bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the Protocatechuate 2,3-Cleavage Pathway Genes
Authors: Kasai Daisuke , Fujinami Toshihiro , Abe Tomokuni , Mase Kohei , Katayama Yoshihiro , Fukuda Masao , Masai Eiji 
Published: August 2009

ABSTRACT

Paenibacillus
sp. (formerly
Bacillus macerans
) strain JJ-1b is able to grow on 4-hydroxybenzoate (4HB) as a sole source of carbon and energy and is known to degrade 4HB via the protocatechuate (PCA) 2,3-cleavage pathway. However, none of the genes involved in this pathway have been identified. In this study, we identified and characterized the JJ-1b genes for the 4HB catabolic pathway via the PCA 2,3-cleavage pathway, which consisted of
praR
and
praABEGFDCHI
. Based on the enzyme activities of cell extracts of
Escherichia coli
carrying
praI
,
praA
,
praH
,
praB
,
praC
, and
praD
, these genes were found to code for 4HB 3-hydroxylase, PCA 2,3-dioxygenase, 5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase, 2-hydroxymuconate-6-semialdehyde dehydrogenase, 4-oxalocrotonate (OCA) tautomerase, and OCA decarboxylase, respectively, which are involved in the conversion of 4HB into 2-hydroxypenta-2,4-dienoate (HPD). The
praE
,
praF
, and
praG
gene products exhibited 45 to 61% amino acid sequence identity to the corresponding enzymes responsible for the catabolism of HPD to pyruvate and acetyl coenzyme A. The deduced amino acid sequence of
praR
showed similarity with those of IclR-type transcriptional regulators. Reverse transcription-PCR analysis revealed that
praABEGFDCHI
constitute an operon, and these genes were expressed during the growth of JJ-1b on 4HB and PCA.
praR-praABEGFDCHI
conferred the ability to grow on 4HB to
E
.
coli
, suggesting that
praEGF
were functional for the conversion of HPD to pyruvate and acetyl coenzyme A. A promoter analysis suggested that
praR
encodes a repressor of the
pra
operon.
Bacillus subtilis
SpoIIIJ and YqjG Function in Membrane Protein Biogenesis
Authors: Saller Manfred J. , Fusetti Fabrizia , Driessen Arnold J. M. 
Published: August 2009

ABSTRACT

In all domains of life Oxa1p-like proteins are involved in membrane protein biogenesis.
Bacillus subtilis
, a model organism for gram-positive bacteria, contains two Oxa1p homologs: SpoIIIJ and YqjG. These molecules appear to be mutually exchangeable, although SpoIIIJ is specifically required for spore formation. SpoIIIJ and YqjG have been implicated in a posttranslocational stage of protein secretion. Here we show that the expression of either
spoIIIJ
or
yqjG
functionally compensates for the defects in membrane insertion due to YidC depletion in
Escherichia coli
. Both SpoIIIJ and YqjG complement the function of YidC in SecYEG-dependent and -independent membrane insertion of subunits of the cytochrome
o
oxidase and F
1
F
o
ATP synthase complexes. Furthermore, SpoIIIJ and YqjG facilitate membrane insertion of F
1
F
o
ATP synthase subunit c from both
E. coli
and
B. subtilis
into inner membrane vesicles of
E. coli
. When isolated from
B. subtilis
cells, SpoIIIJ and YqjG were found to be associated with the entire F
1
F
o
ATP synthase complex, suggesting that they have a role late in the membrane assembly process. These data demonstrate that the
Bacillus
Oxa1p homologs have a role in membrane protein biogenesis rather than in protein secretion.
FlhF and Its GTPase Activity Are Required for Distinct Processes in Flagellar Gene Regulation and Biosynthesis in
Campylobacter jejuni
Authors: Balaban Murat , Joslin Stephanie N. , Hendrixson David R. 
Published: August 2009

