bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcription Antitermination by a Phosphorylated Response Regulator and Cobalamin-Dependent Termination at a B
12
Riboswitch Contribute to Ethanolamine Utilization in Enterococcus faecalis
Authors: Baker Kris Ann , Perego Marta 
Published: March 2011

ABSTRACT

The ability of bacteria to utilize ethanolamine (EA) as a carbon and nitrogen source may confer an advantage for survival, colonization, and pathogenicity in the human intestinal tract.
Enterococcus faecalis
, a Gram-positive human commensal organism, depends on a two-component signaling system (TCS-17) for sensing EA and regulating the expression of the ethanolamine utilization genes. Multiple promoters participate in
eut
gene expression in the presence of EA as the sole carbon source and cobalamin (CoB12), an essential cofactor in the enzymatic degradation process. By means of
in vivo
and
in vitro
approaches, this study characterized the transcriptional activity identified in the
eutT-eutG
intergenic region of the
E. faecalis eut
cluster. Two novel promoters in this region were shown to be active
in vivo
. The distal P2-1 promoter was associated with a B12 riboswitch that terminated transcription in the presence of CoB12. Transcription elongation from the proximal P2-2 promoter was regulated by antitermination mediated by the phosphorylated form of the response regulator of TCS-17 (RR17). 3′-Rapid amplification of cDNA ends (RACE) analyses of the terminated RNA products allowed precise identification of the hairpin loop structures involved in termination/antitermination. The results uncovered the role of the B12 riboswitch and RR17 in
eut
gene expression, adding to the complexity of this regulatory pathway and extending the knowledge of possible means of transcription regulation in Gram-positive organisms.
Full-Length
De Novo
Sequence of the Chlamydophila psittaci Type Strain, 6BC
Authors: Voigt Anja , Schöfl Gerhard , Heidrich Alexander , Sachse Konrad , Saluz Hans Peter 
Published: March 2011

ABSTRACT

Chlamydophila psittaci
is an obligate intracellular zoonotic pathogen, mainly of birds. It is the causative agent of psittacosis in birds and humans. Here we report the full-length
de novo
genome sequence of the avian isolate 6BC, the type strain of the species
C. psittaci
.
Genome Sequence of Acinetobacter calcoaceticus PHEA-2, Isolated from Industry Wastewater
Authors: Zhan Yuhua , Yan Yongliang , Zhang Wei , Yu Haiying , Chen Ming , Lu Wei , Ping Shuzhen , Peng Zixin , Yuan Menglong , Zhou Zhengfu , Elmerich Claudine , Lin Min 
Published: March 2011

ABSTRACT

Genome analysis of
Acinetobacter calcoaceticus
PHEA-2 was undertaken because of the importance of this bacterium for bioremediation of phenol-polluted water and because of the close phylogenetic relationship of this species with the human pathogen
Acinetobacter baumannii
. To our knowledge, this is the first strain of
A. calcoaceticus
whose genome has been sequenced.
Genome Sequence of the Methanotrophic Alphaproteobacterium Methylocystis sp. Strain Rockwell (ATCC 49242)
Authors: Stein Lisa Y. , Bringel Françoise , DiSpirito Alan A. , Han Sukkyun , Jetten Mike S. M. , Kalyuzhnaya Marina G. , Kits K. Dimitri , Klotz Martin G. , Op den Camp Huub J. M. , Semrau Jeremy D. , Vuilleumier Stéphane , Bruce David C. , Cheng Jan-Fang , Davenport Karen W. , Goodwin Lynne , Han Shunsheng , Hauser Loren , Lajus Aurélie , Land Miriam L. , Lapidus Alla , Lucas Susan , Médigue Claudine , Pitluck Sam , Woyke Tanja 
Published: March 2011

ABSTRACT

Methylocystis
sp. strain Rockwell (ATCC 49242) is an aerobic methane-oxidizing alphaproteobacterium isolated from an aquifer in southern California. Unlike most methanotrophs in the
Methylocystaceae
family, this strain has a single
pmo
operon encoding particulate methane monooxygenase but no evidence of the genes encoding soluble methane monooxygenase. This is the first reported genome sequence of a member of the
Methylocystis
species of the
Methylocystaceae
family in the order
Rhizobiales
.
Complete Genome Sequence of the Pathogenic Bacterium Riemerella anatipestifer Strain RA-GD
Authors: Yuan Jianfeng , Liu Wanfei , Sun Mingfei , Song Shuhui , Cai Jianping , Hu Songnian 
Published: March 2011

