bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Tyramine Synthesis by Food-Borne
Enterococcus durans
in Adaptation to the Gastrointestinal Tract Environment
Authors: Fernández de Palencia Pilar , Fernández Maria , Mohedano Maria Luz , Ladero Victor , Quevedo Cristina , Alvarez Miguel A. , López Paloma 
Published: November 2010

ABSTRACT

Biogenic amines in food constitute a human health risk. Here we report that tyramine-producing
Enterococcus durans
strain IPLA655 (from cheese) was able to produce tyramine under conditions simulating transit through the gastrointestinal tract. Activation of the tyramine biosynthetic pathway contributed to binding and immunomodulation of enterocytes.
Integron Prevalence and Diversity in Manured Soil
Authors: Byrne-Bailey K. G. , Gaze W. H. , Zhang L. , Kay P. , Boxall A. , Hawkey P. M. , Wellington E. M. H. 
Published: November 2010

ABSTRACT
The levels of integron abundance and diversity in soil amended with pig slurry were studied. Real-time PCR illustrated a significant increase in class 1 integron prevalence after slurry application, with increased prevalence still evident at 10 months after application. Culture-dependent data revealed 10 genera, including putative human pathogens, carrying class 1 and 2 integrons.
Requirements of the Engineered Leader Peptide of Nisin for Inducing Modification, Export, and Cleavage
Authors: Plat Annechien , Kluskens Leon D. , Kuipers Anneke , Rink Rick , Moll Gert N. 
Published: November 2010

ABSTRACT

Nisin A is a pentacyclic peptide antibiotic produced by
Lactococcus lactis
. The leader peptide of prenisin keeps nisin inactive and has a role in inducing NisB- and NisC-catalyzed modifications of the propeptide and NisT-mediated export. The highly specific NisP cleaves off the leader peptide from fully modified and exported prenisin. We present here a detailed mutagenesis analysis of the nisin leader peptide. For alternative cleavage, we successfully introduced a putative NisP autocleavage site and sites for thrombin, enterokinase, Glu-C, and factor Xa in the C-terminal part of the leader peptide. Replacing residue F-18 with Trp or Thr strongly reduced production. On the other hand, D-19A, F-18H, F-18M, L-16D, L-16K, and L-16A enhanced production. Substitutions within and outside the FNLD box enhanced or reduced the transport efficiency. None of the above substitutions nor even an internal 6His tag from positions −13 to −8 had any effect on the capacity of the leader peptide to induce NisB and NisC modifications. Therefore, these data demonstrate a large mutational freedom. However, simultaneous replacement of the FNLD amino acids by four alanines strongly reduced export and even led to a complete loss of the capacity to induce modifications. Reducing the leader peptide to MSTKDFNLDLR led to 3- or 4-fold dehydration. Taken together, the FNLD box is crucial for inducing posttranslational modifications.
Characterization of Lytic Enzyme Open Reading Frame 9 (ORF9) Derived from
Enterococcus faecalis
Bacteriophage φEF24C
Authors: Uchiyama Jumpei , Takemura Iyo , Hayashi Ikue , Matsuzaki Shigenobu , Satoh Miho , Ujihara Takako , Murakami Masanao , Imajoh Masayuki , Sugai Motoyuki , Daibata Masanori 
Published: November 2010

ABSTRACT

In bacteriophage (phage) therapy against Gram-positive bacteria, such as
Staphylococcus aureus
,
Listeria monocytogenes
, and
Enterococcus faecalis
, members of a genus of SPO1-like viruses are typically employed because of their extreme virulence and broad host spectrum. Phage φEF24C, which is a SPO1-like virus infecting
E. faecalis
, has previously been characterized as a therapeutic phage candidate. In addition to the phage itself, phage endolysin is also recognized as an effective antimicrobial agent. In this study, a putative endolysin gene (
orf9
) of
E. faecalis
phage φEF24C was analyzed
in silico
, and its activity was characterized using the recombinant form. First, bioinformatics analysis predicted that the open reading frame 9 (ORF9) protein is
N
-acetylmuramoyl-
l
-alanine amidase. Second, bacteriolytic and bactericidal activities of ORF9 against
E. faecalis
were confirmed by zymography, decrease of peptidoglycan turbidity, decrease of the viable count, and morphological analysis of ORF9-treated cells. Third, ORF9 did not appear to require Zn
2+
ions for its activity, contrary to the bioinformatics prediction of a Zn
2+
ion requirement. Fourth, the lytic spectrum was from 97.1% (34 out of 35 strains, including vancomycin-resistant strains) of
E. faecalis
strains to 60% (6 out of 10 strains) of
Enterococcus faecium
strains. Fifth,
N
-acetylmuramoyl-
l
-alanine amidase activity of ORF9 was confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and the subsequent MALDI-postsource decay (PSD) analyses. Finally, functional analysis using N- or C-terminally deleted ORF9 mutants suggested that a complete ORF9 molecule is essential for its activity. These results suggested that ORF9 is an endolysin of phage φEF24C and can be a therapeutic alternative to antibiotics.
Application of a Depositional
F
acies
Model to an Acid Mine Drainage Site
Authors: Brown Juliana F. , Jones Daniel S. , Mills Daniel B. , Macalady Jennifer L. , Burgos William D. 
Published: November 2010

