bluuebunny/crossref_metadata_2025_split huggingface dataset:
ThePseudomonas aeruginosaPathogenicity Island PAPI-1 Is Transferred via a Novel Type IV Pilus
Authors: Carter Michelle Qiu , Chen Jianshun , Lory Stephen 
Published: April 2010

ABSTRACTPseudomonas aeruginosais a major cause of nosocomial infections, particularly in immunocompromised patients or in individuals with cystic fibrosis. The notable ability ofP. aeruginosato inhabit a broad range of environments, including humans, is in part due to its large and diverse genomic repertoire. The genomes of most strains contain a significant number of large and small genomic islands, including those carrying virulence determinants (pathogenicity islands). The pathogenicity island PAPI-1 of strain PA14 is a cluster of 115 genes, and some have been shown to be responsible for virulence phenotypes in a number of infection models. We have previously demonstrated that PAPI-1 can be transferred to otherP. aeruginosastrains following excision from the chromosome of the donor. Here we show that PAPI-1 is transferred into recipientP. aeruginosaby a conjugative mechanism, via a type IV pilus, encoded in PAPI-1 by a 10-gene cluster which is closely related to the genes in the enterobacterial plasmid R64. We also demonstrate that the precursor of the major pilus subunit, PilS2, is processed by the chromosomally encoded prepillin peptidase PilD but not its paralog FppA. Our results suggest that the pathogenicity island PAPI-1 may have evolved by acquisition of a conjugation system but that because of its dependence on an essential chromosomal determinant, its transfer is restricted toP. aeruginosaor other species capable of providing a functional prepilin peptidase.
Visualization of Flagella during Bacterial Swarming
Authors: Turner Linda , Zhang Rongjing , Darnton Nicholas C. , Berg Howard C. 
Published: April 2010

ABSTRACT

When cells of
Escherichia coli
are grown in broth and suspended at low density in a motility medium, they swim independently, exploring a homogeneous, isotropic environment. Cell trajectories and the way in which these trajectories are determined by flagellar dynamics are well understood. When cells are grown in a rich medium on agar instead, they elongate, produce more flagella, and swarm. They move in coordinated packs within a thin film of fluid, in intimate contact with one another and with two fixed surfaces, a surfactant monolayer above and an agar matrix below: they move in an inhomogeneous, anisotropic environment. Here we examine swarm-cell trajectories and ways in which these trajectories are determined by flagellar motion, visualizing the cell bodies by phase-contrast microscopy and the flagellar filaments by fluorescence microscopy. We distinguish four kinds of tracks, defining stalls, reversals, lateral movement, and forward movement. When cells are stalled at the edge of a colony, they extend their flagellar filaments outwards, moving fluid over the virgin agar; when cells reverse, changes in filament chirality play a crucial role; when cells move laterally, they are pushed sideways by adjacent cells; and when cells move forward, they are pushed by flagellar bundles in the same way as when they are swimming in bulk aqueous media. These maneuvers are described in this report.
Genetic, Structural, and Antigenic Analyses of Glycan Diversity in the O-Linked Protein Glycosylation Systems of HumanNeisseriaSpecies
Authors: Børud Bente , Aas Finn Erik , Vik Åshild , Winther-Larsen Hanne C. , Egge-Jacobsen Wolfgang , Koomey Michael 
Published: April 2010

ABSTRACTBacterial capsular polysaccharides and lipopolysaccharides are well-established ligands of innate and adaptive immune effectors and often exhibit structural and antigenic variability. Although many surface-localized glycoproteins have been identified in bacterial pathogens and symbionts, it not clear if and how selection impacts associated glycoform structure. Here, a systematic approach was devised to correlate gene repertoire with protein-associated glycoform structure inNeisseriaspecies important to human health and disease. By manipulating the protein glycosylation (pgl) gene content and assessing the glycan structure by mass spectrometry and reactivity with monoclonal antibodies, it was established that protein-associated glycans are antigenically variable and that at least nine distinct glycoforms can be expressedin vitro. These studies also revealed that in addition toNeisseria gonorrhoeaestrain N400, one other gonococcal strain and isolates ofNeisseria meningitidisandNeisseria lactamicaexhibit broad-spectrum O-linked protein glycosylation. Although a strong correlation betweenpglgene content, glycoform expression, and serological profile was observed, there were significant exceptions, particularly with regard to levels of microheterogeneity. This work provides a technological platform for molecular serotyping of neisserial protein glycans and for elucidatingpglgene evolution.
Haloferax volcanii
Flagella Are Required for Motility but Are Not Involved in PibD-Dependent Surface Adhesion
Authors: Tripepi Manuela , Imam Saheed , Pohlschröder Mechthild 
Published: April 2010