ABSTRACT

FlhF proteins are putative GTPases that are often necessary for one or more steps in flagellar organelle development in polarly flagellated bacteria. In
Campylobacter jejuni
, FlhF is required for σ
54
-dependent flagellar gene expression and flagellar biosynthesis, but how FlhF influences these processes is unknown. Furthermore, the GTPase activity of any FlhF protein and the requirement of this speculated activity for steps in flagellar biosynthesis remain uncharacterized. We show here that
C. jejuni
FlhF hydrolyzes GTP, indicating that these proteins are GTPases.
C. jejuni
mutants producing FlhF proteins with reduced GTPase activity were not severely defective for σ
54
-dependent flagellar gene expression, unlike a mutant lacking FlhF. Instead, these mutants had a propensity to lack flagella or produce flagella in improper numbers or at nonpolar locations, indicating that GTP hydrolysis by FlhF is required for proper flagellar biosynthesis. Additional studies focused on elucidating a possible role for FlhF in σ
54
-dependent flagellar gene expression were conducted. These studies revealed that FlhF does not influence production of or signaling between the flagellar export apparatus and the FlgSR two-component regulatory system to activate σ
54
. Instead, our data suggest that FlhF functions in an independent pathway that converges with or works downstream of the flagellar export apparatus-FlgSR pathway to influence σ
54
-dependent gene expression. This study provides corroborative biochemical and genetic analyses suggesting that different activities of the
C. jejuni
FlhF GTPase are required for distinct steps in flagellar gene expression and biosynthesis. Our findings are likely applicable to many polarly flagellated bacteria that utilize FlhF in flagellar biosynthesis processes.
Mechanism of Transcriptional Activation by
Pseudomonas aeruginosa
ExsA
Authors: Vakulskas Christopher A. , Brady Keith M. , Yahr Timothy L. 
Published: August 2009

ABSTRACT

ExsA is a transcriptional activator of the
Pseudomonas aeruginosa
type III secretion system (T3SS). The T3SS consists of >40 genes organized within 10 transcriptional units, each of which is controlled by the transcriptional activator ExsA. ExsA-dependent promoters contain two adjacent ExsA binding sites that when occupied protect the −30 to −70 region from DNase I cleavage. The promoters also possess regions bearing strong resemblance to the consensus −10 and −35 regions of σ
70
-dependent promoters. The spacing distance between the putative −10 and −35 regions of ExsA-dependent promoters, however, is increased by 4 to 5 bp compared to that in typical σ
70
-dependent promoters. In the present study, we demonstrate that ExsA-dependent transcriptional activation requires a 21- or 22-bp spacer length between the −10 and −35 regions. Despite the atypical spacing in this region, in vitro transcription assays using σ
70
-saturated RNA polymerase holoenzyme (RNAP-σ
70
) confirm that ExsA-dependent promoters are indeed σ
70
dependent. Potassium permanganate footprinting experiments indicate that ExsA facilitates an early step in transcriptional initiation. Although RNAP-σ
70
binds to the promoters with low affinity in the absence of ExsA, the activator stimulates transcription by enhancing recruitment of RNAP-σ
70
to the P

exsC

and P

exsD

promoters. Abortive initiation assays confirm that ExsA enhances the equilibrium binding constant for RNAP while having only a modest effect on the isomerization rate constant.
The PqrR Transcriptional Repressor of
Pseudomonas aeruginosa
Transduces Redox Signals via an Iron-Containing Prosthetic Group
Authors: Rungrassamee Wanilada , Ryan Kelly C. , Maroney Michael J. , Pomposiello Pablo J. 
Published: August 2009

ABSTRACT

Inducible defenses against oxidative stress are coordinated by redox-sensitive transcription factors that transduce oxidative damage into differential gene expression. The opportunistic human pathogen
Pseudomonas aeruginosa
has evolved under physiological and host-derived sources of oxidative stress. Previous work showed that the
pqrABC
and
pqrR
genes of
P. aeruginosa
, all lacking known functions, were induced by treatment of three different isolates of
P. aeruginosa
with paraquat (PQ), a superoxide-producing agent. Insertional mutation of the
pqrABCR
genes resulted in hypersensitive phenotypes to a variety of oxidants, although the hypersensitivity to PQ was marginal. Mutation of
pqrR
and complementation assays showed that PqrR regulated the
pqrABC
genes in response to PQ. PqrR, a member of the MarR family of transcriptional regulators, contains a C-terminal region with four conserved cysteines, which suggested redox-regulated transcriptional activity. Purified PqrR bound to two discrete sites at the
pqrA
and
pqrR
regulatory regions. The in vitro DNA binding activity of PqrR was decreased by exposure to air and reconstituted by treatment with
dl
-dithiothreitol. Elemental analysis and preliminary electron paramagnetic resonance experiments showed that PqrR contains iron. Interestingly, site-directed mutagenesis of C-terminal cysteines demonstrated that the four conserved cysteine residues are essential for in vivo redox sensing by PqrR.
Single-Residue Changes in the C-Terminal Disulfide-Bonded Loop of thePseudomonas aeruginosaType IV Pilin Influence Pilus Assembly and Twitching Motility
Authors: Harvey Hanjeong , Habash Marc , Aidoo Francisca , Burrows Lori L. 
Published: August 2009

