bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Genome and Structural Proteome of YuA, a New
Pseudomonas aeruginosa
Phage Resembling M6
Authors: Ceyssens Pieter-Jan , Mesyanzhinov Vadim , Sykilinda Nina , Briers Yves , Roucourt Bart , Lavigne Rob , Robben Johan , Domashin Artem , Miroshnikov Konstantin , Volckaert Guido , Hertveldt Kirsten 
Published: December 2007

ABSTRACT

Pseudomonas aeruginosa
phage YuA (
Siphoviridae
) was isolated from a pond near Moscow, Russia. It has an elongated head, encapsulating a circularly permuted genome of 58,663 bp, and a flexible, noncontractile tail, which is terminally and subterminally decorated with short fibers. The YuA genome is neither Mu- nor λ-like and encodes 78 gene products that cluster in three major regions involved in (i) DNA metabolism and replication, (ii) host interaction, and (iii) phage particle formation and host lysis. At the protein level, YuA displays significant homology with phages M6, φJL001, 73, B3, DMS3, and D3112. Eighteen YuA proteins were identified as part of the phage particle by mass spectrometry analysis. Five different bacterial promoters were experimentally identified using a promoter trap assay, three of which have a σ
54
-specific binding site and regulate transcription in the genome region involved in phage particle formation and host lysis. The dependency of these promoters on the host σ
54
factor was confirmed by analysis of an
rpoN
mutant strain of
P. aeruginosa
PAO1. At the DNA level, YuA is 91% identical to the recently (July 2007) annotated phage M6 of the Lindberg typing set. Despite this level of DNA homology throughout the genome, both phages combined have 15 unique genes that do not occur in the other phage. The genome organization of both phages differs substantially from those of the other known
Pseudomonas
-infecting
Siphoviridae
, delineating them as a distinct genus within this family.
A Point Mutation in the Two-Component Regulator PhoP-PhoR Accounts for the Absence of Polyketide-Derived Acyltrehaloses but Not That of Phthiocerol Dimycocerosates in
Mycobacterium tuberculosis
H37Ra
Authors: Chesne-Seck Marie-Laure , Barilone Nathalie , Boudou Frédéric , Asensio Jesús Gonzalo , Kolattukudy Pappachan E. , Martín Carlos , Cole Stewart T. , Gicquel Brigitte , Gopaul Deshmukh N. , Jackson Mary 
Published: December 2007

ABSTRACT

Similarities between
Mycobacterium tuberculosis phoP-phoR
mutants and the attenuated laboratory strain
M. tuberculosis
H37Ra in terms of morphological and cytochemical properties, lipid content, gene expression and virulence attenuation prompted us to analyze the functionality of this two-component regulator in the latter strain. Sequence analysis revealed a base substitution resulting in a one-amino-acid change in the likely DNA-binding region of PhoP in H37Ra relative to H37Rv. Using gel-shift assays, we show that this mutation abrogates the ability of the H37Ra PhoP protein to bind to a 40-bp segment of its own promoter. Consistent with this result, the
phoP
gene from H37Rv but not that from H37Ra was able to restore the synthesis of sulfolipids, diacyltrehaloses and polyacyltrehaloses in an isogenic
phoP-phoR
knock-out mutant of
M. tuberculosis
Moreover, complementation of H37Ra with
phoP
from H37Rv fully restored sulfolipid, diacyltrehalose and polyacyltrehalose synthesis, clearly indicating that the lack of production of these lipids in H37Ra is solely due to the point mutation in
phoP
. Using a
pks2-3/4
knock-out mutant of
M. tuberculosis
H37Rv, evidence is further provided that the above-mentioned polyketide-derived acyltrehaloses do not significantly contribute to the virulence of the tubercle bacillus in a mouse model of infection. Reasons for the attenuation of H37Ra thus most likely stand in other virulence factors, many of which are expected to belong to the PhoP regulon and another of which, unrelated to PhoP, appears to be the lack of production of phthiocerol dimycocerosates in this strain.
Interplay of Different Transporters in the Mediation of Divalent Heavy Metal Resistance in
Pseudomonas putida
KT2440
Authors: Leedjärv Anu , Ivask Angela , Virta Marko 
Published: December 2007

