bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of Fatty Acid-Producing Corynebacterium glutamicum Strains
Authors: Takeno Seiki , Takasaki Manami , Urabayashi Akinobu , Mimura Akinori , Muramatsu Tetsuhiro , Mitsuhashi Satoshi , Ikeda Masato 
Published: August 2013

ABSTRACTTo date, no information has been made available on the genetic traits that lead to increased carbon flow into the fatty acid biosynthetic pathway ofCorynebacterium glutamicum. To develop basic technologies for engineering, we employed an approach that begins by isolating a fatty acid-secreting mutant without depending on mutagenic treatment. This was followed by genome analysis to characterize its genetic background. The selection of spontaneous mutants resistant to the palmitic acid ester surfactant Tween 40 resulted in the isolation of a desired mutant that produced oleic acid, suggesting that a single mutation would cause increased carbon flow down the pathway and subsequent excretion of the oversupplied fatty acid into the medium. Two additional rounds of selection of spontaneous cerulenin-resistant mutants led to increased production of the fatty acid in a stepwise manner. Whole-genome sequencing of the resulting best strain identified three specific mutations (fasR20,fasA63up, andfasA2623). Allele-specific PCR analysis showed that the mutations arose in that order. Reconstitution experiments with these mutations revealed that onlyfasR20gave rise to oleic acid production in the wild-type strain. The other two mutations contributed to an increase in oleic acid production. Deletion offasRfrom the wild-type strain led to oleic acid production as well. Reverse transcription-quantitative PCR analysis revealed that thefasR20mutation brought about upregulation of thefasAandfasBgenes encoding fatty acid synthases IA and IB, respectively, by 1.31-fold ± 0.11-fold and 1.29-fold ± 0.12-fold, respectively, and of theaccD1gene encoding the β-subunit of acetyl-CoA carboxylase by 3.56-fold ± 0.97-fold. On the other hand, thefasA63upmutation upregulated thefasAgene by 2.67-fold ± 0.16-fold. In flask cultivation with 1% glucose, thefasR20 fasA63upfasA2623triple mutant produced approximately 280 mg of fatty acids/liter, which consisted mainly of oleic acid (208 mg/liter) and palmitic acid (47 mg/liter).
Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations
Authors: Nakagawa Tatsunori , Stahl David A. 
Published: August 2013

ABSTRACT

The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO
2
fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon
Nitrosopumilus maritimus
SCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above the

K
m

for ammonia oxidation (∼500 μM) and the other well below the

K
m

(<10 nM). Transcript levels were generally immediately and differentially repressed when cells transitioned from ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO
2
fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment.
Structural Features of Sugars That Trigger or Support Conidial Germination in the Filamentous Fungus Aspergillus niger
Authors: Hayer Kimran , Stratford Malcolm , Archer David B. 
Published: August 2013

ABSTRACT

The asexual spores (conidia) of
Aspergillus niger
germinate to produce hyphae under appropriate conditions. Germination is initiated by conidial swelling and mobilization of internal carbon and energy stores, followed by polarization and emergence of a hyphal germ tube. The effects of different pyranose sugars, all analogues of
d
-glucose, on the germination of
A. niger
conidia were explored, and we define germination as the transition from a dormant conidium into a germling. Within germination, we distinguish two distinct stages, the initial swelling of the conidium and subsequent polarized growth. The stage of conidial swelling requires a germination trigger, which we define as a compound that is sensed by the conidium and which leads to catabolism of
d
-trehalose and isotropic growth. Sugars that triggered germination and outgrowth included
d
-glucose,
d
-mannose, and
d
-xylose. Sugars that triggered germination but did not support subsequent outgrowth included
d
-tagatose,
d
-lyxose, and 2-deoxy-
d
-glucose. Nontriggering sugars included
d
-galactose,
l
-glucose, and
d
-arabinose. Certain nontriggering sugars, including
d
-galactose, supported outgrowth if added in the presence of a complementary triggering sugar. This division of functions indicates that sugars are involved in two separate events in germination, triggering and subsequent outgrowth, and the structural features of sugars that support each, both, or none of these events are discussed. We also present data on the uptake of sugars during the germination process and discuss possible mechanisms of triggering in the absence of apparent sugar uptake during the initial swelling of conidia.
Substrate-Induced Transcriptional Activation of the MoCel7C Cellulase Gene Is Associated with Methylation of Histone H3 at Lysine 4 in the Rice Blast Fungus Magnaporthe oryzae
Authors: Vu Ba Van , Pham Kieu Thi Minh , Nakayashiki Hitoshi 
Published: August 2013

