bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feedback Regulation of Glucose Transporter Gene Transcription in
Kluyveromyces lactis
by Glucose Uptake
Authors: Milkowski C. , Krampe S. , Weirich J. , Hasse V. , Boles E. , Breunig K. D. 
Published: July 2002

ABSTRACT

In the respirofermentative yeast
Kluyveromyces lactis
, only a single genetic locus encodes glucose transporters that can support fermentative growth. This locus is polymorphic in wild-type isolates carrying either
KHT1
and
KHT2
, two tandemly arranged
HXT-
like genes, or
RAG1
, a low-affinity transporter gene that arose by recombination between
KHT1
and
KHT2
. Here we show that
KHT1
is a glucose-induced gene encoding a low-affinity transporter very similar to Rag1p. Kht2p has a lower
K

m

(3.7 mM) and a more complex regulation. Transcription is high in the absence of glucose, further induced by low glucose concentrations, and repressed at higher glucose concentrations. The response of
KHT1
and
KHT2
gene regulation to high but not to low concentrations of glucose depends on glucose transport. The function of either Kht1p or Kht2p is sufficient to mediate the characteristic response to high glucose, which is impaired in a
kht1 kht2
deletion mutant. Thus, the
KHT
genes are subject to mutual feedback regulation. Moreover, glucose repression of the endogenous β-galactosidase (
LAC4
) promoter and glucose induction of pyruvate decarboxylase were abolished in the
kht1 kht2
mutant. These phenotypes could be partially restored by
HXT
gene family members from
Saccharomyces cerevisiae
. The results indicate that the specific responses to high but not to low glucose concentrations require a high rate of glucose uptake.
DNA Microarray-Based Identification of Genes Controlled by Autoinducer 2-Stimulated Quorum Sensing in
Escherichia coli
Authors: DeLisa Matthew P. , Wu Chi-Fang , Wang Liang , Valdes James J. , Bentley William E. 
Published: July 2002

ABSTRACT

Bacterial cell-to-cell communication facilitates coordinated expression of specific genes in a growth rate-II and cell density-dependent manner, a process known as quorum sensing. While the discovery of a diffusible
Escherichia coli
signaling pheromone, termed autoinducer 2 (AI-2), has been made along with several quorum sensing genes, the overall number and coordination of genes controlled by quorum sensing through the AI-2 signal has not been studied systematically. We investigated global changes in mRNA abundance elicited by the AI-2 signaling molecule through the use of a
luxS
mutant that was unable to synthesize AI-2. Remarkably, 242 genes, comprising ca. 5.6% of the
E. coli
genome, exhibited significant transcriptional changes (either induction or repression) in response to a 300-fold AI-2 signaling differential, with many of the identified genes displaying high induction levels (more than fivefold). Significant induction of
ygeV
, a putative ς
54
-dependent transcriptional activator, and
yhbH
, a ς
54
modulating protein, suggests ς
54
may be involved in
E. coli
quorum sensing.
Biochemical Characterization of Signal Peptidase I from Gram-Positive
Streptococcus pneumoniae
Authors: Peng Sheng-Bin , Wang Li , Moomaw John , Peery Robert B. , Sun Pei-Ming , Johnson Robert B. , Lu Jin , Treadway Patti , Skatrud Paul L. , Wang Q. May 
Published: July 2002

ABSTRACT

Bacterial signal peptidase I is responsible for proteolytic processing of the precursors of secreted proteins. The enzymes from gram-negative and -positive bacteria are different in structure and specificity. In this study, we have cloned, expressed, and purified the signal peptidase I of gram-positive
Streptococcus pneumoniae
. The precursor of streptokinase, an extracellular protein produced in pathogenic streptococci, was identified as a substrate of
S. pneumoniae
signal peptidase I. Phospholipids were found to stimulate the enzymatic activity. Mutagenetic analysis demonstrated that residues serine 38 and lysine 76 of
S. pneumoniae
signal peptidase I are critical for enzyme activity and involved in the active site to form a serine-lysine catalytic dyad, which is similar to LexA-like proteases and
Escherichia coli
signal peptidase I. Similar to LexA-like proteases,
S. pneumoniae
signal peptidase I catalyzes an intermolecular self-cleavage in vitro, and an internal cleavage site has been identified between glycine 36 and histidine 37. Sequence analysis revealed that the signal peptidase I and LexA-like proteases show sequence homology around the active sites and some common properties around the self-cleavage sites. All these data suggest that signal peptidase I and LexA-like proteases are closely related and belong to a novel class of serine proteases.
Clock Control of Ultradian Respiratory Oscillation Found during Yeast Continuous Culture
Authors: Murray Douglas B. , Roller Sibel , Kuriyama Hiroshi , Lloyd David 
Published: July 2002

