhiE
, which was induced by EvgA overexpression. These results suggest that
ydeP
,
ydeO
, and
yhiE
are novel genes related to acid resistance and that EvgA regulates several acid resistance genes. Furthermore, the deletion of
yhiE
completely abolished acid resistance in stationary-phase cells, suggesting that YhiE plays a critical role in stationary-phase acid resistance. The multidrug resistance in an
acrB
deletion mutant caused by EvgA overexpression was completely abolished by deletion of
yhiUV
, while the
emrKY
deletion had no effect on the increase in resistance by EvgA overexpression. In addition, EvgA overexpression did not confer resistance in a
tolC
-deficient strain. These results suggest that YhiUV induced by EvgA overexpression is functionally associated with TolC and contributes to multidrug resistance.
Phenotypes of
lexA
Mutations in
Salmonella enterica
: Evidence for a Lethal
lexA
Null Phenotype Due to the Fels-2 Prophage
Authors: Bunny Kim , Liu Jing , Roth John 
Published: October 2002

ABSTRACT

The LexA protein of
Escherichia coli
represses the damage-inducible SOS regulon, which includes genes for repair of DNA. Surprisingly,
lexA
null mutations in
Salmonella enterica
are lethal even with a
sulA
mutation, which corrects
lexA
lethality in
E. coli
. Nine suppressors of lethality isolated in a
sulA
mutant of
S. enterica
had lost the Fels-2 prophage, and seven of these (which grew better) had also lost the Gifsy-1 and Gifsy-2 prophages. All three phage genomes included a homologue of the
tum
gene of coliphage 186, which encodes a LexA-repressed cI antirepressor. The
tum
homologue of Fels-2 was responsible for
lexA
lethality and had a LexA-repressed promoter. This basis of
lexA
lethality was unexpected because the four prophages of
S. enterica
LT2 are not strongly UV inducible and do not sensitize strains to UV killing. In
S. enterica
,
lexA
(Ind
−
) mutants have the same phenotypes as their
E. coli
counterparts. Although
lexA
null mutants express their error-prone DinB polymerase constitutively, they are not mutators in either
S. enterica
or
E. coli
.
Bacillus subtilisYhaM, a Member of a New Family of 3′-to-5′ Exonucleases in Gram-Positive Bacteria
Authors: Oussenko Irina A. , Sanchez Roberto , Bechhofer David H. 
Published: October 2002

ABSTRACTA strain ofBacillus subtilislacking two 3′-to-5′ exoribonucleases, polynucleotide phosphorylase (PNPase) and RNase R, was used to purify another 3′-to-5′ exoribonuclease, which is encoded by theyhaMgene. YhaM was active in the presence of Mn2+(or Co2+), was inactive in the presence of Mg2+, and could also degrade single-stranded DNA. The half-life of bulk mRNA in a mutant lacking PNPase, RNase R, and YhaM was not significantly different from that of the wild type, suggesting the existence of additional activities that can participate in mRNA turnover. Sequence homologues of YhaM were found only in gram-positive organisms. TheStaphylococcus aureushomologue, CBF1, which had been characterized as a double-stranded DNA binding protein involved in plasmid replication, was also shown to be an Mn2+-dependent exoribonuclease. YhaM protein has a C-terminal “HD domain,” found in metal-dependent phosphohydrolases. By structure modeling, it was shown that YhaM also contains an N-terminal “OB-fold,” present in many oligosaccharide- and oligonucleotide-binding proteins. The combination of these two domains is unique. Thus, YhaM and 10 related proteins from gram-positive organisms constitute a new exonuclease family.
Gene Structure, Organization, Expression, and Potential Regulatory Mechanisms of Arginine Catabolism inEnterococcus faecalis
Authors: Barcelona-Andrés Belén , Marina Alberto , Rubio Vicente 
Published: October 2002