ABSTRACT

The mechanisms involved in substrate-dependent regulation of a
Magnaporthe oryzae
gene encoding a cellulase which we designate MoCel7C (MGG_14954) were investigated. The levels of MoCel7C transcript were dramatically increased more than 1,000-fold, 16 to 24 h after transfer to a medium containing 2% carboxymethylcellulose (CMC), while levels were very low or undetectable in conventional rich medium. Green fluorescent protein reporter assays showed that the MoCel7C promoter was activated by cello-oligosaccharides larger than a pentamer. CMC-induced activation of the MoCel7C promoter was suppressed by glucose and cellobiose. Chromatin immunoprecipitation assays revealed that histone H3 methylation on lysine 4 (H3K4) at the MoCel7C locus was associated with activation of the gene by CMC. Consistently, CMC-induced MoCel7C gene activation was drastically diminished in a knockout (KO) mutant of the MoSET1 gene, which encodes a histone lysine methyltransferase that catalyzes H3K4 methylation in
M. oryzae
. Interestingly, however, MoCel7C transcript levels under noninducing conditions were significantly increased in the MoSET1 KO mutant, suggesting that MoSET1 directly or indirectly plays a role in both activation and suppression of the MoCel7C gene in response to environmental signals. In addition, gene expression and silencing vectors using the MoCel7C promoter were constructed.
Arabinoxylan Oligosaccharide Hydrolysis by Family 43 and 51 Glycosidases from Lactobacillus brevis DSM 20054
Authors: Michlmayr Herbert , Hell Johannes , Lorenz Cindy , Böhmdorfer Stefan , Rosenau Thomas , Kneifel Wolfgang 
Published: August 2013

ABSTRACT

Due to their potential prebiotic properties, arabinoxylan-derived oligosaccharides [(A)XOS] are of great interest as functional food and feed ingredients. While the (A)XOS metabolism of
Bifidobacteriaceae
has been extensively studied, information regarding lactic acid bacteria (LAB) is still limited in this context. The aim of the present study was to fill this important gap by characterizing candidate (A)XOS hydrolyzing glycoside hydrolases (GHs) identified in the genome of
Lactobacillus brevis
DSM 20054. Two putative GH family 43 xylosidases (XynB1 and XynB2) and a GH family 43 arabinofuranosidase (Abf3) were heterologously expressed and characterized. While the function of XynB1 remains unclear, XynB2 could efficiently hydrolyze xylooligosaccharides. Abf3 displayed high specific activity for arabinobiose but could not release arabinose from an (A)XOS preparation. However, two previously reported GH 51 arabinofuranosidases from
Lb. brevis
were able to specifically remove α-1,3-linked arabinofuranosyl residues from arabino-xylooligosaccharides (AXHm3 specificity). These results imply that
Lb. brevis
is at least genetically equipped with functional enzymes in order to hydrolyze the depolymerization products of (arabino)xylans and arabinans. The distribution of related genes in
Lactobacillales
genomes indicates that GH 43 and, especially, GH 51 glycosidase genes are rare among LAB and mainly occur in obligately heterofermentative
Lactobacillus
spp.,
Pediococcus
spp., members of the
Leuconostoc/Weissella
branch, and
Enterococcus
spp. Apart from the prebiotic viewpoint, this information also adds new perspectives on the carbohydrate (i.e., pentose-oligomer) metabolism of LAB species involved in the fermentation of hemicellulose-containing substrates.
Diversity and Ecophysiology of New Isolates of Extremely Acidophilic CS
2
-Converting Acidithiobacillus Strains
Authors: Smeulders Marjan J. , Pol Arjan , Zandvoort Marcel H. , Jetten Mike S. M. , Op den Camp Huub J. M. 
Published: August 2013