ABSTRACT

A short-period autonomous respiratory ultradian oscillation (period ≈ 40 min) occurs during aerobic
Saccharomyces cerevisiae
continuous culture and is most conveniently studied by monitoring dissolved O
2
concentrations. The resulting data are high quality and reveal fundamental information regarding cellular dynamics. The phase diagram and discrete fast Fourier transformation of the dissolved O
2
values revealed a square waveform with at least eight harmonic peaks. Stepwise changes in temperature revealed that the oscillation was temperature compensated at temperatures ranging from 27 to 34°C when either glucose (temperature quotient [Q
10
] = 1.02) or ethanol (Q
10
= 0.82) was used as a carbon source. After alteration of the temperature beyond the temperature compensation region, phase coherence events for individual cells were quickly lost. As the cell doubling rate decreased from 15.5 to 9.2 h (a factor of 1.68), the periodicity decreased by a factor of 1.26. This indicated that there was a degree of nutrient compensation. Outside the range of dilution rates at which stable oscillation occurred, the mode of oscillation changed. The oscillation in respiratory output is therefore under clock control.
Two-Component Sensor Required for Normal Symbiotic Colonization of
Euprymna scolopes
by
Vibrio fischeri
Authors: Visick Karen L. , Skoufos Line M. 
Published: July 2002

ABSTRACT

The light organ of the squid
Euprymna scolopes
is specifically colonized to a high density by the marine bacterium
Vibrio fischeri
. To date, only a few factors contributing to the specificity of this symbiosis have been identified. Using a genetic screen for random transposon mutants defective in initiating the symbiotic association or in colonizing the light organ to high density, we identified a mutant of
V. fischeri
that exhibited an apparent defect in symbiosis initiation. This mutant was not defective in motility, luminescence, or growth in minimal medium, suggesting that it lacks an essential, previously unidentified symbiotic function. By sequence analysis, we showed that the locus inactivated in this mutant encodes a predicted 927-amino-acid protein with a high degree of similarity to the sensor component of hybrid two-component regulatory systems. We have therefore designated this locus
rscS
, for regulator of symbiotic colonization—sensor. Sequence analysis revealed two hydrophobic regions which may result in the formation of a periplasmic loop involved in signal recognition; PhoA fusion data supported this proposed membrane topology. We have investigated the start site of
rscS
transcription by primer extension and identified a putative promoter region. We hypothesize that RscS recognizes a signal associated with the light organ environment and responds by stimulating a putative response regulator that controls protein function or gene expression to coordinate early colonization events. Further studies on RscS, its cognate response regulator, and the signaling conditions will provide important insight into the interaction between
V. fischeri
and
E. scolopes
.
A Novel Serotype-Specific Gene Cassette (
gltA-gltB
) Is Required for Expression of Teichoic Acid-Associated Surface Antigens in
Listeria monocytogenes
of Serotype 4b
Authors: Lei Xiang-He , Fiedler Franz , Lan Zheng , Kathariou Sophia 
Published: July 2002

ABSTRACT

Listeria monocytogenes
serotype 4b strains account for about 40% of sporadic cases and many epidemics of listeriosis. Mutations in a chromosomal locus resulted in loss of reactivity with all three monoclonal antibodies (MAbs) which were specific to serotype 4b and the closely related serotypes 4d and 4e. Here we show that this locus contains a serotype 4b-4d-4e-specific gene cassette (3,071 bp) which consists of two genes,
gltA
and
gltB
, and is flanked by palindromic sequences (51 and 44 nucleotides). Complete loss of reactivity with the three serotype-specific MAbs resulted from insertional inactivation of either
gltA
or
gltB
. The
gltA
and
gltB
mutants were characterized by loss and severe reduction, respectively, of glucose in the teichoic acid, whereas galactose, the other serotype-specific sugar substituent in the teichoic acid, was not affected. Within
L. monocytogenes
, only strains of serotypes 4b, 4d, and 4e harbored the
gltA-gltB
cassette, whereas coding sequences on either side of the cassette were conserved among all serotypes. Comparative genomic analysis of a serotype 1/2b strain showed that the 3,071-bp
gltA-gltB
cassette was replaced by a much shorter (528-bp) and unrelated region, flanked by inverted repeats similar to their counterparts in serotype 4b. These findings indicate that in the evolution of different serotypes of
L. monocytogenes
, this site in the genome has become occupied by serotype-specific sequences which, in the case of serotype 4b, are essential for expression of serotype-specific surface antigens and presence of glucose substituents in the teichoic acids in the cell wall.
umuDC
-Mediated Cold Sensitivity Is a Manifestation of Functions of the UmuD
2
C Complex Involved in a DNA Damage Checkpoint Control
Authors: Sutton Mark D. , Walker Graham C. 
Published: July 2002

