bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of the Peptide Pheromone Plantaricin A and Cocultivation with Lactobacillus sanfranciscensis DPPMA174 on the Exoproteome and the Adhesion Capacity of Lactobacillus plantarum DC400
Authors: Calasso Maria , Di Cagno Raffaella , De Angelis Maria , Campanella Daniela , Minervini Fabio , Gobbetti Marco 
Published: February 2013

ABSTRACT

This study aimed at investigating the extracellular and cell wall-associated proteins (exoproteome) of
Lactobacillus plantarum
DC400 when cultivated on modified chemically defined medium (CDM) supplemented with the chemically synthesized pheromone plantaricin A (PlnA) or cocultured with
L. plantarum
DPPMA20 or
Lactobacillus sanfranciscensis
DPPMA174. Compared to monoculture, two-dimensional gel electrophoresis (2-DE) analysis showed that the exoproteome of
L. plantarum
DC400 was affected by PlnA and cocultivation with strains DPPMA20 and, especially, DPPMA174. The highest similarity of the 2-DE maps was found between DC400 cells cultivated in monoculture and in coculture with strain DPPMA20. Almost all extracellular proteins (22 spots) and cell wall-associated proteins (40 spots) which showed decreased or increased levels of synthesis during growth in CDM supplemented with PlnA and/or in coculture with strain DPPMA20 or DPPMA174 were identified. On the basis of the sequences in the Kyoto Encyclopedia of Genes and Genomes database, changes to the exoproteome concerned proteins involved in quorum sensing (QS), the transport system, stress response, carbohydrate metabolism and glycolysis, oxidation/reduction processes, the proteolytic system, amino acid metabolism, cell wall and catabolic processes, and cell shape, growth, and division. Cultivation with PlnA and cocultivation with strains DPPMA20 and, especially, DPMMA174 markedly increased the capacity of
L. plantarum
DC400 to form biofilms, to adhere to human Caco-2 cells, and to prevent the adhesion of potential intestinal pathogens. These phenotypic traits were in part related to oversynthesized moonlighting proteins (e.g., DnaK and GroEL, pyruvate kinase, enolase, and glyceraldehyde-3-phosphate dehydrogenase) in response to QS mechanisms and interaction with
L. plantarum
DPPMA20 and, especially,
L. sanfranciscensis
DPPMA174.
Development of a Rapid Real-Time PCR Method as a Tool To Quantify Viable Photobacterium phosphoreum Bacteria in Salmon (Salmo salar) Steaks
Authors: Macé Sabrina , Mamlouk Kelthoum , Chipchakova Stoyka , Prévost Hervé , Joffraud Jean-Jacques , Dalgaard Paw , Pilet Marie-France , Dousset Xavier 
Published: February 2013

ABSTRACT

A specific real-time PCR quantification method combined with a propidium monoazide sample treatment step was developed to determine quantitatively the viable population of the
Photobacterium phosphoreum
species group in raw modified-atmosphere-packed salmon. Primers were designed to amplify a 350-bp fragment of the gyrase subunit B gene (
gyrB
) of
P. phosphoreum
. The specificity of the two primers was demonstrated by using purified DNA from 81 strains of 52 different bacterial species. When these primers were used for real-time PCR in pure culture, a good correlation (
R
2
of 0.99) was obtained between this method and conventional enumeration on marine agar (MA). Quantification was linear over 5 log units as confirmed by using inoculated salmon samples. On naturally contaminated fresh salmon, the new real-time PCR method performed successfully with a quantification limit of 3 log CFU/g. A correlation coefficient (
R
2
) of 0.963 was obtained between the PCR method and classic enumeration on MA, followed by identification of colonies (290 isolates identified by real-time PCR or by 16S rRNA gene sequencing). A good correlation with an
R
2
of 0.940 was found between the new PCR method and an available specific conductance method for
P. phosphoreum
. This study presents a rapid tool for producing reliable quantitative data on viable
P. phosphoreum
bacteria in fresh salmon in 6 h. This new culture-independent method will be valuable for future fish inspection, the assessment of raw material quality in fish processing plants, and studies on the ecology of this important specific spoilage microorganism.
Optimization of Magnetosome Production and Growth by the Magnetotactic Vibrio Magnetovibrio blakemorei Strain MV-1 through a Statistics-Based Experimental Design
Authors: Silva Karen T. , Leão Pedro E. , Abreu Fernanda , López Jimmy A. , Gutarra Melissa L. , Farina Marcos , Bazylinski Dennis A. , Freire Denise M. G. , Lins Ulysses 
Published: February 2013

