bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of Xylella fastidiosa to Zinc: Decreased Culturability, Increased Exopolysaccharide Production, and Formation of Resilient Biofilms under Flow Conditions
Authors: Navarrete Fernando , De La Fuente Leonardo 
Published: November 2013

ABSTRACT

The bacterial plant pathogen
Xylella fastidiosa
produces biofilm that accumulates in the host xylem vessels, affecting disease development in various crops and bacterial acquisition by insect vectors. Biofilms are sensitive to the chemical composition of the environment, and mineral elements being transported in the xylem are of special interest for this pathosystem. Here,
X. fastidiosa
liquid cultures were supplemented with zinc and compared with nonamended cultures to determine the effects of Zn on growth, biofilm, and exopolysaccharide (EPS) production under batch and flow culture conditions. The results show that Zn reduces growth and biofilm production under both conditions. However, in microfluidic chambers under liquid flow and with constant bacterial supplementation (closer to conditions inside the host), a dramatic increase in biofilm aggregates was seen in the Zn-amended medium. Biofilms formed under these conditions were strongly attached to surfaces and were not removed by medium flow. This phenomenon was correlated with increased EPS production in stationary-phase cells grown under high Zn concentrations. Zn did not cause greater adhesion to surfaces by individual cells. Additionally, viability analyses suggest that
X. fastidiosa
may be able to enter the viable but nonculturable state
in vitro
, and Zn can hasten the onset of this state. Together, these findings suggest that Zn can act as a stress factor with pleiotropic effects on
X. fastidiosa
and indicate that, although Zn could be used as a bactericide treatment, it could trigger the undesired effect of stronger biofilm formation upon reinoculation events.
Investigation of the
malE
Promoter and MalR, a Positive Regulator of the Maltose Regulon, for an Improved Expression System in Sulfolobus acidocaldarius
Authors: Wagner Michaela , Wagner Alexander , Ma Xiaoqing , Kort Julia Christin , Ghosh Abhrajyoti , Rauch Bernadette , Siebers Bettina , Albers Sonja-Verena 
Published: November 2013

ABSTRACT

In this study, the regulator MalR (Saci_1161) of the TrmB family from
Sulfolobus acidocaldarius
was identified and was shown to be involved in transcriptional control of the maltose regulon (Saci_1660 to Saci_1666), including the ABC transporter (
malEFGK
), α-amylase (
amyA
), and α-glycosidase (
malA
). The Δ
malR
deletion mutant exhibited a significantly decreased growth rate on maltose and dextrin but not on sucrose. The expression of the genes organized in the maltose regulon was induced only in the presence of MalR and maltose in the growth medium, indicating that MalR, in contrast to its TrmB and TrmB-like homologues, is an activator of the maltose gene cluster. Electrophoretic mobility shift assays revealed that the binding of MalR to
malE
was independent of sugars. Here we report the identification of the archaeal maltose regulator protein MalR, which acts as an activator and controls the expression of genes involved in maltose transport and metabolic conversion in
S. acidocaldarius
, and its use for improvement of the
S. acidocaldarius
expression system under the control of an optimized maltose binding protein (
malE
) promoter by promoter mutagenesis.
Anti-Inflammatory Properties of Streptococcus salivarius, a Commensal Bacterium of the Oral Cavity and Digestive Tract
Authors: Kaci Ghalia , Goudercourt Denise , Dennin Véronique , Pot Bruno , Doré Joël , Ehrlich S. Dusko , Renault Pierre , Blottière Hervé M. , Daniel Catherine , Delorme Christine 
Published: November 2013

ABSTRACT

Streptococcus salivarius
is one of the first colonizers of the human oral cavity and gut after birth and therefore may contribute to the establishment of immune homeostasis and regulation of host inflammatory responses. The anti-inflammatory potential of
S. salivarius
was first evaluated
in vitro
on human intestinal epithelial cells and human peripheral blood mononuclear cells. We show that live
S. salivarius
strains inhibited
in vitro
the activation of the NF-κB pathway on intestinal epithelial cells. We also demonstrate that the live
S. salivarius
JIM8772 strain significantly inhibited inflammation in severe and moderate colitis mouse models. These
in vitro
and
in vivo
anti-inflammatory properties were not found with heat-killed
S. salivarius
, suggesting a protective response exclusively with metabolically active bacteria.
Solubility Behavior of Cyanophycin Depending on Lysine Content
Authors: Wiefel Lars , Steinbüchel Alexander 
Published: November 2013

