bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual Transcriptional Regulation of the
Escherichia coli
Phosphate-Starvation-Inducible
psiE
Gene of the Phosphate Regulon by PhoB and the Cyclic AMP (cAMP)-cAMP Receptor Protein Complex
Authors: Kim Soo-Ki , Kimura Sigenobu , Shinagawa Hideo , Nakata Atsuo , Lee Ki-Sung , Wanner Barry L. , Makino Kozo 
Published: July 2002

ABSTRACT

We have shown that the
Escherichia coli
phosphate-starvation-inducible
psiE
gene is regulated by both phosphate and the carbon source by using both
lacZ
and chloramphenicol acetyltransferase gene (
cat
) fusions. Yet, under all conditions tested, a single transcriptional start site lying 7 bp downstream of a predicted −10 region was revealed by primer extension analysis. DNase I footprinting showed that the PhoB transcriptional-activator protein protects two predicted
pho
boxes lying upstream of and near the −35 promoter region. Similar analysis showed that the cyclic AMP (cAMP)-cAMP receptor protein (cAMP-CRP) complex binds a region that overlaps with the downstream
pho
box. These results, together with measurements of the in vivo
psiE
promoter activity under various conditions, show that expression of the
psiE
gene is under direct positive and negative control by PhoB and cAMP-CRP, respectively.
Transcriptional Regulation of the
cpr
Gene Cluster in
ortho
-Chlorophenol-Respiring
Desulfitobacterium dehalogenans
Authors: Smidt Hauke , van Leest Maarten , van der Oost John , de Vos Willem M. 
Published: July 2002

ABSTRACT

To characterize the expression and possible regulation of reductive dehalogenation in halorespiring bacteria, a 11.5-kb genomic fragment containing the
o
-chlorophenol reductive dehalogenase-encoding
cprBA
genes of the gram-positive bacterium
Desulfitobacterium dehalogenans
was subjected to detailed molecular characterization. Sequence analysis revealed the presence of eight designated genes with the order
cprTKZEBACD
and with the same polarity except for
cprT
. The deduced
cprC
and
cprK
gene products belong to the NirI/NosR and CRP-FNR families of transcription regulatory proteins, respectively. CprD and CprE are predicted to be molecular chaperones of the GroEL type, whereas
cprT
may encode a homologue of the trigger factor folding catalysts. Northern blot analysis, reverse transcriptase PCR, and primer extension analysis were used to elucidate the transcriptional organization and regulation of the
cpr
gene cluster. Results indicated halorespiration-specific transcriptional induction of the monocistronic
cprT
gene and the biscistronic
cprBA
and
cprZE
genes. Occasional read-through at
cprC
gives rise to a tetracistronic
cprBACD
transcript. Transcription of
cprBA
was induced 15-fold upon addition of the
o
-chlorophenolic substrate 3-chloro-4-hydroxyphenylacetic acid within 30 min with concomitant induction of dehalogenation activity. Putative regulatory protein binding motifs that to some extent resemble the FNR box were identified in the
cprT-cprK
and
cprK-cprZ
intergenic regions and the promoter at
cprB
, suggesting a role for FNR-like CprK in the control of expression of the
cprTKZEBACD
genes.
radC102
of
Escherichia coli
Is an Allele of
recG
Authors: Lombardo Mary-Jane , Rosenberg Susan M. 
Published: July 2002

