bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Choline-Converting Pathway in
Staphylococcus xylosus
C2A: Genetic and Physiological Characterization
Authors: Rosenstein Ralf , Futter-Bryniok Detlinde , Götz Friedrich 
Published: December 2019

ABSTRACT

A
Staphylococcus xylosus
C2A gene cluster, which encodes enzymes in the pathway for choline uptake and dehydrogenation (
cud
), to form the osmoprotectant glycine betaine, was identified. The
cud
locus comprises four genes, three of which encode proteins with significant similarities to those known to be involved in choline transport and conversion in other organisms. The physiological role of the gene products was confirmed by analysis of
cud
deletion mutants. The fourth gene possibly codes for a regulator protein. Part of the gene cluster was shown to be transcriptionally regulated by choline and elevated NaCl concentrations as inducers.
Structure of a New Glycolipid from the
Mycobacterium avium-Mycobacterium intracellulare
Complex
Authors: Watanabe Motoko , Ohta Akihiro , Sasaki Shun-ichi , Minnikin David E. 
Published: December 2019

ABSTRACT

From the lipid fraction of a freeze-dried cell mass of a strain of the
Mycobacterium avium-Mycobacterium intracellulare
complex, a new glycolipid was isolated and was characterized as 5-mycoloyl-α-arabinofuranosyl (1→1′)-glycerol, mainly on the basis of nuclear magnetic resonance spectroscopy studies.
NahW, a Novel, Inducible Salicylate Hydroxylase Involved in Mineralization of Naphthalene by
Pseudomonas stutzeri
AN10
Authors: Bosch Rafael , Moore Edward R. B. , García-Valdés Elena , Pieper Dietmar H. 
Published: December 2019

ABSTRACT

Two genes,
nahG
and
nahW
, encoding two independent salicylate 1-hydroxylases have been identified in the naphthalene-degrading strain
Pseudomonas stutzeri
AN10. While
nahG
resides in the same transcriptional unit as the
meta
-cleavage pathway genes, forming the naphthalene degradation lower pathway,
nahW
is situated outside but in close proximity to this transcriptional unit. The
nahG
and
nahW
genes of
P. stutzeri
AN10 are induced and expressed upon incubation with salicylate, and the enzymes that are encoded, NahG and NahW, are involved in naphthalene and salicylate metabolism. Both genes,
nahG
and
nahW
, have been cloned in
Escherichia coli
JM109. The overexpression of these genes yields peptides with apparent molecular masses of 46 kDa (NahG) and 43 kDa (NahW), respectively. Both enzymes exhibit broad substrate specificities and metabolize salicylate, methylsalicylates, and chlorosalicylates. However, the relative rates by which the substituted analogs are transformed differ considerably.
Structural and Functional Significance of the FGL Sequence of the Periplasmic Chaperone Caf1M of
Yersinia pestis
Authors: Chapman David A. G. , Zavialov Anton V. , Chernovskaya Tatiana V. , Karlyshev Andrey V. , Zav’yalova Galina A. , Vasiliev Anatoly M. , Dudich Igor V. , Abramov Vyacheslav M. , Zav’yalov Vladimir P. , MacIntyre Sheila 
Published: December 2019

