bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inositol Catabolism, a Key Pathway in
Sinorhizobium meliloti
for Competitive Host Nodulation
Authors: Kohler Petra R. A. , Zheng Jasmine Y. , Schoffers Elke , Rossbach Silvia 
Published: October 2010

ABSTRACT

The nitrogen-fixing symbiont of alfalfa,
Sinorhizobium meliloti
, is able to use
myo
-inositol as the sole carbon source. Putative inositol catabolism genes (
iolA
and
iolRCDEB
) have been identified in the
S. meliloti
genome based on their similarities with the
Bacillus subtilis iol
genes. In this study, functional mutational analysis revealed that the
iolA
and
iolCDEB
genes are required for growth not only with the
myo
-isomer but also for growth with
scyllo
- and
d
-
chiro
-inositol as the sole carbon source. An additional, hypothetical dehydrogenase of the IdhA/MocA/GFO family encoded by the
smc01163
gene was found to be essential for growth with
scyllo
-inositol, whereas the
idhA
-encoded
myo
-inositol dehydrogenase was responsible for the oxidation of
d
-
chiro
-inositol. The putative regulatory
iolR
gene, located upstream of
iolCDEB
, encodes a repressor of the
iol
genes, negatively regulating the activity of the
myo
- and the
scyllo
-inositol dehydrogenases. Mutants with insertions in the
iolA
,
smc01163
, and individual
iolRCDE
genes could not compete against the wild type in a nodule occupancy assay on alfalfa plants. Thus, a functional inositol catabolic pathway and its proper regulation are important nutritional or signaling factors in the
S. meliloti
-alfalfa symbiosis.
Promising Immunomodulatory Effects of Selected Strains of Dairy Propionibacteria as Evidenced
In Vitro
and
In Vivo
Authors: Foligné Benoît , Deutsch Stéphanie-Marie , Breton Jérôme , Cousin Fabien J. , Dewulf Joëlle , Samson Michel , Pot Bruno , Jan Gwénaël 
Published: October 2010

ABSTRACT

Immunomodulatory properties of 10 dairy propionibacteria, analyzed on human peripheral blood mononuclear cells (PBMCs), revealed a highly strain-dependent induction of anti-inflammatory cytokine interleukin 10 (IL-10). Two selected strains of
Propionibacterium freudenreichii
showed a protective effect against two models of colitis in mice, suggesting a probiotic potential predicted by immune-based selection criteria for these cheese starter bacteria.
Abundance and Diversity of Archaeal Ammonia Oxidizers in a Coastal Groundwater System
Authors: Rogers Daniel R. , Casciotti Karen L. 
Published: October 2010

ABSTRACT

Nitrification, the microbially catalyzed oxidation of ammonia to nitrate, is a key process in the nitrogen cycle. Archaea have been implicated in the first part of the nitrification pathway (oxidation of ammonia to nitrite), but the ecology and physiology of these organisms remain largely unknown. This work describes two different populations of sediment-associated ammonia-oxidizing archaea (AOA) in a coastal groundwater system in Cape Cod, MA. Sequence analysis of the ammonia monooxygenase subunit A gene (
amoA
) shows that one population of putative AOA inhabits the upper meter of the sediment, where they may experience frequent ventilation, with tidally driven overtopping and infiltration of bay water supplying dissolved oxygen, ammonium, and perhaps organic carbon. A genetically distinct population occurs deeper in the sediment, in a mixing zone between a nitrate- and oxygen-rich freshwater zone and a reduced, ammonium-bearing saltwater wedge. Both of these AOA populations are coincident with increases in the abundance of group I crenarchaeota 16S rRNA gene copies.
Genetic Characterization of Plasmid-Associated Benzalkonium Chloride Resistance Determinants in a
Listeria monocytogenes
Strain from the 1998-1999 Outbreak
Authors: Elhanafi Driss , Dutta Vikrant , Kathariou Sophia 
Published: October 2010

