bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of the Leucine Response Transcription Factor LeuO in Regulation of the Genes for Sulfa Drug Efflux
Authors: Shimada Tomohiro , Yamamoto Kaneyoshi , Ishihama Akira 
Published: May 2009

ABSTRACT

LeuO, a LysR family transcription factor, exists in a wide variety of bacteria of the family
Enterobacteriaceae
and is involved in the regulation of as yet unidentified genes affecting the stress response and pathogenesis expression. Using genomic screening by systematic evolution of ligands by exponential enrichment (SELEX) in vitro, a total of 106 DNA sequences were isolated from 12 different regions of the
Escherichia coli
genome. All of the SELEX fragments formed complexes in vitro with purified LeuO. After Northern blot analysis of the putative target genes located downstream of the respective LeuO-binding sequence, a total of nine genes were found to be activated by LeuO, while three genes were repressed by LeuO. The LeuO target gene collection included several multidrug resistance genes. A phenotype microarray assay was conducted to identify the gene(s) responsible for drug resistance and the drug species that are under the control of the LeuO target gene(s). The results described herein indicate that the
yjcRQP
operon, one of the LeuO targets, is involved in sensitivity control against sulfa drugs. We propose to rename the
yjcRQP
genes the
sdsRQP
genes (
s
ulfa
d
rug
s
ensitivity determinant).
Gene Expression Patterns Associated with the Biosynthesis of the Sunscreen Scytonemin in
Nostoc punctiforme
ATCC 29133 in Response to UVA Radiation
Authors: Soule Tanya , Garcia-Pichel Ferran , Stout Valerie 
Published: May 2009

ABSTRACT

Under exposure to UV radiation, some cyanobacteria synthesize sunscreen compounds. Scytonemin is a heterocyclic indole-alkaloid sunscreen, the synthesis of which is induced upon exposure to UVA (long-wavelength UV) radiation. We previously identified and characterized an 18-gene cluster associated with scytonemin biosynthesis in the cyanobacterium
Nostoc punctiforme
ATCC 29133; we now report on the expression response of these genes to a step-up shift in UVA exposure. Using quantitative PCR on cDNAs from the
N. punctiforme
transcriptome and primers targeting each of the 18 genes in the cluster, we followed their differential expression in parallel subcultures incubated with and without UVA. All 18 genes are induced by UVA irradiation, with relative transcription levels that generally peak after 48 h of continuous UVA exposure. A five-gene cluster implicated in the process of scytonemin biosynthesis solely on the basis of comparative genomics was also upregulated. Furthermore, we demonstrate that all of the genes in the18-gene region are cotranscribed as part of a single transcriptional unit.
The Crystal Structures of Substrate and Nucleotide Complexes of
Enterococcus faecium
Aminoglycoside-2′′-Phosphotransferase-IIa [APH(2′′)-IIa] Provide Insights into Substrate Selectivity in the APH(2′′) Subfamily
Authors: Young Paul G. , Walanj Rupa , Lakshmi Vendula , Byrnes Laura J. , Metcalf Peter , Baker Edward N. , Vakulenko Sergei B. , Smith Clyde A. 
Published: May 2009