ABSTRACT

Although the genome of
Haloferax volcanii
contains genes (
flgA1
-
flgA2
) that encode flagellins and others that encode proteins involved in flagellar assembly, previous reports have concluded that
H. volcanii
is nonmotile. Contrary to these reports, we have now identified conditions under which
H. volcanii
is motile. Moreover, we have determined that an
H. volcanii
deletion mutant lacking flagellin genes is not motile. However, unlike flagella characterized in other prokaryotes, including other archaea, the
H. volcanii
flagella do not appear to play a significant role in surface adhesion. While flagella often play similar functional roles in bacteria and archaea, the processes involved in the biosynthesis of archaeal flagella do not resemble those involved in assembling bacterial flagella but, instead, are similar to those involved in producing bacterial type IV pili. Consistent with this observation, we have determined that, in addition to disrupting preflagellin processing, deleting
pibD
, which encodes the preflagellin peptidase, prevents the maturation of other
H. volcanii
type IV pilin-like proteins. Moreover, in addition to abolishing swimming motility, and unlike the
flgA1
-
flgA2
deletion, deleting
pibD
eliminates the ability of
H. volcanii
to adhere to a glass surface, indicating that a nonflagellar type IV pilus-like structure plays a critical role in
H. volcanii
surface adhesion.
Biochemical Characterization of the C
4
-Dicarboxylate Transporter DctA from
Bacillus subtilis
Authors: Groeneveld Maarten , Detert Oude Weme Ruud G. J. , Duurkens Ria H. , Slotboom Dirk Jan 
Published: April 2010

ABSTRACT

Bacterial secondary transporters of the DctA family mediate ion-coupled uptake of C
4
-dicarboxylates. Here, we have expressed the DctA homologue from
Bacillus subtilis
in the Gram-positive bacterium
Lactococcus lactis
. Transport of dicarboxylates
in vitro
in isolated membrane vesicles was assayed. We determined the substrate specificity, the type of cotransported ions, the electrogenic nature of transport, and the pH and temperature dependence patterns. DctA was found to catalyze proton-coupled symport of the four C
4
-dicarboxylates from the Krebs cycle (succinate, fumurate, malate, and oxaloacetate) but not of other mono- and dicarboxylates. Because (i) succinate-proton symport was electrogenic (stimulated by an internal negative membrane potential) and (ii) the divalent anionic form of succinate was recognized by DctA, at least three protons must be cotransported with succinate. The results were interpreted in the light of the crystal structure of the homologous aspartate transporter Glt
Ph
from
Pyrococcus horikoshii
.
Loss of the Response Regulator CtrA Causes Pleiotropic Effects on Gene Expression but Does Not Affect Growth Phase Regulation in
Rhodobacter capsulatus
Authors: Mercer Ryan G. , Callister Stephen J. , Lipton Mary S. , Pasa-Tolic Ljiljana , Strnad Hynek , Paces Vaclav , Beatty J. Thomas , Lang Andrew S. 
Published: April 2010

ABSTRACT

The purple nonsulfur photosynthetic bacterium
Rhodobacter capsulatus
has been extensively studied for its metabolic versatility as well as for production of a gene transfer agent called RcGTA. Production of RcGTA is highest in the stationary phase of growth and requires the response regulator protein CtrA. The CtrA protein in
Caulobacter crescentus
has been thoroughly studied for its role as an essential, master regulator of the cell cycle. Although the CtrA protein in
R. capsulatus
shares a high degree of sequence similarity with the
C. crescentus
protein, it is nonessential and clearly plays a different role in this bacterium. We have used transcriptomic and proteomic analyses of wild-type and
ctrA
mutant cultures to identify the genes dysregulated by the loss of CtrA in
R. capsulatus
. We have also characterized gene expression differences between the logarithmic and stationary phases of growth. Loss of CtrA has pleiotropic effects, with dysregulation of expression of ∼6% of genes in the
R. capsulatus
genome. This includes all flagellar motility genes and a number of other putative regulatory proteins but does not appear to include any genes involved in the cell cycle. Quantitative proteomic data supported 88% of the CtrA transcriptome results. Phylogenetic analysis of CtrA sequences supports the hypothesis of an ancestral
ctrA
gene within the alphaproteobacteria, with subsequent diversification of function in the major alphaproteobacterial lineages.
Genome Sequence of
Lentisphaera araneosa
HTCC2155
T
, the Type Species of the Order
Lentisphaerales
in the Phylum
Lentisphaerae
Authors: Thrash J. Cameron , Cho Jang-Cheon , Vergin Kevin L. , Morris Robert M. , Giovannoni Stephen J. 
Published: April 2010