ABSTRACT

Quaternary ammonium compounds such as benzalkonium chloride (BC) are widely used as disinfectants in both food processing and medical environments. BC-resistant strains of
Listeria monocytogenes
have been implicated in multistate outbreaks of listeriosis and have been frequently isolated from food processing plants. However, the genetic basis for BC resistance in
L. monocytogenes
remains poorly understood. In this study, we have characterized a plasmid (pLM80)-associated BC resistance cassette in
L. monocytogenes
H7550, a strain implicated in the 1998-1999 multistate outbreak involving contaminated hot dogs. The BC resistance cassette (
bcrABC
) restored resistance to BC (MIC, 40 μg/ml) in a plasmid-cured derivative of H7550. All three genes of the cassette were essential for imparting BC resistance. The transcription of H7550 BC resistance genes was increased under sublethal (10 μg/ml) BC exposure and was higher at reduced temperatures (4, 8, or 25°C) than at 37°C. The level of transcription was higher at 10 μg/ml than at 20 or 40 μg/ml.
In silico
analysis suggested that the BC resistance cassette was harbored by an IS
1216
composite transposon along with other genes whose functions are yet to be determined. The findings from this study will further our understanding of the adaptations of this organism to disinfectants such as BC and may contribute to the elucidation of possible BC resistance dissemination in
L. monocytogenes
.
PCR Inhibitor Levels in Concentrates of Biosolid Samples Predicted by a New Method Based on Excitation-Emission Matrix Spectroscopy
Authors: Rock Channah , Alum Absar , Abbaszadegan Morteza 
Published: October 2010

ABSTRACT
Biosolids contain a wide variety of organic contaminants that are known for their ability to inhibit PCR. During sample processing, these contaminants are coconcentrated with microorganisms. Elevated concentrations of these compounds in concentrates render samples unsuitable for molecular applications. Glycine-based elution and recovery methods have been shown to generate samples with fewer PCR inhibitory compounds than the current U.S. EPA-recommended method for pathogen recovery from biosolids. Even with glycine-based methods, PCR inhibitors still persist in concentrations that may interfere with nucleic acid amplification. This results in considerable loss of time and resources and increases the probability of false negatives. A method to estimate the degree of inhibition prior to application of molecular methods is desirable. Here we report fluorescence excitation-emission matrix (EEM) profiling as a tool for predicting levels of molecular inhibition in sample concentrates of biosolids.
The Sin3p PAH Domains Provide Separate Functions Repressing Meiotic Gene Transcription in Saccharomyces cerevisiae
Authors: Mallory Michael J. , Law Michael J. , Buckingham Lela E. , Strich Randy 
Published: October 2010

ABSTRACT
Meiotic genes in budding yeast are repressed during vegetative growth but are transiently induced during specific stages of meiosis. Sin3p represses the early meiotic gene (EMG) by bridging the DNA binding protein Ume6p to the histone deacetylase Rpd3p. Sin3p contains four paired amphipathic helix (PAH) domains, one of which (PAH3) is required for repressing several genes expressed during mitotic cell division. This report examines the roles of the PAH domains in mediating EMG repression during mitotic cell division and following meiotic induction. PAH2 and PAH3 are required for mitotic EMG repression, while electrophoretic mobility shift assays indicate that only PAH2 is required for stable Ume6p-promoter interaction. Unlike mitotic repression, reestablishing EMG repression following transient meiotic induction requires PAH3 and PAH4. In addition, the role of Sin3p in reestablishing repression is expanded to include additional loci that it does not control during vegetative growth. These findings indicate that mitotic and postinduction EMG repressions are mediated by two separate systems that utilize different Sin3p domains.
Mapping of theNeisseria meningitidisNadA Cell-Binding Site: Relevance of Predicted α-Helices in the NH2-Terminal and Dimeric Coiled-Coil Regions
Authors: Tavano Regina , Capecchi Barbara , Montanari Paolo , Franzoso Susanna , Marin Oriano , Sztukowska Maryta , Cecchini Paola , Segat Daniela , Scarselli Maria , Aricò Beatrice , Papini Emanuele 
Published: October 2010

ABSTRACTNadA is a trimeric autotransporter protein ofNeisseria meningitidisbelonging to the group of oligomeric coiled-coil adhesins. It is implicated in the colonization of the human upper respiratory tract by hypervirulent serogroup BN. meningitidisstrains and is part of a multiantigen anti-serogroup B vaccine. Structure prediction indicates that NadA is made by a COOH-terminal membrane anchor (also necessary for autotranslocation to the bacterial surface), an intermediate elongated coiled-coil-rich stalk, and an NH2-terminal region involved in cell interaction. Electron microscopy analysis and structure prediction suggest that the apical region of NadA forms a compact and globular domain. Deletion studies proved that the NH2-terminal sequence (residues 24 to 87) is necessary for cell adhesion. In this study, to better define the NadA cell binding site, we exploited (i) a panel of NadA mutants lacking sequences along the coiled-coil stalk and (ii) several oligoclonal rabbit antibodies, and their relative Fab fragments, directed to linear epitopes distributed along the NadA ectodomain. We identified two critical regions for the NadA-cell receptor interaction with Chang cells: the NH2globular head domain and the NH2dimeric intrachain coiled-coil α-helices stemming from the stalk. This raises the importance of different modules within the predicted NadA structure. The identification of linear epitopes involved in receptor binding that are able to induce interfering antibodies reinforces the importance of NadA as a vaccine antigen.
Detrimental Effects of Hypoxia-Specific Expression of Uracil DNA Glycosylase (Ung) in
Mycobacterium smegmatis
Authors: Kurthkoti Krishna , Varshney Umesh 
Published: October 2010