ABSTRACT

Riemerella anatipestifer
is a well-described pathogen of waterfowl and other avian species which can cause a great loss to the poultry industry. Here we obtained the complete genome sequence of
R. anatipestifer
strain RA-GD, which was isolated from an infected duck in Guangzhou, China, and was cultivated in our laboratory.
Prophage-Stimulated Toxin Production in Clostridium difficile NAP1/027 Lysogens
Authors: Sekulovic Ognjen , Meessen-Pinard Mathieu , Fortier Louis-Charles 
Published: March 2011

ABSTRACT

TcdA and TcdB exotoxins are the main virulence factors of
Clostridium difficile
, one of the most deadly nosocomial pathogens. Recent data suggest that prophages can influence the regulation of toxin expression. Here we present the characterization of φCD38-2, a
pac
-type temperate
Siphoviridae
phage that stimulates toxin expression when introduced as a prophage into
C. difficile
. Host range analysis showed that φCD38-2 was able to infect 99/207 isolates of
C. difficile
representing 11 different PCR ribotypes. Of 89 isolates corresponding to the NAP1/027 hypervirulent strain, which recently caused several outbreaks in North America and Europe, 79 (89%) were sensitive to φCD38-2. The complete double-stranded DNA (dsDNA) genome was determined, and a putative function could be assigned to 24 of the 55 open reading frames. No toxins or virulence factors could be identified based on bioinformatics analyses. Our data also suggest that φCD38-2 replicates as a circular plasmid in
C. difficile
lysogens. Upon introduction of φCD38-2 into a NAP1/027 representative isolate, up to 1.6- and 2.1-fold more TcdA and TcdB, respectively, were detected by immunodot blotting in culture supernatants of the lysogen than in the wild-type strain. In addition, real-time quantitative reverse transcriptase PCR (qRT-PCR) analyses showed that the mRNA levels of all five pathogenicity locus (PaLoc) genes were higher in the CD274 lysogen. Our study provides the first genomic sequence of a new
pac
-type
Siphoviridae
phage family member infecting
C. difficile
and brings further evidence supporting the role of prophages in toxin production in this important nosocomial pathogen.
Identification of ArgP and Lrp as Transcriptional Regulators of lysP, the Gene Encoding the Specific Lysine Permease of Escherichia coli
Authors: Ruiz Jimena , Haneburger Ina , Jung Kirsten 
Published: March 2011

ABSTRACT

Expression of
lysP
, which encodes the lysine-specific transporter LysP in
Escherichia coli
, is regulated by the concentration of exogenous available lysine. In this study, the LysR-type transcriptional regulator ArgP was identified as the activator of
lysP
expression. At lysine concentrations higher than 25 μM,
lysP
expression was shut off and phenocopied an
argP
deletion mutant. Purified ArgP-His
6
bound to the
lysP
promoter/control region at a sequence containing a conserved T-N
11
-A motif. Its affinity increased in the presence of lysine but not in the presence of the other known coeffector, arginine.
In vivo
data suggest that lysine-loaded ArgP and arginine-loaded ArgP compete at the
lysP
promoter. We propose that lysine-loaded ArgP prevents
lysP
transcription at the promoter clearance step, as described for the lysine-dependent regulation of
argO
(R. S. Laishram and J. Gowrishankar, Genes Dev. 21:1258-1272, 2007). The global regulator Lrp also bound to the
lysP
promoter/control region. An
lrp
mutant exhibited reduced
lysP
expression in the absence of external lysine. These results indicate that ArgP is a major regulator of
lysP
expression but that Lrp modulates
lysP
transcription under lysine-limiting conditions.
Flagellin Redundancy in Caulobacter crescentus and Its Implications for Flagellar Filament Assembly
Authors: Faulds-Pain Alexandra , Birchall Christopher , Aldridge Christine , Smith Wendy D. , Grimaldi Giulia , Nakamura Shuichi , Miyata Tomoko , Gray Joe , Li Guanglai , Tang Jay X. , Namba Keiichi , Minamino Tohru , Aldridge Phillip D. 
Published: March 2011