ABSTRACT
Study of the synthesis of cyanophycin (CGP) in recombinant organisms focused for a long time mostly on the insoluble form of CGP, due to its easy purification and its putative use as a precursor for biodegradable chemicals. Recently, another form of CGP, which, in contrast to the insoluble form, was soluble at neutral pH, became interesting due to its high lysine content, which was also assumed to be the reason for the solubility of the polymer. In this study, we demonstrate that lysine incorporated into insoluble CGP affected the solubility of the polymer in relation to its lysine content. Insoluble CGP can be separated along a temperature gradient of 90°C to 30°C, where CGP showed an increasing lysine content corresponding to a decreasing temperature needed for solubilization. CGP with less than 3 to 4 mol% lysine did not become soluble even at 90°C, while CGP with 31 mol% lysine was soluble at 30°C. In lysine fractions at higher than 31 mol%, CGP was soluble. The temperature separation will be suitable for improving the downstream processing of CGP synthesized in large-scale fermentations, including faster and more efficient purification of CGP, as well as enrichment and separation of dipeptides and CGP with specific amino acid compositions.
Restoration of Bioactive Lantibiotic Suicin from a Remnant
lan
Locus of Pathogenic Streptococcus suis Serotype 2
Authors: Wang Jian , Gao Yong , Teng Kunling , Zhang Jie , Sun Shutao , Zhong Jin 
Published: November 2013

ABSTRACT

Lantibiotics are ribosomally synthesized, posttranslationally modified antimicrobial peptides. Their biosynthesis genes are usually organized in gene clusters, which are mainly found in Gram-positive bacteria, including pathogenic streptococci. Three highly virulent
Streptococcus suis
serotype 2 strains (98HAH33, 05ZYH33, and SC84) have been shown to contain an 89K pathogenicity island. Here, on these islands, we unveiled and reannotated a putative lantibiotic locus designated
sui
which contains a virulence-associated two-component regulator,
suiK-suiR. In silico
analysis revealed that the putative lantibiotic modification gene
suiM
was interrupted by a 7.9-kb integron and that other biosynthesis-related genes contained various frameshift mutations. By reconstituting the intact
suiM
in
Escherichia coli
together with a semi-
in vitro
biosynthesis system, a putative lantibiotic named suicin was produced with bactericidal activities against a variety of Gram-positive strains, including pathogenic streptococci and vancomycin-resistant enterococci. Ring topology dissection indicated that the 34-amino-acid lantibiotic contained two methyllanthionine residues and one disulfide bridge, which render suicin in an N-terminal linear and C-terminal globular shape. To confirm the function of
suiK-suiR
, SuiR was overexpressed and purified.
In vitro
analysis showed that SuiR could specifically bind to the
suiA
gene promoter. Its coexpression with
suiK
could activate
suiA
gene promoter in
Lactococcus lactis
NZ9000. Conclusively, we obtained a novel lantibiotic suicin by restoring its production from the remnant
sui
locus and demonstrated that virulence-associated SuiK-SuiR regulates its production.
Potential Role of Nitrite for Abiotic Fe(II) Oxidation and Cell Encrustation during Nitrate Reduction by Denitrifying Bacteria
Authors: Klueglein Nicole , Zeitvogel Fabian , Stierhof York-Dieter , Floetenmeyer Matthias , Konhauser Kurt O. , Kappler Andreas , Obst Martin 
Published: November 2013

