bluuebunny/crossref_metadata_2025_split huggingface dataset:
Caenorhabditis elegans, a Model Organism for Investigating Immunity
Authors: Marsh Elizabeth K. , May Robin C. 
Published: January 2012

ABSTRACT

The nematode
Caenorhabditis elegans
has been a powerful experimental organism for almost half a century. Over the past 10 years, researchers have begun to exploit the power of
C. elegans
to investigate the biology of a number of human pathogens. This work has uncovered mechanisms of host immunity and pathogen virulence that are analogous to those involved during pathogenesis in humans or other animal hosts, as well as novel immunity mechanisms which appear to be unique to the worm. More recently, these investigations have uncovered details of the natural pathogens of
C. elegans
, including the description of a novel intracellular microsporidian parasite as well as new nodaviruses, the first identification of viral infections of this nematode. In this review, we consider the application of
C. elegans
to human infectious disease research, as well as consider the nematode response to these natural pathogens.
Comprehensive Set of Integrative Plasmid Vectors for Copper-Inducible Gene Expression in Myxococcus xanthus
Authors: Gómez-Santos Nuria , Treuner-Lange Anke , Moraleda-Muñoz Aurelio , García-Bravo Elena , García-Hernández Raquel , Martínez-Cayuela Marina , Pérez Juana , Søgaard-Andersen Lotte , Muñoz-Dorado José 
Published: January 2012

ABSTRACT

Myxococcus xanthus
is widely used as a model system for studying gliding motility, multicellular development, and cellular differentiation. Moreover,
M. xanthus
is a rich source of novel secondary metabolites. The analysis of these processes has been hampered by the limited set of tools for inducible gene expression. Here we report the construction of a set of plasmid vectors to allow copper-inducible gene expression in
M. xanthus
. Analysis of the effect of copper on strain DK1622 revealed that copper concentrations of up to 500 μM during growth and 60 μM during development do not affect physiological processes such as cell viability, motility, or aggregation into fruiting bodies. Of the copper-responsive promoters in
M. xanthus
reported so far, the multicopper oxidase
cuoA
promoter was used to construct expression vectors, because no basal expression is observed in the absence of copper and induction linearly depends on the copper concentration in the culture medium. Four different plasmid vectors have been constructed, with different marker selection genes and sites of integration in the
M. xanthus
chromosome. The vectors have been tested and gene expression quantified using the
lacZ
gene. Moreover, we demonstrate the functional complementation of the motility defect caused by lack of PilB by the copper-induced expression of the
pilB
gene. These versatile vectors are likely to deepen our understanding of the biology of
M. xanthus
and may also have biotechnological applications.
Function of the Pyruvate Oxidase-Lactate Oxidase Cascade in Interspecies Competition between Streptococcus oligofermentans and Streptococcus mutans
Authors: Liu Lei , Tong Huichun , Dong Xiuzhu 
Published: January 2012

ABSTRACT

Complex interspecies interactions occur constantly between oral commensals and the opportunistic pathogen
Streptococcus mutans
in dental plaque. Previously, we showed that oral commensal
Streptococcus oligofermentans
possesses multiple enzymes for H
2
O
2
production, especially lactate oxidase (Lox), allowing it to out-compete
S. mutans
. In this study, through extensive biochemical and genetic studies, we identified a pyruvate oxidase (
pox
) gene in
S. oligofermentans
. A
pox
deletion mutant completely lost Pox activity, while ectopically expressed
pox
restored activity. Pox was determined to produce most of the H
2
O
2
in the earlier growth phase and log phase, while Lox mainly contributed to H
2
O
2
production in stationary phase. Both
pox
and
lox
were expressed throughout the growth phase, while expression of the
lox
gene increased by about 2.5-fold when cells entered stationary phase. Since lactate accumulation occurred to a large degree in stationary phase, the differential Pox- and Lox-generated H
2
O
2
can be attributed to differential gene expression and substrate availability. Interestingly, inactivation of
pox
causes a dramatic reduction in H
2
O
2
production from lactate, suggesting a synergistic action of the two oxidases in converting lactate into H
2
O
2
. In an
in vitro
two-species biofilm experiment, the
pox
mutant of
S. oligofermentans
failed to inhibit
S. mutans
even though
lox
was active. In summary,
S. oligofermentans
develops a Pox-Lox synergy strategy to maximize its H
2
O
2
formation so as to win the interspecies competition.
Phylogenetic Clustering of Soil Microbial Communities by 16S rRNA but Not 16S rRNA Genes
Authors: DeAngelis Kristen M. , Firestone Mary K. 
Published: January 2012