ABSTRACT

Lower Red Eyes is an acid mine drainage site in Pennsylvania where low-pH Fe(II) oxidation has created a large, terraced iron mound downstream of an anoxic, acidic, metal-rich spring. Aqueous chemistry, mineral precipitates, microbial communities, and laboratory-based Fe(II) oxidation rates for this site were analyzed in the context of a depositional
facies
model. Depositional
facies
were defined as pools, terraces, or microterracettes based on cm-scale sediment morphology, irrespective of the distance downstream from the spring. The sediments were composed entirely of Fe precipitates and cemented organic matter. The Fe precipitates were identified as schwertmannite at all locations, regardless of
facies
. Microbial composition was studied with fluorescence
in situ
hybridization (FISH) and transitioned from a microaerophilic,
Euglena
-dominated community at the spring, to a
Betaproteobacteria
(primarily
Ferrovum
spp.)-dominated community at the upstream end of the iron mound, to a
Gammaproteobacteria
(primarily
Acidithiobacillus
)-dominated community at the downstream end of the iron mound. Microbial community structure was more strongly correlated with pH and geochemical conditions than depositional
facies
. Intact pieces of terrace and pool sediments from upstream and downstream locations were used in flowthrough laboratory reactors to measure the rate and extent of low-pH Fe(II) oxidation. No change in Fe(II) concentration was observed with
60
Co-irradiated sediments or with no-sediment controls, indicating that abiotic Fe(II) oxidation was negligible. Upstream sediments attained lower effluent Fe(II) concentrations compared to downstream sediments, regardless of depositional
facies
.
The Type II Secretion System Is Essential for Erythrocyte Lysis and Gut Colonization by the Leech Digestive Tract Symbiont
Aeromonas veronii
Authors: Maltz Michele , Graf Joerg 
Published: November 2010

ABSTRACT

Hemolysin and the type II secretion system (T2SS) have been shown to be important for virulence in many pathogens, but very few studies have shown their importance in beneficial microbes. Here, we investigated the importance of the type II secretion pathway in the beneficial digestive-tract association of
Aeromonas veronii
and the medicinal leech
Hirudo verbana
and revealed a critical role for the hemolysis of erythrocytes. A mutant with a miniTn
5
insertion in
exeM
, which is involved in forming the inner membrane platform in the T2SS, was isolated by screening mutants for loss of hemolysis on blood agar plates. A hemolysis assay was used to quantify the mutant's deficiency in lysing sheep erythrocytes and revealed a 99.9% decrease compared to the parent strain. The importance of the T2SS in the colonization of the symbiotic host was assessed. Colonization assays revealed that the T2SS is critical for initial colonization of the leech gut. The defect was tied to the loss of hemolysin production by performing a colonization assay with blood containing lysed erythrocytes. This restored the colonization defect in the mutant. Complementation of the mutant using the promoter region and
exeMN
revealed that the T2SS is responsible for secreting hemolysin into the extracellular space and that both the T2SS and hemolysin export by the T2SS are critical for initial establishment of
A. veronii
in the leech gut.
Characterization of Glycoconjugates of Extracellular Polymeric Substances in Tufa-Associated Biofilms by Using Fluorescence Lectin-Binding Analysis
Authors: Zippel B. , Neu T. R. 
Published: November 2010