ABSTRACT

The
radC102
mutation causes mild UV and X-ray sensitivity and was mapped previously to near
pyrE
and
recG
at 82 min on the
Escherichia coli
chromosome (I. Felzenszwalb, N. J. Sargentini, and K. C. Smith, Radiat. Res. 97:615–625, 1984). We report that
radC102
has two striking phenotypes characteristic of
recG
mutations. First, it causes dramatically increased RecA-dependent mutation in a stationary-phase mutation assay. Second, it causes extreme UV sensitivity in combination with
ruv
mutations affecting the RuvABC Holliday junction resolution system. DNA sequencing of the
radC
and
recG
genes in
radC102
strains revealed that the
radC102
mutation creates a stop codon in
recG
that is predicted to truncate the RecG protein at 410 of 603 amino acids. A low-copy-number plasmid carrying the
radC
+
gene did not affect the UV sensitivity of a wild-type strain, a
radC102
strain, or a
recG258
::Tn
10
mini-
kan
strain. We conclude that
radC102
is an allele of
recG
and that the function of the RadC protein remains to be determined.
H-NS Controls
pap
and
daa
Fimbrial Transcription in
Escherichia coli
in Response to Multiple Environmental Cues
Authors: White-Ziegler Christine A. , Villapakkam Anuradha , Ronaszeki Karla , Young Sarah 
Published: July 2002

ABSTRACT

A comparative study was completed to determine the influence of various environmental stimuli on the transcription of three different fimbrial operons in
Escherichia coli
and to determine the role of the histone-like protein H-NS in this environmental regulation. The fimbrial operons studied included the
pap
operon, which encodes pyelonephritis-associated pili (P pili), the
daa
operon, which encodes F1845 fimbriae, and the
fan
operon, which encodes K99 fimbriae. Using
lacZYA
transcriptional fusions within each of the fimbrial operons, we tested temperature, osmolarity, carbon source, rich medium, oxygen levels, pH, amino acids, solid medium, and iron concentration for their effects on fimbrial gene expression. Low temperature, high osmolarity, glucose as a carbon source, and rich medium repressed transcription of all three operons. High iron did not alter transcription of any of the operons tested, whereas the remaining stimuli had effects on individual operons. For the
pap
and
daa
operons, introduction of the
hns651
mutation relieved the repression, either fully or partially, due to low temperature, glucose as a carbon source, rich medium, and high osmolarity. Taken together, these data indicate that there are common environmental cues that regulate fimbrial transcription in
E. coli
and that H-NS is an important environmental regulator for fimbrial transcription in response to several stimuli.
Inducible Metabolism of Phenolic Acids inPediococcus pentosaceusIs Encoded by an Autoregulated Operon Which Involves a New Class of Negative Transcriptional Regulator
Authors: Barthelmebs Lise , Lecomte Bruno , Divies Charles , Cavin Jean-François 
Published: July 2002

ABSTRACTPediococcus pentosaceusdisplays a substrate-inducible phenolic acid decarboxylase (PAD) activity onp-coumaric acid. Based on DNA sequence homologies between the three PADs previously cloned, a DNA probe of theLactobacillus plantarum pdcgene was used to screen aP. pentosaceusgenomic library in order to clone the corresponding gene of this bacteria. One clone detected with this probe displayed a low PAD activity. Subcloning of this plasmid insertion allowed us to determine the part of the insert which contains a 534-bp open reading frame (ORF) coding for a 178-amino-acid protein presenting 81.5% of identity withL. plantarumPDC enzyme. This ORF was identified as thepadAgene. A second ORF was located just downstream of thepadAgene and displayed 37% identity with the product of theBacillus subtilis yfiOgene. Subcloning, transcriptional analysis, and expression studies withEscherichia coliof these two genes under thepadAgene promoter, demonstrated that the genes are organized in an autoregulated bicistronic operonic structure and that the gene located upstream of thepadAgene encodes the transcriptional repressor of thepadAgene. Transcription of thispadoperon inP. pentosaceusis acid phenol dependent.
Role of the H Protein in Assembly of the Photochemical Reaction Center and Intracytoplasmic Membrane in
Rhodospirillum rubrum
Authors: Cheng Yongjian S. , Brantner Christine A. , Tsapin Alexandre , Collins Mary Lynne Perille 
Published: July 2002