ABSTRACT

The
umuDC
genes are part of the
Escherichia coli
SOS response, and their expression is induced as a consequence of DNA damage. After induction, they help to promote cell survival via two temporally separate pathways. First, UmuD and UmuC together participate in a cell cycle checkpoint control; second, UmuD′
2
C enables translesion DNA replication over any remaining unrepaired or irreparable lesions in the DNA. Furthermore, elevated expression of the
umuDC
gene products leads to a cold-sensitive growth phenotype that correlates with a rapid inhibition of DNA synthesis. Here, using two mutant
umuC
alleles, one that encodes a UmuC derivative that lacks a detectable DNA polymerase activity (
umuC104
; D101N) and another that encodes a derivative that is unable to confer cold sensitivity but is proficient for SOS mutagenesis (
umuC125
; A39V), we show that
umuDC
-mediated cold sensitivity can be genetically separated from the role of UmuD′
2
C in SOS mutagenesis. Our genetic and biochemical characterizations of UmuC derivatives bearing nested deletions of C-terminal sequences indicate that
umuDC
-mediated cold sensitivity is not due solely to the single-stranded DNA binding activity of UmuC. Taken together, our analyses suggest that
umuDC
-mediated cold sensitivity is conferred by an activity of the UmuD
2
C complex and not by the separate actions of the UmuD and UmuC proteins. Finally, we present evidence for structural differences between UmuD and UmuD′ in solution, consistent with the notion that these differences are important for the temporal regulation of the two separate physiological roles of the
umuDC
gene products.
Genetic Characterization of a
Sinorhizobium meliloti
Chromosomal Region Involved in Lipopolysaccharide Biosynthesis
Authors: Lagares Antonio , Hozbor Daniela F. , Niehaus Karsten , Otero Augusto J. L. Pich , Lorenzen Jens , Arnold Walter , Pühler Alfred 
Published: July 2002

ABSTRACT

The genetic characterization of a 5.5-kb chromosomal region of
Sinorhizobium meliloti
2011 that contains
lpsB
, a gene required for the normal development of symbiosis with
Medicago
spp., is presented. The nucleotide sequence of this DNA fragment revealed the presence of six genes:
greA
and
lpsB
, transcribed in the forward direction; and
lpsE, lpsD, lpsC
, and
lrp
, transcribed in the reverse direction. Except for
lpsB
, none of the
lps
genes were relevant for nodulation and nitrogen fixation. Analysis of the transcriptional organization of
lpsB
showed that
greA
and
lpsB
are part of separate transcriptional units, which is in agreement with the finding of a DNA stretch homologous to a “nonnitrogen” promoter consensus sequence between
greA
and
lpsB
. The opposite orientation of
lpsB
with respect to its first downstream coding sequence,
lpsE
, indicated that the altered LPS and the defective symbiosis of
lpsB
mutants are both consequences of a primary nonpolar defect in a single gene. Global sequence comparisons revealed that the
greA-lpsB
and
lrp
genes of
S. meliloti
have a genetic organization similar to that of their homologous loci in
R. leguminosarum
bv. viciae. In particular, high sequence similarity was found between the translation product of
lpsB
and a core-related biosynthetic mannosyltransferase of
R. leguminosarum
bv. viciae encoded by the
lpcC
gene. The functional relationship between these two genes was demonstrated in genetic complementation experiments in which the
S. meliloti lpsB
gene restored the wild-type LPS phenotype when introduced into
lpcC
mutants of
R. leguminosarum
. These results support the view that
S. meliloti lpsB
also encodes a mannosyltransferase that participates in the biosynthesis of the LPS core. Evidence is provided for the presence of other
lpsB
-homologous sequences in several members of the family
Rhizobiaceae
.
Expression Characteristics of the Transfer-Related
kilB
Gene Product of
Streptomyces
Plasmid pIJ101: Implications for the Plasmid Spread Function
Authors: Pettis Gregg S. , Ward Naomi , Schully Kevin L. 
Published: July 2002

