bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishing Equivalence for Microbial-Growth-Inhibitory Effects (“Iso-Hurdle Rules”) by Analyzing Disparate Listeria monocytogenes Data with a Gamma-Type Predictive Model
Authors: Pujol Laure , Kan-King-Yu Denis , Le Marc Yvan , Johnston Moira D. , Rama-Heuzard Florence , Guillou Sandrine , McClure Peter , Membré Jeanne-Marie 
Published: December 2011

ABSTRACT

Preservative factors act as hurdles against microorganisms by inhibiting their growth; these are essential control measures for particular food-borne pathogens. Different combinations of hurdles can be quantified and compared to each other in terms of their inhibitory effect (“iso-hurdle”). We present here a methodology for establishing microbial iso-hurdle rules in three steps: (i) developing a predictive model based on existing but disparate data sets, (ii) building an experimental design focused on the iso-hurdles using the model output, and (iii) validating the model and the iso-hurdle rules with new data. The methodology is illustrated with
Listeria monocytogenes
. Existing data from industry, a public database, and the literature were collected and analyzed, after which a total of 650 growth rates were retained. A gamma-type model was developed for the factors temperature, pH, a
w
, and acetic, lactic, and sorbic acids. Three iso-hurdle rules were assessed (40 logcount curves generated): salt replacement by addition of organic acids, sorbic acid replacement by addition of acetic and lactic acid, and sorbic acid replacement by addition of lactic/acetic acid and salt. For the three rules, the growth rates were equivalent in the whole experimental domain (γ from 0.1 to 0.5). The lag times were also equivalent in the case of mild inhibitory conditions (γ ≥ 0.2), while they were longer in the presence of salt than acids under stress conditions (γ < 0.2). This methodology allows an assessment of the equivalence of inhibitory effects without intensive data generation; it could be applied to develop milder formulations which guarantee microbial safety and stability.
Cloning and Characterization of the Polyether Salinomycin Biosynthesis Gene Cluster of Streptomyces albus XM211
Authors: Jiang Chunyan , Wang Hougen , Kang Qianjin , Liu Jing , Bai Linquan 
Published: December 2011

ABSTRACT

Salinomycin is widely used in animal husbandry as a food additive due to its antibacterial and anticoccidial activities. However, its biosynthesis had only been studied by feeding experiments with isotope-labeled precursors. A strategy with degenerate primers based on the polyether-specific epoxidase sequences was successfully developed to clone the salinomycin gene cluster. Using this strategy, a putative epoxidase gene,
slnC
, was cloned from the salinomycin producer
Streptomyces albus
XM211. The targeted replacement of
slnC
and subsequent
trans
-complementation proved its involvement in salinomycin biosynthesis. A 127-kb DNA region containing
slnC
was sequenced, including genes for polyketide assembly and release, oxidative cyclization, modification, export, and regulation. In order to gain insight into the salinomycin biosynthesis mechanism, 13 gene replacements and deletions were conducted. Including
slnC
, 7 genes were identified as essential for salinomycin biosynthesis and putatively responsible for polyketide chain release, oxidative cyclization, modification, and regulation. Moreover, 6 genes were found to be relevant to salinomycin biosynthesis and possibly involved in precursor supply, removal of aberrant extender units, and regulation. Sequence analysis and a series of gene replacements suggest a proposed pathway for the biosynthesis of salinomycin. The information presented here expands the understanding of polyether biosynthesis mechanisms and paves the way for targeted engineering of salinomycin activity and productivity.
Diversity of Five Anaerobic Toluene-Degrading Microbial Communities Investigated Using Stable Isotope Probing
Authors: Sun Weimin , Cupples Alison M. 
Published: December 2011