ABSTRACT

Rhodospirillum rubrum
is a model for the study of membrane formation. Under conditions of oxygen limitation, this facultatively phototrophic bacterium forms an intracytoplasmic membrane that houses the photochemical apparatus. This apparatus consists of two pigment-protein complexes, the light-harvesting antenna (LH) and photochemical reaction center (RC). The proteins of the photochemical components are encoded by the
puf
operon (LHα, LHβ, RC-L, and RC-M) and by
puhA
(RC-H).
R. rubrum puf
interposon mutants do not form intracytoplasmic membranes and are phototrophically incompetent. The
puh
region was cloned, and DNA sequence determination identified open reading frames
bchL
and
bchM
and part of
bchH
;
bchHLM
encode enzymes of bacteriochlorophyll biosynthesis. A
puhA
/G115 interposon mutant was constructed and found to be incapable of phototrophic growth and impaired in intracytoplasmic membrane formation. Comparison of properties of the wild-type and the mutated and complemented strains suggests a model for membrane protein assembly. This model proposes that RC-H is required as a foundation protein for assembly of the RC and highly developed intracytoplasmic membrane. In complemented strains, expression of
puh
occurred under semiaerobic conditions, thus providing the basis for the development of an expression vector. The
puhA
gene alone was sufficient to restore phototrophic growth provided that recombination occurred.
Role of the Dinitrogenase Reductase Arginine 101 Residue in Dinitrogenase Reductase ADP-Ribosyltransferase Binding, NAD Binding, and Cleavage
Authors: Ma Yan , Ludden Paul W. 
Published: July 2002

ABSTRACT

Dinitrogenase reductase is posttranslationally regulated by dinitrogenase reductase ADP-ribosyltransferase (DRAT) via ADP-ribosylation of the arginine 101 residue in some bacteria.
Rhodospirillum rubrum
strains in which the arginine 101 of dinitrogenase reductase was replaced by tyrosine, phenylalanine, or leucine were constructed by site-directed mutagenesis of the
nifH
gene. The strain containing the R101F form of dinitrogenase reductase retains 91%, the strain containing the R101Y form retains 72%, and the strain containing the R101L form retains only 28% of in vivo nitrogenase activity of the strain containing the dinitrogenase reductase with arginine at position 101. In vivo acetylene reduction assays, immunoblotting with anti-dinitrogenase reductase antibody, and [adenylate-
32
P]NAD labeling experiments showed that no switch-off of nitrogenase activity occurred in any of the three mutants and no ADP-ribosylation of altered dinitrogenase reductases occurred either in vivo or in vitro. Altered dinitrogenase reductases from strains UR629 (R101Y) and UR630 (R101F) were purified to homogeneity. The R101F and R101Y forms of dinitrogenase reductase were able to form a complex with DRAT that could be chemically cross-linked by 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide. The R101F form of dinitrogenase reductase and DRAT together were not able to cleave NAD. This suggests that arginine 101 is not critical for the binding of DRAT to dinitrogenase reductase but that the availability of arginine 101 is important for NAD cleavage. Both DRAT and dinitrogenase reductase can be labeled by [carbonyl-
14
C]NAD individually upon UV irradiation, but most
14
C label is incorporated into DRAT when both proteins are present. The ability of R101F dinitrogenase reductase to be labeled by [carbonyl-
14
C]NAD suggested that Arg 101 is not absolutely required for NAD binding.
Nitrogen or Sulfur Starvation Differentially Affects Phycobilisome Degradation and Expression of the
nblA
Gene in
Synechocystis
Strain PCC 6803
Authors: Richaud Catherine , Zabulon Gérald , Joder Annette , Thomas Jean-Claude 
Published: July 2002