ABSTRACT

Microorganisms have been observed to oxidize Fe(II) at neutral pH under anoxic and microoxic conditions. While most of the mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria become encrusted with Fe(III)-rich minerals, photoautotrophic and microaerophilic Fe(II) oxidizers avoid cell encrustation. The Fe(II) oxidation mechanisms and the reasons for encrustation remain largely unresolved. Here we used cultivation-based methods and electron microscopy to compare two previously described nitrate-reducing Fe(II) oxidizers (
Acidovorax
sp. strain BoFeN1 and
Pseudogulbenkiania
sp. strain 2002) and two heterotrophic nitrate reducers (
Paracoccus denitrificans
ATCC 19367 and
P. denitrificans
Pd 1222). All four strains oxidized ∼8 mM Fe(II) within 5 days in the presence of 5 mM acetate and accumulated nitrite (maximum concentrations of 0.8 to 1.0 mM) in the culture media. Iron(III) minerals, mainly goethite, formed and precipitated extracellularly in close proximity to the cell surface. Interestingly, mineral formation was also observed within the periplasm and cytoplasm; intracellular mineralization is expected to be physiologically disadvantageous, yet acetate consumption continued to be observed even at an advanced stage of Fe(II) oxidation. Extracellular polymeric substances (EPS) were detected by lectin staining with fluorescence microscopy, particularly in the presence of Fe(II), suggesting that EPS production is a response to Fe(II) toxicity or a strategy to decrease encrustation. Based on the data presented here, we propose a nitrite-driven, indirect mechanism of cell encrustation whereby nitrite forms during heterotrophic denitrification and abiotically oxidizes Fe(II). This work adds to the known assemblage of Fe(II)-oxidizing bacteria in nature and complicates our ability to delineate microbial Fe(II) oxidation in ancient microbes preserved as fossils in the geological record.
Functional Screening and
In Vitro
Analysis Reveal Thioesterases with Enhanced Substrate Specificity Profiles That Improve Short-Chain Fatty Acid Production in Escherichia coli
Authors: McMahon Matthew D. , Prather Kristala L. J. 
Published: November 2013

ABSTRACT

Short-chain fatty acid (SCFA) biosynthesis is pertinent to production of biofuels, industrial compounds, and pharmaceuticals from renewable resources. To expand on
Escherichia coli
SCFA products, we previously implemented a coenzyme A (CoA)-dependent pathway that condenses acetyl-CoA to a diverse group of short-chain fatty acyl-CoAs. To increase product titers and reduce premature pathway termination products, we conducted
in vivo
and
in vitro
analyses to understand and improve the specificity of the acyl-CoA thioesterase enzyme, which releases fatty acids from CoA. A total of 62 putative bacterial thioesterases, including 23 from the cow rumen microbiome, were inserted into a pathway that condenses acetyl-CoA to an acyl-CoA molecule derived from exogenously provided propionic or isobutyric acid. Functional screening revealed thioesterases that increase production of saturated (valerate), unsaturated (
trans
-2-pentenoate), and branched (4-methylvalerate) SCFAs compared to overexpression of
E. coli
thioesterase
tesB
or native expression of endogenous thioesterases. To determine if altered thioesterase acyl-CoA substrate specificity caused the increase in product titers, six of the most promising enzymes were analyzed
in vitro
. Biochemical assays revealed that the most productive thioesterases rely on promiscuous activity but have greater specificity for product-associated acyl-CoAs than for precursor acyl-CoAs. In this study, we introduce novel thioesterases with improved specificity for saturated, branched, and unsaturated short-chain acyl-CoAs, thereby expanding the diversity of potential fatty acid products while increasing titers of current products. The growing uncertainty associated with protein database annotations denotes this study as a model for isolating functional biochemical pathway enzymes in situations where experimental evidence of enzyme function is absent.
The Pine Bark Adelgid, Pineus strobi, Contains Two Novel Bacteriocyte-Associated Gammaproteobacterial Symbionts
Authors: Toenshoff Elena R. , Szabó Gitta , Gruber Daniela , Horn Matthias 
Published: November 2013

ABSTRACT

Bacterial endosymbionts of the pine bark adelgid,
Pineus strobi
(Insecta: Hemiptera: Adelgidae), were investigated using transmission electron microscopy, 16S and 23S rRNA-based phylogeny, and fluorescence
in situ
hybridization. Two morphologically different symbionts affiliated with the
Gammaproteobacteria
were present in distinct bacteriocytes. One of them (“
Candidatus
Annandia pinicola”) is most closely related to an endosymbiont of
Adelges tsugae
, suggesting that they originate from a lineage already present in ancient adelgids before the hosts diversified into the two major clades,
Adelges
and
Pineus
. The other
P. strobi
symbiont (“
Candidatus
Hartigia pinicola”) represents a novel symbiont lineage in members of the Adelgidae. Our findings lend further support for a complex evolutionary history of the association of adelgids with a phylogenetically diverse set of bacterial symbionts.
An
N
-Acyl Homoserine Lactone Synthase in the Ammonia-Oxidizing Bacterium Nitrosospira multiformis
Authors: Gao Jie , Ma Anzhou , Zhuang Xuliang , Zhuang Guoqiang 
Published: November 2013