ABSTRACT

The periplasmic molecular chaperone Caf1M of
Yersinia pestis
is a typical representative of a subfamily of specific chaperones involved in assembly of surface adhesins with a very simple structure. One characteristic feature of this Caf1M-like subfamily is possession of an extended, variable sequence (termed FGL) between the F1 and subunit binding G1 β-strands. In contrast, FGS subfamily members, characterized by PapD, have a short F1-G1 loop and are involved in assembly of complex pili. To elucidate the structural and functional significance of the FGL sequence, a mutant Caf1M molecule (dCaf1M), in which the 27 amino acid residues between the F1 and G1 β-strands had been deleted, was constructed. Expression of the mutated
caf1M
in
Escherichia coli
resulted in accumulation of high levels of dCaf1M. The far-UV circular dichroism spectra of the mutant and wild-type proteins were indistinguishable and exhibited practically the same temperature and pH dependencies. Thus, the FGL sequence of Caf1M clearly does not contribute significantly to the stability of the protein conformation. Preferential cleavage of Caf1M by trypsin at Lys-119 confirmed surface exposure of this part of the FGL sequence in the isolated chaperone and periplasmic chaperone-subunit complex. There was no evidence of surface-localized Caf1 subunit in the presence of the Caf1A outer membrane protein and dCaf1M. In contrast to Caf1M, dCaf1M was not able to form a stable complex with Caf1 nor could it protect the subunit from proteolytic degradation in vivo. This demonstration that the FGL sequence is required for stable chaperone-subunit interaction, but not for folding of a stable chaperone, provides a sound basis for future detailed molecular analyses of the FGL subfamily of chaperones.
Control of Nitrogen Catabolite Repression Is Not Affected by the tRNA
Gln-CUU
Mutation, Which Results in Constitutive Pseudohyphal Growth of
Saccharomyces cerevisiae
Authors: Beeser Alexander E. , Cooper Terrance G. 
Published: December 2019

ABSTRACT

Saccharomyces cerevisiae
responds to nitrogen availability in several ways. (i) The cell is able to distinguish good nitrogen sources from poor ones through a process designated nitrogen catabolite repression (NCR). Good and poor nitrogen sources do not demonstrably affect the cell cycle other than to influence the cell’s doubling time. (ii) Nitrogen starvation promotes the initiation of sporulation and pseudohyphal growth. (iii) Nitrogen starvation strongly affects the cell cycle; nitrogen-starved cells arrest in G
1
. A specific allele of the
SUP70/CDC65
tRNA
Gln
gene (
sup70-65
) has been reported to be defective in nitrogen signaling associated with pseudohyphal formation, sporulation, and NCR. Our data confirm that pseudohyphal growth occurs gratuitously in
sup70-65
mutants cultured in nitrogen-rich medium at 30°C. However, we find neither any defect in NCR in the
sup70-65
mutant nor any alteration in the control of
YVH1
expression, which has been previously shown to be specifically induced by nitrogen starvation.
Cloning and Characterization of Two Bistructural S-Layer-RTX Proteins from
Campylobacter rectus
Authors: Braun Martin , Kuhnert Peter , Nicolet Jacques , Burnens André P. , Frey Joachim 
Published: December 2019

ABSTRACT

Campylobacter rectus
is an important periodontal pathogen in humans. A surface-layer (S-layer) protein and a cytotoxic activity have been characterized and are thought to be its major virulence factors. The cytotoxic activity was suggested to be due to a pore-forming protein toxin belonging to the RTX (repeats in the structural toxins) family. In the present work, two closely related genes,
csxA
and
csxB
(for
C. rectus
S-layer and RTX protein) were cloned from
C. rectus
and characterized. The Csx proteins appear to be bifunctional and possess two structurally different domains. The N-terminal part shows similarity with S-layer protein, especially SapA and SapB of
C. fetus
and Crs of
C. rectus
. The C-terminal part comprising most of CsxA and CsxB is a domain with 48 and 59 glycine-rich canonical nonapeptide repeats, respectively, arranged in three blocks. Purified recombinant Csx peptides bind Ca
2+
. These are characteristic traits of RTX toxin proteins. The S-layer and RTX domains of Csx are separated by a proline-rich stretch of 48 amino acids. All
C. rectus
isolates studied contained copies of either the
csxA
or
csxB
gene or both;
csx
genes were absent from all other
Campylobacter
and
Helicobacter
species examined. Serum of a patient with acute gingivitis showed a strong reaction to recombinant Csx protein on immunoblots.
Mitomycin Resistance in
Streptomyces lavendulae
Includes a Novel Drug-Binding-Protein-Dependent Export System
Authors: Sheldon Paul J. , Mao Yingqing , He Min , Sherman David H. 
Published: December 2019