ABSTRACT

Mycobacterium tuberculosis
is known to reside latently in a significant fraction of the human population. Although the bacterium possesses an aerobic mode of metabolism, it adapts to persistence under hypoxic conditions such as those encountered in granulomas. While in mammalian systems hypoxia is a recognized DNA-damaging stress, aspects of DNA repair in mycobacteria under such conditions have not been studied. We subjected
M
ycobacterium
smegmatis
, a model organism, to the Wayne's protocol of hypoxia. Analysis of the mRNA of a key DNA repair enzyme, uracil DNA glycosylase (Ung), by real-time reverse transcriptase PCR (RT-PCR) revealed its downregulation during hypoxia. However, within an hour of recovery of the culture under normal oxygen levels, the Ung mRNA was restored. Analysis of Ung by immunoblotting and enzyme assays supported the RNA analysis results. To understand its physiological significance, we misexpressed Ung in
M. smegmatis
by using a hypoxia-responsive promoter of
narK2
from
M. tuberculosis
. Although the misexpression of Ung during hypoxia decreased C-to-T mutations, it compromised bacterial survival upon recovery at normal oxygen levels. RT-PCR analysis of other base excision repair gene transcripts (UdgB and Fpg) suggested that these DNA repair functions also share with Ung the phenomenon of downregulation during hypoxia and recovery with return to normal oxygen conditions. We discuss the potential utility of this phenomenon in developing attenuated strains of mycobacteria.
Proximity of the Start Codon to a Leaderless mRNA's 5′ Terminus Is a Strong Positive Determinant of Ribosome Binding and Expression in
Escherichia coli
Authors: Krishnan Karthik M. , Van Etten William J. , Janssen Gary R. 
Published: October 2010

ABSTRACT

An AUG start codon is an important determinant of ribosome binding and expression of leaderless mRNAs in
Escherichia coli
. Using reporter constructs encoding mRNAs where the AUG start codon is preceded by untranslated leaders of various length and sequence, we find that close proximity of the start codon to the 5′ terminus and the leader sequence are strong determinants of both ribosome binding and expression.
C-Terminal Domain Residues Important for Secretion and Attachment of RgpB in
Porphyromonas gingivalis
Authors: Slakeski Nada , Seers Christine A. , Ng Kaiting , Moore Caroline , Cleal Steven M. , Veith Paul D. , Lo Alvin W. , Reynolds Eric C. 
Published: October 2010

ABSTRACT

Porphyromonas gingivalis
, a periodontal pathogen, expresses a group of surface proteins with a common C-terminal domain (CTD) that are exported by a novel secretion system to the surface, where they are covalently attached. Using RgpB as a model CTD protein, we have produced a series of site-directed mutations in the CTD sequence at conserved residues and at residues that may be modified and, hence, surface attached. The mutant RgpB proteins were expressed in a
P. gingivalis
host lacking functional RgpB and RgpA Arg-specific proteases. The RgpB mutants produced were Y674F, Y674F Y718F, T675Q S679Q T682Q T684Q, T693Q, F695A, D696A, N698A, G699P, G716P, T724Q, T728Q T730Q, and K732Q and a protein with a deletion of residues 692 to 702 (Δ692-702). The mutants were characterized for cell-associated Arg-specific protease activity and for cellular distribution using anti-Rgp antibodies and Western blotting of culture fractions. All the mutants exhibited cell-associated Arg-specific activity similar to that of the positive control except for the D696A and Δ692-702 mutants. For all mutants, except D696A and Δ692-702, the RgpB proteins were found modified and attached to the cell surface, which was the same profile found in the positive-control strain. Only trace amounts of the precursor form of the Δ692-702 mutant were detected in the outer membrane, with none detected in the periplasm or culture fluid although cell transcript levels were normal. The results suggest that residues 692 to 702 of the CTD, in particular, residue D696, have an important role in the attachment of RgpB at the cell surface and that without attachment secretion does not occur.
Functional Analysis of Molybdopterin Biosynthesis in Mycobacteria Identifies a Fused Molybdopterin Synthase in
Mycobacterium tuberculosis
Authors: Williams Monique J. , Kana Bavesh D. , Mizrahi Valerie 
Published: October 2010