ABSTRACT
We evaluated phylogenetic clustering of bacterial and archaeal communities from redox-dynamic subtropical forest soils that were defined by 16S rRNA and rRNA gene sequences. We observed significant clustering for the RNA-based communities but not the DNA-based communities, as well as increasing clustering over time of the highly active taxa detected by only rRNA.
The Histone-Like Nucleoid Structuring Protein (H-NS) Is a Repressor of Vibrio cholerae Exopolysaccharide Biosynthesis (
vps
) Genes
Authors: Wang Hongxia , Ayala Julio C. , Silva Anisia J. , Benitez Jorge A. 
Published: January 2012

ABSTRACT

The capacity of
Vibrio cholerae
to form biofilms has been shown to enhance its survival in the aquatic environment and play important roles in pathogenesis and disease transmission. In this study, we demonstrated that the histone-like nucleoid structuring protein is a repressor of exopolysaccharide (
vps
) biosynthesis genes and biofilm formation.
Ring-Cleaving Dioxygenases with a Cupin Fold
Authors: Fetzner Susanne 
Published: January 2012

ABSTRACTRing-cleaving dioxygenases catalyze key reactions in the aerobic microbial degradation of aromatic compounds. Many pathways converge to catecholic intermediates, which are subject toorthoormetacleavage by intradiol or extradiol dioxygenases, respectively. However, a number of degradation pathways proceed via noncatecholic hydroxy-substituted aromatic carboxylic acids like gentisate, salicylate, 1-hydroxy-2-naphthoate, or aminohydroxybenzoates. The ring-cleaving dioxygenases active toward these compounds belong to the cupin superfamily, which is characterized by a six-stranded β-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. Most cupin-type ring cleavage dioxygenases use an FeIIcenter for catalysis, and the proposed mechanism is very similar to that of the canonical (type I) extradiol dioxygenases. The metal ion is presumed to act as an electron conduit for single electron transfer from the metal-bound substrate anion to O2, resulting in activation of both substrates to radical species. The family of cupin-type dioxygenases also involves quercetinase (flavonol 2,4-dioxygenase), which opens up two C-C bonds of the heterocyclic ring of quercetin, a wide-spread plant flavonol. Remarkably, bacterial quercetinases are capable of using different divalent metal ions for catalysis, suggesting that the redox properties of the metal are relatively unimportant for the catalytic reaction. The major role of the active-site metal ion could be to correctly position the substrate and to stabilize transition states and intermediates rather than to mediate electron transfer. The tentative hypothesis that quercetinase catalysis involves direct electron transfer from metal-bound flavonolate to O2is supported by model chemistry.
Biology and Genome Sequence of Streptococcus mutans Phage M102AD
Authors: Delisle Allan L. , Guo Ming , Chalmers Natalia I. , Barcak Gerard J. , Rousseau Geneviève M. , Moineau Sylvain 
Published: January 2012

ABSTRACT

M102AD is the new designation for a
Streptococcus mutans
phage described in 1993 as phage M102. This change was necessitated by the genome analysis of another
S. mutans
phage named M102, which revealed differences from the genome sequence reported here. Additional host range analyses confirmed that
S. mutans
phage M102AD infects only a few serotype c strains. Phage M102AD adsorbed very slowly to its host, and it cannot adsorb to serotype e and f strains of
S. mutans
. M102AD adsorption was blocked by c-specific antiserum. Phage M102AD also adsorbed equally well to heat-treated and trypsin-treated cells, suggesting carbohydrate receptors. Saliva and polysaccharide production did not inhibit plaque formation. The genome of this siphophage consisted of a linear, double-stranded, 30,664-bp DNA molecule, with a GC content of 39.6%. Analysis of the genome extremities indicated the presence of a 3′-overhang
cos
site that was 11 nucleotides long. Bioinformatic analyses identified 40 open reading frames, all in the same orientation. No lysogeny-related genes were found, indicating that phage M102AD is strictly virulent. No obvious virulence factor gene candidates were found. Twelve proteins were identified in the virion structure by mass spectrometry. Comparative genomic analysis revealed a close relationship between
S. mutans
phages M102AD and M102 as well as with
Streptococcus thermophilus
phages. This study also highlights the importance of conducting research with biological materials obtained from recognized microbial collections.
Different Virucidal Activities of Hyperbranched Quaternary Ammonium Coatings on Poliovirus and Influenza Virus
Authors: Tuladhar Era , de Koning Martijn C. , Fundeanu Irina , Beumer Rijkelt , Duizer Erwin 
Published: January 2012

