bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of the
Streptomyces coelicolor
Calcium-Dependent Antibiotic by
absA
, Encoding a Cluster-Linked Two-Component System
Authors: Ryding N. Jamie , Anderson Todd B. , Champness Wendy C. 
Published: April 2009

ABSTRACT

The
Streptomyces coelicolor absA
two-component system was initially identified through analysis of mutations in the sensor kinase
absA1
that caused inhibition of all four antibiotics synthesized by this strain. Previous genetic analysis had suggested that the phosphorylated form of AbsA2 acted as a negative regulator of antibiotic biosynthesis in
S. coelicolor
(T. B. Anderson, P. Brian, and W. C. Champness, Mol. Microbiol. 39:553–566, 2001). Genomic sequence data subsequently provided by the Sanger Centre (Cambridge, United Kingdom) revealed that
absA
was located within the gene cluster for production of one of the four antibiotics, calcium-dependent antibiotic (CDA). In this paper we have identified numerous transcriptional start sites within the CDA cluster and have shown that the original antibiotic-negative mutants used to identify
absA
exhibit a stronger negative regulation of promoters upstream of the proposed CDA biosynthetic genes than of promoters in the clusters responsible for production of actinorhodin and undecylprodigiosin. The same antibiotic-negative mutants also showed an increase in transcription from a promoter divergent to that of
absA
, upstream of a putative ABC transporter, in addition to an increase in transcription of
absA
itself. Interestingly, the negative regulation of the biosynthetic transcripts did not appear to be mediated by transcriptional regulation of
cdaR
(a gene encoding a homolog of the pathway-specific regulators of the
act
and
red
clusters) or by any other recognizable transcriptional regulator associated with the cluster. The role of
absA
in regulating the expression of the diverse antibiotic biosynthesis clusters in the genome is discussed in light of its location in the
cda
cluster.
Role of Menaquinones in Fe(III) Reduction by Membrane Fractions of
Shewanella putrefaciens
Authors: Saffarini Daad A. , Blumerman Seth L. , Mansoorabadi Karen J. 
Published: April 2009

ABSTRACT

Two Tn
5
-generated mutants of
Shewanella putrefaciens
with insertions in
menD
and
menB
were isolated and analyzed. Both mutants were deficient in the use of several terminal electron acceptors, including Fe(III). This deficiency was overcome by the addition of menaquinone (vitamin K
2
). Isolated membrane fractions from both mutants were unable to reduce Fe(III) in the absence of added menaquinone when formate was used as the electron donor. These results indicate that menaquinones are essential components for the reduction of Fe(III) by both whole cells and purified membrane fractions when formate or lactate is used as the electron donor.
Evidence for a Fourth Hydrogenase in
Desulfovibrio fructosovorans
Authors: Casalot Laurence , De Luca Gilles , Dermoun Zorah , Rousset Marc , de Philip Pascale 
Published: April 2009

ABSTRACT

A strain devoid of the three hydrogenases characterized for
Desulfovibrio fructosovorans
was constructed using marker exchange mutagenesis. As expected, the H
2
-dependent methyl viologen reduction activity of the strain was null, but physiological studies showed no striking differences between the mutated and wild-type strains. The H
+
-D
2
exchange activity measured in the mutated strain indicates the presence of a fourth hydrogenase in
D. fructosovorans
.
Integrative Genetic Element That Reverses the Usual Target Gene Orientation
Authors: Zhao Sihui , Williams Kelly P. 
Published: April 2009

ABSTRACT

A genetic element integrating site specifically into a prokaryotic gene usually carries a copy of the 3′ portion of that gene that restores the active gene even as the original is disrupted. A cryptic element in
Mesorhizobium loti
instead carries a copy of the 5′ end of the tRNA gene into which it integrated. This has implications for the evolution of new integrase-site combinations.
Replication-Dependent Recruitment of the β-Subunit of DNA Polymerase III from Cytosolic Spaces to Replication Forks in
Escherichia coli
Authors: Onogi Toshinari , Ohsumi Katsufumi , Katayama Tsutomu , Hiraga Sota 
Published: April 2009