ABSTRACT

Information on the genome content of deeply branching phyla with very few cultured members is invaluable for expanding understanding of microbial evolution.
Lentisphaera araneosa
HTCC2155
T
was isolated from the Oregon coast using dilution-to-extinction culturing. It is a marine heterotroph found in surface and mesopelagic waters in both the Pacific and Atlantic oceans and has the unusual property of producing a net-like matrix of secreted exopolysaccharide. Here we present the genome sequence of
L. araneosa
HTCC2155
T
, importantly, one of only two sequenced members of the phylum
Lentisphaerae
.
Direct Targets of CodY in
Staphylococcus aureus
Authors: Majerczyk Charlotte D. , Dunman Paul M. , Luong Thanh T. , Lee Chia Y. , Sadykov Marat R. , Somerville Greg A. , Bodi Kip , Sonenshein Abraham L. 
Published: April 2010

ABSTRACT

More than 200 direct CodY target genes in
Staphylococcus aureus
were identified by genome-wide analysis of
in vitro
DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules, and virulence. The virulence genes regulated by CodY fell into three groups. One group was dependent on the Agr system for its expression; these genes were indirectly regulated by CodY through its repression of the
agr
locus. A second group was regulated directly by CodY. The third group, which includes genes for alpha-toxin and capsule synthesis, was regulated by CodY in two ways, i.e., by direct repression and by repression of the
agr
locus. Since
S. aureus
CodY was activated
in vitro
by the branched chain amino acids and GTP, CodY appears to link changes in intracellular metabolite pools with the induction of numerous adaptive responses, including virulence.
The LysR-Type Nitrogen Assimilation Control Protein Forms Complexes with Both Long and Short DNA Binding Sites in the Absence of Coeffectors
Authors: Rosario Christopher J. , Frisch Ryan L. , Bender Robert A. 
Published: April 2010

ABSTRACT

Most LysR-type transcriptional regulators (LTTRs) function as tetramers when regulating gene expression. The nitrogen assimilation control protein (NAC) generally functions as a dimer when binding to DNA and activating transcription. However, at some sites, NAC binds as a tetramer. Like many LTTRs, NAC tetramers can recognize sites with long footprints (74 bp for the site at
nac
) with a substantial DNA bend or short footprints (56 bp for the site at
cod
) with less DNA bending. However, unlike other LTTRs, NAC can recognize both types of sites in the absence of physiologically relevant coeffectors, suggesting that the two conformers of the NAC tetramer (extended and compact) are interchangeable without the need for any modification to induce or stabilize the change. In order for NAC to bind as a tetramer, three interactions must exist: an interaction between the two NAC dimers and an interaction between each NAC dimer and its corresponding binding site. The interaction between one dimer and its DNA site can be weak (recognizing a half-site rather than a full dimer-binding site), but the other two interactions must be strong. Since the conformation of the NAC tetramer (extended or compact) is determined by the nature of the DNA site without the intervention of a small molecule, we argue that the coeffector that determines the conformation of the NAC tetramer is the DNA site to which it binds.
Glucose Metabolism in
Legionella pneumophila
: Dependence on the Entner-Doudoroff Pathway and Connection with Intracellular Bacterial Growth
Authors: Harada Eiji , Iida Ken-Ichiro , Shiota Susumu , Nakayama Hiroaki , Yoshida Shin-Ichi 
Published: April 2010