ABSTRACT

Intermycelial transfer of
Streptomyces
plasmid pIJ101 occurs prior to cellular differentiation and is mediated by plasmid functions that are also required for production of zones of growth-inhibited recipient cells (i.e., pocks) that develop around individual donors during mating on agar medium. Several other pIJ101 functions, including that of the
kilB
gene, whose unregulated expression on pIJ101 is lethal, are required for normal pock size and so have been postulated to mediate intramycelial spread of the plasmid throughout recipient cells. Using antibodies raised against a KilB fusion protein expressed in
Escherichia coli
, native KilB protein was detected throughout development of pIJ101-containing
Streptomyces lividans
cells, with the concentration of KilB increasing dramatically and reaching a maximum during the final stages (i.e., sporulation and secondary metabolism) of cellular differentiation. Insertion of the
kilB
gene of pIJ101 into the
S. lividans
chromosome in cells lacking the pIJ101 KorB protein, which normally represses
kilB
gene transcription, resulted in elevated but still temporally increasing amounts of KilB. The increased expression or accumulation of the KilB spread protein throughout cellular differentiation of
S. lividans
, which leads to maximum KilB concentrations during developmental stages that occur far later than when intermycelial transfer of pIJ101 is mediated, supports the existence of a subsequent intramycelial component to the pIJ101 spread function. The results also suggest that intramycelial spread of pIJ101 molecules within the recipient extends beyond intercompartmental movements within the substrate mycelia and includes undetermined steps within the spore-yielding aerial hyphae as well.
Identification of Specific Residues in Colicin E1 Involved in Immunity Protein Recognition
Authors: Lindeberg Magdalen , Cramer William A. 
Published: July 2002

ABSTRACT
The basis of specificity between pore-forming colicins and immunity proteins was explored by interchanging residues between colicins E1 (ColE1) and 10 (Col10) and testing for altered recognition by their respective immunity proteins, Imm and Cti. A total of 34 divergent residues in the pore-forming domain of ColE1 between residues 419 and 501, a region previously shown to contain the specificity determinants for Imm, were mutagenized to the corresponding Col10 sequences. The residue changes most effective in converting ColE1 to the Col10 phenotype are residue 448 at the N terminus of helix VI and residues 470, 472, and 474 at the C terminus of helix VII. Mutagenesis of helix VI residues 416 to 419 in Col10 to the corresponding ColE1 sequence resulted in increased recognition by Imm and loss of recognition by Cti.
Transcriptional Activation of the
Bacillus subtilis ackA
Promoter Requires Sequences Upstream of the CcpA Binding Site
Authors: Moir-Blais Tessa R. , Grundy Frank J. , Henkin Tina M. 
Published: July 2002

ABSTRACT

Carbon catabolite protein A (CcpA) is a global regulator of carbon metabolism in gram-positive bacteria, repressing transcription of genes for the utilization of secondary carbon sources in the presence of a readily metabolized carbon source and activating transcription of genes, such as
ackA
and
pta
, that are required for carbon excretion. The promoter region of the
Bacillus subtilis ackA
gene contains two catabolite responsive elements (
cre
sites), of which only the site closest to the promoter (
cre2
) binds CcpA to activate transcription. A region immediately upstream of the
cre2
site is also important for transcriptional activation. The required elements in this region were further defined by mutagenesis. CcpA binds to the
ackA
promoter region in gel shift assays even in the presence of mutations in the upstream element that block transcriptional activation, indicating that this region has a function other than promoting binding of CcpA.
Roles ofhilCandhilDin Regulation ofhilAExpression inSalmonella entericaSerovar Typhimurium
Authors: Lucas Robin L. , Lee Catherine A. 
Published: July 2002

ABSTRACTSequences between −332 and −39 upstream of thehilApromoter are required for repression ofhilA. An unidentified repressor is thought to bind these upstream repressing sequences (URS) to inhibithilAexpression. Two AraC-like transcriptional regulators encoded onSalmonellapathogenicity island 1 (SPI1), HilC and HilD, bind to the URS to counteract the repression ofhilA. The URS is required for regulation ofhilAby osmolarity, oxygen, PhoP/PhoQ, and SirA/BarA. Here, we show that FadD, FliZ, PhoB, and EnvZ/OmpR also require the URS to regulatehilA. These environmental and regulatory factors may affecthilAexpression by altering the expression or activity of HilC, HilD, or the unknown repressor. To begin investigating these possibilities, we tested the effects of environmental and regulatory factors onhilCandhilDexpression. We also examinedhilAregulation whenhilCorhilDwas disrupted or expressed to a high level. AlthoughhilCis regulated by all environmental conditions and regulatory factors that modulatehilAexpression,hilCis not required for the regulation ofhilAby any conditions or factors except EnvZ/OmpR. In contrast,hilDis absolutely required forhilAexpression, but environmental conditions and regulatory factors have little or no effect onhilDexpression. We speculate that EnvZ/OmpR regulateshilAby altering the expression and/or activity ofhilC, while all other regulatory conditions and mutations regulatehilAby modulatinghilDposttranscriptionally. We also discuss models in which the regulation ofhilAexpression is mediated by modulation of the expression or activity of one or more repressors.
Trypsin Mediates Growth Phase-Dependent Transcriptional Regulation of Genes Involved in Biosynthesis of Ruminococcin A, a Lantibiotic Produced by a
Ruminococcus gnavus
Strain from a Human Intestinal Microbiota
Authors: Gomez Ana , Ladiré Monique , Marcille Françoise , Fons Michel 
Published: July 2002