ABSTRACT

The growth and magnetosome production of the marine magnetotactic vibrio
Magnetovibrio blakemorei
strain MV-1 were optimized through a statistics-based experimental factorial design. In the optimized growth medium, maximum magnetite yields of 64.3 mg/liter in batch cultures and 26 mg/liter in a bioreactor were obtained.
Monitoring the Perturbation of Soil and Groundwater Microbial Communities Due to Pig Production Activities
Authors: Hong Pei-Ying , Yannarell Anthony C. , Dai Qinghua , Ekizoglu Melike , Mackie Roderick I. 
Published: February 2013

ABSTRACT

This study aimed to determine if biotic contaminants originating from pig production farms are disseminated into soil and groundwater microbial communities. A spatial and temporal sampling of soil and groundwater in proximity to pig production farms was conducted, and quantitative PCR (Q-PCR) was utilized to determine the abundances of tetracycline resistance genes (i.e.,
tetQ
and
tetZ
) and integrase genes (i.e.,
intI1
and
intI2
). We observed that the abundances of
tetZ
,
tetQ
,
intI1
, and
intI2
in the soils increased at least 6-fold after manure application, and their abundances remained elevated above the background for up to 16 months. Q-PCR further determined total abundances of up to 5.88 × 10
9
copies/ng DNA for
tetZ
,
tetQ
,
intI1
, and
intI2
in some of the groundwater wells that were situated next to the manure lagoon and in the facility well used to supply water for one of the farms. We further utilized 16S rRNA-based pyrosequencing to assess the microbial communities, and our comparative analyses suggest that most of the soil samples collected before and after manure application did not change significantly, sharing a high Bray-Curtis similarity of 78.5%. In contrast, an increase in
Bacteroidetes
and sulfur-oxidizing bacterial populations was observed in the groundwaters collected from lagoon-associated groundwater wells. Genera associated with opportunistic human and animal pathogens, such as
Acinetobacter
,
Arcobacter
,
Yersinia
, and
Coxiella
, were detected in some of the manure-treated soils and affected groundwater wells. Feces-associated bacteria such as
Streptococcus
,
Erysipelothrix
, and
Bacteroides
were detected in the manure, soil, and groundwater ecosystems, suggesting a perturbation of the soil and groundwater environments by invader species from pig production activities.
Characterization of a Novel Panton-Valentine Leukocidin (PVL)-Encoding Staphylococcal Phage and Its Naturally PVL-Lacking Variant
Authors: El Haddad Lynn , Moineau Sylvain 
Published: February 2013

ABSTRACT

A new siphophage (LH1) was isolated from raw milk using a
Staphylococcus aureus
ST352 host. Its genome (46,048 bp, 57 open reading frames) includes the two genes encoding Panton-Valentine leukocidin (PVL), a virulence factor usually harbored by
S. aureus
prophages. Nine structural proteins were identified, including a tail protein generated through a +1 frameshift. A phage lytic mutant was isolated, and its analysis revealed the deletion of genes coding for the PVL and an integrase. The deletion likely occurred through recombination between direct repeats.
Shewanella spp. Use Acetate as an Electron Donor for Denitrification but Not Ferric Iron or Fumarate Reduction
Authors: Yoon Sukhwan , Sanford Robert A. , Löffler Frank E. 
Published: February 2013

ABSTRACT

Lactate but not acetate oxidation was reported to support electron acceptor reduction by
Shewanella
spp. under anoxic conditions. We demonstrate that the denitrifiers
Shewanella loihica
strain PV-4 and
Shewanella denitrificans
OS217 utilize acetate as an electron donor for denitrification but not for fumarate or ferric iron reduction.
Cross-Sectional Study Reveals High Prevalence of Clostridium difficile Non-PCR Ribotype 078 Strains in Australian Veal Calves at Slaughter
Authors: Knight Daniel R. , Thean Sara , Putsathit Papanin , Fenwick Stan , Riley Thomas V. 
Published: February 2013