ABSTRACT

Glucose metabolism in
Legionella pneumophila
was studied by focusing on the Entner-Doudoroff (ED) pathway with a combined genetic and biochemical approach. The bacterium utilized exogenous glucose for synthesis of acid-insoluble cell components but manifested no discernible increase in the growth rate. Assays with permeabilized cell preparations revealed the activities of three enzymes involved in the pathway, i.e., glucokinase, phosphogluconate dehydratase, and 2-dehydro-3-deoxy-phosphogluconate aldolase, presumed to be encoded by the
glk
,
edd
, and
eda
genes, respectively. Gene-disrupted mutants for the three genes and the
ywtG
gene encoding a putative sugar transporter were devoid of the ability to metabolize exogenous glucose, indicating that the pathway is almost exclusively responsible for glucose metabolism and that the
ywtG
gene product is the glucose transporter. It was also established that these four genes formed part of an operon in which the gene order was
edd-glk-eda-ywtG
, as predicted by genomic information. Intriguingly, while the mutants exhibited no appreciable change in growth characteristics
in vitro
, they were defective in multiplication within eukaryotic cells, strongly indicating that the ED pathway must be functional for the intracellular growth of the bacterium to occur. Curiously, while the deficient glucose metabolism of the
ywtG
mutant was successfully complemented by the
ywtG
+
gene supplied in
trans
via plasmid, its defect in intracellular growth was not. However, the latter defect was also manifested in wild-type cells when a plasmid carrying the mutant
ywtG
gene was introduced. This phenomenon, resembling so-called dominant negativity, awaits further investigation.
A Novel Hydrolytic Dehalogenase for the Chlorinated Aromatic Compound Chlorothalonil
Authors: Wang Guangli , Li Rong , Li Shunpeng , Jiang Jiandong 
Published: April 2010

ABSTRACT

Dehalogenases play key roles in the detoxification of halogenated aromatics. Interestingly, only one hydrolytic dehalogenase for halogenated aromatics, 4-chlorobenzoyl-coenzyme A (CoA) dehalogenase, has been reported. Here, we characterize another novel hydrolytic dehalogenase for a halogenated aromatic compound from the 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil)-degrading strain of
Pseudomonas
sp. CTN-3, which we have named Chd. Chd catalyzes a hydroxyl substitution at the 4-chlorine atom of chlorothalonil. The metabolite of the Chd dehalogenation, 4-hydroxy-trichloroisophthalonitrile, was identified by reverse-phase high-performance liquid chromatography (HPLC), tandem mass spectrometry (MS/MS), and nuclear magnetic resonance (NMR). Chd dehalogenates chlorothalonil under anaerobic and aerobic conditions and does not require the presence of cofactors such as CoA and ATP. Chd contains a putative conserved domain of the metallo-β-lactamase superfamily and shows the highest identity with several metallohydrolases (24 to 29%). Chd is a monomer (36 kDa), and the isoelectric point (pI) of Chd is estimated to be 4.13. Chd has a dissociation constant (

K
m

) of 0.112 mM and an overall catalytic rate (
k
cat
) of 207 s
−1
for chlorothalonil. Chd is completely inhibited by 1,10-phenanthroline, diethyl pyrocarbonate, and
N
-bromosuccinic acid. Site-directed mutagenesis of Chd revealed that histidines 128 and 157, serine 126, aspartates 45, 130 and 184, and tryptophan 241 were essential for the dehalogenase activity. Chd differs from other reported hydrolytic dehalogenases based on the analysis of amino acid sequences and catalytic mechanisms. This study provides an excellent dehalogenase candidate for mechanistic study of hydrolytic dehalogenation of halogenated aromatic compound.
Multiple Interaction Domains in FtsL, a Protein Component of the Widely Conserved Bacterial FtsLBQ Cell Division Complex
Authors: Gonzalez Mark D. , Akbay Esra A. , Boyd Dana , Beckwith Jon 
Published: April 2010

ABSTRACTA bioinformatic analysis of nearly 400 genomes indicates that the overwhelming majority of bacteria possess homologs of theEscherichia coliproteins FtsL, FtsB, and FtsQ, three proteins essential for cell division in that bacterium. These three bitopic membrane proteins form a subcomplexin vivo, independent of the other cell division proteins. Here we analyze the domains ofE. coliFtsL that are involved in the interaction with other cell division proteins and important for the assembly of the divisome. We show that FtsL, as we have found previously with FtsB, packs an enormous amount of information in its sequence for interactions with proteins upstream and downstream in the assembly pathway. Given their size, it is likely that the sole function of the complex of these two proteins is to act as a scaffold for divisome assembly.
Mutagenesis and Functional Characterization of the Four Domains of GlnD, a Bifunctional Nitrogen Sensor Protein
Authors: Zhang Yaoping , Pohlmann Edward L. , Serate Jose , Conrad Mary C. , Roberts Gary P. 
Published: April 2010