ABSTRACTTime-series DNA-stable isotope probing (SIP) was used to identify the microbes assimilating carbon from [13C]toluene under nitrate- or sulfate-amended conditions in a range of inoculum sources, including uncontaminated and contaminated soil and wastewater treatment samples. In all, five different phylotypes were found to be responsible for toluene degradation, and these included previously identified toluene degraders as well as novel toluene-degrading microorganisms. In microcosms constructed from granular sludge and amended with nitrate, the putative toluene degraders were classified in the genusThauera, whereas in nitrate-amended microcosms constructed from a different source (agricultural soil), microorganisms in the familyComamonadaceae(genus unclassified) were the key putative degraders. In one set of sulfate-amended microcosms (agricultural soil), the putative toluene degraders were identified as belonging to the classClostridia(genusDesulfosporosinus), while in other sulfate-amended microcosms, the putative degraders were in the classDeltaproteobacteria, within the familySyntrophobacteraceae(digester sludge) orDesulfobulbaceae(contaminated soil) (genus unclassified for both). Partial benzylsuccinate synthase gene (bssA, the functional gene for anaerobic toluene degradation) sequences were obtained for some samples, and quantitative PCR targeting this gene, along with SIP, was further used to confirm anaerobic toluene degradation by the identified species. The study illustrates the diversity of toluene degraders across different environments and highlights the utility of ribosomal and functional gene-based SIP for linking function with identity in microbial communities.
Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation
Authors: Murakami Shinnosuke , Fujishima Kosuke , Tomita Masaru , Kanai Akio 
Published: December 2011

ABSTRACT

Studies of small noncoding RNAs (sRNAs) have been conducted predominantly using culturable organisms, and the acquisition of further information about sRNAs from global environments containing uncultured organisms now is very important. In this study, hot spring water (57°C, pH 8.1) was collected directly from the underground environment at depths of 250 to 1,000 m in Yunohama, Japan, and small RNA sequences obtained from the environment were analyzed. A phylogenetic analysis of both archaeal and bacterial 16S rRNA gene sequences was conducted, and the results suggested the presence of unique species in the environment, corresponding to the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) group and three new
Betaproteobacteria
. A metatranscriptomic analysis identified 64,194 (20,057 nonredundant) cDNA sequences. Of these cDNAs, 90% were either tRNAs, tRNA fragments, rRNAs, or rRNA fragments, whereas 2,181 reads (10%) were classified as previously uncharacterized putative candidate sRNAs. Among these, 15 were particularly abundant, 14 of which showed no sequence similarity to any known noncoding RNA, and at least six of which form very stable RNA secondary structures. The analysis of a large number of tRNA fragments suggested that unique relationships exist between the anticodons of the tRNAs and the sites of tRNA degradation. Previous bacterial tRNA degradation studies have been limited to specific organisms, such as
Escherichia coli
and
Streptomyces coelicolor
, and the current results suggest that specific tRNA decay occurs more frequently than previously expected.
Carbapenem-Hydrolyzing GES-5-Encoding Gene on Different Plasmid Types Recovered from a Bacterial Community in a Sewage Treatment Plant
Authors: Girlich Delphine , Poirel Laurent , Szczepanowski Rafael , Schlüter Andreas , Nordmann Patrice 
Published: December 2011

ABSTRACT

Plasmids pRSB113 and pRSB115 were recovered from an activated sludge bacterial community of a municipal wastewater treatment plant in Germany. Both plasmids carry the same
bla
GES-5
carbapenemase gene, located within two distinct class 1 integrons. These plasmids have different backbones, belong to different incompatibility groups, and could replicate in both
Pseudomonas aeruginosa
and
Escherichia coli
.
Identification and Characterization of the LysR-Type Transcriptional Regulator HsdR for Steroid-Inducible Expression of the 3α-Hydroxysteroid Dehydrogenase/Carbonyl Reductase Gene in Comamonas testosteroni
Authors: Gong Wenjie , Xiong Guangming , Maser Edmund 
Published: December 2011

ABSTRACT

3α-Hydroxysteroid dehydrogenase/carbonyl reductase (3α-HSD/CR) from
Comamonas testosteroni
is a key enzyme in steroid degradation in soil and water. 3α-HSD/CR gene (
hsdA
) expression can be induced by steroids like testosterone and progesterone. Previously, we have shown that the induction of
hsdA
expression by steroids is a derepression where steroidal inducers bind to two repressors, RepA and RepB, thereby preventing the blocking of
hsdA
transcription and translation, respectively (G. Xiong and E. Maser, J. Biol. Chem.
276:
9961-9970, 2001; G. Xiong, H. J. Martin, and E. Maser, J. Biol. Chem.
278
:47400–47407, 2003). In the present study, a new LysR-type transcriptional factor, HsdR, for 3α-HSD/CR expression in
C. testosteroni
has been identified. The
hsdR
gene is located 2.58 kb downstream from
hsdA
on the
C. testosteroni
ATCC 11996 chromosome with an orientation opposite that of
hsdA
. The
hsdR
gene was cloned and recombinant HsdR protein was produced, as was anti-HsdR polyclonal antibodies. While heterologous transformation systems revealed that HsdR activates the expression of the
hsdA
gene, electrophoresis mobility shift assays showed that HsdR specifically binds to the
hsdA
promoter region. Interestingly, the activity of HsdR is dependent on decreased repression by RepA. Furthermore,
in vitro
binding assays indicated that HsdR can come into contact with RNA polymerase. As expected, an
hsdR
knockout mutant expressed low levels of 3α-HSD/CR compared to that of wild-type
C. testosteroni
after testosterone induction. In conclusion, HsdR is a positive transcription factor for the
hsdA
gene and promotes the induction of 3α-HSD/CR expression in
C. testosteroni
.
CTX-M-15 Extended-Spectrum β-Lactamase in a Shiga Toxin-Producing Escherichia coli Isolate of Serotype O111:H8
Authors: Valat Charlotte , Haenni Marisa , Saras Estelle , Auvray Frédéric , Forest Karine , Oswald Eric , Madec Jean-Yves 
Published: December 2011