ABSTRACT

According to in silico analysis, the genome of
Pseudomonas putida
KT2440 encodes at least four Zn/Cd/Pb efflux transporters—two P-type ATPases (CadA1 and CadA2) and two
czc
chemiosmotic transporters (CzcCBA1 and CzcCBA2). In this study we showed that all these transporters are functional, but under laboratory conditions only two of them were involved in the mediation of heavy metal resistance in
P. putida
KT2440. CadA2 conferred Cd
2+
and Pb
2+
resistance, whereas CzcCBA1 was involved in export of Zn
2+
, Cd
2+
, and possibly Pb
2+
. CadA1, although nonfunctional in
P. putida
, improved Zn
2+
resistance and slightly improved Cd
2+
resistance when it was expressed in
Escherichia coli
. CzcCBA2 contributed to Zn resistance of a
czcA1
-defective
P. putida
strain or when the CzcA2 subunit was overexpressed in a transporter-deficient strain. It seemed that CzcA2 could complex with CzcC1 and CzcB1 subunits and therefore complement the loss of CzcA1. The CzcCBA2 transporter itself, however, did not function. Expression of
cadA1
,
cadA2
, and
czcCBA1
was induced by heavy metals, and the expression levels were dependent on the growth medium and growth phase. Expression of
cadA2
and
czcCBA1
was nonspecific; both genes were induced by Zn
2+
, Cd
2+
, Pb
2+
, Ni
2+
, Co
2+
, and Hg
2+
. On the other hand, remarkably, expression of
cadA1
was induced only by Zn
2+
. Possible roles of distinct but simultaneously functioning transporters are discussed.
Influence of thespxBGene on Competence inStreptococcus pneumoniae
Authors: Bättig Patrick , Mühlemann Kathrin 
Published: December 2007

ABSTRACTInStreptococcus pneumoniaeexpression of pyruvate oxidase (SpxB) peaks during the early growth phase, coincident with the time of natural competence. This study investigated whether SpxB influences parameters of competence, such as spontaneous transformation frequency, expression of competence genes, and DNA release. Knockout of thespxBgene in strain D39 abolished spontaneous transformation (compared to a frequency of 6.3 × 10−6in the parent strain [P< 0.01]). It also reduced expression levels ofcomCandrecAas well as DNA release from bacterial cells significantly during the early growth phase, coincident with the time of spontaneous competence in the parent strain. In thespxBmutant, supplementation with competence-stimulating peptide 1 (CSP-1) restored transformation (rate, 1.8 × 10−2). This speaks against the role of SpxB as a necessary source of energy for competence. Neither supplementation with CSP-1 nor supplementation with the SpxB products H2O2and acetate altered DNA release. Supplementation of the parent strain with catalase did not reduce DNA release significantly. In conclusion, the pneumococcalspxBgene influences competence; however, the mechanism remains elusive.
Ma-LMM01 Infecting Toxic
Microcystis aeruginosa
Illuminates Diverse Cyanophage Genome Strategies
Authors: Yoshida Takashi , Nagasaki Keizo , Takashima Yukari , Shirai Yoko , Tomaru Yuji , Takao Yoshitake , Sakamoto Shigetaka , Hiroishi Shingo , Ogata Hiroyuki 
Published: December 2007

ABSTRACT

Cyanobacteria and their phages are significant microbial components of the freshwater and marine environments. We identified a lytic phage, Ma-LMM01, infecting
Microcystis aeruginosa
, a cyanobacterium that forms toxic blooms on the surfaces of freshwater lakes. Here, we describe the first sequenced freshwater cyanomyovirus genome of Ma-LMM01. The linear, circularly permuted, and terminally redundant genome has 162,109 bp and contains 184 predicted protein-coding genes and two tRNA genes. The genome exhibits no colinearity with previously sequenced genomes of cyanomyoviruses or other
Myoviridae
. The majority of the predicted genes have no detectable homologues in the databases. These findings indicate that Ma-LMM01 is a member of a new lineage of the
Myoviridae
family. The genome lacks homologues for the photosynthetic genes that are prevalent in marine cyanophages. However, it has a homologue of
nblA
, which is essential for the degradation of the major cyanobacteria light-harvesting complex, the phycobilisomes. The genome codes for a site-specific recombinase and two prophage antirepressors, suggesting that it has the capacity to integrate into the host genome. Ma-LMM01 possesses six genes, including three coding for transposases, that are highly similar to homologues found in cyanobacteria, suggesting that recent gene transfers have occurred between Ma-LMM01 and its host. We propose that the Ma-LMM01 NblA homologue possibly reduces the absorption of excess light energy and confers benefits to the phage living in surface waters. This phage genome study suggests that light is central in the phage-cyanobacterium relationships where the viruses use diverse genetic strategies to control their host's photosynthesis.
Structure of [NiFe] Hydrogenase Maturation Protein HypE from
Escherichia coli
and Its Interaction with HypF
Authors: Rangarajan Erumbi S. , Asinas Abdalin , Proteau Ariane , Munger Christine , Baardsnes Jason , Iannuzzi Pietro , Matte Allan , Cygler Miroslaw 
Published: December 2007