ABSTRACT

Sequence analysis of
Streptomyces lavendulae
NRRL 2564 chromosomal DNA adjacent to the mitomycin resistance locus
mrd
(encoding a previously described mitomycin-binding protein [P. Sheldon, D. A. Johnson, P. R. August, H.-W. Liu, and D. H. Sherman, J. Bacteriol. 179:1796–1804, 1997]) revealed a putative mitomycin C (MC) transport gene (
mct
) encoding a hydrophobic polypeptide that has significant amino acid sequence similarity with several actinomycete antibiotic export proteins. Disruption of
mct
by insertional inactivation resulted in an
S. lavendulae
mutant strain that was considerably more sensitive to MC. Expression of
mct
in
Escherichia coli
conferred a fivefold increase in cellular resistance to MC, led to the synthesis of a membrane-associated protein, and correlated with reduced intracellular accumulation of the drug. Coexpression of
mct
and
mrd
in
E. coli
resulted in a 150-fold increase in resistance, as well as reduced intracellular accumulation of MC. Taken together, these data provide evidence that MRD and Mct function as components of a novel drug export system specific to the mitomycins.
Cyclic AMP Can Decrease Expression of Genes Subject to Catabolite Repression in
Saccharomyces cerevisiae
Authors: Zaragoza Oscar , Lindley Chris , Gancedo Juana M. 
Published: December 2019

ABSTRACT

External cyclic AMP (cAMP) hindered the derepression of gluconeogenic enzymes in a
pde2
mutant of
Saccharomyces cerevisiae
, but it did not prevent invertase derepression. cAMP reduced nearly 20-fold the transcription driven by upstream activation sequence (UAS1

FBP1

) from
FBP1
, encoding fructose-1,6-bisphosphatase; it decreased 2-fold the activation of transcription by UAS2

FBP1

. Nuclear extracts from cells derepressed in the presence of cAMP were impaired in the formation of specific UAS

FBP1

-protein complexes in band shift experiments. cAMP does not appear to act through the repressing protein Mig1. Control of
FBP1
transcription through cAMP is redundant with other regulatory mechanisms.
Bordetella pertussis waaAEncodes a Monofunctional 2-Keto-3-Deoxy-d-manno-Octulosonic Acid Transferase That Can Complement anEscherichia coli waaAMutation
Authors: Isobe Tomoko , White Kimberley A. , Allen Andrew G. , Peacock Michael , Raetz Christian R. H. , Maskell Duncan J. 
Published: December 2019

ABSTRACTBordetella pertussislipopolysaccharide (LPS) contains a single 2-keto-3-deoxy-d-manno-octulosonic acid (Kdo) residue, whereas LPS fromEscherichia colicontains at least two. Here we report thatB. pertussis waaAencodes an enzyme capable of transferring only a single Kdo during the biosynthesis of LPS and that this activity is sufficient to complement anE. coli waaAmutation.
Function of Coenzyme F
420
in Aerobic Catabolism of 2,4,6-Trinitrophenol and 2,4-Dinitrophenol by
Nocardioides simplex
FJ2-1A
Authors: Ebert Sybille , Rieger Paul-Gerhard , Knackmuss Hans-Joachim 
Published: December 2019

ABSTRACT

2,4,6-Trinitrophenol (picric acid) and 2,4-dinitrophenol were readily biodegraded by the strain
Nocardioides simplex
FJ2-1A. Aerobic bacterial degradation of these π-electron-deficient aromatic compounds is initiated by hydrogenation at the aromatic ring. A two-component enzyme system was identified which catalyzes hydride transfer to picric acid and 2,4-dinitrophenol. Enzymatic activity was dependent on NADPH and coenzyme F
420
. The latter could be replaced by an authentic preparation of coenzyme F
420
from
Methanobacterium thermoautotrophicum
. One of the protein components functions as a NADPH-dependent F
420
reductase. A second component is a hydride transferase which transfers hydride from reduced coenzyme F
420
to the aromatic system of the nitrophenols. The N-terminal sequence of the F
420
reductase showed high homology with an F
420
-dependent NADP reductase found in archaea. In contrast, no N-terminal similarity to any known protein was found for the hydride-transferring enzyme.
Identification and Characterization of a New Porin Gene of
Klebsiella pneumoniae
: Its Role in β-Lactam Antibiotic Resistance
Authors: Doménech-Sánchez Antonio , Hernández-Allés Santiago , Martínez-Martínez Luis , Benedí Vicente J. , Albertí Sebastián 
Published: December 2019