ABSTRACTAlthoughEnteroccus faecalisis the paradigm for biochemical studies on the arginine deiminase (ADI) pathway of fermentative arginine catabolism, little genetic information exists on this pathway in this organism. We fill this important gap by characterizing, in an 8,228-bp region cloned from a λgt11 genomic library ofE. faecalis, a five-gene cluster forming a transcriptional unit (revealed by Northern blots and primer extension inE. faecalis) that corresponds to the ADI operon. Four additional genes in the opposite DNA strand and one in the same DNA strand are also identified. Studies on the protein products, including heterologous expression and/or sequence comparisons, allow us to ascertain or propose functions for all but 1 of the 10 genes. The ADI operon genes,arcABCRD, encode, respectively, ADI, ornithine transcarbamylase, carbamate kinase, a putative Crp/Fnr-type regulator (ArcR), and a putative ornithine-arginine antiporter (ArcD). Arginine induces the expression ofarcABCRD, most likely by means of two homologous ArgR/AhrC-type regulators encoded by two genes,argR1andargR2, that precedearcABCRDin each DNA strand and that are transcribed monocistronically, their transcription being influenced differentially by glucose and arginine. Potential ArgR1/ArgR2 (double and single) binding sequences are found in the promoter regions ofarcAand ofargR1/argR2themselves. In addition, putative binding sequences for ArcR and for CcpA are found, respectively, in theargR1/argR2andarcApromoter regions. Of the three other genes identified, two form a transcriptional unit and encode a putative metal-sensitive transcriptional regulator (ArsR) and a cysteine protease.
Genes Coding for a New Pathway of Aerobic Benzoate Metabolism in
Azoarcus evansii
Authors: Gescher Johannes , Zaar Annette , Mohamed Magdy , Schägger Hermann , Fuchs Georg 
Published: October 2002

ABSTRACT

A new pathway for aerobic benzoate oxidation has been postulated for
Azoarcus evansii
and for a
Bacillus stearothermophilus
-like strain. Benzoate is first transformed into benzoyl coenzyme A (benzoyl-CoA), which subsequently is oxidized to 3-hydroxyadipyl-CoA and then to 3-ketoadipyl-CoA; all intermediates are CoA thioesters. The genes coding for this benzoate-induced pathway were investigated in the β-proteobacterium
A. evansii
. They were identified on the basis of N-terminal amino acid sequences of purified benzoate metabolic enzymes and of benzoate-induced proteins identified on two-dimensional gels. Fifteen genes probably coding for the benzoate pathway were found to be clustered on the chromosome. These genes code for the following functions: a putative ATP-dependent benzoate transport system, benzoate-CoA ligase, a putative benzoyl-CoA oxygenase, a putative isomerizing enzyme, a putative ring-opening enzyme, enzymes for β-oxidation of CoA-activated intermediates, thioesterase, and lactone hydrolase, as well as completely unknown enzymes belonging to new protein families. An unusual putative regulator protein consists of a regulator protein and a shikimate kinase I-type domain. A deletion mutant with a deletion in one gene (
boxA
) was unable to grow with benzoate as the sole organic substrate, but it was able to grow with 3-hydroxybenzoate and adipate. The data support the proposed pathway, which postulates operation of a new type of ring-hydroxylating dioxygenase acting on benzoyl-CoA and nonoxygenolytic ring cleavage. A β-oxidation-like metabolism of the ring cleavage product is thought to lead to 3-ketoadipyl-CoA, which finally is cleaved into succinyl-CoA and acetyl-CoA.
Postgenomic Analysis of Four Novel Antigens of Group A
Streptococcus
: Growth Phase-Dependent Gene Transcription and Human Serologic Response
Authors: Reid Sean D. , Green Nicole M. , Sylva Gail L. , Voyich Jovanka M. , Stenseth Elisha T. , DeLeo Frank R. , Palzkill Timothy , Low Donald E. , Hill Harry R. , Musser James M. 
Published: October 2002

ABSTRACT

Analysis of three group A
Streptococcus
genomes (serotypes M1, M3, and M18) recently identified four previously undescribed genes that encode extracellular proteins. Each of these genes encode proteins with an LPXTG amino acid motif that covalently links many virulence factors produced by gram-positive bacteria to the cell surface. Western immunoblot analysis of serum samples obtained from 80 patients with invasive infections, noninvasive soft tissue infections, pharyngitis, and rheumatic fever indicated that these four proteins are expressed in vivo. However, the level of gene transcript and the time of maximal gene transcription varied in representative serotype M1, M3, and M18 strains. Surface expression of two proteins was confirmed by flow cytometry. Studies using a mouse infection model suggest that antibodies specific for one of the proteins (Spy0843) may contribute to a protective host immune response against a serotype M1 infection. These results are additional evidence that postgenomic strategies provide new ways to identify and investigate novel bacterial proteins that may participate in host-pathogen interactions or serve as targets for therapeutics research.