ABSTRACT

Freshwater tufa deposits are the result of calcification associated with biofilms dominated by cyanobacteria. Recent investigations highlighted the fact that the formation of microbial calcium carbonates is mainly dependent on the saturation index, which is determined by pH, the ion activity of Ca
2+
and CO
3
2−
, and the occurrence of extracellular polymeric substances (EPS) produced by microorganisms. EPS, which contain carboxyl and/or hydroxyl groups, can strongly bind cations. This may result in inhibition of CaCO
3
precipitation. In contrast, the formation of templates for crystal nucleation was reported by many previous investigations. The purposes of this study were (i) to characterize the
in situ
distribution of EPS glycoconjugates in tufa-associated biofilms of two German hard-water creeks by employing fluorescence lectin-binding analysis (FLBA), (ii) to verify the specific lectin-binding pattern by competitive-inhibition assays, and (iii) to assess whether carbonates are associated with structural EPS domains. Three major
in situ
EPS domains (cyanobacterial, network-like, and cloud-like structures) were detected by FLBA in combination with laser scanning microscopy (LSM). Based on lectin specificity, the EPS glycoconjugates produced by cyanobacteria contained mainly fucose, amino sugars (
N
-acetyl-glucosamine and
N
-acetyl-galactosamine), and sialic acid. Tufa deposits were irregularly covered by network-like EPS structures, which may originate from cyanobacterial EPS secretions. Cloud-like EPS glycoconjugates were dominated by sialic acid, amino sugars, and galactose. In some cases calcium carbonate crystals were associated with cyanobacterial EPS glycoconjugates. The detection of amino sugars and calcium carbonate in close association with decaying sheath material indicated that microbially mediated processes might be important for calcium carbonate precipitation in freshwater tufa systems.
Mechanisms of Contact-Mediated Killing of Yeast Cells on Dry Metallic Copper Surfaces
Authors: Quaranta Davide , Krans Travis , Santo Christophe Espírito , Elowsky Christian G. , Domaille Dylan W. , Chang Christopher J. , Grass Gregor 
Published: November 2010

ABSTRACT

Surfaces made of copper or its alloys have strong antimicrobial properties against a wide variety of microorganisms. However, the molecular mode of action responsible for the antimicrobial efficacy of metallic copper is not known. Here, we show that dry copper surfaces inactivate
Candida albicans
and
Saccharomyces cerevisiae
within minutes in a process called contact-mediated killing. Cellular copper ion homeostasis systems influenced the kinetics of contact-mediated killing in both organisms. Deregulated copper ion uptake through a hyperactive
S. cerevisiae
Ctr1p (ScCtr1p) copper uptake transporter in
Saccharomyces
resulted in faster inactivation of mutant cells than of wild-type cells. Similarly, lack of the
C. albicans
Crp1p (CaCrp1p) copper-efflux P-type ATPase or the metallothionein CaCup1p caused more-rapid killing of
Candida
mutant cells than of wild-type cells.
Candida
and
Saccharomyces
took up large quantities of copper ions as soon as they were in contact with copper surfaces, as indicated by inductively coupled plasma mass spectroscopy (ICP-MS) analysis and by the intracellular copper ion-reporting dye coppersensor-1. Exposure to metallic copper did not cause lethality through genotoxicity, deleterious action on a cell's genetic material, as indicated by a mutation assay with
Saccharomyces
. Instead, toxicity mediated by metallic copper surfaces targeted membranes in both yeast species. With the use of Live/Dead staining, onset of rapid and extensive cytoplasmic membrane damage was observed in cells from copper surfaces. Fluorescence microscopy using the indicator dye DiSBaC
2
(3) indicated that cell membranes were depolarized. Also, during contact-mediated killing, vacuoles first became enlarged and then disappeared from the cells. Lastly, in metallic copper-stressed yeasts, oxidative stress in the cytoplasm and in mitochondria was elevated.
Prevalence ofHelicobacterpullorumin Conventional, Organic, and Free-Range Broilers and Typing of Isolates
Authors: Manfreda Gerardo , Parisi Antonio , Lucchi Alex , Zanoni Renato Giulio , De Cesare Alessandra 
Published: November 2010

