bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Lactobacillus fermentum on Beta2 Toxin Production by Clostridium perfringens
Authors: Allaart Janneke G. , van Asten Alphons J. A. M. , Vernooij Johannes C. M. , Gröne Andrea 
Published: May 2011

ABSTRACT

Clostridium perfringens
, although a member of the normal gut flora, is also an important cause of intestinal disease in animals and, to a lesser extent, in humans. Disease is associated with the production of one or more toxins, and little is known about environmental influences on the production of these toxins. One of the health-promoting effects of lactic acid bacteria (LAB) is the establishment and maintenance of a low pH in the intestine since an acidic environment inhibits the growth of many potentially harmful bacteria. Here, the effect of the LAB
Lactobacillus fermentum
on beta2 toxin production by
C. perfringens
is described. Coculturing of
C. perfringens
with
L. fermentum
showed that under
in vitro
conditions,
L. fermentum
was capable of silencing beta2 toxin production by
C. perfringens
without influencing bacterial viability. The reduction in toxin production was shown to be most likely a result of the decline in pH. Quantitative PCR showed that the reduction in beta2 toxin production was due to a decrease in
cpb2
mRNA. These results suggest that in the intestine, the production of beta2 toxin by
C. perfringens
might be regulated by other members of the normal intestinal flora.
Planktonic versus Biofilm Catabolic Communities: Importance of the Biofilm for Species Selection and Pesticide Degradation
Authors: Verhagen Pieter , De Gelder Leen , Hoefman Sven , De Vos Paul , Boon Nico 
Published: May 2011

ABSTRACT
Chloropropham-degrading cultures were obtained from sludge and soil samples by using two different enrichment techniques: (i) planktonic enrichments in shaken liquid medium and (ii) biofilm enrichments on two types of solid matrixes (plastic chips and gravel). Denaturing gradient gel electrophoresis fingerprinting showed that planktonic and biofilm cultures had a different community composition depending on the presence and type of added solid matrix during enrichment. This was reflected in the unique chloropropham-degrading species that could be isolated from the different cultures. Planktonic and biofilm cultures also differed in chloropropham-degrading activity. With biofilm cultures, slower chloropropham removal was observed, but with less build-up of the toxic intermediate 3-chloroaniline. Disruption of the biofilm architecture resulted in degradation characteristics shifting toward those of the free suspensions, indicating the importance of a well-established biofilm structure for good performance. These results show that biofilm-mediated enrichment techniques can be used to select for pollutant-degrading microorganisms that like to proliferate in a biofilm and that cannot be isolated using conventional shaken-liquid procedures. Furthermore, the influence of the biofilm architecture on the pesticide degradation characteristics suggests that for bioaugmentation the use of biofilm catabolic communities might be a proficient alternative to using planktonic freely suspended cultures.
The Polyketide MPBD Initiates the SDF-1 Signaling Cascade That Coordinates Terminal Differentiation in Dictyostelium
Authors: Anjard Christophe , Su Yongxuan , Loomis William F. 
Published: May 2011

ABSTRACT

Dictyostelium
uses a wide array of chemical signals to coordinate differentiation as it switches from a unicellular to a multicellular organism. MPBD, the product of the polyketide synthase encoded by
stlA
, regulates stalk and spore differentiation by rapidly stimulating the release of the phosphopeptide SDF-1. By analyzing specific mutants affected in MPBD or SDF-1 production, we delineated a signal transduction cascade through the membrane receptor CrlA coupled to Gα1, leading to the inhibition of GskA so that the precursor of SDF-1 is released. It is then processed by the extracellular protease of TagB on prestalk cells. SDF-1 apparently acts through the adenylyl cyclase ACG to activate the cyclic AMP (cAMP)-dependent protein kinase A (PKA) and trigger the production of more SDF-1. This signaling cascade shows similarities to the SDF-2 signaling pathway, which acts later to induce rapid spore encapsulation.
Age of Inoculum Strongly Influences Persister Frequency and Can Mask Effects of Mutations Implicated in Altered Persistence
Authors: Luidalepp Hannes , Jõers Arvi , Kaldalu Niilo , Tenson Tanel 
Published: May 2011