ABSTRACTPilA, the major pilin subunit ofPseudomonas aeruginosatype IV pili (T4P), is a principal structural component. PilA has a conserved C-terminal disulfide-bonded loop (DSL) that has been implicated as the pilus adhesinotope. Structural studies have suggested that DSL is involved in intersubunit interactions within the pilus fiber. PilA mutants with single-residue substitutions, insertions, or deletions in the DSL were tested for pilin stability, pilus assembly, and T4P function. Mutation of either Cys residue of the DSL resulted in pilins that were unable to assemble into fibers. Ala replacements of the intervening residues had a range of effects on assembly or function, as measured by changes in surface pilus expression and twitching motility. Modification of the C-terminal P-X-X-C type II beta-turn motif, which is one of the few highly conserved features in pilins across various species, caused profound defects in assembly and twitching motility. Expression of pilins with suspected assembly defects in apilA pilTdouble mutant unable to retract T4P allowed us to verify which subunits were physically unable to assemble. Use of two different PilA antibodies showed that the DSL may be an immunodominant epitope in intact pili compared with pilin monomers. Sequence diversity of the type IVa pilins likely reflects an evolutionary compromise between retention of function and antigenic variation. The consequences of DSL sequence changes should be evaluated in the intact protein since it is technically feasible to generate DSL-mimetic peptides with mutations that will not appear in the natural repertoire due to their deleterious effects on assembly.
The
Vibrio cholerae
Flagellar Regulatory Hierarchy Controls Expression of Virulence Factors
Authors: Syed Khalid Ali , Beyhan Sinem , Correa Nidia , Queen Jessica , Liu Jirong , Peng Fen , Satchell Karla J. F. , Yildiz Fitnat , Klose Karl E. 
Published: August 2009

ABSTRACT

Vibrio cholerae
is a motile bacterium responsible for the disease cholera, and motility has been hypothesized to be inversely regulated with virulence. We examined the transcription profiles of
V. cholerae
strains containing mutations in flagellar regulatory genes (
rpoN
,
flrA
,
flrC
, and
fliA
) by utilizing whole-genome microarrays. Results revealed that flagellar transcription is organized into a four-tiered hierarchy. Additionally, genes with proven or putative roles in virulence (e.g.,
ctx
,
tcp
, hemolysin, and type VI secretion genes) were upregulated in flagellar regulatory mutants, which was confirmed by quantitative reverse transcription-PCR. Flagellar regulatory mutants exhibit increased hemolysis of human erythrocytes, which was due to increased transcription of the thermolabile hemolysin (
tlh
). The flagellar regulatory system positively regulates transcription of a diguanylate cyclase, CdgD, which in turn regulates transcription of a novel hemagglutinin (
frhA
) that mediates adherence to chitin and epithelial cells and enhances biofilm formation and intestinal colonization in infant mice. Our results demonstrate that the flagellar regulatory system modulates the expression of nonflagellar genes, with induction of an adhesin that facilitates colonization within the intestine and repression of virulence factors maximally induced following colonization. These results suggest that the flagellar regulatory hierarchy facilitates correct spatiotemporal expression patterns for optimal
V. cholerae
colonization and disease progression.
Two Essential Arginine Residues in the T Components of Energy-Coupling Factor Transporters
Authors: Neubauer Olivia , Alfandega Anja , Schoknecht Janna , Sternberg Ulrich , Pohlmann Anne , Eitinger Thomas 
Published: August 2009

ABSTRACT
Energy-coupling factor (ECF) transporters, a recently discovered class of importers of micronutrients, are composed of a substrate-specific transmembrane component (S component) and a conserved energy-coupling module consisting of a transmembrane protein (T component) and pairs of ABC ATPases (A proteins). Based on utilization of a dedicated (subclass I) or shared (subclass II) energy-coupling module, ECF systems fall into two subclasses. The T components are the least-characterized proteins of ECF importers, and their function is essentially unknown. Using RcBioN and LmEcfT, the T units of the subclass I biotin transporter (RcBioMNY) of a gram-negative bacterium and of the subclass II folate, pantothenate, and riboflavin transporters of a lactic acid bacterium, respectively, we analyzed the role of two strongly conserved short motifs, each containing an arginine residue. Individual replacement of the two Arg residues in RcBioN reduced ATPase activity, an indicator of the transporter function, by two-thirds without affecting the modular assembly of the RcBioMNY complex. A double Arg-to-Glu replacement destroyed the complex and abolished ATPase activity. The corresponding single mutation in motif II of LmEcfT, as well as a double mutation, led to loss of the T unit from the subclass II ECF transporters and inactivated these systems. A single Arg-to-Glu replacement in motif I, however, abolished vitamin uptake activity without affecting assembly of the modules. Our results indicate that the conserved motif I in T components is essential for intramolecular signaling and, in cooperation with motif II, for subunit assembly of modular ECF transporters.
The
Mycoplasma genitalium
MG_454 Gene Product Resists Killing by Organic Hydroperoxides
Authors: Saikolappan Sankaralingam , Sasindran Smitha J. , Yu Hongwei D. , Baseman Joel B. , Dhandayuthapani Subramanian 
Published: August 2009