ABSTRACT

Recent reports in North America and Europe of
Clostridium difficile
being isolated from livestock and retail meats of bovine origin have raised concerns about the risk to public health. To assess the situation in Australia, we investigated the prevalence and genetic diversity of
C. difficile
in adult cattle and calves at slaughter. Carcass washings, gastrointestinal contents, and feces were collected from abattoirs across five Australian states. Selective culture, toxin profiling, and PCR ribotyping were performed. The prevalence of
C. difficile
was 56% (203/360 samples) in feces from <7-day-old calves, 3.8% (1/26) in 2- to 6-month-old calves, and 1.8% (5/280) in adult cattle. Three PCR ribotypes (RTs), RT127, RT033, and RT126, predominated in <7-day-old calves and comprised 77.8% (158/203 samples) of isolates. RT056, which has not been reported in cattle before, was found in 16 <7-day-old calves (7.7%). Surprisingly, RT078 strains, which dominate production animal carriage studies in the Northern Hemisphere, were not isolated.
Transcriptional Regulation of the Copper Transporter Mfc1 in Meiotic Cells
Authors: Beaudoin Jude , Ioannoni Raphaël , Mailloux Stéphane , Plante Samuel , Labbé Simon 
Published: February 2013

ABSTRACT

Mfc1 is a meiosis-specific protein that mediates copper transport during the meiotic program in
Schizosaccharomyces pombe
. Although the
mfc1
+
gene is induced at the transcriptional level in response to copper deprivation, the molecular determinants that are required for its copper starvation-dependent induction are unknown. Promoter deletion and site-directed mutagenesis have allowed identification of a new
cis
-regulatory element in the promoter region of the
mfc1
+
gene. This
cis
-acting regulatory sequence containing the sequence TCGGCG is responsible for transcriptional activation of
mfc1
+
under low-copper conditions. The TCGGCG sequence contains a CGG triplet known to serve as a binding site for members of the Zn
(2)
Cys
(6)
binuclear cluster transcriptional regulator family. In agreement with this fact, one member of this group of regulators, denoted Mca1, was found to be required for maximum induction of
mfc1
+
gene expression. Analysis of Mca1 cellular distribution during meiosis revealed that it colocalizes with both chromosomes and sister chromatids during early, middle, and late phases of the meiotic program. Cells lacking Mca1 exhibited a meiotic arrest at metaphase I under low-copper conditions. Binding studies revealed that the N-terminal 150-residue segment of Mca1 expressed as a fusion protein in
Escherichia coli
specifically interacts with the TCGGCG sequence of the
mfc1
+
promoter. Taken together, these results identify the
cis
-regulatory TCGGCG sequence and the transcription factor Mca1 as critical components for activation of the meiotic copper transport
mfc1
+
gene in response to copper starvation.
Cysteine Protease Inhibitor (AcStefin) Is Required for Complete Cyst Formation of Acanthamoeba
Authors: Lee Jung-Yub , Song Su-Min , Moon Eun-Kyung , Lee Yu-Ran , Jha Bijay Kumar , Danne Dinzouna-Boutamba Sylvatrie , Cha Hee-Jae , Yu Hak Sun , Kong Hyun-Hee , Chung Dong-Il , Hong Yeonchul 
Published: February 2013

ABSTRACT

The encystation of
Acanthamoeba
leads to the formation of resilient cysts from vegetative trophozoites. This process is essential for parasite survival under unfavorable conditions, such as those associated with starvation, low temperatures, and biocides. Furthermore, cysteine proteases have been implicated in the massive turnover of intracellular components required for encystation. Thus, strict modulation of the activities of cysteine proteases is required to protect
Acanthamoeba
from intracellular damage. However, mechanisms underlying the control of protease activity during encystation have not been established in
Acanthamoeba
. In the present study, we identified and characterized
Acanthamoeba
cysteine protease inhibitor (AcStefin), which was found to be highly expressed during encystation and to be associated with lysosomes by fluorescence microscopy. Recombinant AcStefin inhibited various cysteine proteases, including human cathepsin B, human cathepsin L, and papain. Transfection with small interfering RNA against AcStefin increased cysteine protease activity during encystation and resulted in incomplete cyst formation, reduced excystation efficiency, and a significant reduction in cytoplasmic area. Taken together, these results indicate that AcStefin is involved in the modulation of cysteine proteases and that it plays an essential role during the encystation of
Acanthamoeba
.
Adhesins in Human Fungal Pathogens: Glue with Plenty of Stick
Authors: de Groot Piet W. J. , Bader Oliver , de Boer Albert D. , Weig Michael , Chauhan Neeraj 
Published: February 2013