ABSTRACT

We report the discovery of a CTX-M-15-producing
Escherichia coli
(STEC) of serogroup O111:H8, a major serotype responsible for human enterohemorrhagic
Escherichia coli
(EHEC) infections. In line with the recent CTX-M-15/O104:H4
E. coli
outbreak, these data may reflect an accelerating spread of resistance to expanded-spectrum cephalosporins within the
E. coli
population, including STEC isolates.
Absence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex CC398 as a Nasal Colonizer of Pigs Raised in an Alternative System
Authors: Cuny Christiane , Friedrich Alexander W. , Witte Wolfgang 
Published: December 2011

ABSTRACT

Livestock-associated methicillin-resistant
Staphylococcus aureus
(LA-MRSA) ST398 isolated from pigs raised in conventional farms was previously reported. Here we report a study on 25 farms adhering to an alternative system. LA-MRSA ST398 was not detected in nasal swabs from 178 pigs or from 89 humans working and living on these farms.
Requirement for RNA Helicase CsdA for Growth of Yersinia pseudotuberculosis IP32953 at Low Temperatures
Authors: Palonen Eveliina , Lindström Miia , Somervuo Panu , Johansson Per , Björkroth Johanna , Korkeala Hannu 
Published: December 2011

ABSTRACT

The expression of
csdA
, encoding an RNA helicase, was induced at 3°C in
Yersinia pseudotuberculosis
. The role of CsdA in
Y. pseudotuberculosis
under cold conditions was confirmed by impaired growth of insertional
csdA
mutants at 3°C. The results suggest that CsdA is crucial for
Y. pseudotuberculosis
survival in the chilled food chain.
Lactic Acid Bacterium and Yeast Microbiotas of 19 Sourdoughs Used for Traditional/Typical Italian Breads: Interactions between Ingredients and Microbial Species Diversity
Authors: Minervini Fabio , Di Cagno Raffaella , Lattanzi Anna , De Angelis Maria , Antonielli Livio , Cardinali Gianluigi , Cappelle Stefan , Gobbetti Marco 
Published: December 2011

ABSTRACT

The study of the microbiotas of 19 Italian sourdoughs used for the manufacture of traditional/typical breads allowed the identification, through a culture-dependent approach, of 20 and 4 species of lactic acid bacteria (LAB) and yeasts, respectively. Numerically, the most frequent LAB isolates were
Lactobacillus sanfranciscensis
(ca. 28% of the total LAB isolates),
Lactobacillus plantarum
(ca. 16%), and
Lactobacillus paralimentarius
(ca. 14%).
Saccharomyces cerevisiae
was identified in 16 sourdoughs.
Candida humilis
,
Kazachstania barnettii
, and
Kazachstania exigua
were also identified. As shown by principal component analysis (PCA), a correlation was found between the ingredients, especially the type of flour, the microbial community, and the biochemical features of sourdoughs.
Triticum durum
flours were characterized by the high level of maltose, glucose, fructose, and free amino acids (FAA) correlated with the sole or main presence of obligately heterofermentative LAB, the lowest number of facultatively heterofermentative strains, and the low cell density of yeasts in the mature sourdoughs. This study highlighted, through a comprehensive and comparative approach, the dominant microbiotas of 19 Italian sourdoughs, which determined some of the peculiarities of the resulting traditional/typical Italian breads.
Enigmatic Presence of Mitochondrial Complex I in Trypanosoma brucei Bloodstream Forms
Authors: Surve Sachin , Heestand Meredith , Panicucci Brian , Schnaufer Achim , Parsons Marilyn 
Published: December 2011