ABSTRACT

The majority of cells transferred from stationary-phase culture into fresh medium resume growth quickly, while a few remain in a nongrowing state for longer. These temporarily nonproliferating bacteria are tolerant of several bactericidal antibiotics and constitute a main source of persisters. Several genes have been shown to influence the frequency of persisters in
Escherichia coli
, although the exact mechanism underlying persister formation is unknown. This study demonstrates that the frequency of persisters is highly dependent on the age of the inoculum and the medium in which it has been grown. The
hipA7
mutant had 1,000 times more persisters than the wild type when inocula were sampled from younger stationary-phase cultures. When started after a long stationary phase, the two displayed equal and elevated persister frequencies. The lower persister frequencies of
glpD
,
dnaJ
, and
surA
knockout strains were increased to the level of the wild type when inocula aged. The
mqsR
and
phoU
deletions showed decreased persister levels only when the inocula were from aged cultures, while
sucB
and
ygfA
deletions had decreased persister levels irrespective of the age of the inocula. A dependency on culture conditions underlines the notion that during screening for mutants with altered persister frequencies, the exact experimental details are of great importance. Unlike ampicillin and norfloxacin, which always leave a fraction of bacteria alive, amikacin killed all cells in the growth resumption experiment. It was concluded that the frequency of persisters depends on the conditions of inoculum cultivation, particularly its age, and the choice of antibiotic.
The xnp1 P2-Like Tail Synthesis Gene Cluster Encodes Xenorhabdicin and Is Required for Interspecies Competition
Authors: Morales-Soto Nydia , Forst Steven A. 
Published: May 2011

ABSTRACT

Xenorhabdus nematophila
, the mutualistic bacterium of the nematode
Steinernema carpocapsae
, produces the R-type bacteriocin called xenorhabdicin, which is thought to confer a competitive advantage for growth in the insect host. We have identified a P2-like tail synthesis gene cluster (
xnp1
) that is required for xenorhabdicin production. The
xnp1
genes were expressed constitutively during growth and were induced by mitomycin C. Deletion of either the sheath (
xnpS1
) or fiber (
xnpH1
) genes eliminated xenorhabdicin production. Production of R-type bacteriocins in a host organism had not been shown previously. We show that xenorhabdicin is produced in the hemocoel of insects infected with the wild type but not with the Δ
xnpS1
deletion strain. Xenorhabdicin prepared from the wild-type strain killed the potential competitor
Photorhabdus luminescens
TT01.
P. luminescens
was eliminated during coculture with wild-type
X. nematophila
but not with the Δ
xnpS1
strain. Furthermore,
P. luminescens
inhibited reproduction of
S. carpocapsae
in insect larvae, while coinjection with wild-type
X. nematophila
, but not the Δ
xnpS1
, strain restored normal reproduction, demonstrating that xenorhabdicin was required for killing
P. luminescens
and protecting the nematode partner. Xenorhabdicin killed
X. nematophila
from
Steinernema anatoliense
, demonstrating for the first time that it possesses intraspecies activity. In addition, activity was variable against diverse strains of
Xenorhabdus
and
Photorhabdus
and was not correlated with phylogenetic distance. These findings are discussed in the context of the role of xenorhabdicin in the life cycle of the mutualistic bacterium
X. nematophila
.
Characterization of DNA Binding Sites of the ComE Response Regulator from Streptococcus mutans
Authors: Hung David C. I. , Downey Jennifer S. , Ayala Eduardo A. , Kreth Jens , Mair Richard , Senadheera Dilani B. , Qi Fengxia , Cvitkovitch Dennis G. , Shi Wenyuan , Goodman Steven D. 
Published: May 2011

ABSTRACT

In
Streptococcus mutans
, both competence and bacteriocin production are controlled by ComC and the ComED two-component signal transduction system. Recent studies of
S. mutans
suggested that purified ComE binds to two 11-bp direct repeats in the
nlmC-comC
promoter region, where ComE activates
nlmC
and represses
comC
. In this work, quantitative binding studies and DNase I footprinting analysis were performed to calculate the equilibrium dissociation constant and further characterize the binding site of ComE. We found that ComE protects sequences inclusive of both direct repeats, has an equilibrium dissociation constant in the nanomolar range, and binds to these two direct repeats cooperatively. Furthermore, similar direct repeats were found upstream of
cslAB
,
comED
,
comX
,
ftf
,
vicRKX
,
gtfD
,
gtfB
,
gtfC
, and
gbpB.
Quantitative binding studies were performed on each of these sequences and showed that only
cslAB
has a similar specificity and high affinity for ComE as that seen with the upstream region of
comC
. A mutational analysis of the binding sequences showed that ComE does not require both repeats to bind DNA with high affinity, suggesting that single site sequences in the genome may be targets for ComE-mediated regulation. Based on the mutational analysis and DNase I footprinting analysis, we propose a consensus ComE binding site, TCBTAAAYSGT.
Characterization of Peptide Chain Length and Constituency Requirements for YejABEF-Mediated Uptake of Microcin C Analogues
Authors: Vondenhoff Gaston H. M. , Blanchaert Bart , Geboers Sophie , Kazakov Teymur , Datsenko Kirill A. , Wanner Barry L. , Rozenski Jef , Severinov Konstantin , Van Aerschot Arthur 
Published: May 2011