ABSTRACT

Understanding the pathogenesis of an infectious disease is critical for developing new methods to prevent infection and diagnose or cure disease. Adherence of microorganisms to host tissue is a prerequisite for tissue invasion and infection. Fungal cell wall adhesins involved in adherence to host tissue or abiotic medical devices are critical for colonization leading to invasion and damage of host tissue. Here, with a main focus on pathogenic
Candida
species, we summarize recent progress made in the field of adhesins in human fungal pathogens and underscore the importance of these proteins in establishment of fungal diseases.
Identification and Characterization of MalA in the Maltose/Maltodextrin Operon of Sulfolobus acidocaldarius DSM639
Authors: Choi Kyoung-Hwa , Hwang Sungmin , Cha Jaeho 
Published: February 2013

ABSTRACT

A putative maltose/maltodextrin operon was found in the
Sulfolobus acidocaldarius
DSM639 genome. The gene cluster consisted of 7 genes (
malA
,
trmB
,
amyA
,
malG
,
malF
,
malE
, and
malK
). Here, we report the identification of MalA, which is responsible for the hydrolysis of maltose or maltodextrin to glucose in
S. acidocaldarius
. The transcription level of
malA
was increased 3-fold upon the addition of maltose or starch to the medium. Moreover, the α-glucosidase activity for maltose as a substrate in cell extracts of
S. acidocaldarius
DSM639 was also 11- and 10-fold higher during growth in YT medium (Brock's mineral salts, 0.1% [wt/vol] tryptone, and 0.005% [wt/vol] yeast extract) containing maltose or starch, respectively, than during growth on other sugars. The gene encoding MalA was cloned and expressed in
S. acidocaldarius
. The enzyme purified from the organism was a dodecamer in its active state and showed strong maltose-hydrolyzing activity at 100°C and pH 5.0. MalA was remarkably thermostable, with half-lives of 33.8 h, 10.6 h, and 1.8 h at 95°C, 100°C, and 105°C, respectively. Substrate specificity and kinetic studies of MalA with maltooligosaccharides indicated that MalA efficiently hydrolyzed maltose to maltopentaose, which is a typical characteristic of GH31-type α-glucosidases. However, glycogen or starch was not hydrolyzed. Reverse transcription-PCR, sugar uptake, and growth studies of the wild-type DSM639 and Δ
malEFG
mutant on different sugars demonstrated that MalA located in the
mal
operon gene cluster is involved in maltose and starch metabolism in
S. acidocaldarius
.
Interplay between Type 1A Topoisomerases and Gyrase in Chromosome Segregation in Escherichia coli
Authors: Usongo Valentine , Tanguay Cynthia , Nolent Flora , Bessong Jill Egbe , Drolet Marc 
Published: February 2013

ABSTRACTEscherichia colipossesses two type 1A topoisomerases, Topo I (topA) and Topo III (topB). Topo I relaxes excess negative supercoiling, andtopAmutants can grow only in the presence of compensatory mechanisms, such as gyrase mutations.topBmutants grow as well as wild-type cells.In vitro, Topo III, but not Topo I, can efficiently decatenate DNA during replication. However,in vivo, a chromosome segregation defect is seen only when both type 1A topoisomerases are absent. Here we present experimental evidence for an interplay between gyrase and type 1A topoisomerases in chromosome segregation. We found that both the growth defect and the Par−phenotypes of agyrB(Ts) mutant at nonpermissive temperatures were significantly corrected by deletingtopA, but only whentopBwas present. Overproducing Topo IV, the major cellular decatenase, could not substitute fortopB. We also show that overproducing Topo III at a very high level could suppress the Par−phenotype. We previously found that the growth and chromosome segregation defects of a tripletopA rnhA gyrB(Ts) mutant in which gyrase supercoiling activity was strongly inhibited could be corrected by overproducing Topo III (V. Usongo, F. Nolent, P. Sanscartier, C. Tanguay, S. Broccoli, I. Baaklini, K. Drlica, and M. Drolet, Mol. Microbiol.69:968-981, 2008). We show here that this overproduction could be bypassed by substituting thegyrB(Ts) allele for agyrB+one or by growing cells in a minimal medium, conditions that reduced bothtopA- andrnhA-dependent unregulated replication. Altogether, our data point to a role for Topo III in chromosome segregation when gyrase is inefficient and suggest that Topo I plays an indirect role via supercoiling regulation.
Structural and Functional Roles of Carotenoids in Chlorosomes
Authors: Pšenčík Jakub , Arellano Juan B. , Collins Aaron M. , Laurinmäki Pasi , Torkkeli Mika , Löflund Benita , Serimaa Ritva E. , Blankenship Robert E. , Tuma Roman , Butcher Sarah J. 
Published: February 2013