ABSTRACT

The β-subunit of DNA polymerase III is located as one or two condensed clusters within the nucleoid-occupied space in exponentially growing cells of
Escherichia coli
. When chromosome replication is terminated after incubation at nonpermissive temperature in a temperature-sensitive
dnaC
mutant, the β-subunit is located in the cytosolic spaces of the cell poles.
Corynebacterium glutamicumUtilizes both Transsulfuration and Direct Sulfhydrylation Pathways for Methionine Biosynthesis
Authors: Hwang Byung-Joon , Yeom Hye-Jin , Kim Younhee , Lee Heung-Shick 
Published: April 2009

ABSTRACTA direct sulfhydrylation pathway for methionine biosynthesis inCorynebacterium glutamicumwas found. The pathway was catalyzed bymetYencodingO-acetylhomoserine sulfhydrylase. The genemetY, located immediately upstream ofmetA, was found to encode a protein of 437 amino acids with a deduced molecular mass of 46,751 Da. In accordance with DNA and protein sequence data, the introduction ofmetYintoC. glutamicumresulted in the accumulation of a 47-kDa protein in the cells and a 30-fold increase inO-acetylhomoserine sulfhydrylase activity, showing the efficient expression of the cloned gene. Although disruption of themetBgene, which encodes cystathionine γ-synthase catalyzing the transsulfuration pathway of methionine biosynthesis, or themetYgene was not enough to lead to methionine auxotrophy, an additional mutation in themetYor themetBgene resulted in methionine auxotrophy. The growth pattern of themetYmutant strain was identical to that of themetBmutant strain, suggesting that both methionine biosynthetic pathways function equally well. In addition, anEscherichia coli metBmutant could be complemented by transformation of the strain with a DNA fragment carrying corynebacterialmetYandmetAgenes. These data clearly show thatC. glutamicumutilizes both transsulfuration and direct sulfhydrylation pathways for methionine biosynthesis. AlthoughmetYandmetAare in close proximity to one another, separated by 143 bp on the chromosome, deletion analysis suggests that they are expressed independently. As withmetA, methionine could also repress the expression ofmetY. The repression was also observed withmetB, but the degree of repression was more severe withmetY,which shows almost complete repression at 0.5 mM methionine in minimal medium. The data suggest a physiologically distinctive role of the direct sulfhydrylation pathway inC. glutamicum.
YopD and LcrH Regulate Expression of
Yersinia enterocolitica
YopQ by a Posttranscriptional Mechanism and Bind to
yopQ
RNA
Authors: Anderson Deborah M. , Ramamurthi Kumaran S. , Tam Christina , Schneewind Olaf 
Published: April 2009

ABSTRACT

Pathogenic yersiniae secrete 14 Yop proteins via the type III pathway. Synthesis of YopQ occurs when the type III machinery is activated by a low-calcium signal, but not when the calcium concentration is above 100 μM. To characterize the mechanism that regulates the expression of
yopQ
, mutants that permit synthesis of YopQ in the presence of calcium were isolated. Yersiniae bearing deletion mutations in
yopN
,
tyeA
,
sycN
, or
yscB
synthesized and secreted YopQ in both the presence and the absence of calcium. In contrast, yersiniae with a deletion in
yopD
or
lcrH
synthesized YopQ in the presence of calcium but did not secrete the polypeptide. These variants displayed no defect in YopQ secretion under low-calcium conditions, revealing that
yopD
and
lcrH
are required for the regulation of
yopQ
expression. Experiments with transcriptional and translational fusions to the
npt
reporter gene suggest that
yopD
and
lcrH
regulate
yopQ
expression at a posttranscriptional step. YopD and LcrH form a complex in the bacterial cytosol and bind
yopQ
mRNA. Models that can account for posttranscriptional regulatory mechanisms of
yop
expression are discussed.
Amino Acid- and Purine Ribonucleoside-Induced Germination of
Bacillus anthracis
ΔSterne Endospores:
gerS
Mediates Responses to Aromatic Ring Structures
Authors: Ireland John A. W. , Hanna Philip C. 
Published: April 2009