ABSTRACT

Biofiltration of industrial carbon disulfide (CS
2
)-contaminated waste air streams results in the acidification of biofilters and therefore reduced performance, high water use, and increased costs. To address these issues, we isolated 16 extremely acidophilic CS
2
-converting
Acidithiobacillus thiooxidans
strains that tolerated up to 6% (vol/vol) sulfuric acid. The ecophysiological properties of five selected strains (2Bp, Sts 4-3, S1p, G8, and BBW1) were compared. These five strains had pH optima between 1 (2Bp) and 2 (S1p). Their affinities for CS
2
ranged between 80 (G8) and 130 (2Bp) μM. Strains S1p, G8, and BBW1 had more hydrophobic cell surfaces and produced less extracellular polymeric substance than did strains 2Bp and Sts 4-3. All five strains converted about 80% of the S added as CS
2
to S
0
when CS
2
was supplied in excess. The rate of S
0
consumption varied between 7 (Sts 4-3) and 63 (S1p) nmol O
2
min
−1
ml culture
−1
. Low S
0
consumption rates correlated partly with low levels of cell attachment to externally produced S
0
globules. During chemostat growth, the relative amount of CS
2
hydrolase in the cell increased with decreasing growth rates. This resulted in more S
0
accumulation during CS
2
overloads at low growth rates. Intermittent interruptions of the CS
2
supply affected all five strains. Strains S1p, G8, and BBW1 recovered from 24 h of starvation within 4 h, and strains 2Bp and Sts 4-3 recovered within 24 h after CS
2
was resupplied. We recommend the use of mixtures of
Acidithiobacillus
strains in industrial biofilters.
Novel Mono-, Di-, and Trimethylornithine Membrane Lipids in Northern Wetland Planctomycetes
Authors: Moore Eli K. , Hopmans Ellen C. , Rijpstra W. Irene C. , Villanueva Laura , Dedysh Svetlana N. , Kulichevskaya Irina S. , Wienk Hans , Schoutsen Frans , Sinninghe Damsté Jaap S. 
Published: August 2013

ABSTRACT

Northern peatlands represent a significant global carbon store and commonly originate from
Sphagnum
moss-dominated wetlands. These ombrotrophic ecosystems are rain fed, resulting in nutrient-poor, acidic conditions. Members of the bacterial phylum
Planctomycetes
are highly abundant and appear to play an important role in the decomposition of
Sphagnum
-derived litter in these ecosystems. High-performance liquid chromatography coupled to high-resolution accurate-mass mass spectrometry (HPLC-HRAM/MS) analysis of lipid extracts of four isolated planctomycetes from wetlands of European north Russia revealed novel ornithine membrane lipids (OLs) that are mono-, di-, and trimethylated at the ε-nitrogen position of the ornithine head group. Nuclear magnetic resonance (NMR) analysis of the isolated trimethylornithine lipid confirmed the structural identification. Similar fatty acid distributions between mono-, di-, and trimethylornithine lipids suggest that the three lipid classes are biosynthetically linked, as in the sequential methylation of the terminal nitrogen in phosphatidylethanolamine to produce phosphatidylcholine. The mono-, di-, and trimethylornithine lipids described here represent the first report of methylation of the ornithine head groups in biological membranes. Various bacteria are known to produce OLs under phosphorus limitation or fatty-acid-hydroxylated OLs under thermal or acid stress. The sequential methylation of OLs, leading to a charged choline-like moiety in the trimethylornithine lipid head group, may be an adaptation to provide membrane stability under acidic conditions without the use of scarce phosphate in nutrient-poor ombrotrophic wetlands.
Cumate-Inducible Gene Expression System for Sphingomonads and Other Alphaproteobacteria
Authors: Kaczmarczyk Andreas , Vorholt Julia A. , Francez-Charlot Anne 
Published: August 2013

ABSTRACT

Tunable promoters represent a pivotal genetic tool for a wide range of applications. Here we present such a system for sphingomonads, a phylogenetically diverse group of bacteria that have gained much interest for their potential in bioremediation and their use in industry and for which no dedicated inducible gene expression system has been described so far. A strong, constitutive synthetic promoter was first identified through a genetic screen and subsequently combined with the repressor and the operator sites of the
Pseudomonas putida
F1
cym
/
cmt
system. The resulting promoter, termed P
Q5
, responds rapidly to the inducer cumate and shows a maximal induction ratio of 2 to 3 orders of magnitude in the different sphingomonads tested. Moreover, it was also functional in other
Alphaproteobacteria
, such as the model organisms
Caulobacter crescentus
,
Paracoccus denitrificans
, and
Methylobacterium extorquens
. In the noninduced state, expression from P
Q5
is low enough to allow gene depletion analysis, as demonstrated with the essential gene
phyP
of
Sphingomonas
sp. strain Fr1. A set of P
Q5
-based plasmids has been constructed allowing fusions to affinity tags or fluorescent proteins.
Prevalences of Shiga Toxin Subtypes and Selected Other Virulence Factors among Shiga-Toxigenic Escherichia coli Strains Isolated from Fresh Produce
Authors: Feng Peter C. H. , Reddy Shanker 
Published: August 2013