ABSTRACT

Nitrogen (N) limitation in cyanobacteria is well documented: a reduced growth rate is observed, accompanied by a cessation of phycobiliprotein synthesis and an ordered degradation of phycobilisomes (PBS). This leads to a dramatic bleaching phenomenon known as chlorosis. In
Synechococcus
strain PCC 7942, bleaching due to PBS degradation is also observed under sulfur (S) or phosphorus (P) limitation, and all three are under the control of the
nblA
gene product, a 59-amino-acid polypeptide which is overexpressed under N, S, and P starvation (J. L. Collier, and A. R. Grossman, EMBO J. 13:1039–1047, 1994). Cyanobase sequence data for
Synechocystis
strain PCC 6803 indicate the presence of two tandem open reading frames (sll0452 and sll0453) homologous to
nblA
. We cloned the two genes, identified a unique 5′ mRNA end suggestive of a single transcription start site, and studied
nblA
expression under conditions of N or S starvation by Northern hybridization: transcripts were detected only under N starvation (no signal is detected in replete medium or with S starvation), whether
nblA1
or
nblA2
was used as a probe. Mutations in
nblA1
and
nblA2
were constructed by insertion of a kanamycin cassette; both mutations were nonbleaching under N starvation.
Synechocystis
strain PCC 6803 does not bleach under S starvation, consistent with the absence of
nblA
induction in these conditions. These results were confirmed by analysis of the PBS components: sequential degradation of phycocyanin and associated linkers was observed only under conditions of N starvation. This indicates differences between
Synechocystis
strain PCC 6803 and
Synechococcus
strain PCC 7942 in their regulatory and signaling pathways leading to N- and S-starved phenotypes.
CAP1
, an Adenylate Cyclase-Associated Protein Gene, Regulates Bud-Hypha Transitions, Filamentous Growth, and Cyclic AMP Levels and Is Required for Virulence of
Candida albicans
Authors: Bahn Yong-Sun , Sundstrom Paula 
Published: July 2002

ABSTRACT

In response to a wide variety of environmental stimuli, the opportunistic fungal pathogen
Candida albicans
exits the budding cycle, producing germ tubes and hyphae concomitant with expression of virulence genes, such as that encoding hyphal wall protein 1 (
HWP1
). Biochemical studies implicate cyclic AMP (cAMP) increases in promoting bud-hypha transitions, but genetic evidence relating genes that control cAMP levels to bud-hypha transitions has not been reported. Adenylate cyclase-associated proteins (CAPs) of nonpathogenic fungi interact with Ras and adenylate cyclase to increase cAMP levels under specific environmental conditions. To initiate studies on the relationship between cAMP signaling and bud-hypha transitions in
C. albicans
, we identified, cloned, characterized, and disrupted the
C. albicans CAP1
gene.
C. albicans
strains with inactivated
CAP1
budded in conditions that led to germ tube formation in isogenic strains with
CAP1
. The addition of 10 mM cAMP and dibutyryl cAMP promoted bud-hypha transitions and filamentous growth in the
cap1/cap1
mutant in liquid and solid media, respectively, showing clearly that cAMP promotes hypha formation in
C. albicans
. Increases in cytoplasmic cAMP preceding germ tube emergence in strains having
CAP1
were markedly diminished in the budding
cap1/cap1
mutant.
C. albicans
strains with deletions of both alleles of
CAP1
were avirulent in a mouse model of systemic candidiasis. The avirulence of a germ tube-deficient
cap1/cap1
mutant coupled with the role of Cap1 in regulating cAMP levels shows that the Cap1-mediated cAMP signaling pathway is required for bud-hypha transitions, filamentous growth, and the pathogenesis of candidiasis.
Dehalogenation, Denitration, Dehydroxylation, and Angular Attack on Substituted Biphenyls and Related Compounds by a Biphenyl Dioxygenase
Authors: Seeger Michael , Cámara Beatriz , Hofer Bernd 
Published: July 2002