ABSTRACT

Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H
2
as an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction center involving Fe and Ni metal ions and a small subunit containing one or more Fe-S clusters. Maturation of the [NiFe] hydrogenase involves assembly of nonproteinaceous ligands on the large subunit by accessory proteins encoded by the
hyp
operon. HypE is an essential accessory protein and participates in the synthesis of two cyano groups found in the large subunit. We report the crystal structure of
Escherichia coli
HypE at 2.0-Å resolution. HypE exhibits a fold similar to that of PurM and ThiL and forms dimers. The C-terminal catalytically essential Cys336 is internalized at the dimer interface between the N- and C-terminal domains. A mechanism for dehydration of the thiocarbamate to the thiocyanate is proposed, involving Asp83 and Glu272. The interactions of HypE and HypF were characterized in detail by surface plasmon resonance and isothermal titration calorimetry, revealing a

K
d

(dissociation constant) of ∼400 nM. The stoichiometry and molecular weights of the complex were verified by size exclusion chromatography and gel scanning densitometry. These experiments reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]
2
heterotetramer which exists in a dynamic equilibrium with the EF heterodimer. The surface plasmon resonance results indicate that a conformational change occurs upon heterodimerization which facilitates formation of a productive complex as part of the carbamate transfer reaction.
Pseudomonas aeruginosa
Exhibits Sliding Motility in the Absence of Type IV Pili and Flagella
Authors: Murray Thomas S. , Kazmierczak Barbara I. 
Published: December 2007

ABSTRACT

Pseudomonas aeruginosa
exhibits swarming motility on 0.5 to 1% agar plates in the presence of specific carbon and nitrogen sources. We have found that PAO1 double mutants expressing neither flagella nor type IV pili (
fliC pilA
) display sliding motility under the same conditions. Sliding motility was inhibited when type IV pilus expression was restored; like swarming motility, it also decreased in the absence of rhamnolipid surfactant production. Transposon insertions in
gacA
and
gacS
increased sliding motility and restored tendril formation to spreading colonies, while transposon insertions in
retS
abolished motility. These changes in motility were not accompanied by detectable changes in rhamnolipid surfactant production or by the appearance of bacterial surface structures that might power sliding motility. We propose that
P. aeruginosa
requires flagella during swarming to overcome adhesive interactions mediated by type IV pili. The apparent dependence of sliding motility on environmental cues and regulatory pathways that also affect swarming motility suggests that both forms of motility are influenced by similar cohesive factors that restrict translocation, as well as by dispersive factors that facilitate spreading. Studies of sliding motility may be particularly well-suited for identifying factors other than pili and flagella that affect community behaviors of
P. aeruginosa
.
Mesaconyl-Coenzyme A Hydratase, a New Enzyme of Two Central Carbon Metabolic Pathways in Bacteria
Authors: Zarzycki Jan , Schlichting Ansgar , Strychalsky Nina , Müller Michael , Alber Birgit E. , Fuchs Georg 
Published: December 2007

ABSTRACT

The coenzyme A (CoA)-activated C
5
-dicarboxylic acids mesaconyl-CoA and β-methylmalyl-CoA play roles in two as yet not completely resolved central carbon metabolic pathways in bacteria. First, these compounds are intermediates in the 3-hydroxypropionate cycle for autotrophic CO
2
fixation in
Chloroflexus aurantiacus
, a phototrophic green nonsulfur bacterium. Second, mesaconyl-CoA and β-methylmalyl-CoA are intermediates in the ethylmalonyl-CoA pathway for acetate assimilation in various bacteria, e.g., in
Rhodobacter sphaeroides
,
Methylobacterium extorquens
, and
Streptomyces
species. In both cases, mesaconyl-CoA hydratase was postulated to catalyze the interconversion of mesaconyl-CoA and β-methylmalyl-CoA. The putative genes coding for this enzyme in
C. aurantiacus
and
R. sphaeroides
were cloned and heterologously expressed in
Escherichia coli
, and the proteins were purified and studied. The recombinant homodimeric 80-kDa proteins catalyzed the reversible dehydration of
erythro
-β-methylmalyl-CoA to mesaconyl-CoA with rates of 1,300 μmol min
−1
mg protein
−1
. Genes coding for similar enzymes with two (
R
)-enoyl-CoA hydratase domains are present in the genomes of
Roseiflexus
,
Methylobacterium
,
Hyphomonas
,
Rhodospirillum
,
Xanthobacter
,
Caulobacter
,
Magnetospirillum
,
Jannaschia
,
Sagittula
,
Parvibaculum
,
Stappia
,
Oceanicola
,
Loktanella
,
Silicibacter
,
Roseobacter
,
Roseovarius
,
Dinoroseobacter
,
Sulfitobacter
,
Paracoccus
, and
Ralstonia
species. A similar yet distinct class of enzymes containing only one hydratase domain was found in various other bacteria, such as
Streptomyces
species. The role of this widely distributed new enzyme is discussed.
Role of the Clp System in Stress Tolerance, Biofilm Formation, and Intracellular Invasion inPorphyromonas gingivalis
Authors: Capestany Cindy A. , Tribble Gena D. , Maeda Kazuhiko , Demuth Donald R. , Lamont Richard J. 
Published: December 2007