ABSTRACT

Specific combinations of amino acids or purine ribonucleosides and amino acids are required for efficient germination of endospores of
Bacillus anthracis
ΔSterne, a plasmidless strain, at ligand concentrations in the low-micromolar range. The amino acid
l
-alanine was the only independent germinant in
B. anthracis
and then only at concentrations of >10 mM. Inosine and
l
-alanine both play major roles as cogerminants with several other amino acids acting as efficient cogerminants (His, Pro, Trp, and Tyr combining with
l
-alanine and Ala, Cys, His, Met, Phe, Pro, Ser, Trp, Tyr, and Val combining with inosine). An ortholog to the
B. subtilis
tricistronic germination receptor operon
gerA
was located on the
B. anthracis
chromosome and named
gerS
. Disruption of
gerS
completely eliminated the ability of
B. anthracis
endospores to respond to amino-acid and inosine-dependent germination responses. The
gerS
mutation also produced a significant microlag in the aromatic-amino-acid-enhanced-alanine germination pathways. The
gerS
disruption appeared to specifically affect use of aromatic chemicals as cogerminants with alanine and inosine. We conclude that efficient germination of
B. anthracis
endospores requires multipartite signals and that
gerS
-encoded proteins act as an aromatic-responsive germination receptor.
Periplasmic Nitrate Reductase (NapABC Enzyme) Supports Anaerobic Respiration byEscherichia coliK-12
Authors: Stewart Valley , Lu Yiran , Darwin Andrew J. 
Published: April 2009

ABSTRACTPeriplasmic nitrate reductase (NapABC enzyme) has been characterized from a variety of proteobacteria, especiallyParacoccus pantotrophus. Whole-genome sequencing ofEscherichia colirevealed the structural genesnapFDAGHBC, which encode NapABC enzyme and associated electron transfer components.E. colialso expresses two membrane-bound proton-translocating nitrate reductases, encoded by thenarGHJIandnarZYWVoperons. We measured reduced viologen-dependent nitrate reductase activity in a series of strains with combinations ofnarandnapnull alleles. ThenapFoperon-encoded nitrate reductase activity was not sensitive to azide, as shown previously for theP. pantotrophusNapA enzyme. A strain carrying null alleles ofnarGandnarZgrew exponentially on glycerol with nitrate as the respiratory oxidant (anaerobic respiration), whereas a strain also carrying a null allele ofnapAdid not. By contrast, the presence ofnapA+had no influence on the more rapid growth ofnarG+strains. These results indicate that periplasmic nitrate reductase, like fumarate reductase, can function in anaerobic respiration but does not constitute a site for generating proton motive force. The time course of Φ(napF-lacZ) expression during growth in batch culture displayed a complex pattern in response to the dynamic nitrate/nitrite ratio. Our results are consistent with the observation that Φ(napF-lacZ) is expressed preferentially at relatively low nitrate concentrations in continuous cultures (H. Wang, C.-P. Tseng, and R. P. Gunsalus, J. Bacteriol. 181:5303-5308, 1999). This finding and other considerations support the hypothesis that NapABC enzyme may function inE. coliwhen low nitrate concentrations limit the bioenergetic efficiency of nitrate respiration via NarGHI enzyme.
YplA Is Exported by the Ysc, Ysa, and Flagellar Type III Secretion Systems ofYersinia enterocolitica
Authors: Young Briana M. , Young Glenn M. 
Published: April 2009