ABSTRACT

The attack by the
bph
-encoded biphenyl dioxygenase of
Burkholderia
sp. strain LB400 on a number of symmetrical
ortho
-substituted biphenyls or quasi
ortho
-substituted biphenyl analogues has been investigated. 2,2′-Difluoro-, 2,2′-dibromo-, 2,2′-dinitro-, and 2,2′-dihydroxybiphenyl were accepted as substrates. Dioxygenation of all of these compounds showed a strong preference for the semisubstituted pair of vicinal
ortho
and
meta
carbons, leading to the formation of 2′-substituted 2,3-dihydroxybiphenyls by subsequent elimination of HX (X = F, Br, NO
2
, or OH). All of these products were further metabolized by 2,3-dihydroxybiphenyl 1,2-dioxygenases of
Burkholderia
sp. strain LB400 or of
Rhodococcus globerulus
P6. Dibenzofuran and dibenzodioxin, which may be regarded as analogues of doubly
ortho
-substituted biphenyls or diphenylethers, respectively, were attacked at the “quasi
ortho
” carbon (the angular position 4a) and its neighbor. This shows that an aromatic ring-hydroxylating dioxygenase of class IIB is able to attack angular carbons. The catechols formed, 2,3,2′-trihydroxybiphenyl and 2,3,2′-trihydroxydiphenylether, were further metabolized by 2,3-dihydroxybiphenyl 1,2-dioxygenase. While angular attack by the biphenyl dioxygenase was the main route of dibenzodioxin oxidation, lateral dioxygenation leading to dihydrodiols was the major reaction with dibenzofuran. These results indicate that this enzyme is capable of hydroxylating
ortho
or angular carbons carrying a variety of substituents which exert electron-withdrawing inductive effects. They also support the view that the conversions of phenols into catechols by ring-hydroxylating dioxygenases, such as the transformation of 2,2′-dihydroxybiphenyl into 2,3,2′-trihydroxybiphenyl, are the results of di- rather than of monooxygenations. Lateral dioxygenation of dibenzofuran and subsequent dehydrogenation and extradiol dioxygenation by a number of biphenyl-degrading strains yielded intensely colored dead-end products. Thus, dibenzofuran can be a useful chromogenic indicator for the activity of the first three enzymes of biphenyl catabolic pathways.
Maximal Expression of Membrane-Bound Nitrate Reductase in
Paracoccus
Is Induced by Nitrate via a Third FNR-Like Regulator Named NarR
Authors: Wood Nicholas J. , Alizadeh Tooba , Bennett Scott , Pearce Joanne , Ferguson Stuart J. , Richardson David J. , Moir James W. B. 
Published: July 2002

ABSTRACT

Respiratory reduction of nitrate to nitrite is the first key step in the denitrification process that leads to nitrate loss from soils. In
Paracoccus pantotrophus
, the enzyme system that catalyzes this reaction is encoded by the
narKGHJI
gene cluster. Expression of this cluster is maximal under anaerobic conditions in the presence of nitrate. Upstream from
narK
is
narR
, a gene encoding a member of the FNR family of transcriptional activators.
narR
is transcribed divergently from the other
nar
genes. Mutational analysis reveals that NarR is required for maximal expression of the membrane-bound nitrate reductase genes and
narK
but has no other regulatory function related to denitrification. NarR is shown to require nitrate and/or nitrite is order to activate gene expression. The N-terminal region of the protein lacks the cysteine residues that are required for formation of an oxygen-sensitive iron-sulfur cluster in some other members of the FNR family. Also, NarR lacks a crucial residue involved in interactions of this family of regulators with the ς
70
subunit of RNA polymerase, indicating that a different mechanism is used to promote transcription.
narR
is also found in
Paracoccus denitrificans
, indicating that this species contains at least three FNR homologues.
Molecular Physiology of Sugar Catabolism in
Lactococcus lactis
IL1403
Authors: Even Sergine , Lindley Nic D. , Cocaign-Bousquet Muriel 
Published: July 2002

