bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Autolysis-Dependent Extracellular DNA Release by
Enterococcus faecalis
Extracellular Proteases Influences Biofilm Development
Authors: Thomas Vinai Chittezham , Thurlow Lance R. , Boyle Dan , Hancock Lynn E. 
Published: June 2008

ABSTRACT

Enterococci are major contributors of hospital-acquired infections and have emerged as important reservoirs for the dissemination of antibiotic resistance traits. The ability to form biofilms on medical devices is an important aspect of pathogenesis in the hospital environment. The
Enterococcus faecalis
Fsr quorum system has been shown to regulate biofilm formation through the production of gelatinase, but the mechanism has been hitherto unknown. Here we show that both gelatinase (GelE) and serine protease (SprE) contribute to biofilm formation by
E. faecalis
and provide clues to how the activity of these proteases governs this developmental process. Confocal imaging of biofilms suggested that GelE
−
mutants were significantly reduced in biofilm biomass compared to the parental strain, whereas the absence of SprE appeared to accelerate the progression of biofilm development. The phenotype observed in a SprE
−
mutant was linked to an observed increase in autolytic rate compared to the parental strain. Culture supernatant analysis and confocal microscopy confirmed the inability of mutants deficient in GelE to release extracellular DNA (eDNA) in planktonic and biofilm cultures, whereas cells deficient in SprE produced significantly more eDNA as a component of the biofilm matrix. DNase I treatment of
E. faecalis
biofilms reduced the accumulation of biofilm, implying a critical role for eDNA in biofilm development. In conclusion, our data suggest that the interplay of two secreted and coregulated proteases—GelE and SprE—is responsible for regulating autolysis and the release of high-molecular-weight eDNA, a critical component for the development of
E. faecalis
biofilms.
FtsW Is a Dispensable Cell Division Protein Required for Z-Ring Stabilization during Sporulation Septation in
Streptomyces coelicolor
Authors: Mistry Bhavesh V. , Del Sol Ricardo , Wright Chris , Findlay Kim , Dyson Paul 
Published: June 2008

ABSTRACT

The conserved
rodA
and
ftsW
genes encode polytopic membrane proteins that are essential for bacterial cell elongation and division, respectively, and each gene is invariably linked with a cognate class B high-molecular-weight penicillin-binding protein (HMW PBP) gene. Filamentous differentiating
Streptomyces coelicolor
possesses four such gene pairs. Whereas
rodA
, although not its cognate HMW PBP gene, is essential in these bacteria, mutation of SCO5302 or SCO2607 (
sfr
) caused no gross changes to growth and septation. In contrast, disruption of either
ftsW
or the cognate
ftsI
gene blocked the formation of sporulation septa in aerial hyphae. The inability of spiral polymers of FtsZ to reorganize into rings in aerial hyphae of these mutants indicates an early pivotal role of an FtsW-FtsI complex in cell division. Concerted assembly of the complete divisome was unnecessary for Z-ring stabilization in aerial hyphae as
ftsQ
mutants were found to be blocked at a later stage in cell division, during septum closure. Complete cross wall formation occurred in vegetative hyphae in all three
fts
mutants, indicating that the typical bacterial divisome functions specifically during nonessential sporulation septation, providing a unique opportunity to interrogate the function and dependencies of individual components of the divisome in vivo.
RadC, a Misleading Name?
Authors: Attaiech Laetitia , Granadel Chantal , Claverys Jean-Pierre , Martin Bernard 
Published: June 2008

ABSTRACTThe pfam04002 annotation describes RadC as a bacterial DNA repair protein. Although theradCgene is expressed specifically during competence for genetic transformation inStreptococcus pneumoniae, we report thatradCmutants exhibit normal uptake and processing of transforming DNA. They also display normal sensitivity to DNA-damaging agents, providing no support for the rad epithet.
Functional Characterization and Metal Ion Specificity of the Metal-Citrate Complex Transporter from
Streptomyces coelicolor
Authors: Lensbouer Joshua J. , Patel Ami , Sirianni Joseph P. , Doyle Robert P. 
Published: June 2008