ABSTRACTHelicobacterpullorumrepresents a potential food-borne pathogen, and avian species appear to be a relevant reservoir of this organism. In this study, the prevalence ofH.pullorumwas investigated at 30 conventional farms where 169 ceca from 34 flocks were tested, at eight organic farms where 39 ceca from eight flocks were tested, and at seven free-range farms where 40 ceca from eight flocks were tested. All of the ceca were obtained from healthy broiler chickens. Moreover, amplified fragment length polymorphism, pulsed-field gel electrophoresis, and automated ribotyping were employed to estimate the levels of genetic variability ofH.pullorumbroiler isolates within and between flocks. Overall, Gram-negative, slender, curved rods, identified asH.pullorumby PCR, were isolated at 93.3% of the farms tested. The percentage of positive free-range farms (54.2%) was significantly lower than that of conventional (100%) or organic (100%) farms (P< 0.001). The level of within-flock genetic variability, calculated as the number of flocks colonized by isolates genetically different by all of the typing methods, was 34.9%. Isolates showing identical profiles by each typing method were observed in 11.6% of the flocks, but they were never detected between flocks. However, groups of isolates clustered together with an overall similarity level of ≥85%. Our results suggest that even though a high level of genetic variability is attributable toH.pullorumbroiler isolates, their hierarchical genotyping produces data useful for epidemiological investigations.
Characterization of Three Lactic Acid Bacteria and Their Isogenic
ldh
Deletion Mutants Shows Optimization for
Y
ATP
(Cell Mass Produced per Mole of ATP) at Their Physiological pHs
Authors: Fiedler Tomas , Bekker Martijn , Jonsson Maria , Mehmeti Ibrahim , Pritzschke Anja , Siemens Nikolai , Nes Ingolf , Hugenholtz Jeroen , Kreikemeyer Bernd 
Published: November 2010

ABSTRACT

Several lactic acid bacteria use homolactic acid fermentation for generation of ATP. Here we studied the role of the lactate dehydrogenase enzyme on the general physiology of the three homolactic acid bacteria
Lactococcus lactis
,
Enterococcus faecalis
, and
Streptococcus pyogenes
. Of note, deletion of the
ldh
genes hardly affected the growth rate in chemically defined medium under microaerophilic conditions. However, the growth rate was affected in rich medium. Furthermore, deletion of
ldh
affected the ability for utilization of various substrates as a carbon source. A switch to mixed acid fermentation was observed during glucose-limited continuous growth and was dependent on the growth rate for
S. pyogenes
and on the pH for
E. faecalis
. In
S. pyogenes
and
L. lactis
, a change in pH resulted in a clear change in
Y
ATP
(cell mass produced per mole of ATP). The pH that showed the highest
Y
ATP
corresponded to the pH of the natural habitat of the organisms.
Anaerobic Obligatory Xylitol Production inEscherichia coliStrains Devoid of Native Fermentation Pathways
Authors: Akinterinwa Olubolaji , Cirino Patrick C. 
Published: November 2010

ABSTRACTAnaerobic glucose oxidation was coupled to xylose reduction in a nonfermentativeEscherichia colistrain expressing NADPH-dependent xylose reductase. Xylitol production serves as the primary means of NAD(P)+regeneration, as glucose is converted primarily to acetate and CO2. The membrane-bound transhydrogenase PntAB is required to achieve the maximum theoretical yield of four moles of xylitol per mole of glucose consumed.
Metatranscriptome Analysis for Insight into Whole-Ecosystem Gene Expression during Spontaneous Wheat and Spelt Sourdough Fermentations
Authors: Weckx Stefan , Allemeersch Joke , Van der Meulen Roel , Vrancken Gino , Huys Geert , Vandamme Peter , Van Hummelen Paul , De Vuyst Luc 
Published: November 2010

ABSTRACT
Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, including sourdough-derived products. Despite their limited metabolic capacity, LAB contribute considerably to important characteristics of fermented foods, such as extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Triggered by the considerable amount of LAB genomic information that became available during the last decade, transcriptome and, by extension, metatranscriptome studies have become one of the most appropriate research approaches to study whole-ecosystem gene expression in more detail. In this study, microarray analyses were performed using RNA sampled during four 10-day spontaneous sourdough fermentations carried out in the laboratory with an in-house-developed LAB functional gene microarray. For data analysis, a new algorithm was developed to calculate a net expression profile for each of the represented genes, allowing use of the microarray analysis beyond the species level. In addition, metabolite target analyses were performed on the sourdough samples to relate gene expression with metabolite production. The results revealed the activation of different key metabolic pathways, the ability to use carbohydrates other than glucose (e.g., starch and maltose), and the conversion of amino acids as a contribution to redox equilibrium and flavor compound generation in LAB during sourdough fermentation.
Proteolytic Cleavage of Covalently Linked Cell Wall Proteins by Candida albicans Sap9 and Sap10
Authors: Schild Lydia , Heyken Antje , de Groot Piet W. J. , Hiller Ekkehard , Mock Marlen , de Koster Chris , Horn Uwe , Rupp Steffen , Hube Bernhard 
Published: November 2010