ABSTRACT

Most mycobacterial species possess a full complement of genes for the biosynthesis of molybdenum cofactor (MoCo). However, a distinguishing feature of members of the
Mycobacterium tuberculosis
complex is their possession of multiple homologs associated with the first two steps of the MoCo biosynthetic pathway. A mutant of
M. tuberculosis
lacking the
moaA1-moaD1
gene cluster and a derivative in which
moaD2
was also deleted were significantly impaired for growth in media containing nitrate as a sole nitrogen source, indicating a reduced availability of MoCo to support the assimilatory function of the MoCo-dependent nitrate reductase, NarGHI. However, the double mutant displayed residual respiratory nitrate reductase activity, suggesting that it retains the capacity to produce MoCo. The
M. tuberculosis moaD
and
moaE
homologs were further analyzed by expressing these genes in mutant strains of
M. smegmatis
that lacked one or both of the sole molybdopterin (MPT) synthase-encoding genes,
moaD2
and
moaE2
, and were unable to grow on nitrate, presumably as a result of the loss of MoCo-dependent nitrate assimilatory activity. Expression of
M. tuberculosis moaD2
in the
M. smegmatis moaD2
mutant and of
M. tuberculosis moaE1
or
moaE2
in the
M. smegmatis moaE2
mutant restored nitrate assimilation, confirming the functionality of these genes in MPT synthesis. Expression of
M. tuberculosis moaX
also restored MoCo biosynthesis in
M. smegmatis
mutants lacking
moaD2
,
moaE2
, or both, thus identifying MoaX as a fused MPT synthase. By implicating multiple synthase-encoding homologs in MoCo biosynthesis, these results suggest that important cellular functions may be served by their expansion in
M. tuberculosis
.
Plantazolicin, a Novel Microcin B17/Streptolysin S-Like Natural Product from
Bacillus amyloliquefaciens
FZB42
Authors: Scholz Romy , Molohon Katie J. , Nachtigall Jonny , Vater Joachim , Markley Andrew L. , Süssmuth Roderich D. , Mitchell Douglas A. , Borriss Rainer 
Published: October 2010

ABSTRACT

Here we report on a novel

t

hiazole/

o

xazole-

m

odified

m

icrocin (TOMM) from
Bacillus amyloliquefaciens
FZB42, a Gram-positive soil bacterium. This organism is well known for stimulating plant growth and biosynthesizing complex small molecules that suppress the growth of bacterial and fungal plant pathogens. Like microcin B17 and streptolysin S, the TOMM from
B. amyloliquefaciens
FZB42 undergoes extensive posttranslational modification to become a bioactive natural product. Our data show that the modified peptide bears a molecular mass of 1,335 Da and displays antibacterial activity toward closely related Gram-positive bacteria. A cluster of 12 genes that covers ∼10 kb is essential for the production, modification, export, and self-immunity of this natural product. We have named this compound plantazolicin (PZN), based on the association of several producing organisms with plants and the incorporation of azole heterocycles, which derive from Cys, Ser, and Thr residues of the precursor peptide.
Acis-Encoded Antisense Small RNA Regulated by the HP0165-HP0166 Two-Component System Controls Expression ofureBinHelicobacter pylori
Authors: Wen Yi , Feng Jing , Scott David R. , Marcus Elizabeth A. , Sachs George 
Published: October 2010

ABSTRACTExpression of urease is essential for gastric colonization byHelicobacter pylori.The increased level of urease in gastric acidity is due, in part, to acid activation of the two-component system (TCS) consisting of the membrane sensor HP0165 and its response regulator, HP0166, which regulates transcription of the seven genes of the urease gene cluster. We now find that there are two majorureABtranscripts: a 2.7-kb full-lengthureABtranscript and a 1.4-kb truncated transcript lacking 3′ureB. Acidic pH (pH 4.5) results in a significant increase in transcription ofureAB, while neutral pH (pH 7.4) increases the truncated 1.4-kb transcript. Northern blot analysis with sense RNA and strand-specific oligonucleotide probes followed by 5′ rapid amplification of cDNA ends detects an antisense small RNA (sRNA) encoded by the 5′ureBnoncoding strand consisting of ∼290 nucleotides (5′ureB-sRNA). Deletion of HP0165 elevates the level of the truncated 1.4-kb transcript along with that of the 5′ureB-sRNA at both pH 7.4 and pH 4.5. Overexpression of 5′ureB-sRNA increases the 1.4-kb transcript, decreases the 2.7-kb transcript, and decreases urease activity. Electrophoretic mobility shift assay shows that unphosphorylated HP0166 binds specifically to the 5′ureB-sRNA promoter. The ability of the HP0165-HP0166 TCS to both increase and decreaseureBexpression at low and high pHs, respectively, facilitates gastric habitation and colonization over the wide range of intragastric pHs experienced by the organism.
The Rcs Signal Transduction Pathway Is Triggered by Enterobacterial Common Antigen Structure Alterations inSerratia marcescens
Authors: Castelli María E. , Véscovi Eleonora García 
Published: October 2010