ABSTRACTYersinia enterocoliticamaintains three different pathways for type III protein secretion. Each pathway requires the activity of a specific multicomponent apparatus or type III secretion system (TTSS). Two of the TTSSs are categorized as contact-dependent systems which have been shown in a number of different symbiotic and pathogenic bacteria to influence interactions with host organisms by targeting effector proteins into the cytosol of eukaryotic cells. The third TTSS is required for the assembly of flagella and the secretion of the phospholipase YplA, which has been implicated inY. enterocoliticavirulence. In this study, YplA was expressed from a constitutive promoter in strains that contained only a single TTSS. It was determined that each of the three TTSSs is individually sufficient for YplA secretion. Environmental factors such as temperature, calcium availability, and sodium chloride concentration affected the contribution of each system to extracellular protein secretion and, under some conditions, more than one TTSS appeared to operate simultaneously. This suggests that some proteins might normally be exported by more than one TTSS inY. enterocolitca.
Two Novel Type III-Secreted Proteins of
Xanthomonas campestris
pv. vesicatoria Are Encoded within the
hrp
Pathogenicity Island
Authors: Noël Laurent , Thieme Frank , Nennstiel Dirk , Bonas Ulla 
Published: April 2009

ABSTRACT

The Hrp type III protein secretion system (TTSS) is essential for pathogenicity of gram-negative plant pathogen
Xanthomonas campestris
pv. vesicatoria. cDNA-amplified fragment length polymorphism and reverse transcription-PCR analyses identified new genes, regulated by key
hrp
regulator HrpG, in the regions flanking the
hrp
gene cluster. Sequence analysis revealed genes encoding HpaG, a predicted leucine-rich repeat-containing protein, the lysozyme-like HpaH protein, and XopA and XopD, which are similar in sequence to Hpa1 from
Xanthomonas oryzae
pv. oryzae and PsvA from
Pseudomonas syringae
, respectively. XopA and XopD (
Xanthomonas
outer proteins) are secreted by the
Xanthomonas
Hrp TTSS and thus represent putative effector proteins. Mutations in
xopA
, but not in
xopD
, resulted in reduced bacterial growth in planta and delayed plant reactions in susceptible and resistant host plants. Since the
xopD
promoter contains a putative
hrp
box, which is characteristic of
hrpL
-regulated genes in
P. syringae
and
Erwinia
spp., the gene was probably acquired by horizontal gene transfer. Interestingly, the regions flanking the
hrp
gene cluster also contain insertion sequences and genes for a putative transposase and a tRNA
Arg
. These features suggest that the
hrp
gene cluster of
X. campestris
pv. vesicatoria is part of a pathogenicity island.
rRNA Promoter Activity in the Fast-Growing Bacterium
Vibrio natriegens
Authors: Aiyar Sarah E. , Gaal Tamas , Gourse Richard L. 
Published: April 2009

ABSTRACT

The bacterium
Vibrio natriegens
can double with a generation time of less than 10 min (R. G. Eagon, J. Bacteriol. 83:736-737, 1962), a growth rate that requires an extremely high rate of protein synthesis. We show here that
V. natriegens
' high potential for protein synthesis results from an increase in ribosome numbers with increasing growth rate, as has been found for other bacteria. We show that
V. natriegens
contains a large number of rRNA operons, and its rRNA promoters are extremely strong. The
V. natriegens
rRNA core promoters are at least as active in vitro as
Escherichia coli
rRNA core promoters with either
E. coli
RNA polymerase (RNAP) or
V. natriegens
RNAP, and they are activated by UP elements, as in
E. coli
. In addition, the
E. coli
transcription factor Fis activated
V. natriegens rrn
P1 promoters in vitro. We conclude that the high capacity for ribosome synthesis in
V. natriegens
results from a high capacity for rRNA transcription, and the high capacity for rRNA transcription results, at least in part, from the same factors that contribute most to high rates of rRNA transcription in
E. coli
, i.e., high gene dose and strong activation by UP elements and Fis.
Cel9M, a New Family 9 Cellulase of the
Clostridium cellulolyticum
Cellulosome
Authors: Belaich Anne , Parsiegla Goetz , Gal Laurent , Villard Claude , Haser Richard , Belaich Jean-Pierre 
Published: April 2009