ABSTRACT

The metabolic characteristics of
Lactococcus lactis
IL1403 were examined on two different growth media with respect to the physiological response to two sugars, glucose and galactose. Analysis of specific metabolic rates indicated that despite significant variations in the rates of both growth and sugar consumption, homolactic fermentation was maintained for all cultures due to the low concentration of either pyruvate-formate lyase or alcohol dehydrogenase. When the ionophore monensin was added to the medium, flux through glycolysis was not increased, suggesting a catabolic flux limitation, which, with the low intracellular concentrations of glycolytic intermediates and high in vivo glycolytic enzyme capacities, may be at the level of sugar transport. To assess transcription, a novel DNA macroarray technology employed RNA labeled in vitro with digoxigenin and detection of hybrids with an alkaline phosphatase-antidigoxigenin conjugate. This method showed that several genes of glycolysis were expressed to higher levels on glucose and that the genes of the mixed-acid pathway were expressed to higher levels on galactose. When rates of enzyme synthesis are compared to transcript concentrations, it can be deduced that some translational regulation occurs with threefold-higher translational efficiency in cells grown on glucose.
Novel Topology of BfpE, a Cytoplasmic Membrane Protein Required for Type IV Fimbrial Biogenesis in Enteropathogenic
Escherichia coli
Authors: Blank T. Eric , Donnenberg Michael S. 
Published: July 2002

ABSTRACT

Enteropathogenic
Escherichia coli
(EPEC) produces the bundle-forming pilus (BFP), a type IV fimbria that has been implicated in virulence, autoaggregation, and localized adherence to epithelial cells. The
bfpE
gene is one of a cluster of
bfp
genes previously shown to encode functions that direct BFP biosynthesis. Here, we show that an EPEC strain carrying a nonpolar mutation in
bfpE
fails to autoaggregate, adhere to HEp-2 cells, or form BFP, thereby demonstrating that BfpE is required for BFP biogenesis. BfpE is a cytoplasmic membrane protein of the GspF family. To determine the membrane topology of BfpE, we fused
bfpE
derivatives containing 3′ truncations and/or internal deletions to alkaline phosphatase and/or β-galactosidase reporter genes, whose products are active only when localized to the periplasm or cytoplasm, respectively. In addition, we constructed BfpE sandwich fusions using a dual alkaline phosphatase/β-galactosidase reporter cassette and analyzed BfpE deletion derivatives by sucrose density flotation gradient fractionation. The data from these analyses support a topology in which BfpE contains four hydrophobic transmembrane (TM) segments, a large cytoplasmic segment at its N terminus, and a large periplasmic segment near its C terminus. This topology is dramatically different from that of OutF, another member of the GspF family, which has three TM segments and is predominantly cytoplasmic. These findings provide a structural basis for predicting protein-protein interactions required for assembly of the BFP biogenesis machinery.
Structure-Function Analysis of BfpB, a Secretin-Like Protein Encoded by the Bundle-Forming-Pilus Operon of Enteropathogenic
Escherichia coli
Authors: Schmidt Sarah A. , Bieber David , Ramer Sandra W. , Hwang Jaiweon , Wu Cheng-Yen , Schoolnik Gary 
Published: July 2002

ABSTRACT

Production of type IV bundle-forming pili by enteropathogenic
Escherichia coli
(EPEC) requires BfpB, an outer-membrane lipoprotein and member of the secretin protein superfamily. BfpB was found to compose a ring-shaped, high-molecular-weight outer-membrane complex that is stable in 4% sodium dodecyl sulfate at temperatures of ≤65°C. Chemical cross-linking and immunoprecipitation experiments disclosed that the BfpB multimeric complex interacts with BfpG, and mutational studies showed that BfpG is required for the formation and/or stability of the multimer but not for the outer-membrane localization of BfpB. Formation of the BfpB multimer also does not require BfpA, the repeating subunit of the pilus filament. Functional studies of the BfpB-BfpG complex revealed that its presence confers vancomycin sensitivity, indicating that it may form an incompletely gated channel through the outer membrane. BfpB expression is also associated with accumulation of EPEC proteins in growth medium, suggesting that it may support both pilus biogenesis and protein secretion.