ABSTRACT

Bacterial flagella play key roles in surface attachment and host-bacterial interactions as well as driving motility. Here, we have investigated the ability of
Caulobacter crescentus
to assemble its flagellar filament from six flagellins: FljJ, FljK, FljL, FljM, FljN, and FljO. Flagellin gene deletion combinations exhibited a range of phenotypes from no motility or impaired motility to full motility. Characterization of the mutant collection showed the following: (i) that there is no strict requirement for any one of the six flagellins to assemble a filament; (ii) that there is a correlation between slower swimming speeds and shorter filament lengths in Δ
fljK
Δ
fljM
mutants; (iii) that the flagellins FljM to FljO are less stable than FljJ to FljL; and (iv) that the flagellins FljK, FljL, FljM, FljN, and FljO alone are able to assemble a filament.
Unexpected Diversity of Chlorite Dismutases: a Catalytically Efficient Dimeric Enzyme from Nitrobacter winogradskyi
Authors: Mlynek Georg , Sjöblom Björn , Kostan Julius , Füreder Stephanie , Maixner Frank , Gysel Kira , Furtmüller Paul Georg , Obinger Christian , Wagner Michael , Daims Holger , Djinović-Carugo Kristina 
Published: March 2011

ABSTRACT

Chlorite dismutase (Cld) is a unique heme enzyme catalyzing the conversion of ClO
2
−
to Cl
−
and O
2
. Cld is usually found in perchlorate- or chlorate-reducing bacteria but was also recently identified in a nitrite-oxidizing bacterium of the genus
Nitrospira
. Here we characterized a novel Cld-like protein from the chemolithoautotrophic nitrite oxidizer
Nitrobacter winogradskyi
which is significantly smaller than all previously known chlorite dismutases. Its three-dimensional (3D) crystal structure revealed a dimer of two identical subunits, which sharply contrasts with the penta- or hexameric structures of other chlorite dismutases. Despite a truncated N-terminal domain in each subunit, this novel enzyme turned out to be a highly efficient chlorite dismutase (

K
m

= 90 μM;
k
cat
= 190 s
−1
;
k
cat
/

K
m

= 2.1 × 10
6
M
−1
s
−1
), demonstrating a greater structural and phylogenetic diversity of these enzymes than was previously known. Based on comparative analyses of Cld sequences and 3D structures, signature amino acid residues that can be employed to assess whether uncharacterized Cld-like proteins may have a high chlorite-dismutating activity were identified. Interestingly, proteins that contain all these signatures and are phylogenetically closely related to the novel-type Cld of
N. winogradskyi
exist in a large number of other microbes, including other nitrite oxidizers.
Chlamydia trachomatis Secretion of an Immunodominant Hypothetical Protein (CT795) into Host Cell Cytoplasm
Authors: Qi Manli , Lei Lei , Gong Siqi , Liu Quanzhong , DeLisa Matthew P. , Zhong Guangming 
Published: March 2011

ABSTRACT

The
Chlamydia
-specific hypothetical protein CT795 was dominantly recognized by human antisera produced during
C. trachomatis
infection but not by animal antisera raised against dead chlamydia organisms. The immundominant region recognized by the human antibodies was mapped to the N-terminal fragment T22-S69. The endogenous CT795 was detected in the cytoplasm of host cells during
C. trachomatis
infection and was highly enriched in the host cytosolic fraction but absent in the purified chlamydia organisms, suggesting that CT795 is synthesized and secreted into host cell cytoplasm without incorporation into the organisms. All
C. trachomatis
serovars tested secreted CT795. A predicted signal peptide of CT795 directed the mature PhoA to cross
Escherichia coli
inner membranes. The secretion of CT795 in
Chlamydia
-infected cells was inhibited by a C
16
compound targeting signal peptidase I, but not by a C
1
compound known to block the type III secretion pathway. These results suggest that CT795, like CPAF (a
Chlamydia
-secreted virulence factor), is secreted into the host cell cytoplasm via a sec-dependent mechanism and not by a type III secretion pathway. The above characterizations of CT795 have provided important information for further understanding the potential roles of CT795 in
C. trachomatis
pathogenesis.
Heme Utilization by Nontypeable Haemophilus influenzae Is Essential and Dependent on Sap Transporter Function
Authors: Mason Kevin M. , Raffel Forrest K. , Ray William C. , Bakaletz Lauren O. 
Published: March 2011