ABSTRACT

Chlorosomes are large light-harvesting complexes found in three phyla of anoxygenic photosynthetic bacteria. Chlorosomes are primarily composed of self-assembling pigment aggregates. In addition to the main pigment, bacteriochlorophyll
c
,
d
, or
e
, chlorosomes also contain variable amounts of carotenoids. Here, we use X-ray scattering and electron cryomicroscopy, complemented with absorption spectroscopy and pigment analysis, to compare the morphologies, structures, and pigment compositions of chlorosomes from
Chloroflexus aurantiacus
grown under two different light conditions and
Chlorobaculum tepidum
. High-purity chlorosomes from
C. aurantiacus
contain about 20% more carotenoid per bacteriochlorophyll
c
molecule when grown under low light than when grown under high light. This accentuates the light-harvesting function of carotenoids, in addition to their photoprotective role. The low-light chlorosomes are thicker due to the overall greater content of pigments and contain domains of lamellar aggregates. Experiments where carotenoids were selectively extracted from intact chlorosomes using hexane proved that they are located in the interlamellar space, as observed previously for species belonging to the phylum
Chlorobi
. A fraction of the carotenoids are localized in the baseplate, where they are bound differently and cannot be removed by hexane. In
C. tepidum
, carotenoids cannot be extracted by hexane even from the chlorosome interior. The chemical structure of the pigments in
C. tepidum
may lead to π-π interactions between carotenoids and bacteriochlorophylls, preventing carotenoid extraction. The results provide information about the nature of interactions between bacteriochlorophylls and carotenoids in the protein-free environment of the chlorosome interior.
Regulation of Lipid Biosynthesis, Sliding Motility, and Biofilm Formation by a Membrane-Anchored Nucleoid-Associated Protein of Mycobacterium tuberculosis
Authors: Ghosh Soumitra , Indi Shantinath S. , Nagaraja Valakunja 
Published: February 2013

ABSTRACT

Bacteria use a number of small basic proteins for organization and compaction of their genomes. By their interaction with DNA, these nucleoid-associated proteins (NAPs) also influence gene expression. Rv3852, a NAP of
Mycobacterium tuberculosis
, is conserved among the pathogenic and slow-growing species of mycobacteria. Here, we show that the protein predominantly localizes in the cell membrane and that the carboxy-terminal region with the propensity to form a transmembrane helix is necessary for its membrane localization. The protein is involved in genome organization, and its ectopic expression in
Mycobacterium smegmatis
resulted in altered nucleoid morphology, defects in biofilm formation, sliding motility, and change in apolar lipid profile. We demonstrate its crucial role in regulating the expression of KasA, KasB, and GroEL1 proteins, which are in turn involved in controlling the surface phenotypes in mycobacteria.
Crystallographic Study To Determine the Substrate Specificity of an
l
-Serine-Acetylating Enzyme Found in the
d
-Cycloserine Biosynthetic Pathway
Authors: Oda Kosuke , Matoba Yasuyuki , Kumagai Takanori , Noda Masafumi , Sugiyama Masanori 
Published: February 2013

ABSTRACT

DcsE, one of the enzymes found in the
d
-cycloserine biosynthetic pathway, displays a high sequence homology to
l
-homoserine
O
-acetyltransferase (HAT), but it prefers
l
-serine over
l
-homoserine as the substrate. To clarify the substrate specificity, in the present study we determined the crystal structure of DcsE at a 1.81-Å resolution, showing that the overall structure of DcsE is similar to that of HAT, whereas a turn region to form an oxyanion hole is obviously different between DcsE and HAT: in detail, the first and last residues in the turn of DcsE are Gly
52
and Pro
55
, respectively, but those of HAT are Ala and Gly, respectively. In addition, more water molecules were laid on one side of the turn region of DcsE than on that of HAT, and a robust hydrogen-bonding network was formed only in DcsE. We created a HAT-like mutant of DcsE in which Gly
52
and Pro
55
were replaced by Ala and Gly, respectively, showing that the mutant acetylates
l
-homoserine but scarcely acetylates
l
-serine. The crystal structure of the mutant DcsE shows that the active site, including the turn and its surrounding waters, is similar to that of HAT. These findings suggest that a methyl group of the first residue in the turn of HAT plays a role in excluding the binding of
l
-serine to the substrate-binding pocket. In contrast, the side chain of the last residue in the turn of DcsE may need to form an extensive hydrogen-bonding network on the turn, which interferes with the binding of
l
-homoserine.