ABSTRACT
Microcin C (McC), a natural antibacterial compound consisting of a heptapeptide attached to a modified adenosine, is actively taken up by the YejABEF transporter, after which it is processed by cellular aminopeptidases, releasing the nonhydrolyzable aminoacyl adenylate, an inhibitor of aspartyl-tRNA synthetase. McC analogues with variable length of the peptide moiety were synthesized and evaluated in order to characterize the substrate preferences of the YejABEF transporter. It was shown that a minimal peptide chain length of 6 amino acids and the presence of an N-terminal formyl-methionyl-arginyl sequence are required for transport.
Comparative Genomics of the Dormancy Regulons in Mycobacteria
Authors: Gerasimova Anna , Kazakov Alexey E. , Arkin Adam P. , Dubchak Inna , Gelfand Mikhail S. 
Published: May 2011

ABSTRACT

In response to stresses,
Mycobacterium
cells become dormant. This process is regulated by the DosR transcription factor. In
Mycobacterium tuberculosis
, the dormancy regulon is well characterized and contains the
dosR
gene itself and
dosS
and
dosT
genes encoding DosR kinases, nitroreductases (
acg
;
Rv3131
), diacylglycerol acyltransferase (DGAT) (
Rv3130c
), and many universal stress proteins (USPs). In this study, we apply comparative genomic analysis to characterize the DosR regulons in nine
Mycobacterium
genomes,
Rhodococcus
sp. RHA1,
Nocardia farcinica
, and
Saccharopolyspora erythraea.
The regulons are highly labile, containing eight core gene groups (regulators, kinases, USPs, DGATs, nitroreductases, ferredoxins, heat shock proteins, and the orthologs of the predicted kinase [Rv2004c] from
M. tuberculosis
) and 10 additional genes with more restricted taxonomic distribution that are mostly involved in anaerobic respiration. The largest regulon is observed in
M. marinum
and the smallest in
M. abscessus
. Analysis of large gene families encoding USPs, nitroreductases, and DGATs demonstrates a mosaic distribution of regulated and nonregulated members, suggesting frequent acquisition and loss of DosR-binding sites.
Deciphering the Electron Transport Pathway for Graphene Oxide Reduction by Shewanella oneidensis MR-1
Authors: Jiao Yongqin , Qian Fang , Li Yat , Wang Gongming , Saltikov Chad W. , Gralnick Jeffrey A. 
Published: May 2011

ABSTRACTWe determined that graphene oxide reduction byShewanella oneidensisMR-1 requires the Mtr respiratory pathway by analyzing a range of mutants lacking these proteins. Electron shuttling compounds increased the graphene oxide reduction rate 3- to 5-fold. These results may help facilitate the use of bacteria for large-scale graphene production.
Broad-Spectrum Biofilm Inhibition by Kingella kingae Exopolysaccharide
Authors: Bendaoud Meriem , Vinogradov Evgeny , Balashova Nataliya V. , Kadouri Daniel E. , Kachlany Scott C. , Kaplan Jeffrey B. 
Published: May 2011

ABSTRACT

Cell-free extracts prepared from
Kingella kingae
colony biofilms were found to inhibit biofilm formation by
Aggregatibacter actinomycetemcomitans
,
Klebsiella pneumoniae
,
Staphylococcus aureus
,
Staphylococcus epidermidis
,
Candida albicans
, and
K. kingae
. The extracts evidently inhibited biofilm formation by modifying the physicochemical properties of the cell surface, the biofilm matrix, and the substrate. Chemical and biochemical analyses indicated that the biofilm inhibition activity in the
K. kingae
extract was due to polysaccharide. Structural analyses showed that the extract contained two major polysaccharides. One was a linear polysaccharide with the structure →6)-α-
d
-GlcNAc
p
-(1→5)-β-
d
-OclA
p
-(2→, which was identical to a capsular polysaccharide produced by
Actinobacillus pleuropneumoniae
serotype 5. The second was a novel linear polysaccharide, designated PAM galactan, with the structure →3)-β-
d
-Gal
f
-(1→6)-β-
d
-Gal
f
-(1→. Purified PAM galactan exhibited broad-spectrum biofilm inhibition activity. A cluster of three
K. kingae
genes encoding UDP-galactopyranose mutase (
ugm
) and two putative galactofuranosyl transferases was sufficient for the synthesis of PAM galactan in
Escherichia coli
. PAM galactan is one of a growing number of bacterial polysaccharides that exhibit antibiofilm activity. The biological roles and potential technological applications of these molecules remain unknown.
Phenazine-1-Carboxylic Acid Promotes Bacterial Biofilm Development via Ferrous Iron Acquisition
Authors: Wang Yun , Wilks Jessica C. , Danhorn Thomas , Ramos Itzel , Croal Laura , Newman Dianne K. 
Published: May 2011