ABSTRACT
Virucidal activity of immobilized quaternary ammonium compounds (IQACs) coated onto glass and plastic surfaces was tested against enveloped influenza A (H1N1) virus and nonenveloped poliovirus Sabin1. The IQACs tested were virucidal against the influenza virus within 2 min, but no virucidal effect against poliovirus was found in 6 h.
Tumor Necrosis Factor Alpha Modulates the Dynamics of the Plasminogen-Mediated Early Interaction between Bifidobacterium animalis subsp.
lactis
and Human Enterocytes
Authors: Centanni Manuela , Bergmann Simone , Turroni Silvia , Hammerschmidt Sven , Chhatwal Gursharan Singh , Brigidi Patrizia , Candela Marco 
Published: January 2012

ABSTRACT

The capacity to intervene with the host plasminogen system has recently been considered an important component in the interaction process between
Bifidobacterium animalis
subsp.
lactis
and the human host. However, its significance in the bifidobacterial microecology within the human gastrointestinal tract is still an open question. Here we demonstrate that human plasminogen favors the
B. animalis
subsp.
lactis
BI07 adhesion to HT29 cells. Prompting the HT29 cell capacity to activate plasminogen, tumor necrosis factor alpha (TNF-α) modulated the plasminogen-mediated bacterium-enterocyte interaction, reducing the bacterial adhesion to the enterocytes and enhancing migration to the luminal compartment.
Analysis of the Functions of Recombination-Related Genes in the Generation of Large Chromosomal Deletions by Loop-Out Recombination in Aspergillus oryzae
Authors: Takahashi Tadashi , Ogawa Masahiro , Koyama Yasuji 
Published: January 2012

ABSTRACT

Loop-out-type recombination is a type of intrachromosomal recombination followed by the excision of a chromosomal region. The detailed mechanism underlying this recombination and the genes involved in loop-out recombination remain unknown. In the present study, we investigated the functions of
ku70
,
ligD
,
rad52
,
rad54
, and
rdh54
in the construction of large chromosomal deletions via loop-out recombination and the effect of the position of the targeted chromosomal region on the efficiency of loop-out recombination in
Aspergillus oryzae
. The efficiency of generation of large chromosomal deletions in the near-telomeric region of chromosome 3, including the aflatoxin gene cluster, was compared with that in the near-centromeric region of chromosome 8, including the tannase gene. In the Δ
ku70
and Δ
ku70-rdh54
strains, only precise loop-out recombination occurred in the near-telomeric region. In contrast, in the Δ
ligD
, Δ
ku70-rad52
, and Δ
ku70-rad54
strains, unintended chromosomal deletions by illegitimate loop-out recombination occurred in the near-telomeric region. In addition, large chromosomal deletions via loop-out recombination were efficiently achieved in the near-telomeric region, but barely achieved in the near-centromeric region, in the Δ
ku70
strain. Induction of DNA double-strand breaks by I-SceI endonuclease facilitated large chromosomal deletions in the near-centromeric region. These results indicate that
ligD
,
rad52
, and
rad54
play a role in the generation of large chromosomal deletions via precise loop-out-type recombination in the near-telomeric region and that loop-out recombination between distant sites is restricted in the near-centromeric region by chromosomal structure.
Mitochondrial Sorting and Assembly Machinery Subunit Sam37 in Candida albicans: Insight into the Roles of Mitochondria in Fitness, Cell Wall Integrity, and Virulence
Authors: Qu Yue , Jelicic Branka , Pettolino Filomena , Perry Andrew , Lo Tricia L. , Hewitt Victoria L. , Bantun Farkad , Beilharz Traude H. , Peleg Anton Y. , Lithgow Trevor , Djordjevic Julianne T. , Traven Ana 
Published: January 2012