ABSTRACT

Shiga-toxigenic
Escherichia coli
(STEC) strains were isolated from a variety of fresh produce, but mostly from spinach, with an estimated prevalence rate of 0.5%. A panel of 132 produce STEC strains were characterized for the presence of virulence and putative virulence factor genes and for Shiga toxin subtypes. About 9% of the isolates were found to have the
eae
gene, which encodes the intimin binding protein, and most of these belonged to known pathogenic STEC serotypes, such as O157:H7 and O26:H11, or to serotypes that reportedly have caused human illness. Among the
eae
-negative strains, there were three O113:H21 strains and one O91:H21 strain, which historically have been implicated in illness and therefore may be of concern as well. The
ehxA
gene, which encodes enterohemolysin, was found in ∼60% of the isolates, and the
saa
and
subAB
genes, which encode STEC agglutinating adhesin and subtilase cytotoxin, respectively, were found in ∼30% of the isolates. However, the precise roles of these three putative virulence factors in STEC pathogenesis have not yet been fully established. The
stx
1a
and
stx
2a
subtypes were present in 22% and 56%, respectively, of the strains overall and were the most common subtypes among produce STEC strains. The
stx
2d
subtype was the second most common subtype (28% overall), followed by
stx
2c
(7.5%), and only 2 to 3% of the produce STEC strains had the
stx
2e
and
stx
2g
subtypes. Almost half of the produce STEC strains had only partial serotypes or were untyped, and most of those that were identified belonged to unremarkable serotypes. Considering the uncertainties of some of these Stx subtypes and putative virulence factors in causing human illness, it is difficult to determine the health risk of many of these produce STEC strains.
Modeling of Fungal and Bacterial Spore Germination under Static and Dynamic Conditions
Authors: Peleg Micha , Normand Mark D. 
Published: August 2013

ABSTRACT
Isothermal germination curves, sigmoid and nonsigmoid, can be described by a variety of models reminiscent of growth models. Two of these, which are consistent with the percent of germinated spores being initially zero, were selected: one, Weibullian (or “stretched exponential”), for more or less symmetric curves, and the other, introduced by Dantigny's group, for asymmetric curves (P. Dantigny, S. P.-M. Nanguy, D. Judet-Correia, and M. Bensoussan, Int. J. Food Microbiol. 146:176–181, 2011). These static models were converted into differential rate models to simulate dynamic germination patterns, which passed a test for consistency. In principle, these and similar models, if validated experimentally, could be used to predict dynamic germination from isothermal data. The procedures to generate both isothermal and dynamic germination curves have been automated and posted as freeware on the Internet in the form of interactive Wolfram demonstrations. A fully stochastic model of individual and small groups of spores, developed in parallel, shows that when the germination probability is constant from the start, the germination curve is nonsigmoid. It becomes sigmoid if the probability monotonically rises from zero. If the probability rate function rises and then falls, the germination reaches an asymptotic level determined by the peak's location and height. As the number of individual spores rises, the germination curve of their assemblies becomes smoother. It also becomes more deterministic and can be described by the empirical phenomenological models.
A Translocation Motif in Relaxase TrwC Specifically Affects Recruitment by Its Conjugative Type IV Secretion System
Authors: Alperi Anabel , Larrea Delfina , Fernández-González Esther , Dehio Christoph , Zechner Ellen L. , Llosa Matxalen 
Published: August 2013