ABSTRACTClp proteases and chaperones are ubiquitous among prokaryotes and eukaryotes, and in many pathogenic bacteria the Clp stress response system is also involved in regulation of virulence properties. In this study, the roles of ClpB, ClpC, and ClpXP in stress resistance, homotypic and heterotypic biofilm formation, and intracellular invasion in the oral opportunistic pathogenPorphyromonas gingivaliswere investigated. Absence of ClpC and ClpXP, but not ClpB, resulted in diminished tolerance to high temperatures. Response to oxidative stress was not affected by the loss of any of the Clp proteins. TheclpCandclpXPmutants demonstrated elevated monospecies biofilm formation, and the absence of ClpXP also enhanced heterotypicP. gingivalis-Streptococcus gordoniibiofilm formation. Allclpmutants adhered to gingival epithelial cells to the same level as the wild type; however, ClpC and ClpXP were found to be necessary for entry into host epithelial cells. ClpB did not play a role in entry but was required for intracellular replication and survival. ClpXP negatively regulated the surface exposure of the minor fimbrial (Mfa) protein subunit ofP. gingivalis, which stimulates biofilm formation but interferes with epithelial cell entry. Collectively, these results show that the Clp protease complex and chaperones control several processes that are important for the colonization and survival ofP. gingivalisin the oral cavity.
The Complete Genome Sequence of
Actinobacillus pleuropneumoniae
L20 (Serotype 5b)
Authors: Foote Simon J. , Bossé Janine T. , Bouevitch Anne B. , Langford Paul R. , Young N. Martin , Nash John H. E. 
Published: December 2007

ABSTRACT

There are 16 capsule-based serotypes of
Actinobacillus pleuropneumoniae
, all of which are capable of causing disease in pigs. Here we report the finished and annotated genome sequence of the reference serotype 5b strain L20. This strain has a rough appearance and readily forms biofilms, as is typical for most field isolates (6).
The epidemiology of rock-climbing injuries
Authors: Jones G , Asghar A , Llewellyn D J 
Published: December 2007

Objectives:To determine the prevalence and nature of rock-climbing injuries, and the factors associated with these injuries.Design:A retrospective cross-sectional study.Setting:Rock climbers were recruited at five outdoor and six indoor climbing venues in the UK.Participants:201 active rock climbers (163 male, 38 female climbers) aged 16–62 years.Assessment of risk factors:Rock climbing behaviours and key demographics.Main outcome measures:Injuries requiring medical attention or withdrawal from participation for ⩾1 day.Results:Around 50% of climbers had sustained ⩾1 injury in the past 12 months, causing a total of 275 distinct anatomical injuries. 21 climbers (10%) had sustained acute climbing injuries as a result of a fall, 67 (33%) had chronic overuse injuries, and 57 (28%) had acute injuries caused by strenuous climbing moves. Dedicated climbers participating in different forms of rock climbing more often and at a higher level of technical difficulty may be more prone to injury, particularly overuse injuries of the finger and shoulder. The principal sources of treatment or advice sought by climbers were physiotherapists (18%), other climbers (14%) and doctors (11%).Conclusions:Climbing frequency and technical difficulty are associated with climbing injuries occurring at both indoor and outdoor venues, particularly cumulative trauma to the upper extremities.
A prospective cohort study of the incidence of injuries among junior Australian football players: evidence for an effect of playing-age level
Authors: Romiti M , Finch C F , Gabbe B 
Published: December 2007