ABSTRACT

Klebsiella pneumoniae
porin genes were analyzed to detect mutations accounting for the porin deficiency observed in many β-lactam-resistant strains. PCR and Southern blot analysis revealed the existence of a third porin gene in addition to the OmpK36 and OmpK35 porin genes previously described. This new porin gene was designated
ompK37
and is present in all of the clinical isolates tested. The OmpK37 porin gene was cloned, sequenced, and overexpressed in
Escherichia coli
. In contrast to that of the major porins, OmpK37 porin expression was only detectable by Western blot analysis in porin-deficient β-lactam-resistant strains, suggesting strong down regulation under standard laboratory conditions. Functional characterization suggested a narrower pore for the OmpK37 porin than for
K. pneumoniae
porins OmpK36 and OmpK35. This correlated with the susceptibility to certain β-lactam antibiotics, since a
K. pneumoniae
strain expressing porin OmpK37, but not porin OmpK36 or OmpK35, was less susceptible to β-lactam antibiotics than the same strain expressing either porin OmpK36 or OmpK35.
Adherence of
Staphylococcus aureus
Is Enhanced by an Endogenous Secreted Protein with Broad Binding Activity
Authors: Palma Marco , Haggar Axana , Flock Jan-Ingmar 
Published: December 2019

ABSTRACT

A novel mechanism for enhancement of adherence of
Staphylococcus aureus
to host components is described. A secreted protein, Eap (extracellular adherence protein), was purified from the supernatant of
S. aureus
Newman and found to be able to bind to at least seven plasma proteins, e.g., fibronectin, the α-chain of fibrinogen, and prothrombin, and to the surface of
S. aureus
. Eap bound much less to cells of
Staphylococcus epidermidis
,
Streptococcus mutans
, or
Escherichia coli
. The protein can form oligomeric forms and is able to cause agglutination of
S. aureus
. Binding of
S. aureus
to fibroblasts and epithelial cells was significantly enhanced by addition of Eap, presumably due to its affinity both for plasma proteins on the cells and for the bacteria.
Characterization of the Major Control Region of
Vibrio cholerae
Bacteriophage K139: Immunity, Exclusion, and Integration
Authors: Nesper Jutta , Blaß Julia , Fountoulakis Michael , Reidl Joachim 
Published: December 2019

ABSTRACT

The temperate bacteriophage K139 is highly associated with pathogenic O1
Vibrio cholerae
strains. The nucleotide sequence of the major control region of K139 was determined. The sequences of four (
cox
,
cII
,
cI
, and
int
) of the six deduced open reading frames and their gene order indicated that K139 is related to the P2 bacteriophage family. Two genes of the lysogenic transcript from the mapped promoter P
L
encode homologs to the proteins CI and Int, with deduced functions in prophage formation and maintenance. Between the
cI
and
int
genes, two additional genes were identified:
orf2
, which has no significant similarity to any other gene, and the formerly characterized gene
glo
. Further analysis revealed that Orf2 is involved in preventing superinfection. In a previous report, we described that mutations in
glo
cause an attenuation effect in the cholera mouse model (J. Reidl and J. J. Mekalanos, Mol. Microbiol. 18:685–701, 1995). In this report, we present strong evidence that Glo participates in phage exclusion. Glo was characterized to encode a 13.6-kDa periplasmic protein which inhibits phage infection at an early step, hence preventing reinfection of vibriophage K139 into K139 lysogenic cells. Immediately downstream of gene
int
, the
attP
site was identified. Upon analysis of the corresponding
attB
site within the
V. cholerae
chromosome, it became evident that phage K139 is integrated between the flagellin genes
flaA
and
flaC
of O1 El Tor and O139
V. cholerae
lysogenic strains.
The C-Terminal Sequence of the λ Holin Constitutes a Cytoplasmic Regulatory Domain
Authors: Bläsi Udo , Fraisl Peter , Chang Chung-Yu , Zhang Ning , Young Ry 
Published: December 2019