ABSTRACT

A new cellulosomal protein from
Clostridium cellulolyticum
Cel9M was characterized. The protein contains a catalytic domain belonging to family 9 and a dockerin domain. Cel9M is active on carboxymethyl cellulose, and the hydrolysis of this substrate is accompanied by a decrease in viscosity. Cel9M has a slight, albeit significant, activity on both Avicel and bacterial microcrystalline cellulose, and the main soluble sugar released is cellotetraose. Saccharification of bacterial microcrystalline cellulose by Cel9M in association with two other family 9 enzymes from
C. cellulolyticum
, namely, Cel9E and Cel9G, was measured, and it was found that Cel9M acts synergistically with Cel9E. Complexation of Cel9M with the mini-CipC1 containing the cellulose binding domain, the X2 domain, and the first cohesin domain of the scaffoldin CipC of the bacterium did not significantly increase the hydrolysis of Avicel and bacterial microcrystalline cellulose.
In Vitro Serial Passage of
Staphylococcus aureus
: Changes in Physiology, Virulence Factor Production, and
agr
Nucleotide Sequence
Authors: Somerville Greg A. , Beres Stephen B. , Fitzgerald J. Ross , DeLeo Frank R. , Cole Robert L. , Hoff Jessica S. , Musser James M. 
Published: April 2009

ABSTRACT

Recently, we observed that
Staphylococcus aureus
strains newly isolated from patients had twofold-higher aconitase activity than a strain passaged extensively in vitro, leading us to hypothesize that aconitase specific activity decreases over time during in vitro passage. To test this hypothesis, a strain recovered from a patient with toxic shock syndrome was serially passaged for 6 weeks, and the aconitase activity was measured. Aconitase specific activity decreased 38% (
P
< 0.001) by the sixth week in culture. During serial passage,
S. aureus
existed as a heterogeneous population with two colony types that had pronounced (wild type) or negligible zones of beta-hemolytic activity. The cell density-sensing accessory gene regulatory (
agr
) system regulates beta-hemolytic activity. Surprisingly, the percentage of colonies with a wild-type beta-hemolytic phenotype correlated strongly with aconitase specific activity (ρ = 0.96), suggesting a common cause of the decreased aconitase specific activity and the variation in percentage of beta-hemolytic colonies. The loss of the beta-hemolytic phenotype also coincided with the occurrence of mutations in the
agrC
coding region or the intergenic region between
agrC
and
agrA
in the derivative strains. Our results demonstrate that in vitro growth is sufficient to result in mutations within the
agr
operon. Additionally, our results demonstrate that
S. aureus
undergoes significant phenotypic and genotypic changes during serial passage and suggest that vigilance should be used when extrapolating data obtained from the study of high-passage strains.
Conserved Low-Affinity Nickel-Binding Amino Acids Are Essential for the Function of the Nickel Permease NixA of
Helicobacter pylori
Authors: Wolfram Lutz , Bauerfeind Peter 
Published: April 2009

ABSTRACT

Nickel acquisition is necessary for urease activity, a major virulence factor of the human gastric pathogen
Helicobacter pylori
. The nickel permease NixA of
H. pylori
is a member of the single-component nickel-cobalt transporter family. To identify functionally relevant amino acids of NixA, single-site exchanges were introduced into NixA via PCR-based mutagenesis. This study investigated one of the recognition motifs for this family in transmembrane segment III and other conserved amino acids, mostly with possible nickel-binding capacities. The mutant alleles were expressed in
Escherichia coli
, and activity of the altered permeases was analyzed by measuring nickel accumulation and urease activity. Expression was checked by immunoblotting after sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a NixA-specific antibody. Replacement of Phe-75 and His-79—both part of the characteristic sequence motif—and of Asn-127, Thr-195, and Ser-197 with alanine abolished nickel uptake in the
E. coli
system. The results were unchanged if these amino acids were replaced with residues more similar to the original amino acid. The phenotype of the null mutants was independent of the culture medium. Mutation of Val-82, Tyr-242, Thr-260, His-181, and His-15 strongly affected uptake activity under nickel limitation on complex Luria-Bertani medium but had little effect in minimal medium. Eight other conserved amino acids (Ser-80, Ser-81, Phe-119, Trp-180, Tyr-183, Trp-244, Pro-249, and Asn-256) were found to be dispensable for the function of NixA. These results show that atypical nickel-binding amino acids play an important function in nickel uptake and that most of the essential amino acids are clustered in conserved motifs.
Charged Amino Acids Conserved in the Aromatic Acid/H
+
Symporter Family of Permeases Are Required for 4-Hydroxybenzoate Transport by PcaK from
Pseudomonas putida
Authors: Ditty Jayna L. , Harwood Caroline S. 
Published: April 2009