ABSTRACT

Aminoglycoside-2′′-phosphotransferase-IIa [APH(2′′)-IIa] is one of a number of homologous bacterial enzymes responsible for the deactivation of the aminoglycoside family of antibiotics and is thus a major component in bacterial resistance to these compounds. APH(2′′)-IIa produces resistance to several clinically important aminoglycosides (including kanamycin and gentamicin) in both gram-positive and gram-negative bacteria, most notably in
Enterococcus
species. We have determined the structures of two complexes of APH(2′′)-IIa, the binary gentamicin complex and a ternary complex containing adenosine-5′-(β,γ-methylene)triphosphate (AMPPCP) and streptomycin. This is the first crystal structure of a member of the APH(2′′) family of aminoglycoside phosphotransferases. The structure of the gentamicin-APH(2′′)-IIa complex was solved by multiwavelength anomalous diffraction methods from a single selenomethionine-substituted crystal and was refined to a crystallographic
R
factor of 0.210 (
R
free
, 0.271) at a resolution of 2.5 Å. The structure of the AMPPCP-streptomycin complex was solved by molecular replacement using the gentamicin-APH(2′′)-IIa complex as the starting model. The enzyme has a two-domain structure with the substrate binding site located in a cleft in the C-terminal domain. Gentamicin binding is facilitated by a number of conserved acidic residues lining the binding cleft, with the A and B rings of the substrate forming the majority of the interactions. The inhibitor streptomycin, although binding in the same pocket as gentamicin, is orientated such that no potential phosphorylation sites are adjacent to the catalytic aspartate residue. The binding of gentamicin and streptomycin provides structural insights into the substrate selectivity of the APH(2′′) subfamily of aminoglycoside phosphotransferases, specifically, the selectivity between the 4,6-disubstituted and the 4,5-disubstituted aminoglycosides.
Gemfibrozil Inhibits
Legionella pneumophila
and
Mycobacterium tuberculosis
Enoyl Coenzyme A Reductases and Blocks Intracellular Growth of These Bacteria in Macrophages
Authors: Reich-Slotky Ronit , Kabbash Christina A. , Della-Latta Phyllis , Blanchard John S. , Feinmark Steven J. , Freeman Sherry , Kaplan Gilla , Shuman Howard A. , Silverstein Samuel C. 
Published: May 2009

ABSTRACT

We report here that gemfibrozil (GFZ) inhibits axenic and intracellular growth of
Legionella pneumophila
and of 27 strains of wild-type and multidrug-resistant
Mycobacterium tuberculosis
in bacteriological medium and in human and mouse macrophages, respectively. At a concentration of 0.4 mM, GFZ completely inhibited
L. pneumophila
fatty acid synthesis, while at 0.12 mM it promoted cytoplasmic accumulation of polyhydroxybutyrate. To assess the mechanism(s) of these effects, we cloned an
L. pneumophila
FabI enoyl reductase homolog that complemented for growth an
Escherichia coli
strain carrying a temperature-sensitive enoyl reductase and rendered the complemented
E. coli
strain sensitive to GFZ at the nonpermissive temperature. GFZ noncompetitively inhibited this
L. pneumophila
FabI homolog, as well as
M. tuberculosis
InhA and
E. coli
FabI.
3′-Phosphoadenosine-5′-Phosphate Phosphatase Activity Is Required for Superoxide Stress Tolerance inStreptococcus mutans
Authors: Zhang Jiaqin , Biswas Indranil 
Published: May 2009

ABSTRACTAerobic microorganisms have evolved different strategies to withstand environmental oxidative stresses generated by various reactive oxygen species (ROS). For the facultative anaerobic human oral pathogenStreptococcus mutans, the mechanisms used to protect against ROS are not fully understood, since it does not possess catalase, an enzyme that degrades hydrogen peroxide. In order to elucidate the genes that are essential for superoxide stress response, methyl viologen (MV)-sensitive mutants ofS. mutanswere generated via ISS1mutagenesis. Screening of approximately 2,500 mutants revealed six MV-sensitive mutants, each containing an insertion in one of five genes, including a highly conserved hypothetical gene, SMU.1297. Sequence analysis suggests that SMU.1297 encodes a hypothetical protein with a high degree of homology to theBacillus subtilisYtqI protein, which possesses an oligoribonuclease activity that cleaves nano-RNAs and a phosphatase activity that degrades 3′-phosphoadenosine-5′-phosphate (pAp) and 3′-phosphoadenosine-5′-phosphosulfate (pApS) to produce AMP; the latter activity is similar to the activity of theEscherichia coliCysQ protein, which is required for sulfur assimilation. SMU.1297 was deleted using a markerless Cre-loxP-based strategy; the SMU.1297 deletion mutant was just as sensitive to MV as the ISS1insertion mutant. Complementation of the deletion mutant with wild-type SMU.1297, intrans, restored the parental phenotype. Biochemical analyses with purified SMU.1297 protein demonstrated that it has pAp phosphatase activity similar to that of YtqI but apparently lacks an oligoribonuclease activity. The ability of SMU.1297 to dephosphorylate pApS in vivo was confirmed by complementation of anE. coli cysQmutant with SMU.1297 intrans. Thus, our results suggest that SMU.1297 is involved in superoxide stress tolerance inS. mutans. Furthermore, the distribution of homologs of SMU.1297 in streptococci indicates that this protein is essential for superoxide stress tolerance in these organisms.
Uptake of Glycerol-2-Phosphate via the
ugp
-Encoded Transporter in
Escherichia coli
K-12
Authors: Yang Kechao , Wang Mi , Metcalf William W. 
Published: May 2009