ABSTRACT

Bacterial strategies of innate immune evasion and essential metabolic functions are critical for commensal-host homeostasis. Previously, we showed that Sap translocator function is necessary for nontypeable
Haemophilus influenzae
(NTHI) behaviors that mediate diseases of the human airway. Antimicrobial peptide (AP) lethality is limited by binding mediated by the Sap complex. SapA shares homology with the dipeptide-binding protein (DppA) and the heme-binding lipoprotein (HbpA), both of which have previously been shown to bind the iron-containing compound heme, whose acquisition is essential for
Haemophilus
survival. Computational modeling revealed conserved SapA residues, similarly modeled to mediate heme binding in HbpA. Here, we directly demonstrate that SapA bound heme and was essential for heme utilization by iron-starved NTHI. Further, the Sap translocator permease mediated heme transport into the bacterial cytoplasm, thus defining a heretofore unknown mechanism of intracytoplasmic membrane heme transport in
Haemophilus
. Since we demonstrate multiple ligand specificity for the SapA-binding protein, we tested whether APs would compete with heme for SapA binding. We showed that human β-defensins 2 and 3, human cathelicidin LL-37, human neutrophil protein 1, and melittin displaced heme bound to SapA, thus supporting a hierarchy wherein immune evasion supercedes even the needed iron acquisition functions of the Sap system.
The Maturation Factors HoxR and HoxT Contribute to Oxygen Tolerance of Membrane-Bound [NiFe] Hydrogenase in Ralstonia eutropha H16
Authors: Fritsch Johannes , Lenz Oliver , Friedrich Bärbel 
Published: March 2011

ABSTRACT

The membrane-bound [NiFe] hydrogenase (MBH) of
Ralstonia eutropha
H16 undergoes a complex maturation process comprising cofactor assembly and incorporation, subunit oligomerization, and finally twin-arginine-dependent membrane translocation. Due to its outstanding O
2
and CO tolerance, the MBH is of biotechnological interest and serves as a molecular model for a robust hydrogen catalyst. Adaptation of the enzyme to oxygen exposure has to take into account not only the catalytic reaction but also biosynthesis of the intricate redox cofactors. Here, we report on the role of the MBH-specific accessory proteins HoxR and HoxT, which are key components in MBH maturation at ambient O
2
levels. MBH-driven growth on H
2
is inhibited or retarded at high O
2
partial pressure (pO
2
) in mutants inactivated in the
hoxR
and
hoxT
genes. The ratio of mature and nonmature forms of the MBH small subunit is shifted toward the precursor form in extracts derived from the mutant cells grown at high pO
2
. Lack of
hoxR
and
hoxT
can phenotypically be restored by providing O
2
-limited growth conditions. Analysis of copurified maturation intermediates leads to the conclusion that the HoxR protein is a constituent of a large transient protein complex, whereas the HoxT protein appears to function at a final stage of MBH maturation. UV-visible spectroscopy of heterodimeric MBH purified from
hoxR
mutant cells points to alterations of the Fe-S cluster composition. Thus, HoxR may play a role in establishing a specific Fe-S cluster profile, whereas the HoxT protein seems to be beneficial for cofactor stability under aerobic conditions.
Monofunctional Transglycosylases Are Not Essential for Staphylococcus aureus Cell Wall Synthesis
Authors: Reed Patricia , Veiga Helena , Jorge Ana M. , Terrak Mohammed , Pinho Mariana G. 
Published: March 2011

ABSTRACT

The polymerization of peptidoglycan is the result of two types of enzymatic activities: transglycosylation, the formation of linear glycan chains, and transpeptidation, the formation of peptide cross-bridges between the glycan strands.
Staphylococcus aureus
has four penicillin binding proteins (PBP1 to PBP4) with transpeptidation activity, one of which, PBP2, is a bifunctional enzyme that is also capable of catalyzing transglycosylation reactions. Additionally, two monofunctional transglycosylases have been reported in
S. aureus
: MGT, which has been shown to have
in vitro
transglycosylase activity, and a second putative transglycosylase, SgtA, identified only by sequence analysis. We have now shown that purified SgtA has
in vitro
transglycosylase activity and that both MGT and SgtA are not essential in
S. aureus.
However, in the absence of PBP2 transglycosylase activity, MGT but not SgtA becomes essential for cell viability. This indicates that
S. aureus
cells require one transglycosylase for survival, either PBP2 or MGT, both of which can act as the sole synthetic transglycosylase for cell wall synthesis. We have also shown that both MGT and SgtA interact with PBP2 and other enzymes involved in cell wall synthesis in a bacterial two-hybrid assay, suggesting that these enzymes may work in collaboration as part of a larger, as-yet-uncharacterized cell wall-synthetic complex.
Properties of CsnR, the Transcriptional Repressor of the Chitosanase Gene,
csnA
, of Streptomyces lividans
Authors: Dubeau Marie-Pierre , Poulin-Laprade Dominic , Ghinet Mariana Gabriela , Brzezinski Ryszard 
Published: March 2011