ABSTRACT

Secondary transporters of citrate in complex with metal ions belong to the bacterial CitMHS family, about which little is known. The transport of metal-citrate complexes in
Streptomyces coelicolor
has been investigated. The best cofactor for citrate uptake in
Streptomyces coelicolor
is Fe
3+
, but uptake was also noted for Ca
2+
, Pb
2+
, Ba
2+
, and Mn
2+
. Uptake was not observed with the Mg
2+
, Ni
2+
, or Co
2+
cofactor. The transportation of iron- and calcium-citrate makes these systems unique among the CitMHS family members reported to date. No complementary uptake akin to that observed for the CitH (Ca
2+
, Ba
2+
, Sr
2+
) and CitM (Mg
2+
, Ni
2+
, Mn
2+
, Co
2+
, Zn
2+
) systems of
Bacillus subtilis
was noted. Competitive experiments using EGTA confirmed that metal-citrate complex formation promoted citrate uptake. Uptake of free citrate was not observed. The open reading frame postulated as being responsible for the metal-citrate transport observed in
Streptomyces coelicolor
was cloned and overexpressed in
Escherichia coli
strains with the primary Fe
3+
-citrate transport system (
fecABCDE
) removed. Functional expression was successful, with uptake of Ca
2+
-citrate, Fe
3+
-citrate, and Pb
2+
-citrate observed. No free-citrate transport was observed in IPTG (isopropyl-β-
d
-thiogalactopyranoside)-induced or -uninduced
E. coli
. Metabolism of the Fe
3+
-citrate and Ca
2+
-citrate complexes, but not the Pb
2+
-citrate complex, was observed. Rationalization is based on the difference in metal-complex coordination upon binding of the metal by citrate.
Stability of the
cbb
3
-Type Cytochrome Oxidase Requires Specific CcoQ-CcoP Interactions
Authors: Peters Annette , Kulajta Carmen , Pawlik Grzegorz , Daldal Fevzi , Koch Hans-Georg 
Published: June 2008

ABSTRACT

Cytochrome
cbb
3
-type oxidases are members of the heme copper oxidase superfamily and are composed of four subunits. CcoN contains the heme
b
-Cu
B
binuclear center where oxygen is reduced, while CcoP and CcoO are membrane-bound
c
-type cytochromes thought to channel electrons from the donor cytochrome into the binuclear center. Like many other bacterial members of this superfamily, the cytochrome
cbb
3
-type oxidase contains a fourth, non-cofactor-containing subunit, which is termed CcoQ. In the present study, we analyzed the role of CcoQ on the stability and activity of
Rhodobacter capsulatus cbb
3
-type oxidase. Our data showed that CcoQ is a single-spanning membrane protein with a N
out
-C
in
topology. In the absence of CcoQ,
cbb
3
-type oxidase activity is significantly reduced, irrespective of the growth conditions. Blue native polyacrylamide gel electrophoresis analyses revealed that the lack of CcoQ specifically impaired the stable recruitment of CcoP into the
cbb
3
-type oxidase complex. This suggested a specific CcoQ-CcoP interaction, which was confirmed by chemical cross-linking. Collectively, our data demonstrated that in
R. capsulatus
CcoQ was required for optimal
cbb
3
-type oxidase activity because it stabilized the interaction of CcoP with the CcoNO core complex, leading subsequently to the formation of the active 230-kDa
cbb
3
-type oxidase complex.
Fur-Dependent Detoxification of Organic Acids by
rpoS
Mutants during Prolonged Incubation under Aerobic, Phosphate Starvation Conditions
Authors: Guillemet Mélanie L. , Moreau Patrice L. 
Published: June 2008

ABSTRACT

The activity of amino acid-dependent acid resistance systems allows
Escherichia coli
to survive during prolonged incubation under phosphate (P
i
) starvation conditions. We show in this work that
rpoS
-null mutants incubated in the absence of any amino acid survived during prolonged incubation under aerobic, P
i
starvation conditions. Whereas
rpoS
+
cells incubated with glutamate excreted high levels of acetate,
rpoS
mutants grew on acetic acid. The characteristic metabolism of
rpoS
mutants required the activity of Fur (ferric uptake regulator) in order to decrease the synthesis of the small RNA RyhB that might otherwise inhibit the synthesis of iron-rich proteins. We propose that RpoS (σ
S
) and the small RNA RyhB contribute to decrease the synthesis of iron-rich proteins required for the activity of the tricarboxylic acid (TCA) cycle, which redirects the metabolic flux toward the production of acetic acid at the onset of stationary phase in
rpoS
+
cells. In contrast, Fur activity, which represses
ryhB
, and the lack of RpoS activity allow a substantial activity of the TCA cycle to continue in stationary phase in
rpoS
mutants, which decreases the production of acetic acid and, eventually, allows growth on acetic acid and P
i
excreted into the medium. These data may help explain the fact that a high frequency of
E. coli rpoS
mutants is found in nature.
Identification and Utility of FdmR1 as a
Streptomyces
Antibiotic Regulatory Protein Activator for Fredericamycin Production in
Streptomyces griseus
ATCC 49344 and Heterologous Hosts
Authors: Chen Yihua , Wendt-Pienkowski Evelyn , Shen Ben 
Published: June 2008