ABSTRACT

Recent studies indicate that mitochondrial functions impinge on cell wall integrity, drug tolerance, and virulence of human fungal pathogens. However, the mechanistic aspects of these processes are poorly understood. We focused on the mitochondrial outer membrane SAM (
S
orting and
A
ssembly
M
achinery) complex subunit Sam37 in
Candida albicans
. Inactivation of
SAM37
in
C. albicans
leads to a large reduction in fitness, a phenotype not conserved with the model yeast
Saccharomyces cerevisiae
. Our data indicate that slow growth of the
sam37ΔΔ
mutant results from mitochondrial DNA loss, a new function for Sam37 in
C. albicans
, and from reduced activity of the essential SAM complex subunit Sam35. The
sam37ΔΔ
mutant was hypersensitive to drugs that target the cell wall and displayed altered cell wall structure, supporting a role for Sam37 in cell wall integrity in
C. albicans
. The sensitivity of the mutant to membrane-targeting antifungals was not significantly altered. The
sam37ΔΔ
mutant was avirulent in the mouse model, and bioinformatics showed that the fungal Sam37 proteins are distant from their animal counterparts and could thus represent potential drug targets. Our study provides the first direct evidence for a link between mitochondrial function and cell wall integrity in
C. albicans
and is further relevant for understanding mitochondrial function in fitness, antifungal drug tolerance, and virulence of this major pathogen. Beyond the relevance to fungal pathogenesis, this work also provides new insight into the mitochondrial and cellular roles of the SAM complex in fungi.
Characterization of the Unusual Bidirectional
ves
Promoters Driving VESA1 Expression and Associated with Antigenic Variation in Babesia bovis
Authors: Wang Xinyi , Xiao Yu-Ping , Bouchut Anne , Al-Khedery Basima , Wang Hongbin , Allred David R. 
Published: January 2012

ABSTRACT

Rapid clonal antigenic variation in
Babesia bovis
involves the
v
ariant
e
rythrocyte
s
urface
a
ntigen-1 (VESA1) protein expressed on the infected-erythrocyte surface. Because of the significance of this heterodimeric protein for demonstrated mechanisms of parasite survival and virulence, there is a need to understand how expression of the
ves
multigene family encoding this protein is controlled. As an initial step toward this goal, we present here initial characterization of the
ves
promoter driving transcription of VESA1a and -1b subunits. A series of transfection constructs containing various sequence elements from the
in vivo
locus of active
ves
transcription (LAT) were used to drive expression of the firefly luciferase gene in a dual luciferase-normalized assay. The results of this approach reveal the presence of two bidirectional promoter activities within the 434-bp intergenic region (IGr), influenced by putative regulatory sequences embedded within the flanking
ves
1α and
ves
1β genes. Repressor-like effects on the apposing gene were observed for intron 1 of both
ves
1α and
ves
1β. This effect is apparently not dependent upon intronic promoter activity and acts only in
cis
. The expression of genes within the
ves
family is likely modulated by local elements embedded within
ves
coding sequences outside the intergenic promoter region in concert with chromatin modifications. These results provide a framework to help us begin to understand gene regulation during antigenic variation in
B. bovis
.
Fur-Mediated Activation of Gene Transcription in the Human Pathogen Neisseria gonorrhoeae
Authors: Yu Chunxiao , Genco Caroline Attardo 
Published: January 2012

ABSTRACT

It is well established that the
f
erric
u
ptake
r
egulatory protein (Fur) functions as a transcriptional repressor in diverse microorganisms. Recent studies demonstrated that Fur also functions as a transcriptional activator. In this study we defined Fur-mediated activation of gene transcription in the sexually transmitted disease pathogen
Neisseria gonorrhoeae
. Analysis of 37 genes which were previously determined to be iron induced and which contained putative Fur boxes revealed that only 30 of these genes exhibited reduced transcription in a gonococcal
fur
mutant strain. Fur-mediated activation was established by examining binding of Fur to the putative promoter regions of 16 Fur-activated genes with variable binding affinities observed. Only ∼50% of the newly identified Fur-regulated genes bound Fur
in vitro
, suggesting that additional regulatory circuits exist which may function through a Fur-mediated indirect mechanism. The gonococcal Fur-activated genes displayed variable transcription patterns in a
fur
mutant strain, which correlated with the position of the Fur box in each (promoter) region. These results suggest that Fur-mediated direct transcriptional activation is fulfilled by multiple mechanisms involving either competing with a repressor or recruiting RNA polymerase. Collectively, our studies have established that gonococcal Fur functions as an activator of gene transcription through both direct and indirect mechanisms.
Transcriptional and Posttranscriptional Events Control Copper-Responsive Expression of a Rhodobacter capsulatus Multicopper Oxidase
Authors: Rademacher Corinna , Moser Roman , Lackmann Jan-Wilm , Klinkert Birgit , Narberhaus Franz , Masepohl Bernd 
Published: January 2012