ABSTRACT

The opportunistic pathogen
Pseudomonas aeruginosa
forms biofilms, which render it more resistant to antimicrobial agents. Levels of iron in excess of what is required for planktonic growth have been shown to promote biofilm formation, and therapies that interfere with ferric iron [Fe(III)] uptake combined with antibiotics may help treat
P. aeruginosa
infections. However, use of these therapies presumes that iron is in the Fe(III) state in the context of infection. Here we report the ability of phenazine-1-carboxylic acid (PCA), a common phenazine made by all phenazine-producing pseudomonads, to help
P. aeruginosa
alleviate Fe(III) limitation by reducing Fe(III) to ferrous iron [Fe(II)]. In the presence of PCA, a
P. aeruginosa
mutant lacking the ability to produce the siderophores pyoverdine and pyochelin can still develop into a biofilm. As has been previously reported (P. K. Singh, M. R. Parsek, E. P. Greenberg, and M. J. Welsh, Nature 417:552-555, 2002), biofilm formation by the wild type is blocked by subinhibitory concentrations of the Fe(III)-binding innate-immunity protein conalbumin, but here we show that this blockage can be rescued by PCA. FeoB, an Fe(II) uptake protein, is required for PCA to enable this rescue. Unlike PCA, the phenazine pyocyanin (PYO) can facilitate biofilm formation via an iron-independent pathway. While siderophore-mediated Fe(III) uptake is undoubtedly important at early stages of infection, these results suggest that at later stages of infection, PCA present in infected tissues may shift the redox equilibrium between Fe(III) and Fe(II), thereby making iron more bioavailable.
Structure of Burkholderia cepacia UDP-Glucose Dehydrogenase (UGD) BceC and Role of Tyr10 in Final Hydrolysis of UGD Thioester Intermediate
Authors: Rocha Joana , Popescu Alma O. , Borges Patrícia , Mil-Homens Dalila , Moreira Leonilde M. , Sá-Correia Isabel , Fialho Arsénio M. , Frazão Carlos 
Published: May 2011

ABSTRACT

Members of the
Burkholderia cepacia
complex (BCC) are serious respiratory pathogens in immunocompromised individuals and in patients with cystic fibrosis (CF). They are exceptionally resistant to many antimicrobial agents and have the capacity to spread between patients, leading to a decline in lung function and necrotizing pneumonia. BCC members often express a mucoid phenotype associated with the secretion of the exopolysaccharide (EPS) cepacian. There is much evidence supporting the fact that cepacian is a major virulence factor of BCC. UDP-glucose dehydrogenase (UGD) is responsible for the NAD-dependent 2-fold oxidation of UDP-glucose (UDP-Glc) to UDP-glucuronic acid (UDP-GlcA), which is a key step in cepacian biosynthesis. Here, we report the structure of BceC, determined at 1.75-Å resolution. Mutagenic studies were performed on the active sites of UGDs, and together with the crystallographic structures, they elucidate the molecular mechanism of this family of sugar nucleotide-modifying enzymes. Superposition with the structures of human and other bacterial UGDs showed an active site with high structural homology. This family contains a strictly conserved tyrosine residue (Y10 in BceC; shown in italics) within the glycine-rich motif (GXG
Y
XG) of its N-terminal Rossmann-like domain. We constructed several BceC Y10 mutants, revealing only residual dehydrogenase activity and thus highlighting the importance of this conserved residue in the catalytic activity of BceC. Based on the literature of the UGD/GMD nucleotide sugar 6-dehydrogenase family and the kinetic and structural data we obtained for BceC, we determined Y10 as a key catalytic residue in a UGD rate-determining step, the final hydrolysis of the enzymatic thioester intermediate.
Characterization of a Novel Heat Shock Protein (Hsp22.5) Involved in the Pathogenesis of Mycobacterium tuberculosis
Authors: Abomoelak Bassam , Marcus Sarah A. , Ward Sarah K. , Karakousis Petros C. , Steinberg Howard , Talaat Adel M. 
Published: May 2011