Objective:To determine the rate of injury in junior Australian football, and to describe the patterns and severity of these injuries across nine levels of play (U9 to U18).Design:Prospective cohort study.Setting:Junior Australian football games and training sessions were observed for 54 teams from New South Wales and Victoria over the 2004 playing season.Participants:Six teams from each level of play were invited to participate in the study. Overall, data were collected for 51 teams over 40 208 hours of player exposure.Independent variables:Participation and injury data were collected prospectively.Main outcome measures:Injury was defined as “any trauma that causes some disability or pain”. Injury severity was identified by the action of players immediately after the injury event.Results:The overall injury rate was 18.0 (95% CI 16.6 to 19.3) injuries per 1000 player hours. The main cause of injury was body contact (67.3%). There was an increased frequency of sprains and strains, and injury severity with increasing level of play. The rates of injury for players who stayed off the field (6.4 injuries per 1000 hours, 95% CI 5.6 to 7.2) or were advised to seek off-field medical advice (5.0 injuries per 1000 hours, 95% CI 4.3 to 5.7) were low.Conclusion:Compared with the adult game, junior Australian football is relatively safe. However, injury rates increase as children progress across age-determined levels of play towards the more adult form of the game.
Workload demands in professional multi-stage cycling races of varying duration
Authors: Rodríguez-Marroyo J A , García-López J , Juneau C-É , Villa J G 
Published: December 2007

Objetive:To analyse and compare the workload exerted by professional cyclists in 5-day, 8-day and 21-day stage races (5-SR, 8-SR, 21-SR).Methods:The study subjects were 30 professional cyclists competing in 10 5-SR, 5 8-SR and 5 21-SR. Heart rate (HR) was measured during the races and categorised into three intensity zones: Z1 (below the ventilatory threshold (VT)), Z2 (between VT and the respiratory compensation threshold (RCT)) and Z3 (above RCT). The training impulse (TRIMP) was calculated by multiplying the sum of the time spent in each zone by 1, 2 and 3, respectively. Monotony (average TRIMP/SD) and strain (total TRIMP×monotony) were also calculated for each race type.Results:The average time spent in Z3 during each stage was significantly (p<0.05) higher for 5-SR (∼31 min) and 8-SR (∼28 min) than for 21-SR (∼14 min). Daily TRIMP values in 5-SR (∼400) and 8-SR (∼395) were also higher than in 21-SR (∼370). Monotony was similar across races (∼3) but strain was about three times higher for 21-SR than for 5-SR and 8-SR.Conclusions:The cyclists’ effort by stage was less for 21-SR than for 5-SR and 8-SR. Competition strain and monotony accumulated during longer races influence the choice of strategies adopted by cyclists. It is likely that the intensity of each stage is modulated by total race duration, with longer races averaging the lowest daily workload.
First40Ar/39Ar age constraints for the Caledonian evolution of the Trans–European Suture Zone in NE Germany
Authors: DALLMEYER R. D. , GIESE U. , GLASMACHER U. , PICKEL W. 
Published: December 2007

From three Rügen boreholes (G14, Rügen 5, Loissin 1) across the Caledonian deformation front four Lower Palaeozoic slate samples and three detrital muscovite concentrates from associated sandstones have been analysed by40Ar/39Ar analysis. Microprobe analysis of the detrital muscovites show homogeneous, but distinct chemical compositions for each concentrate. Particulate organic matter reflectance and illite crystallinity indicate that all the analysed whole–rock samples have experienced anchizonal metamorphic conditions.40Ar/39Ar analysis of the samples from the G14 and Loissin 1 wells give almost identical results. Muscovite concentrates define plateau ages ofc.830 Ma and show an isotopic rejuvenation of low–temperature increments around 440 Ma. Whole–rock slate samples give plateau ages ofc.440 Ma andc.427 Ma. Isotopic rejuvenation in the low–temperature increments prior to 350 Ma in the Loissin 1 sample can be attributed to the Permo–Carbonifereous volcanism which is known from this borehole. In contrast, samples from the borehole Rügen 5 show a different isotope pattern. A muscovite concentrate defines a plateau age of 609 Ma. Two whole rock slate samples give internally discordant but identical40Ar/39Ar spectra with consistent isotopic rejuvenation from high– to low–temperature increments from 510 Ma to 420 Ma.While for the G14 and Loissin 1 sandstone samples a Baltica–derived provenance can be assumed, greywackes of Rügen 5 indicate a Cadomian–influenced Perigondwanan detrital source. According to the results of whole–rock slate samples the main Caledonian tectonothermal event in NE–Germany occurred around the Ordovician–Silurian boundary or in the early Silurian (450–425 Ma). From these data the Rügen Palaeozoic appears as an allochthonous Caledonian nappe complex which has been thrust much further onto the Baltic shield than previously thought.