ABSTRACT

The fredericamycin (FDM) A biosynthetic gene cluster, cloned previously from
Streptomyces griseus
ATCC 49344, contains three putative regulatory genes,
fdmR
,
fdmR1
, and
fdmR2
. Their deduced gene products show high similarity to members of the
Streptomyces
antibiotic regulatory protein (SARP) family (FdmR1) or to MarR-like regulators (FdmR and FdmR2). Here we provide experimental data supporting FdmR1 as a SARP-type activator. Inactivation of
fdmR1
abolished FDM biosynthesis, and FDM production could be restored to the
fdmR1
::
aac(3)IV
mutant by expressing
fdmR1
in
trans
. Reverse transcription-PCR transcriptional analyses revealed that up to 26 of the 28 genes within the
fdm
gene cluster, with the exception of
fdmR
and
fdmT2
, were under the positive control of FdmR1, directly or indirectly. Overexpression of
fdmR1
in
S. griseus
improved the FDM titer 5.6-fold (to about 1.36 g/liter) relative to that of wild-type
S. griseus
. Cloning of the complete
fdm
cluster into an integrative plasmid and subsequent expression in heterologous hosts revealed that considerable amounts of FDMs could be produced in
Streptomyces albus
but not in
Streptomyces lividans
. However, the
S. lividans
host could be engineered to produce FDMs via constitutive expression of
fdmR1
; FDM production in
S. lividans
could be enhanced further by overexpressing
fdmC
, encoding a putative ketoreductase, concomitantly with
fdmR1
. Taken together, these studies demonstrate the viability of engineering FDM biosynthesis and improving FDM titers in both the native producer
S. griseus
and heterologous hosts, such as
S. albus
and
S. lividans
. The approach taken capitalizes on FdmR1, a key activator of the FDM biosynthetic machinery.
Induction by Cationic Antimicrobial Peptides and Involvement in Intrinsic Polymyxin and Antimicrobial Peptide Resistance, Biofilm Formation, and Swarming Motility of PsrA in
Pseudomonas aeruginosa
Authors: Gooderham W. James , Bains Manjeet , McPhee Joseph B. , Wiegand Irith , Hancock Robert E. W. 
Published: June 2008

ABSTRACT

Pseudomonas aeruginosa
is an important opportunistic pathogen that causes infections that can be extremely difficult to treat due to its high intrinsic antibiotic resistance and broad repertoire of virulence factors, both of which are highly regulated. It is demonstrated here that the
psrA
gene, encoding a transcriptional regulator, was upregulated in response to subinhibitory concentrations of cationic antimicrobial peptides. Compared to the wild type and the complemented mutant, a
P. aeruginosa
PAO1
psrA
::Tn
5
mutant displayed intrinsic supersusceptibility to polymyxin B, a last-resort antimicrobial used against multidrug-resistant infections, and the bovine neutrophil antimicrobial peptide indolicidin; this supersusceptibility phenotype correlated with increased outer membrane permeabilization by these agents. The
psrA
mutant was also defective in simple biofilm formation, rapid attachment, and swarming motility, all of which could be complemented by the cloned
psrA
gene. The role of PsrA in global gene regulation was studied by comparing the
psrA
mutant to the wild type by microarray analysis, demonstrating that 178 genes were up- or downregulated ≥2-fold (
P
≤ 0.05). Dysregulated genes included those encoding certain known PsrA targets, those encoding the type III secretion apparatus and effectors, adhesion and motility genes, and a variety of metabolic, energy metabolism, and outer membrane permeability genes. This suggests that PsrA might be a key regulator of antimicrobial peptide resistance and virulence.
Localization of the Germination Protein GerD to the Inner Membrane in
Bacillus subtilis
Spores
Authors: Pelczar Patricia L. , Setlow Peter 
Published: June 2008