ABSTRACT

During phenotypic characterization of various
Escherichia coli
mutants, we observed that Δ
phoA
strains are capable of using glycerol-2-phosphate (G2P) as a sole source of phosphorus. Mutations in the
ugpBAECQ
operon eliminated this phenotype, suggesting that G2P is a previously unrecognized substrate for the binding protein-dependent Ugp transporter.
orf4
of the
Bacillus cereus sigB
Gene Cluster Encodes a General Stress-Inducible Dps-Like Bacterioferritin
Authors: Wang Shin-Wei , Chen Chien-Yen , Tseng Joseph T. , Liang Shih-Hsiung , Chen Ssu-Ching , Hsieh Chienyan , Chen Yen-hsu , Chen Chien-Cheng 
Published: May 2009

ABSTRACT

The function of
orf4
in the
sigB
cluster in
Bacillus cereus
ATCC 14579 remains to be explored. Amino-acid sequence analysis has revealed that Orf4 is homologous with bacterioferritins and Dps. In this study, we generated an
orf4
-null mutant and produced recombinant protein rOrf4 to establish the role of
orf4
. In vitro, the purified rOrf4 was found to exist in two distinct forms, a dimeric form and a polymer form, through size exclusion analysis. The latter form exhibited a unique filament structure, in contrast to the typical spherical tetracosamer structure of bacterioferritins; the former can be induced to form rOrf4 polymers immediately after the addition of FeCl
2
. Catalysis of the oxidation of ferrous irons by ferroxidase activity was detected with rOrf4, and the mineralized irons were subsequently sequestered only in the rOrf4 polymer. Moreover, rOrf4 exerted DNA-protective activity against oxidative damage via DNA binding in a nonspecific manner, as is seen with Dps. In vivo, deletion of
orf4
had no effect on activation of the alternative sigma factor σ
B
, and therefore,
orf4
is not associated with σ
B
regulation; however,
orf4
can be significantly upregulated upon environmental stress but not H
2
O
2
treatment.
B. cereus
strains with constitutive Orf4 expression exhibited a viability higher than that of the
orf4
-null mutant, under specific oxidative stress or heat shock. Taken together, these results suggest that Orf4 functions as a Dps-like bacterioferritin in response to environmental stress and can provide cell protection from oxidative damage through iron sequestration and DNA binding.
The
ldhA
Gene, Encoding Fermentative
l
-Lactate Dehydrogenase of
Corynebacterium glutamicum
, Is under the Control of Positive Feedback Regulation Mediated by LldR
Authors: Toyoda Koichi , Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki 
Published: May 2009