ABSTRACT

The presence of mitochondrial respiratory complex I in the pathogenic bloodstream stages of
Trypanosoma brucei
has been vigorously debated: increased expression of mitochondrially encoded functional complex I mRNAs is countered by low levels of enzymatic activity that show marginal inhibition by the specific inhibitor rotenone. We now show that epitope-tagged versions of multiple complex I subunits assemble into α and β subcomplexes in the bloodstream stage and that these subcomplexes require the mitochondrial genome for their assembly. Despite the presence of these large (740- and 855-kDa) multisubunit complexes, the electron transport activity of complex I is not essential under experimental conditions since null mutants of two core genes (
NUBM
and
NUKM
) showed no growth defect
in vitro
or in mouse infection. Furthermore, the null mutants showed no decrease in NADH:ubiquinone oxidoreductase activity, suggesting that the observed activity is not contributed by complex I. This work conclusively shows that despite the synthesis and assembly of subunit proteins, the enzymatic function of the largest respiratory complex is neither significant nor important in the bloodstream stage. This situation appears to be in striking contrast to that for the other respiratory complexes in this parasite, where physical presence in a life-cycle stage always indicates functional significance.
Resolving Phenylalanine Metabolism Sheds Light on Natural Synthesis of Penicillin G in Penicillium chrysogenum
Authors: Veiga Tânia , Solis-Escalante Daniel , Romagnoli Gabriele , ten Pierick Angela , Hanemaaijer Mark , Deshmuhk Amit , Wahl Aljoscha , Pronk Jack T. , Daran Jean-Marc 
Published: December 2011

ABSTRACT

The industrial production of penicillin G by
Penicillium chrysogenum
requires the supplementation of the growth medium with the side chain precursor phenylacetate. The growth of
P. chrysogenum
with phenylalanine as the sole nitrogen source resulted in the extracellular production of phenylacetate and penicillin G. To analyze this natural pathway for penicillin G production, chemostat cultures were switched to [U-
13
C]phenylalanine as the nitrogen source. The quantification and modeling of the dynamics of labeled metabolites indicated that phenylalanine was (i) incorporated in nascent protein, (ii) transaminated to phenylpyruvate and further converted by oxidation or by decarboxylation, and (iii) hydroxylated to tyrosine and subsequently metabolized via the homogentisate pathway. The involvement of the homogentisate pathway was supported by the comparative transcriptome analysis of
P. chrysogenum
cultures grown with phenylalanine and with (NH
4
)
2
SO
4
as the nitrogen source. This transcriptome analysis also enabled the identification of two putative 2-oxo acid decarboxylase genes (Pc13g9300 and Pc18g01490). cDNAs of both genes were cloned and expressed in the 2-oxo-acid-decarboxylase-free
Saccharomyces cerevisiae
strain CEN.PK711-7C (
pdc1 pdc5 pdc6Δ aro10Δ thi3Δ
). The introduction of Pc13g09300 restored the growth of this
S. cerevisiae
mutant on glucose and phenylalanine, thereby demonstrating that Pc13g09300 encodes a dual-substrate pyruvate and phenylpyruvate decarboxylase, which plays a key role in an Ehrlich-type pathway for the production of phenylacetate in
P. chrysogenum
. These results provide a basis for the metabolic engineering of
P. chrysogenum
for the production of the penicillin G side chain precursor phenylacetate.
Surface-Localized Spermidine Protects the Pseudomonas aeruginosa Outer Membrane from Antibiotic Treatment and Oxidative Stress
Authors: Johnson Lori , Mulcahy Heidi , Kanevets Uliana , Shi Yan , Lewenza Shawn 
Published: December 2011