ABSTRACT

GerD of
Bacillus subtilis
is a protein essential for normal spore germination with either
l
-alanine or a mixture of
l
-asparagine,
d
-glucose,
d
-fructose, and potassium ions. GerD's amino acid sequence suggests that it may be a lipoprotein, indicating a likely location in a membrane. Location in the spore's outer membrane seems unlikely, since removal of this membrane does not result in a
gerD
spore germination phenotype, suggesting that GerD is likely in the spore's inner membrane. In order to localize GerD within spores, FLAG-tagged GerD constructs were made, found to be functional in spore germination, and detected in immunoblots of spore extracts as not only monomers but also dimers and trimers. Upon fractionation of spore extracts, GerD-FLAG was found in the inner membrane fraction from dormant spores and was present at ∼2,000 molecules/spore. GerD-FLAG in the inner membrane fraction was solubilized by Triton X-100, suggesting that GerD is a lipoprotein, and the protein was also solubilized by 0.5 M NaCl. GerD-FLAG was not processed proteolytically in a
B. subtilis
strain lacking
gerF
(
lgt
), which encodes prelipoprotein diacylglycerol transferase (Lgt), indicating that when GerD does not have a diacylglycerol moiety, signal sequence processing does not occur. However, unprocessed GerD-FLAG still gave bands corresponding to monomers and dimers of slightly higher molecular weight than that of GerD-FLAG from a strain with Lgt, further suggesting that GerD is a lipoprotein. Upon spore germination, much GerD became soluble and then appeared to be degraded as the germinated spores outgrew and initiated vegetative growth. All of these results suggest that GerD is a lipoprotein associated with the dormant spore's inner membrane that may be released in some fashion from this membrane upon spore germination.
Insights into Plant Cell Wall Degradation from the Genome Sequence of the Soil Bacterium
Cellvibrio japonicus
Authors: DeBoy Robert T. , Mongodin Emmanuel F. , Fouts Derrick E. , Tailford Louise E. , Khouri Hoda , Emerson Joanne B. , Mohamoud Yasmin , Watkins Kisha , Henrissat Bernard , Gilbert Harry J. , Nelson Karen E. 
Published: June 2008

ABSTRACT

The plant cell wall, which consists of a highly complex array of interconnecting polysaccharides, is the most abundant source of organic carbon in the biosphere. Microorganisms that degrade the plant cell wall synthesize an extensive portfolio of hydrolytic enzymes that display highly complex molecular architectures. To unravel the intricate repertoire of plant cell wall-degrading enzymes synthesized by the saprophytic soil bacterium
Cellvibrio japonicus
, we sequenced and analyzed its genome, which predicts that the bacterium contains the complete repertoire of enzymes required to degrade plant cell wall and storage polysaccharides. Approximately one-third of these putative proteins (57) are predicted to contain carbohydrate binding modules derived from 13 of the 49 known families. Sequence analysis reveals approximately 130 predicted glycoside hydrolases that target the major structural and storage plant polysaccharides. In common with that of the colonic prokaryote
Bacteroides thetaiotaomicron
, the genome of
C. japonicus
is predicted to encode a large number of GH43 enzymes, suggesting that the extensive arabinose decorations appended to pectins and xylans may represent a major nutrient source, not just for intestinal bacteria but also for microorganisms that occupy terrestrial ecosystems. The results presented here predict that
C. japonicus
possesses an extensive range of glycoside hydrolases, lyases, and esterases. Most importantly, the genome of
C. japonicus
is remarkably similar to that of the gram-negative marine bacterium,
Saccharophagus degradans
2-40
T
. Approximately 50% of the predicted
C. japonicus
plant-degradative apparatus appears to be shared with
S. degradans
, consistent with the utilization of plant-derived complex carbohydrates as a major substrate by both organisms.
Human papillomaviruses do not play an aetiological role in Müllerian adenosarcomas of the uterine cervix
Authors: Mumba E , Ali H , Turton D , Cooper K , Grayson W 
Published: June 2008

Aim:To determine if human papillomaviruses (HPVs) play a role in the histogenesis of adenosarcomas of the uterine cervix.Methods:Nine archival cases of primary cervical adenosarcoma were studied. The HPV status of the nine histologically proven tumours was investigated by non-isotopic in situ hybridisation (NISH) and PCR. NISH was performed using digoxigenin labelled probes to HPV types 6, 11, 16, 18, 31 and 33. PCR used GP5+/GP6+ primers to the HPV L1 gene.Results:Neither the benign epithelial components nor the malignant stromal components of the 9 neoplasms harboured nuclear NISH signals for the HPV types investigated. Amplimers of the HPV L1 gene were not detected by PCR in any of the tumours studied.Conclusion:HPVs do not appear to play an aetiological role in cervical adenosarcomas. This suggests that a different histogenetic pathway for this rare tumour type must exist.
Correlation of cyclin D1 transcript levels, transcript type and protein expression with proliferation and histology among mantle cell lymphoma
Authors: Shakir R , Ngo N , Naresh K N 
Published: June 2008