ABSTRACT

Corynebacterium glutamicum ldhA
encodes
l
-lactate dehydrogenase, a key enzyme that couples
l
-lactate production to reoxidation of NADH formed during glycolysis. We previously showed that in the absence of sugar, SugR binds to the
ldhA
promoter region, thereby repressing
ldhA
expression. In this study we show that LldR is another protein that binds to the
ldhA
promoter region, thus regulating
ldhA
expression. LldR has hitherto been characterized as an
l
-lactate-responsive transcriptional repressor of
l
-lactate utilization genes. Transposon mutagenesis of a reporter strain carrying a chromosomal
ldhA
promoter-
lacZ
fusion (P
ldhA
-
lacZ
) revealed that
ldhA
disruption drastically decreased expression of P
ldhA
-
lacZ
. P
ldhA
-
lacZ
expression in the
ldhA
mutant was restored by deletion of
lldR
, suggesting that LldR acts as a repressor of
ldhA
in the absence of
l
-lactate and the LldR-mediated repression is not relieved in the
ldhA
mutant due to its inability to produce
l
-lactate.
lldR
deletion did not affect P
ldhA
-
lacZ
expression in the wild-type background during growth on either glucose, acetate, or
l
-lactate. However, it upregulated P
ldhA
-
lacZ
expression in the
sugR
mutant background during growth on acetate. The binding sites of LldR and SugR are located around the −35 and −10 regions of the
ldhA
promoter, respectively.
C. glutamicum ldhA
expression is therefore primarily repressed by SugR in the absence of sugar. In the presence of sugar, SugR-mediated repression of
ldhA
is alleviated, and
ldhA
expression is additionally enhanced by LldR inactivation in response to
l
-lactate produced by LdhA.
The
Sinorhizobium meliloti
LpxXL and AcpXL Proteins Play Important Roles in Bacteroid Development within Alfalfa
Authors: Haag Andreas F. , Wehmeier Silvia , Beck Sebastian , Marlow Victoria L. , Fletcher Vivien , James Euan K. , Ferguson Gail P. 
Published: May 2009

ABSTRACT

Free-living
Sinorhizobium meliloti lpxXL
and
acpXL
mutants lack lipid A very-long-chain fatty acids (VLCFAs) and have reduced competitiveness in alfalfa. We demonstrate that LpxXL and AcpXL play important but distinct roles in bacteroid development and that LpxXL is essential for the modification of
S. meliloti
bacteroid lipid A with VLCFAs.
Intact Flagellar Motor of
Borrelia burgdorferi
Revealed by Cryo-Electron Tomography: Evidence for Stator Ring Curvature and Rotor/C-Ring Assembly Flexion
Authors: Liu Jun , Lin Tao , Botkin Douglas J. , McCrum Erin , Winkler Hanspeter , Norris Steven J. 
Published: May 2009

ABSTRACT

The bacterial flagellar motor is a remarkable nanomachine that provides motility through flagellar rotation. Prior structural studies have revealed the stunning complexity of the purified rotor and C-ring assemblies from flagellar motors. In this study, we used high-throughput cryo-electron tomography and image analysis of intact
Borrelia burgdorferi
to produce a three-dimensional (3-D) model of the in situ flagellar motor without imposing rotational symmetry. Structural details of
B. burgdorferi
, including a layer of outer surface proteins, were clearly visible in the resulting 3-D reconstructions. By averaging the 3-D images of ∼1,280 flagellar motors, a ∼3.5-nm-resolution model of the stator and rotor structures was obtained.
flgI
transposon mutants lacked a torus-shaped structure attached to the flagellar rod, establishing the structural location of the spirochetal P ring. Treatment of intact organisms with the nonionic detergent NP-40 resulted in dissolution of the outermost portion of the motor structure and the C ring, providing insight into the in situ arrangement of the stator and rotor structures. Structural elements associated with the stator followed the curvature of the cytoplasmic membrane. The rotor and the C ring also exhibited angular flexion, resulting in a slight narrowing of both structures in the direction perpendicular to the cell axis. These results indicate an inherent flexibility in the rotor-stator interaction. The FliG switching and energizing component likely provides much of the flexibility needed to maintain the interaction between the curved stator and the relatively symmetrical rotor/C-ring assembly during flagellar rotation.
Site-Specific Recombination in the Cyanobacterium
Anabaena
sp. Strain PCC 7120 Catalyzed by the Integrase of Coliphage HK022
Authors: Melnikov Olga , Zaritsky Arieh , Zarka Aliza , Boussiba Sammy , Malchin Natalia , Yagil Ezra , Kolot Mikhail 
Published: May 2009