ABSTRACT

Tuberculosis is a worldwide health problem, given that one-third of the world's population is currently infected with
Mycobacterium tuberculosis
. Understanding the regulation of virulence on the molecular level will provide a better understanding of how
M. tuberculosis
can establish chronic infection. Using
in vivo
microarray analysis (IVMA), we previously identified a group of genes that are activated in BALB/c mouse lungs compared to
in vitro
cultures, including the
rv0990c
gene. Our analysis indicated that this gene is a member of the heat shock regulon and was activated under other stress conditions, including survival in macrophages or during the late phase of chronic tuberculosis in the murine lungs. Deletion of
rv0990c
from the genome of
M. tuberculosis
strain H37Rv affected the transcriptional profiles of many genes (
n
= 382) and operons involved in mycobacterial survival, including the dormancy regulon, ATP synthesis, respiration, protein synthesis, and lipid metabolism. Comparison of the proteomes of the mutant to those of the wild-type strain further confirmed the differential expression of 15 proteins, especially those involved in the heat shock response (e.g., DnaK and GrpE). Finally, the
rv0990c
mutant strain showed survival equivalent to that of the isogenic wild-type strain during active tuberculosis in guinea pigs, despite showing significant attenuation in BALB/c mice during the chronic phase of the disease. Overall, we suggest that
rv0990c
encodes a heat shock protein that plays an important role in mycobacterial virulence. Hence, we renamed
rv0990c
heat shock protein 22.5 (
hsp22.5
), reflecting its molecular mass.
S
-Adenosylmethionine-Binding Properties of a Bacterial Phospholipid
N
-Methyltransferase
Authors: Aktas Meriyem , Gleichenhagen Jan , Stoll Raphael , Narberhaus Franz 
Published: May 2011

ABSTRACT

The presence of the membrane lipid phosphatidylcholine (PC) in the bacterial membrane is critically important for many host-microbe interactions. The phospholipid
N
-methyltransferase PmtA from the plant pathogen
Agrobacterium tumefaciens
catalyzes the formation of PC by a three-step methylation of phosphatidylethanolamine via monomethylphosphatidylethanolamine and dimethylphosphatidylethanolamine. The methyl group is provided by
S
-adenosylmethionine (SAM), which is converted to
S
-adenosylhomocysteine (SAH) during transmethylation. Despite the biological importance of bacterial phospholipid
N
-methyltransferases, little is known about amino acids critical for binding to SAM or phospholipids and catalysis. Alanine substitutions in the predicted SAM-binding residues E58, G60, G62, and E84 in
A. tumefaciens
PmtA dramatically reduced SAM-binding and enzyme activity. Homology modeling of PmtA satisfactorily explained the mutational results. The enzyme is predicted to exhibit a consensus topology of the SAM-binding fold consistent with cofactor interaction as seen with most structurally characterized SAM-methyltransferases. Nuclear magnetic resonance (NMR) titration experiments and
14
C-SAM-binding studies revealed binding constants for SAM and SAH in the low micromolar range. Our study provides first insights into structural features and SAM binding of a bacterial phospholipid
N
-methyltransferase.
Identification of Ten Anabaena sp. Genes That under Aerobic Conditions Are Required for Growth on Dinitrogen but Not for Growth on Fixed Nitrogen
Authors: Lechno-Yossef Sigal , Fan Qing , Wojciuch Elizabeth , Wolk C. Peter 
Published: May 2011

ABSTRACT

Heterocysts are specialized cells required for aerobic fixation of dinitrogen by certain filamentous cyanobacteria. Numerous genes involved in the differentiation and function of heterocysts in
Anabaena
sp. strain PCC 7120 have been identified by mutagenizing and screening for mutants that require fixed nitrogen for growth in the presence of oxygen. We have verified that 10
Anabaena
sp. genes,
all1338
,
all1591
,
alr1728
,
all3278
,
all3520
,
all3582
,
all3850
,
all4019
,
alr4311
, and
all4388
, identified initially by transposon mutagenesis, are such genes by complementing or reconstructing the original mutation and by determining whether the mutant phenotype might be due to a polar effect of the transposon. Elucidation of the roles of these genes should enhance understanding of heterocyst biology.