ABSTRACT

Charged amino acids in the predicted transmembrane portion of PcaK, a permease from
Pseudomonas putida
that transports 4-hydroxybenzoate (4-HBA), were required for 4-HBA transport, and they were also required for
P
.
putida
to have a chemotactic response to 4-HBA. An essential amino acid motif (DGXD) containing aspartate residues is located in the first transmembrane segment of PcaK and is conserved in the aromatic acid/H
+
symporter family of the major facilitator superfamily of transporters.
Glucose-Resistant Sporulation in
Bacillus subtilis crsA47
Mutants Does Not Depend on Promoter Switching at the
spo0A
Gene
Authors: Dixon Laurie G. , Spiegelman George B. 
Published: April 2009

ABSTRACT

We have found that sporulation in
Bacillus subtilis crsA47
mutants does not require the σ
H
-dependent promoter of the
spo0A
gene. This implies that the glucose-resistant sporulation phenotype of this strain is not related to the switch from the vegetative-stage σ
A
-dependent promoter to the σ
H
-dependent promoter at the
spo0A
gene.
New Class of IMP Cyclohydrolases in
Methanococcus jannaschii
Authors: Graupner Marion , Xu Huimin , White Robert H. 
Published: April 2009

ABSTRACT

The enzyme responsible for observed IMP cyclohydrolase activity in
Methanococcus jannaschii
was purified and sequenced: its genetic locus was found to correspond to gene MJ0626. The MJ0626 gene was cloned, and its protein product was expressed in
Escherichia coli
and shown to catalyze the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to IMP. The enzyme has no sequence similarity to known enzymes, and its catalytic properties appear distinct from any characterized IMP cyclohydrolase. The
purO
gene for the enzyme is currently found only in the domain
Archaea
.
AmfS, an Extracellular Peptidic Morphogen in
Streptomyces griseus
Authors: Ueda Kenji , Oinuma Ken-Ichi , Ikeda Go , Hosono Kuniaki , Ohnishi Yasuo , Horinouchi Sueharu , Beppu Teruhiko 
Published: April 2009

ABSTRACT

The
amf
gene cluster was previously identified as a regulator for the onset of aerial-mycelium formation in
Streptomyces griseus
. The nucleotide sequences of
amf
and its counterparts in other species revealed a conserved gene organization consisting of five open reading frames. A nonsense mutation in
amfS
, encoding a 43-amino-acid peptide, caused significant blocking of aerial-mycelium formation and streptomycin production, suggesting its role as a regulatory molecule. Extracellular-complementation tests for the aerial-mycelium-deficient phenotype of the
amfS
mutant demonstrated that AmfS was secreted by the wild-type strain. A null mutation in
amfBA
, encoding HlyB-like membrane translocators, abolished the extracellular AmfS activity without affecting the wild-type morphology, which suggests that AmfBA is involved not in production but in export of AmfS. A synthetic C-terminal octapeptide partially induced aerial-mycelium formation in the
amfS
mutant, which suggests that an AmfS derivative, but not AmfS itself, serves as an extracellular morphogen.