ABSTRACT

GlnD is a bifunctional uridylyltransferase/uridylyl-removing enzyme (UTase/UR) and is believed to be the primary sensor of nitrogen status in the cell by sensing the level of glutamine in enteric bacteria. It plays an important role in nitrogen assimilation and metabolism by reversibly regulating the modification of P
II
protein; P
II
in turn regulates a variety of other proteins. GlnD appears to have four distinct domains: an N-terminal nucleotidyltransferase (NT) domain; a central HD domain, named after conserved histidine and aspartate residues; and two C-terminal ACT domains, named after three of the allosterically regulated enzymes in which this domain is found. Here we report the functional analysis of these domains of GlnD from
Escherichia coli
and
Rhodospirillum rubrum
. We confirm the assignment of UTase activity to the NT domain and show that the UR activity is a property specifically of the HD domain: substitutions in this domain eliminated UR activity, and a truncated protein lacking the NT domain displayed UR activity. The deletion of C-terminal ACT domains had little effect on UR activity itself but eliminated the ability of glutamine to stimulate that activity, suggesting a role for glutamine sensing by these domains. The deletion of C-terminal ACT domains also dramatically decreased UTase activity under all conditions tested, but some of these effects are due to the competition of UTase activity with unregulated UR activity in these variants.
PALINDROMES AND ORDERINGS IN ARTIN GROUPS
Authors: DELOUP FLORIAN 
Published: April 2010

The braid group Bn, endowed with Artin's presentation, admits two distinguished involutions. One is the anti-automorphism rev : Bn→Bn, [Formula: see text], defined by reading braids in the reverse order (from right to left instead of left to right). Another one is the conjugation τ : x ↦ Δ-1xΔ by the generalized half-twist (Garside element).More generally, the involution rev is defined for all Artin groups (equipped with Artin's presentation) and the involution τ is defined for all Artin groups of finite type. A palindrome is an element invariant under rev. We study palindromes and palindromes invariant under τ in Artin groups of finite type. Our main results are the injectivity of the map [Formula: see text] in all finite-type Artin groups, the existence of a left-order compatible with rev for Artin groups of type A, B, D, and the existence of a decomposition for general palindromes. The uniqueness of the latter decomposition requires that the Artin groups carry a left-order.
KORSELT NUMBERS AND SETS
Authors: BOUALLÈGUE KAIS , ECHI OTHMAN , PINCH RICHARD G. E. 
Published: April 2010

Let α ∈ ℤ\{0}. A positive integer N is said to be an α-Korselt number (Kα-number, for short) if N ≠ α and p - α divides N - α for each prime divisor p of N. We are concerned, here, with both a numerical and theoretical study of composite squarefree Korselt numbers. The paper contains two main results. The first one shows that for α ∈ ℤ\{0}, the following properties hold: (i) If α ≤ 1, then each composite squarefree Kα-number has at least three prime factors. (ii) Suppose that α > 1. Let p < q be two prime numbers and N ≔ pq. If N is an α-Korselt number, then p < q ≤ 4α - 3. In particular, there are only finitely many α-Korselt numbers with exactly two prime factors. Let α ∈ ℕ\{0}; by an α-Williams number (Wα-number, for short) we mean a positive integer which is both a Kα-number and a K-α-number. Our second main result shows that if p, 3p - 2, 3p + 2 are all prime, then their product is a (3p)-Williams number.
Upgrading or Decline? Globalization, Retail Structure, and Labour in the Chilean Textile and Clothing Industry
Authors: Reinecke Gerhard 
Published: April 2010

Trade liberalization has plunged the textile and clothing industry in many countries — both in the developed and developing world — into a crisis with important employment losses. Important differences across countries exist regarding the extent of decline, the productivity performance, and the working conditions for the remaining workers in this industry. Based on elements of global commodity chain analysis and the varieties of capitalism (VoC) approach, these different patterns have been explained for developed countries, placing particular emphasis on the scope and effective implementation of industry-wide minimum wages and labour regulations, as well as on retail concentration. In this article, we apply the above framework to Chile, where the process of downsizing of the industry has followed the least virtuous pattern, with meagre productivity results and precarization of remaining employment. Part of the remaining textile and clothing employment has moved to the informal economy and sweatshop-type enterprises. This outcome is explained by the high degree of retail concentration in Chile, the virtual absence of sectoral collective bargaining and the partial coverage of labour inspection among micro and small enterprises.