ABSTRACTThe enterobacterial common antigen (ECA) is a highly conserved exopolysaccharide in Gram-negative bacteria whose role remains largely uncharacterized. In a previous work, we have demonstrated that disrupting the integrity of the ECA biosynthetic pathway imposed severe deficiencies to theSerratia marcescensmotile (swimming and swarming) capacity. In this work, we show that alterations in the ECA structure activate the Rcs phosphorelay, which results in the repression of the flagellar biogenesis regulatory cascade. In addition, a detailed analysis ofweccluster mutant strains, which provoke the disruption of the ECA biosynthesis at different levels of the pathway, suggests that the absence of the periplasmic ECA cyclic structure could constitute a potential signal detected by the RcsF-RcsCDB phosphorelay. We also identify SMA1167 as a member of theS. marcescensRcs regulon and show that high osmolarity induces Rcs activity in this bacterium. These results provide a new perspective from which to understand the phylogenetic conservation of ECA among enterobacteria and the basis for the virulence attenuation detected inwecmutant strains in other pathogenic bacteria.
The
Burkholderia cenocepacia
LysR-Type Transcriptional Regulator ShvR Influences Expression of Quorum-Sensing, Protease, Type II Secretion, and
afc
Genes
Authors: O'Grady Eoin P. , Nguyen David T. , Weisskopf Laure , Eberl Leo , Sokol Pamela A. 
Published: October 2010

ABSTRACT

Burkholderia cenocepacia
is a significant opportunistic pathogen in individuals with cystic fibrosis. ShvR, a LysR-type transcriptional regulator, has previously been shown to influence colony morphology, biofilm formation, virulence in plant and animal infection models, and some quorum-sensing-dependent phenotypes. In the present study, it was shown that ShvR negatively regulates its own expression, as is typical for LysR-type regulators. The production of quorum-sensing signal molecules was detected earlier in growth in the
shvR
mutant than in the wild type, and ShvR repressed expression of the quorum-sensing regulatory genes
cepIR
and
cciIR
. Microarray analysis and transcriptional fusions revealed that ShvR regulated over 1,000 genes, including the zinc metalloproteases
zmpA
and
zmpB
. The
shvR
mutant displayed increased gene expression of the type II secretion system and significantly increased protease and lipase activities. Both ShvR and CepR influence expression of a 24-kb genomic region adjacent to
shvR
that includes the
afcA
and
afcC
operons, required for the production of an antifungal agent; however, the reduction in expression was substantially greater in the
shvR
mutant than in the
cepR
mutant. Only the
shvR
mutation resulted in reduced antifungal activity against
Rhizoctonia solani.
ShvR, but not CepR, was shown to directly regulate expression of the
afcA
and
afcC
promoters. In summary, ShvR was determined to have a significant influence on the expression of quorum-sensing, protease, lipase, type II secretion, and
afc
genes.
In Vitro
Studies of Peptidoglycan Binding and Hydrolysis by the
Bacillus anthracis
Germination-Specific Lytic Enzyme SleB
Authors: Heffron Jared D. , Sherry Nora , Popham David L. 
Published: October 2010

ABSTRACT

The
Bacillus anthracis
endospore loses resistance properties during germination when its cortex peptidoglycan is degraded by germination-specific lytic enzymes (GSLEs). Although this event normally employs several GSLEs for complete cortex removal, the SleB protein alone can facilitate enough cortex hydrolysis to produce vulnerable spores. As a means to better understand its enzymatic function, SleB was overexpressed, purified, and tested
in vitro
for depolymerization of cortex by measurement of optical density loss and the solubilization of substrate. Its ability to bind peptidoglycan was also investigated. SleB functions independently as a lytic transglycosylase on both intact and fragmented cortex. Most of the muropeptide products that SleB generates are large and are potential substrates for other GSLEs present in the spore. Study of a truncated protein revealed that SleB has two domains. The N-terminal domain is required for stable peptidoglycan binding, while the C-terminal domain is the region of peptidoglycan hydrolytic activity. The C-terminal domain also exhibits dependence on cortex containing muramic-δ-lactam in order to carry out hydrolysis. As the conditions and limitations for SleB activity are further elucidated, they will enable the development of treatments that stimulate premature germination of
B. anthracis
spores, greatly simplifying decontamination measures.