ABSTRACT

The integrase (Int) of the λ-like coliphage HK022 catalyzes the site-specific integration and excision of the phage DNA into and from the chromosome of its host,
Escherichia coli
. Int recognizes two different pairs of recombining sites
attP
×
attB
and
attL
×
attR
for integration and excision, respectively. This system was adapted to the cyanobacterium
Anabaena
sp. strain PCC 7120 as a potential tool for site-specific gene manipulations in the cyanobacterium. Two plasmids were consecutively cointroduced by conjugation into
Anabaena
cells, one plasmid that expresses HK022 Int recombinase and the other plasmid that carries the excision substrate

P
glnA

-
attL
-T1/T2-
attR
-
lacZ
, where T1/T2 are the strong transcription terminators of
rrnB
, to prevent expression of the
lacZ
reporter under the constitutive promoter

P
glnA

. The Int-catalyzed site-specific recombination reaction was monitored by the expression of
lacZ
emanating as a result of T1/T2 excision. Int catalyzed the site-specific excision reaction in
Anabaena
cells when its substrate was located either on the plasmid or on the chromosome with no need to supply an accessory protein, such as integration host factor and excisionase (Xis), which are indispensable for this reaction in its host,
E. coli
.
Involvement of Two Transport Systems and a Specific Porin in the Uptake of Phthalate by
Burkholderia
spp
Authors: Chang Hung-Kuang , Dennis Jonathan J. , Zylstra Gerben J. 
Published: May 2009

ABSTRACT

Burkholderia
spp. that degrade phthalate have an ABC transporter-type phthalate transport system (OphFGH) and a specific porin (OphP) in addition to a permease-type phthalate transporter (OphD). OphFGH has a lower
K

m

and higher
V
max
than OphD, which affects how the bacteria grow. OphP is involved in both mechanisms of transport.
High-Force Generation Is a Conserved Property of Type IV Pilus Systems
Authors: Clausen Martin , Jakovljevic Vladimir , Søgaard-Andersen Lotte , Maier Berenike 
Published: May 2009

ABSTRACT

The type IV pilus (T4P) system of
Neisseria gonorrhoeae
is the strongest linear molecular motor reported to date, but it is unclear whether high-force generation is conserved between bacterial species. Using laser tweezers, we found that the average stalling force of single-pilus retraction in
Myxococcus xanthus
of 149 ± 14 pN exceeds the force generated by
N. gonorrhoeae
. Retraction velocities including a bimodal distribution were similar between
M. xanthus
and
N. gonorrhoeae
, but force-dependent directional switching was not. Force generation by pilus retraction is energized by the ATPase PilT. Surprisingly, an
M. xanthus
mutant lacking PilT apparently still retracted T4P, although at a reduced frequency. The retraction velocity was comparable to the high-velocity mode in the wild type at low forces but decreased drastically when the force increased, with an average stalling force of 70 ± 10 pN. Thus,
M. xanthus
harbors at least two different retraction motors. Our results demonstrate that the major physical properties are conserved between bacteria that are phylogenetically distant and pursue very different lifestyles.
Genome Sequence ofAzotobacter vinelandii, an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes
Authors: Setubal João C. , dos Santos Patricia , Goldman Barry S. , Ertesvåg Helga , Espin Guadelupe , Rubio Luis M. , Valla Svein , Almeida Nalvo F. , Balasubramanian Divya , Cromes Lindsey , Curatti Leonardo , Du Zijin , Godsy Eric , Goodner Brad , Hellner-Burris Kaitlyn , Hernandez José A. , Houmiel Katherine , Imperial Juan , Kennedy Christina , Larson Timothy J. , Latreille Phil , Ligon Lauren S. , Lu Jing , Mærk Mali , Miller Nancy M. , Norton Stacie , O'Carroll Ina P. , Paulsen Ian , Raulfs Estella C. , Roemer Rebecca , Rosser James , Segura Daniel , Slater Steve , Stricklin Shawn L. , Studholme David J. , Sun Jian , Viana Carlos J. , Wallin Erik , Wang Baomin , Wheeler Cathy , Zhu Huijun , Dean Dennis R. , Dixon Ray , Wood Derek 
Published: May 2009