Background:Cyclin D1 expression is central to mantle cell lymphoma (MCL) biology. The cyclin D1 gene produces two forms of mRNA: long (D1L) and short (D1S) versions.Aims:To study the relationship between histology, cyclin D1 mRNA (transcript) levels, cyclin D1 transcript type, cyclin D1 protein expression by immunohistochemistry (IHC), and proliferation (Ki-67%).Methods:17 MCLs were initially studied for: levels of expression of cyclin D1 transcripts and for cyclin D1 transcript type by reverse-transcriptase PCR; intensity and percentage cyclin D1 protein expression by IHC; and Ki-67% by IHC. The relationship between cyclin D1 protein expression and proliferation was further validated on an independent set of 23 MCLs.Results:MCLs expressed variable levels of cyclin D1 at both transcript and protein levels. Furthermore, D1L and D1S were the predominant transcripts in 69% and 31% of cases, respectively. While only 9% of cases with dominance of D1L had blastoid histology, 60% of the cases with dominance of the D1S had blastoid features. Furthermore, the levels of D1L showed direct correlation with cyclin D1 protein expression and Ki-67%. Among these cases, and in the independent set of MCLs (n = 40), the level of cyclin D1 protein expression directly correlated with Ki-67%.Conclusions:MCLs express variable levels of cyclin D1 transcripts and protein, and have variable proliferation (Ki-67%). Cases with dominance of D1S transcripts are more likely to be of blastoid morphology. There is correlation between D1L transcripts levels, cyclin D1 protein expression and Ki-67%.
Fine needle aspiration cytology of papillary lesions of the breast: how accurate is the diagnosis?
Authors: Tse G M K , Ma T K F , Lui P C W , Ng D C H , Yu A M C , Vong J S L , Niu Y , Chaiwun B , Lam W W M , Tan P H 
Published: June 2008

Background:Cytological diagnosis of mammary papillary lesions is difficult.Aim:To review the previous cytology diagnosis of 23 papillomas and 11 papillary carcinomas and specific cytological features that may assist in differentiating these entities.Methods:The cytology preparations were reviewed for: (i) overall cellularity; (ii) epithelial cell ball devoid of fibrovascular cores; (iii) background single cells; and (iv) papillary fragments and their morphology.Results:The overall diagnostic accuracy was 59%, atypical rate was 24%, and the error (combined false positive and negative) rate was 17%. For overall cellularity, 6, 14 and 3 cases of papillomas, and 6, 3 and 2 cases of papillary carcinomas showed low, moderate and high cellularity, respectively. Cell balls were present in mild to moderate number in 20 papillomas and 10 papillary carcinomas. The background single cells were absent, or present in low or moderate to high numbers in 7, 10 and 6 papillomas, and 3, 3 and 5 papillary carcinomas, respectively. Papillary fragments were absent, or present in small, moderate or large quantities in 9, 4, 8 and 2 papillomas, and 6, 3, 1 and 1 papillary carcinomas, respectively. There was no demonstrable quantitative difference between papilloma and papillary carcinoma for all these parameters. Qualitatively, the cell balls and single cells showed a higher degree of atypia in papillary carcinoma, and the papillary fragments were more elaborate and slender.Conclusion:Cytological diagnosis of papillary lesions shows a significant error rate with overlapping features. Cellular atypia and fragments with long and slender papillae with ramifying edges favour papillary carcinoma.
Do patients with low volume prostate cancer have prostate specific antigen recurrence following radical prostatectomy?
Authors: Furusato B , Rosner I L , Osborn D , Ali A , Srivastava S , Davis C J , Sesterhenn I A , McLeod D G 
Published: June 2008

Aims:The objective of this study was to determine the incidence of prostate specific antigen (PSA) relapse in patients with low volume prostate cancer following radical prostatectomy.Methods:Between 1993 and 2001, 50 of 717 patients had total tumour volumes of less than 0.5 cm3 following radical prostatectomy. Biochemical recurrence was defined as two consecutive values of serum PSA levels of 0.2 ng/ml or greater.Results:Median follow-up of the 50 patients was 58 months. In five of the 50 patients (10%), PSA recurrence was observed. All of these five cases had Gleason score of 3+3 (well and/or moderately differentiated), organ confined and surgical margin negative tumours. In three of the five cases, capsular incision resulted in benign glands extending into the surgical margin.Conclusions:Five of 50 cases had PSA failure. In three of the five patients, benign glands located in the margin could explain the “PSA recurrence”. However, in the other two patients, none of the pathological parameters correlated with measurable PSA levels. The explanation for their PSA failure is unclear.