ABSTRACT

The copper-regulated
Rhodobacter capsulatus cutO
(multicopper oxidase) gene confers copper tolerance and is carried in the tricistronic
orf635
-
cutO
-
cutR
operon. Transcription of
cutO
strictly depends on the promoter upstream of
orf635
, as demonstrated by
lacZ
reporter fusions to nested promoter fragments. Remarkably,
orf635
expression was not affected by copper availability, whereas
cutO
and
cutR
were expressed only in the presence of copper. Differential regulation was abolished by site-directed mutations within the
orf635
-
cutO
intergenic region, suggesting that this region encodes a copper-responsive mRNA element. Bioinformatic predictions and RNA structure probing experiments revealed an intergenic stem-loop structure as the candidate mRNA element. This is the first posttranscriptional copper response mechanism reported in bacteria.
Inactivation of Haemophilus influenzae Lipopolysaccharide Biosynthesis Genes Interferes with Outer Membrane Localization of the Hap Autotransporter
Authors: Spahich Nicole A. , Hood Derek W. , Moxon E. Richard , St. Geme Joseph W. 
Published: January 2012

ABSTRACT

Nontypeable
Haemophilus influenzae
is a major cause of localized respiratory tract disease and initiates infection by colonizing the nasopharynx. Colonization requires adherence to host epithelial cells, which is mediated by surface proteins such as the Hap adhesin. In this study, we identified a relationship between Hap levels in the outer membrane and lipopolysaccharide (LPS) biosynthesis enzymes. We found that mutation of the
rfaF
,
pgmB
,
lgtC
,
kfiC
,
orfE
,
rfbP
,
lsgB
, or
lsgD
genes, which are involved in the synthesis of the LPS oligosaccharide core in
H. influenzae
strain Rd/HapS243A, resulted in loss of Hap in the bacterial outer membrane and a decrease in
hap
transcript levels. In contrast, the same mutations had no effect on outer membrane localization of
H. influenzae
P5 or IgA1 protease or levels of
p5
or
iga1
transcripts, suggesting a Hap-specific effect. Elimination of the HtrA periplasmic protease resulted in a return of Hap to the outer membrane and restoration of
hap
transcript levels. Consistently, in
lgtC
phase-off bacteria, Hap was absent from the outer membrane, and
hap
transcript levels were reduced. Hap localization and
hap
transcript levels were not related to LPS size but to the functions of the LPS biosynthesis enzymes themselves. We speculate that the lack of certain LPS biosynthesis enzymes causes Hap to mislocalize and accumulate in the periplasm, where it is degraded by HtrA. This degradation then leads to a decrease in
hap
transcript levels. Together, these data highlight a novel interplay between Hap and LPS biosynthesis that can influence
H. influenzae
interactions with the host.
Transcriptional and Metabolomic Consequences of
luxS
Inactivation Reveal a Metabolic Rather than Quorum-Sensing Role for LuxS in Lactobacillus reuteri 100-23
Authors: Wilson Charlotte M. , Aggio Raphael B. M. , O'Toole Paul W. , Villas-Boas Silas , Tannock Gerald W. 
Published: January 2012

ABSTRACT

Autoinducer-2 (AI-2)-mediated quorum sensing has been extensively studied in relation to the regulation of microbial behavior. There are, however, two potential roles for the AI-2 synthase (LuxS). The first is in the production of AI-2 and the second is as an enzyme in the activated methyl cycle, where it catalyzes the conversion of S-ribosylhomocysteine to homocysteine. The by-product of the reaction catalyzed by LuxS is (
S
)-4,5-dihydroxy-2,3-pentanedione, which spontaneously forms the furanones known collectively as AI-2. The mammalian gut contains a complex collection of bacterial species so a method of interspecies communication might influence community structure and function.
Lactobacillus reuteri
100-23 is an autochthonous inhabitant of the rodent forestomach, where it adheres to the nonsecretory epithelium, forming a biofilm. Microarray comparisons of gene expression profiles of the
L. reuteri
100-23 wild type and a
luxS
mutant under different culture conditions revealed altered transcription of genes encoding proteins associated with cysteine biosynthesis/oxidative stress response, urease activity, and sortase-dependent proteins. Metabolomic analysis showed that the
luxS
mutation affected cellular levels of fermentation products, fatty acids and amino acids. Cell density-dependent changes (log phase versus stationary phase growth) in gene transcription were not detected, indicating that AI-2 was unlikely to be involved in gene regulation mediated by quorum sensing in
L. reuteri
100-23.