ABSTRACT

Mycoplasma genitalium
is the smallest self-replicating organism and a successful human pathogen associated with a range of genitourinary maladies. As a consequence of its restricted genome size, genes that are highly conserved in other bacteria are absent in
M. genitalium
. Significantly, genes that encode antioxidants like superoxide dismutase and catalase-peroxidase are lacking. Nevertheless, comparative genomics has revealed that MG_454 of
M. genitalium
encodes a protein with putative function as an organic hydroperoxide reductase (Ohr). In this study, we found that an
M. genitalium
transposon mutant that lacks expression of MG_454 was sensitive to killing by
t
-butyl hydroperoxide and cumene hydroperoxide. To understand whether this sensitivity to hydroperoxides was linked to MG_454, we cloned this gene behind an arabinose-inducible
PBAD
promoter in plasmid pHERD20T and transformed this construct (pHERDMG454) into a
Pseudomonas aeruginosa
strain having deletion in its
ohr
gene (
ohr
mutant) and showing sensitivity to organic hydroperoxides. The
P. aeruginosa ohr
mutant harboring pHERDMG454, when induced with arabinose, was able to reverse its sensitivity to organic hydroperoxides, thus supporting the notion that the product of MG_454 resists organic hydroperoxides in
M. genitalium
. Surprisingly, real-time reverse transcription-PCR showed that expression of MG_454 in
M. genitalium
was not elevated in response to oxidative stress but was elevated in response to physical stresses, like salt (NaCl) and heat. Although failure of MG_454 to respond to oxidative stress in
M. genitalium
implies the absence of a known oxidative stress response regulator in the genome of
M. genitalium
, elevated expression of MG_454 due to physical stress suggests its control by an unidentified regulator.
Effects of a low-frequency sound wave therapy programme on functional capacity, blood circulation and bone metabolism in frail old men and women
Authors: Zheng A. , Sakari R. , Cheng SM , Hietikko A. , Moilanen P. , Timonen J. , Fagerlund KM , Kärkkäinen M. , Alèn M. , Cheng S. 
Published: August 2009

Objective: To evaluate the effects of a low-frequency sound wave therapy programme on functional capacity, blood circulation and bone metabolism of the frail elderly. Design: Single-blind, randomized, controlled trial. Setting: Two senior service centres. Subjects: Forty-nine volunteers (14 males and 35 females) aged 62—93 years with up to 12 diagnosed diseases were allocated in either the intervention group (n = 30) or control group (n = 19). Intervention: The intervention group underwent sound wave therapy, 3—5 times a week for 30 minutes per session over a period of 6 months. The control group received no intervention. Main measurements: Blood pressure, functional capacity, mobility, bone density, biochemical markers, isometric muscle strength, balance, and skin surface temperature. Results: Compared with the control group, the intervention group’s mobility and the amount of self-reported kilometres walked per week increased by 3 km (P<0.05), while levels of cholesterol (4.97 (0.72) to 4.52 (0.65) mmol/L, P =0.019), low-density lipoprotein (2.82 (0.72) to 2.45 (0.61) mmol/L, P =0.022), bone markers of total osteocalcin (11.0 (6.5) to 10.3 (5.9) ng/mL, P =0.048)) and tartrate-resistant acid phosphatase isoform 5b (2.50 (1.0) to 2.41 (1.1) IU/L, P =0.021)) decreased. The average skin surface temperature was significantly higher during active sessions at the end of the intervention than in the beginning (P = 0.004). No change was found during placebo sessions. Conclusions: Low-frequency sound wave therapy may have the potential to promote well-being of frail elderly subjects via improved functional capacity, especially in subjects who are too frail to undertake exercise.
Effects of exercise programmes on quality of life in osteoporotic and osteopenic postmenopausal women: a systematic review and meta-analysis
Authors: Li Wei-Chun , Chen Yi-Chan , Yang Rong-Sen , Tsauo Jau-Yih 
Published: August 2009