ABSTRACT

Type IV secretion system (T4SS) substrates are recruited through a translocation signal that is poorly defined for conjugative relaxases. The relaxase TrwC of plasmid R388 is translocated by its cognate conjugative T4SS, and it can also be translocated by the VirB/D4 T4SS of
Bartonella henselae
, causing DNA transfer to human cells. In this work, we constructed a series of TrwC variants and assayed them for DNA transfer to bacteria and human cells to compare recruitment requirements by both T4SSs. Comparison with other reported relaxase translocation signals allowed us to determine two putative translocation sequence (TS) motifs, TS1 and TS2. Mutations affecting TS1 drastically affected conjugation frequencies, while mutations affecting either motif had only a mild effect on DNA transfer rates through the VirB/D4 T4SS of
B. henselae
. These results indicate that a single substrate can be recruited by two different T4SSs through different signals. The C terminus affected DNA transfer rates through both T4SSs tested, but no specific sequence requirement was detected. The addition of a
Bartonella
intracellular delivery (BID) domain, the translocation signal for the
Bartonella
VirB/D4 T4SS, increased DNA transfer up to 4% of infected human cells, providing an excellent tool for DNA delivery to specific cell types. We show that the R388 coupling protein TrwB is also required for this high-efficiency TrwC-BID translocation. Other elements apart from the coupling protein may also be involved in substrate recognition by T4SSs.
Regulation of Host Hemoglobin Binding by the Staphylococcus aureus Clp Proteolytic System
Authors: Farrand Allison J. , Reniere Michelle L. , Ingmer Hanne , Frees Dorte , Skaar Eric P. 
Published: August 2013

ABSTRACTProtein turnover is a key process for bacterial survival mediated by intracellular proteases. Proteolytic degradation reduces the levels of unfolded and misfolded peptides that accumulate in the cell during stress conditions. Three intracellular proteases, ClpP, HslV, and FtsH, have been identified in the Gram-positive bacteriumStaphylococcus aureus, a pathogen responsible for significant morbidity and mortality worldwide. Consistent with their crucial role in protein turnover, ClpP, HslV, and FtsH affect a number of cellular processes, including metabolism, stress responses, and virulence. The ClpP protease is believed to be the principal degradation machinery inS. aureus. This study sought to identify the effect of the Clp protease on theiron-regulatedsurfacedeterminant (Isd) system, which extracts heme-iron from host hemoglobin during infection and is critical toS. aureuspathogenesis. Inactivation of components of the Clp protease alters abundance of several Isd proteins, including the hemoglobin receptor IsdB. Furthermore, the observed changes in IsdB abundance are the result of transcriptional regulation, since transcription ofisdBis decreased byclpPorclpXinactivation. In contrast, inactivation ofclpCenhancesisdBtranscription and protein abundance. Loss ofclpPorclpXimpairs host hemoglobin binding and utilization and results in severe virulence defects in a systemic mouse model of infection. These findings suggest that the Clp proteolytic system is important for regulating nutrient iron acquisition inS. aureus. The Clp protease and Isd complex are widely conserved in bacteria; therefore, these data reveal a novel Clp-dependent regulation pathway that may be present in other bacterial pathogens.
ppGpp-Dependent Negative Control of DNA Replication of Shiga Toxin-Converting Bacteriophages in Escherichia coli
Authors: Nowicki Dariusz , Kobiela Wioletta , Węgrzyn Alicja , Węgrzyn Grzegorz , Szalewska-Pałasz Agnieszka 
Published: August 2013

ABSTRACT

The pathogenicity of enterohemorrhagic
Escherichia coli
(EHEC) strains depends on the production of Shiga toxins that are encoded on lambdoid prophages. Effective production of these toxins requires prophage induction and subsequent phage replication. Previous reports indicated that lytic development of Shiga toxin-converting bacteriophages is inhibited in amino acid-starved bacteria. However, those studies demonstrated that inhibition of both phage-derived plasmid replication and production of progeny virions occurred during the stringent as well as the relaxed response to amino acid starvation, i.e., in the presence as well as the absence of high levels of ppGpp, an alarmone of the stringent response. Therefore, we asked whether ppGpp influences DNA replication and lytic development of Shiga toxin-converting bacteriophages. Lytic development of 5 such bacteriophages was tested in an
E. coli
wild-type strain and an isogenic mutant that does not produce ppGpp (ppGpp
0
). In the absence of ppGpp, production of progeny phages was significantly (in the range of an order of magnitude) more efficient than in wild-type cells. Such effects were observed in infected bacteria as well as after prophage induction. All tested bacteriophages formed considerably larger plaques on lawns formed by ppGpp
0
bacteria than on those formed by wild-type
E. coli
. The efficiency of synthesis of phage DNA and relative amount of lambdoid plasmid DNA were increased in cells devoid of ppGpp relative to bacteria containing a basal level of this nucleotide. We conclude that ppGpp negatively influences the lytic development of Shiga toxin-converting bacteriophages and that phage DNA replication efficiency is limited by the stringent control alarmone.