ABSTRACTExtracellular DNA acts as a cation chelator and induces the expression of antibiotic resistance genes regulated by Mg2+levels. Here we report the characterization of novel DNA-induced genes inPseudomonas aeruginosathat are annotated as homologs of the spermidine synthesis genesspeD(PA4773) andspeE(PA4774). The addition of sublethal concentrations of DNA and membrane-damaging antibiotics induced expression of the genesPA4773toPA4775, as shown using transcriptionalluxfusions and quantitative RT-PCR. Exogenous polyamine addition prevented DNA- and peptide-mediated gene induction. Mutation ofPA4774resulted in an increased outer membrane (OM) susceptibility phenotype upon polymyxin B, CP10A, and gentamicin treatment. When the membrane-localized fluorescent probe C11-BODIPY581/591was used as an indicator of peroxidation of membrane lipids, thePA4774::luxmutant demonstrated an increased susceptibility to oxidative membrane damage from H2O2treatment. Addition of exogenous polyamines protected the membranes of thePA4774::luxmutant from polymyxin B and H2O2treatment. Polyamines from the outer surface were isolated and shown to contain putrescine and spermidine by using high-performance liquid chromatography and mass spectrometry. ThePA4774::luxmutant did not produce spermidine on the cell surface, but genetic complementation restored surface spermidine production as well as the antibiotic and oxidative stress resistance phenotypes of the membrane. We have identified new functions for spermidine on the cell surface and propose that polyamines are produced under Mg2+-limiting conditions as an organic polycation to bind lipopolysaccharide (LPS) and to stabilize and protect the outer membrane against antibiotic and oxidative damage.
The Translocation Domain in Trimeric Autotransporter Adhesins Is Necessary and Sufficient for Trimerization and Autotransportation
Authors: Mikula Kornelia M. , Leo Jack C. , Łyskowski Andrzej , Kedracka-Krok Sylwia , Pirog Artur , Goldman Adrian 
Published: December 2011

ABSTRACT

Trimeric autotransporter adhesins (TAAs) comprise one of the secretion pathways of the type V secretion system. The mechanism of their translocation across the outer membrane remains unclear, but it most probably occurs by the formation of a hairpin inside the β-barrel translocation unit, leading to transportation of the passenger domain from the C terminus to the N terminus through the lumen of the β-barrel. We further investigated the phenomenon of autotransportation and the rules that govern it. We showed by coexpressing different
Escherichia coli
immunoglobulin-binding (Eib) proteins that highly similar TAAs could form stochastically mixed structures (heterotrimers). We further investigated this phenomenon by coexpressing two more distantly related TAAs, EibA and YadA. These, however, did not form heterotrimers; indeed, coexpression was lethal to the cells, leading to elimination of one or another of the genes. However, substituting in either protein the barrel of the other one so that the barrels were identical led to formation of heterotrimers as for Eibs. Our work shows that trimerization of the β-barrel, but not the passenger domain, is necessary and sufficient for TAA secretion while the passenger domain is not.
Genes Involved in Immunity to and Secretion of Aureocin A53, an Atypical Class II Bacteriocin Produced by Staphylococcus aureus A53
Authors: Nascimento Janaína dos Santos , Coelho Marcus Lívio Varella , Ceotto Hilana , Potter Amina , Fleming Luana Rocha , Salehian Zhian , Nes Ingolf F. , Bastos Maria do Carmo de Freire 
Published: December 2011

ABSTRACT

Aureocin A53 is an antimicrobial peptide produced by
Staphylococcus aureus
A53. The genetic determinants involved in aureocin A53 production and immunity to its action are organized in at least four transcriptional units encoded by the 10.4-kb plasmid pRJ9. One transcriptional unit carries only the bacteriocin structural gene,
aucA
. No immunity gene is found downstream of
aucA
, as part of the same transcriptional unit. Further downstream of
aucA
is found an operon which contains the three genes
aucEFG
, whose products seem to associate to form a dedicated ABC transporter. When
aucEFG
were expressed in RN4220, an aureocin A53-sensitive
S. aureus
strain, this strain became partially resistant to the bacteriocin. A gene disruption mutant in
aucE
was defective in aureocin A53 externalization and more sensitive to aureocin A53 than the wild-type strain, showing that
aucEFG
are involved in immunity to aureocin A53 by active extrusion of the bacteriocin. Full resistance to aureocin A53 was exhibited by transformants carrying, besides
aucEFG
, the operon formed by two genes,
aucIB
and
aucIA
, located between
aucA
and
aucEFG
and carried in the opposite strand. AucIA and AucIB share similarities with hypothetical proteins not found in the gene clusters of other bacteriocins. A gene disruption mutant in
orf8
, located upstream of
aucA
and whose product exhibits about 50% similarity to a number of hypothetical membrane proteins found in many Gram-positive bacteria, was strongly affected in aureocin A53 externalization but resistant to aureocin A53, suggesting that Orf8 is also involved in aureocin A53 secretion.