Objective: To examine the effect of exercise therapy on quality of life in postmenopausal women with osteoporosis or osteopenia. Methods: We searched MEDLINE, CINAHL, PEDro, EMBASE and the Cochrane library from January 1966 to March 2007. Two reviewers independently selected all studies that met predetermined inclusion criteria. Randomized controlled trials that used the Short Form 36 of the Medical Outcome Study (SF-36) questionnaire or the Quality of Life Questionnaire of the European Foundation for Osteoporosis (QUALEFFO) as outcome measures were selected. The PEDro Scale was applied to rate the quality of each article. All studies had a quality score above 5/10. Meta-analysis was facilitated by RevMan 4.1. Results: Four randomized controlled trials met the inclusion criteria, involving a total of 256 participants. Results revealed that the exercise groups showed significant improvements in the domains of physical function, pain, role physical and vitality (P<0.05). Furthermore, intervention with combined exercise programmes had better effects on physical function, pain and vitality domains than controls. Group exercise programmes also produced better results in these three domains. A short-duration exercise programme produced more improvement in physical function, role physical and vitality, whereas a long-duration exercise programme resulted in more improvement in physical function and pain domains. Conclusions: This meta-analysis revealed better improvement in physical function, pain, role physical and vitality in the exercise groups. Combined exercise and group exercise programmes showed better outcomes in the physical function, pain and vitality domains, but different durations of exercise programme showed improvement in different domains.
Development and validation of the Utrecht Scale for Evaluation of Clinical Rehabilitation (USER)
Authors: Post Marcel WM , van de Port Ingrid GL , Kap Bert , Berdenis van Berlekom Steven H 
Published: August 2009

Objective: The Utrecht Scale for Evaluation of Rehabilitation (USER) is a measure of functional independence that covers physical functioning (mobility, self-care), cognitive functioning and additional domains of pain, fatigue and mood. USER is implemented in the Netherlands as a generic rehabilitation outcome measure. This article reports the development and psychometric characteristics of USER. Design: (1) Inter-rater reliability study and (2) responsiveness study with measurements at admission and at discharge from clinical rehabilitation. Setting: Three rehabilitation facilities in the Netherlands. Patients: Rehabilitation inpatients (N = 319). Interventions: Not applicable. Main outcome measures: Effect size (ES) and standardized response mean (SRM) of USER scales were compared to those of the Barthel Index, Functional Independence Measure (FIM) and to relevant scales of the SF-36. Results: Inter-rater reliability of USER was satisfactory to good. Strong correlations were found between the physical and cognitive functioning scores of USER, the Barthel Index and FIM (0.84—0.94). Correlations between USER pain, fatigue and mood scores and SF-36 scores were also strong (0.58—0.84). Responsiveness of USER physical functioning (1.0—1.2) was very good and slightly better than responsiveness of the Barthel Index (0.9—1.1) and the FIM motor score (0.8—1.1). Responsiveness of the USER cognitive score was below standard (0.2—0.3), but better than responsiveness of the FIM cognitive scores (0.1—0.2). Conclusions: USER is a reliable, valid and responsive measure of functional independence that can be used as an alternative for the FIM. The pain, fatigue and mood scores were adapted after this study and need additional validation.
Angiotensin II reduces membranous angiotensin-converting enzyme 2 in pressurized human aortic endothelial cells
Authors: Iizuka Kenji , Kusunoki Asami , Machida Takuji , Hirafuji Masahiko 
Published: August 2009

Introduction. We applied pressure stress to human aortic endothelial cells (HAEC) and investigated whether mechanical pressure stress and/or angiotensin II (Ang II) affected angiotensin-converting enzyme (ACE) 2. We then tested whether the administration of nifedipine had a demonstrable and possibly beneficial effect. Methods. A pulsatile atmospheric pressure with or without Ang II was loaded on HAECs. The expression of ACE2 was studied by immunoblots and reverse transcription/real-time polymerase chain reaction. Results. The pulsatile mechanical pressure increased the expression of ACE2 mRNA by approximately 80%. Supplementation of Ang II (1 μM) with pulsatile mechanical pressure decreased the expression of ACE2 mRNA by approximately 54%. Pulsatile atmospheric pressure increased ACE2 protein, but supplementation of Ang II (1 μM) also increased ACE2 protein, and the latter failed to show significant change compared to pressurized control without Ang II. Ang II administration reduced ACE2 protein in the membranous fraction under pressurized condition. Administration of nifedipine (1 μM) protected cells from this ACE2 protein reduction at the HAEC membrane. Conclusions. These results indicate that pulsatile mechanical pressure and Ang II affect ACE2 in HAECs. Our findings suggest that blood pressure reduction with a calcium channel blocker is beneficial for the conservation of ACE2, and may provide a potential therapeutic target beyond blood pressure lowering in hypertensive patients.