ABSTRACT

Ruminococcin A (RumA) is a trypsin-dependent lantibiotic produced by
Ruminococcus gnavus
E1, a gram-positive strict anaerobic strain isolated from a human intestinal microbiota. A 12.8-kb region from
R. gnavus
E1 chromosome, containing the biosynthetic gene cluster of RumA, has been cloned and sequenced. It consisted of 13 open reading frames, organized in three operons with predicted functions in lantibiotic biosynthesis, signal transduction regulation, and immunity. One unusual feature of the locus is the presence of three almost identical structural genes, all of them encoding the RumA precursor. In order to determine the role of trypsin in RumA production, the transcription of the
rum
genes has been investigated under inducing and noninducing conditions. Trypsin activity is needed for the growth phase-dependent transcriptional activation of RumA operons. Our results suggest that bacteriocin production by
R. gnavus
E1 is controlled through a complex signaling mechanism involving the proteolytic processing of a putative extracellular inducer-peptide by trypsin, a specific environmental cue of the digestive ecosystem.
Escherichia coliDNA Polymerase III Can Replicate Efficiently past a T-Tcis-synCyclobutane Dimer if DNA Polymerase V and the 3′ to 5′ Exonuclease Proofreading Function Encoded bydnaQAre Inactivated
Authors: Borden Angela , O'Grady Paul I. , Vandewiele Dominique , Fernández de Henestrosa Antonio R. , Lawrence Christopher W. , Woodgate Roger 
Published: July 2002

ABSTRACTAlthough very little replication past a T-Tcis-syncyclobutane dimer normally takes place inEscherichia coliin the absence of DNA polymerase V (Pol V), we previously observed as much as half of the wild-type bypass frequency in Pol V-deficient (ΔumuDC) strains if the 3′ to 5′ exonuclease proofreading activity of the Pol III ε subunit was also disabled bymutD5. This observation might be explained in at least two ways. In the absence of Pol V, wild-type Pol III might bind preferentially to the blocked primer terminus but be incapable of bypass, whereas the proofreading-deficient enzyme might dissociate more readily, providing access to bypass polymerases. Alternatively, even though wild-type Pol III is generally regarded as being incapable of lesion bypass, proofreading-impaired Pol III might itself perform this function. We have investigated this issue by examining dimer bypass frequencies in ΔumuDC mutD5strains that were also deficient for Pol I, Pol II, and Pol IV, both singly and in all combinations. Dimer bypass frequencies were not decreased in any of these strains and indeed in some were increased to levels approaching those found in strains containing Pol V. Efficient dimer bypass was, however, entirely dependent on the proofreading deficiency imparted bymutD5, indicating the surprising conclusion that bypass was probably performed by themutD5Pol III enzyme itself. This mutant polymerase does not replicate past the much more distorted T-T (6-4) photoadduct, however, suggesting that it may only replicate past lesions, like the T-T dimer, that form base pairs normally.
Nitric Oxide Metabolism in
Neisseria meningitidis
Authors: Anjum Muna F. , Stevanin Tânia M. , Read Robert C. , Moir James W. B. 
Published: July 2002

ABSTRACT

Neisseria meningitidis
, the causative agent of meningococcal disease in humans, is likely to be exposed to nitrosative stress during natural colonization and disease. The genome of
N. meningitidis
includes the genes
aniA
and
norB
, predicted to encode nitrite reductase and nitric oxide (NO) reductase, respectively. These gene products should allow the bacterium to denitrify nitrite to nitrous oxide. We show that
N. meningitidis
can support growth microaerobically by the denitrification of nitrite via NO and that
norB
is required for anaerobic growth with nitrite. NorB and, to a lesser extent, the
cycP
gene product cytochrome
c
′ are able to counteract toxicity due to exogenously added NO. Expression of these genes by
N. meningitidis
during colonization and disease may confer protection against exogenous or endogenous nitrosative stress.