ABSTRACTAzotobacter vinelandiiis a soil bacterium related to thePseudomonasgenus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. In response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. Here we report the complete genome sequence ofA. vinelandiiDJ, which has a single circular genome of 5,365,318 bp. In order to reconcile an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes,A. vinelandiiis specialized in terms of its complement of respiratory proteins. It is able to produce alginate, a polymer that further protects the organism from excess exogenous oxygen, and it has multiple duplications of alginate modification genes, which may alter alginate composition in response to oxygen availability. The genome analysis identified the chromosomal locations of the genes coding for the three known oxygen-sensitive nitrogenases, as well as genes coding for other oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and formate dehydrogenase. These findings offer new prospects for the wider application ofA. vinelandiias a host for the production and characterization of oxygen-sensitive proteins.
Interactions of DNA with Biofilm-Derived Membrane Vesicles
Authors: Schooling Sarah R. , Hubley Amanda , Beveridge Terry J. 
Published: May 2009

ABSTRACT
The biofilm matrix contributes to the chemistry, structure, and function of biofilms. Biofilm-derived membrane vesicles (MVs) and DNA, both matrix components, demonstrated concentration-, pH-, and cation-dependent interactions. Furthermore, MV-DNA association influenced MV surface properties. This bears consequences for the reactivity and availability for interaction of matrix polymers and other constituents.
Two-Step Assembly Dynamics of theBacillussubtilisDivisome
Authors: Gamba Pamela , Veening Jan-Willem , Saunders Nigel J. , Hamoen Leendert W. , Daniel Richard A. 
Published: May 2009

ABSTRACTCell division in bacteria is carried out by about a dozen proteins which assemble at midcell and form a complex known as the divisome. To study the dynamics and temporal hierarchy of divisome assembly inBacillussubtilis, we have examined the in vivo localization pattern of a set of division proteins fused to green fluorescent protein in germinating spores and vegetative cells. Using time series and time-lapse microscopy, we show that the FtsZ ring assembles early and concomitantly with FtsA, ZapA, and EzrA. After a time delay of at least 20% of the cell cycle, a second set of division proteins, including GpsB, FtsL, DivIB, FtsW, Pbp2B, and DivIVA, are recruited to midcell. Together, our data provide in vivo evidence for two-step assembly of the divisome. Interestingly, overproduction of FtsZ advances the temporal assembly of EzrA but not of DivIVA, suggesting that a signal different from that of FtsZ polymerization drives the assembly of late divisome proteins. Microarray analysis shows that FtsZ depletion or overexpression does not significantly alter the transcription of division genes, supporting the hypothesis that cell division inB.subtilisis mainly regulated at the posttranscriptional level.
Identification of ORF636 in Phage φSLT Carrying Panton-Valentine Leukocidin Genes, Acting as an Adhesion Protein for a Poly(Glycerophosphate) Chain of Lipoteichoic Acid on the Cell Surface of
Staphylococcus aureus
Authors: Kaneko Jun , Narita-Yamada Sachiko , Wakabayashi Yukari , Kamio Yoshiyuki 
Published: May 2009

ABSTRACT

The temperate phage φSLT of
Staphylococcus aureus
carries genes for Panton-Valentine leukocidin. Here, we identify ORF636, a constituent of the phage tail tip structure, as a recognition/adhesion protein for a poly(glycerophosphate) chain of lipoteichoic acid on the cell surface of
S. aureus
. ORF636 bound specifically to
S. aureus
; it did not bind to any other staphylococcal species or to several gram-positive bacteria.