ABSTRACT

The C-terminal domains of holins are highly hydrophilic and contain clusters of consecutive basic and acidic residues, with the overall net charge predicted to be positive. The C-terminal domain of λ S was found to be cytoplasmic, as defined by protease accessibility in spheroplasts and inverted membrane vesicles. C-terminal nonsense mutations were constructed in
S
and found to be lysis proficient, as long as at least one basic residue is retained at the C terminus. In general, the normal intrinsic scheduling of S function is deranged, resulting in early lysis. However, the capacity of each truncated lytic allele for inhibition by the S107 inhibitor product of
S
is retained. The K97am allele, when incorporated into the phage context, confers a plaque-forming defect because its early lysis significantly reduces the burst size. Finally, a C-terminal frameshift mutation was isolated as a suppressor of the even more severe early lysis defect of the mutant
S
A52G, which causes lysis at or before the time when the first phage particle is assembled in the cell. This mutation scrambles the C-terminal sequence of
S
, resulting in a predicted net charge increase of +4, and retards lysis by about 30 min, thus permitting a viable quantity of progeny to accumulate. Thus, the C-terminal domain is not involved in the formation of the lethal membrane lesion nor in the “dual-start” regulation conserved in lambdoid holins. Instead, the C-terminal sequence defines a cytoplasmic regulatory domain which affects the timing of lysis. Comparison of the C-terminal sequences of within holin families suggests that these domains have little or no structure but act as reservoirs of charged residues that interact with the membrane to effect proper lysis timing.
Histidine Operon Deattenuation in
dnaA
Mutants of
Salmonella typhimurium
Correlates with a Decrease in the Gene Dosage Ratio between tRNA
His
and Histidine Biosynthetic Loci
Authors: Blanc-Potard Anne-Beatrice , Figueroa-Bossi Nara , Bossi Lionello 
Published: December 2019

ABSTRACT

Expression of the histidine operon of
Salmonella typhimurium
is increased in
dnaA
(Ts) mutants at 37°C. This effect requires an intact
his
attenuator and can be suppressed by increasing the gene copy number of the
hisR
locus, which encodes the tRNA
His
. We present data which suggest that the
his
deattenuation defect in
dnaA
(Ts) mutants results from the loss of a gene dosage gradient between the
hisR
locus, close to
oriC
, and the
his
operon, far from
oriC
. Some of the conclusions drawn here may apply to other operons as well.
The C-Terminal Domain of DnaQ Contains the Polymerase Binding Site
Authors: Taft-Benz Sharon A. , Schaaper Roel M. 
Published: December 2019

ABSTRACT

The
Escherichia coli dnaQ
gene encodes the 3′→5′ exonucleolytic proofreading (ɛ) subunit of DNA polymerase III (Pol III). Genetic analysis of
dnaQ
mutants has suggested that ɛ might consist of two domains, an N-terminal domain containing the exonuclease and a C-terminal domain essential for binding the polymerase (α) subunit. We have created truncated forms of
dnaQ
resulting in ɛ subunits that contain either the N-terminal or the C-terminal domain. Using the yeast two-hybrid system, we analyzed the interactions of the single-domain ɛ subunits with the α and θ subunits of the Pol III core. The DnaQ991 protein, consisting of the N-terminal 186 amino acids, was defective in binding to the α subunit while retaining normal binding to the θ subunit. In contrast, the NΔ186 protein, consisting of the C-terminal 57 amino acids, exhibited normal binding to the α subunit but was defective in binding to the θ subunit. A strain carrying the
dnaQ991
allele exhibited a strong, recessive mutator phenotype, as expected from a defective α binding mutant. The data are consistent with the existence of two functional domains in ɛ, with the C-terminal domain responsible for polymerase binding.
Phosphorylation of HPr and Crh by HprK, Early Steps in the Catabolite Repression Signalling Pathway for the
Bacillus subtilis
Levanase Operon
Authors: Martin-Verstraete Isabelle , Deutscher Josef , Galinier Anne 
Published: December 2019