ABSTRACT

A palindromic sequence is present in the intergenic region preceding the chitosanase gene
csnA
(SSPG_06922) of
Streptomyces lividans
TK24. This sequence was also found in front of putative chitosanase genes in several other actinomycete genomes and upstream genes encoding putative transcriptional regulators of the ROK family, including
csnR
(SSPG_04872) in
S. lividans
. The latter was examined as a possible transcriptional regulator (CsnR) of chitosanase gene expression.
In vitro
, purified CsnR bound strongly to the palindromic sequences of the
csnA
and
csnR
genes (equilibrium dissociation constant [

K
D

] = 0.032 and 0.040 nM, respectively). Binding was impaired in the presence of chitosan oligosaccharides and
d
-glucosamine, and chitosan dimer was found to be the best effector, as determined by an equilibrium competition experiment and 50% inhibitory concentration (IC
50
) determination, while glucose,
N
-acetyl-glucosamine, and galactosamine had no effect.
In vivo
, comparison of the
S. lividans
wild type and ΔCsnR strains using β-lactamase reporter genes showed that CsnR represses the expression of
csnA
and of its own gene, which was confirmed by quantitative PCR (qPCR). CsnR is localized at the beginning of a gene cluster, possibly an operon, the organization of which is conserved through many actinomycete genomes. The CsnR-mediated chitosanase regulation mechanism seems to be widespread among actinomycetes.
Functional Analysis of the Holin-Like Proteins of Mycobacteriophage Ms6
Authors: Catalão Maria João , Gil Filipa , Moniz-Pereira José , Pimentel Madalena 
Published: March 2011

ABSTRACT

The mycobacteriophage Ms6 is a temperate double-stranded DNA (dsDNA) bacteriophage which, in addition to the predicted endolysin (LysA)-holin (Gp4) lysis system, encodes three additional proteins within its lysis module: Gp1, LysB, and Gp5. Ms6 Gp4 was previously described as a class II holin-like protein. By analysis of the amino acid sequence of Gp4, an N-terminal signal-arrest-release (SAR) domain was identified, followed by a typical transmembrane domain (TMD), features which have previously been observed for pinholins. A second putative holin gene (
gp5
) encoding a protein with a predicted single TMD at the N-terminal region was identified at the end of the Ms6 lytic operon. Neither the putative class II holin nor the single TMD polypeptide could trigger lysis in pairwise combinations with the endolysin LysA in
Escherichia coli
. One-step growth curves and single-burst-size experiments of different Ms6 derivatives with deletions in different regions of the lysis operon demonstrated that the gene products of
gp4
and
gp5
, although nonessential for phage viability, appear to play a role in controlling the timing of lysis: an Ms6 mutant with a deletion of
gp4
(Ms6

Δ
gp4

) caused slightly accelerated lysis, whereas an Ms6

Δ
gp5

deletion mutant delayed lysis, which is consistent with holin function. Additionally, cross-linking experiments showed that Ms6 Gp4 and Gp5 oligomerize and that both proteins interact. Our results suggest that in Ms6 infection, the correct and programmed timing of lysis is achieved by the combined action of Gp4 and Gp5.
Chemoreceptors and Flagellar Motors Are Subterminally Located in Close Proximity at the Two Cell Poles in Spirochetes
Authors: Xu Hongbin , Raddi Gianmarco , Liu Jun , Charon Nyles W. , Li Chunhao 
Published: March 2011

ABSTRACT

Green fluorescent protein (GFP) fusions, immunofluorescence microscopy, and cryo-electron tomography revealed that the chemoreceptors of the Lyme disease spirochete
Borrelia burgdorferi
form long, thin arrays near both cell poles. These arrays are in close proximity to the flagellar motors. This information provides a basis for further understanding motility, chemotaxis, and protein localization in spirochetes.
Understanding Barrett's columnar lined oesophagus from the patients' perspective: qualitative analysis of semistructured interviews with patients
Authors: Griffiths Helen , Davies Ruth 
Published: March 2011

ObjectivesTo explore patients' views and perspectives on their experience of living with Barrett's columnar lined oesophagus (CLO) and being part of an endoscopic surveillance programme.DesignQualitative semistructured interviews.SettingDistrict General Hospital.Subjects22 men with diagnosis of Barrett's CLO between the ages of 50 and 70 years.ResultsAll subjects had received some information about Barrett's CLO and had a heightened awareness of the cancer risk. However, many had misinterpreted or poorly assimilated the information and overall health literacy levels were low. From their stories a ‘Model of Uncertainty’ in Barrett's surveillance was developed as a focus for healthcare professionals to ensure that the service users' perspective is considered in future service development.ConclusionPatients' assimilation of information should not be assumed by healthcare professionals but rather should be verified for individual patients. The model developed highlights the factors found to influence patients' knowledge and understanding of Barrett's CLO.