ABSTRACT

The cell wall of the human-pathogenic fungus
Candida albicans
is a robust but also dynamic structure which mediates adaptation to changing environmental conditions during infection. Sap9 and Sap10 are cell surface-associated proteases which function in
C. albicans
cell wall integrity and interaction with human epithelial cells and neutrophils. In this study, we have analyzed the enzymatic properties of Sap9 and Sap10 and investigated whether these proteases cleave proteins on the fungal cell surface. We show that Sap9 and Sap10, in contrast to other aspartic proteases, exhibit a near-neutral pH optimum of proteolytic activity and prefer the processing of peptides containing basic or dibasic residues. However, both proteases also cleaved at nonbasic sites, and not all tested peptides with dibasic residues were processed. By digesting isolated cell walls with Sap9 or Sap10, we identified the covalently linked cell wall proteins (CWPs) Cht2, Ywp1, Als2, Rhd3, Rbt5, Ecm33, and Pga4 as
in vitro
protease substrates. Proteolytic cleavage of the chitinase Cht2 and the glucan-cross-linking protein Pir1 by Sap9 was verified using hemagglutinin (HA) epitope-tagged versions of both proteins. Deletion of the
SAP9
and
SAP10
genes resulted in a reduction of cell-associated chitinase activity similar to that upon deletion of
CHT2
, suggesting a direct influence of Sap9 and Sap10 on Cht2 function. In contrast, cell surface changes elicited by
SAP9
and
SAP10
deletion had no major impact on the phagocytosis and killing of
C. albicans
by human macrophages. We propose that Sap9 and Sap10 influence distinct cell wall functions by proteolytic cleavage of covalently linked cell wall proteins.
Hph1 and Hph2 Are Novel Components of the Sec63/Sec62 Posttranslational Translocation Complex That Aid in Vacuolar Proton ATPase Biogenesis
Authors: Piña Francisco J. , O'Donnell Allyson F. , Pagant Silvere , Piao Hai Lan , Miller John P. , Fields Stanley , Miller Elizabeth A. , Cyert Martha S. 
Published: November 2010

ABSTRACT

Hph1 and Hph2 are homologous integral endoplasmic reticulum (ER) membrane proteins required for
Saccharomyces cerevisiae
survival under environmental stress conditions. To investigate the molecular functions of Hph1 and Hph2, we carried out a split-ubiquitin-membrane-based yeast two-hybrid screen and identified their interactions with Sec71, a subunit of the Sec63/Sec62 complex, which mediates posttranslational translocation of proteins into the ER. Hph1 and Hph2 likely function in posttranslational translocation, as they interact with other Sec63/Sec62 complex subunits, i.e., Sec72, Sec62, and Sec63.
hph1
Δ
hph2
Δ cells display reduced vacuole acidification; increased instability of Vph1, a subunit of vacuolar proton ATPase (V-ATPase); and growth defects similar to those of mutants lacking V-ATPase activity.
sec71
Δ cells exhibit similar phenotypes, indicating that Hph1/Hph2 and the Sec63/Sec62 complex function during V-ATPase biogenesis. Hph1/Hph2 and the Sec63/Sec62 complex may act together in this process, as vacuolar acidification and Vph1 stability are compromised to the same extent in
hph1
Δ
hph2
Δ and
hph1
Δ
hph2
Δ
sec71
Δ cells. In contrast, loss of Pkr1, an ER protein that promotes posttranslocation assembly of Vph1 with V-ATPase subunits, further exacerbates
hph1
Δ
hph2
Δ phenotypes, suggesting that Hph1 and Hph2 function independently of Pkr1-mediated V-ATPase assembly. We propose that Hph1 and Hph2 aid Sec63/Sec62-mediated translocation of specific proteins, including factors that promote efficient biogenesis of V-ATPase, to support yeast cell survival during environmental stress.
The Rag4 Glucose Sensor Is Involved in the Hypoxic Induction of
KlPDC1
Gene Expression in the Yeast Kluyveromyces lactis
Authors: Micolonghi C. , Wésolowski-Louvel M. , Bianchi M. M. 
Published: November 2010

ABSTRACT

Kluyveromyces lactis
is a yeast which cannot grow under strict anaerobiosis. To date, no factors responsible for oxygen sensing and oxygen-dependent regulation of metabolism have been identified. In this paper we present the identification of the glucose sensor Rag4 as a factor essential for oxygen-dependent regulation of the fermentative pathway.