ABSTRACT

Carbon catabolite repression (CCR) of
Bacillus subtilis
catabolic genes is mediated by CcpA and in part by P-Ser–HPr. For certain operons, Crh, an HPr-like protein, is also implicated in CCR. In this study we demonstrated that in
ptsH1 crh1
and
hprK
mutants, expression of the
lev
operon was completely relieved from CCR and that both P-Ser–HPr and P-Ser–Crh stimulated the binding of CcpA to the
cre
sequence of the
lev
operon.
Isolation and Characterization of the
Saccharomyces cerevisiae XPT1
Gene Encoding Xanthine Phosphoribosyl Transferase
Authors: Guetsova M. L. , Crother T. R. , Taylor M. W. , Daignan-Fornier B. 
Published: December 2019

ABSTRACT

A new
Saccharomyces cerevisiae
gene,
XPT1
, was isolated as a multicopy suppressor of a hypoxanthine phosphoribosyl transferase (HPRT) defect. Disruption of
XPT1
affects xanthine utilization in vivo and results in a severe reduction of xanthine phosphoribosyl transferase (XPRT) activity while HPRT is unaffected. We conclude that
XPT1
encodes XPRT in yeast.
Field Evaluation of a Combination of Monospecific Enzyme-Linked Immunosorbent Assays for Type-Specific Diagnosis of Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2 Infections in HIV-Seropositive Persons in Abidjan, Ivory Coast
Authors: Nkengasong John N. , Maurice Chantal , Koblavi Stéphania , Kalou Mireille , Bile Celestin , Yavo Daniel , Boateng Emmanuel , Wiktor Stefan Z. , Greenberg Alan E. 
Published: December 2019

ABSTRACTSerologic distinction between human immunodeficiency virus type 1 (HIV-1) and HIV-2 infection is made difficult because of the cross-reactivity and high cost of existing differentiation assays. An evaluation of a strategy based on a combination of monospecific enzyme-linked immunosorbent assays (ELISAs) (CME), was carried out in Abidjan, Ivory Coast, where both HIV-1 and HIV-2 are present, to determine its accuracy and cost-effectiveness. A total of 1,608 (428 HIV-1-positive, 361 HIV-2-positive, 371 dually HIV-1 and HIV-2 [HIV-D] reactive, and 448 HIV-negative) sera that had been serotyped by a line immunoassay (Peptilav) were tested retrospectively by an HIV-1-monospecific (Wellcozyme HIV Recombinant ELISA) and an HIV-2-monospecific (ICE*-HIV-2) assay. The CME strategy gave concordant results for all of the 428 sera scored as HIV-1 by Peptilav. Of the 361 sera scored as HIV-2 by Peptilav, 316 (87.5%) were scored as HIV-2 by CME; the remaining 45 sera were positive by both monospecific ELISAs (mean optical density ratios, 1.36 for Wellcozyme and 11.30 for ICE*-HIV-2) and were classified as HIV-D by CME. Of the 371 sera classified as HIV-D by Peptilav, 344 (92.7%), 21, and 6 were scored as HIV-D, HIV-1, and HIV-2, respectively, by CME. Additional testing of the discrepant samples by two HIV differentiation assays (RIBA and INNO-LIA) gave results that agreed with those by CME for most of the sera. In addition, 267 other sera were tested prospectively by both CME and Peptilav. In the prospective evaluation, CME results agreed with those by Peptilav for all 106 HIV-1 sera and 40 of the 41 HIV-2 sera. However, of the 120 sera scored as HIV-D by Peptilav, 69 (57.5%), 47 (39.2%), and 4 (3.3%) were scored as HIV-D, HIV-1 only, and HIV-2 only, respectively, by CME. All 47 samples scored as HIV-1 by CME and two of four HIV-2 sera gave concordant results by RIBA, whereas 29 of 47 sera scored as HIV-1 by CME and all four HIV-2 sera gave concordant results by INNO-LIA. The reagent cost for the CME strategy was 59% lower than the cost of the Peptilav strategy. These results suggest that a combination of highly sensitive and specific commercially available monospecific ELISAs is a reliable and cost-effective strategy for type-specific serodiagnosis of HIV-1 and HIV-2 infections in HIV-seropositive persons and therefore represents a recommended strategy in areas where both HIV-1 and HIV-2 are endemic.