ABSTRACT

The chemolithoautotrophic bacterium
Nitrosospira multiformis
is involved in affecting the process of nitrogen cycling. Here we report the existence and characterization of a functional quorum sensing signal synthase in
N. multiformis
. One gene (
nmuI
) playing a role in generating a protein with high levels of similarity to
N
-acyl homoserine lactone (AHL) synthase protein families was identified. Two AHLs (C
14
-AHL and 3-oxo-C
14
-AHL) were detected using an AHL biosensor and liquid chromatography-mass spectrometry (LC-MS) when
nmuI
, producing a LuxI homologue, was introduced into
Escherichia coli
. However, by extracting
N. multiformis
culture supernatants with acidified ethyl acetate, no AHL product was obtained that was capable of activating the biosensor or being detected by LC-MS. According to reverse transcription-PCR, the
nmuI
gene is transcribed in
N. multiformis
, and a LuxR homolog (NmuR) in this ammonia-oxidizing strain showed great sensitivity to long-chain AHL signals by solubility assay. A degradation experiment demonstrated that the absence of AHL signals might be attributed to the possible AHL-inactivating activities of this strain. To summarize, an AHL synthase gene (
nmuI
) acting as a long-chain AHL producer has been found in a chemolithotrophic ammonia-oxidizing microorganism, and the results provide an opportunity to complete the knowledge of the regulatory networks in
N. multiformis
.
3-Hydroxybutyrate Oligomer Hydrolase and 3-Hydroxybutyrate Dehydrogenase Participate in Intracellular Polyhydroxybutyrate and Polyhydroxyvalerate Degradation in Paracoccus denitrificans
Authors: Lu Jing , Takahashi Akira , Ueda Shunsaku 
Published: November 2013

ABSTRACT

Genes encoding 3-hydroxybutyrate oligomer hydrolase (PhaZc) and 3-hydroxybutyrate dehydrogenase (Hbd) were isolated from
Paracoccus denitrificans
. PhaZc and Hbd were overproduced as His-tagged proteins in
Escherichia coli
and purified by affinity and gel filtration chromatography. Purified His-tagged proteins had molecular masses of 31 kDa and 120 kDa (a tetramer of 29-kDa subunits). The His-tagged PhaZc hydrolyzed not only 3-hydroxybutyrate oligomers but also 3-hydroxyvalerate oligomers. The His-tagged Hbd catalyzed the dehydrogenation of 3-hydroxyvalerate as well as 3-hydroxybutyrate. When both enzymes were included in the same enzymatic reaction system with 3-hydroxyvalerate dimer, sequential reactions occurred, suggesting that PhaZc and Hbd play an important role in the intracellular degradation of poly(3-hydroxyvalerate). When the
phaZc
gene was disrupted in
P. denitrificans
by insertional inactivation, the mutant strain lost PhaZc activity. When the
phaZc
-disrupted
P. denitrificans
was complemented with
phaZc
, PhaZc activity was restored. These results suggest that
P. denitrificans
carries a single
phaZc
gene. Disruption of the
phaZc
gene in
P. denitrificans
affected the degradation rate of PHA.
Corexit 9500 Inactivates Two Enveloped Viruses of Aquatic Animals but Enhances the Infectivity of a Nonenveloped Fish Virus
Authors: Pham P. H. , Huang Y. J. , Chen C. , Bols N. C. 
Published: November 2013

ABSTRACTThe effects of Corexit 9500, a dispersant used to clean up oil spills, on invertebrates, lower vertebrates, birds, and human health have been examined, but there is a significant lack of study of the effect of this dispersant on aquatic viruses. In this study, the effects of Corexit 9500 on four aquatic viruses of differing structural composition were examined. Corexit 9500 reduced the titer of the enveloped viral hemorrhagic septicemia virus (VHSV) at all concentrations (10% to 0.001%) examined. The titer of frog virus 3 (FV3), a virus with both enveloped and nonenveloped virions, was reduced only at the high Corexit 9500 concentrations (10% to 0.1%). Corexit 9500 was unable to reduce the titer of nonenveloped infectious pancreatic necrosis virus (IPNV) but enhanced the titer of chum salmon reovirus (CSV) by 2 to 4 logs. With the ability to inactivate enveloped viruses and possibly enhance some nonenveloped viruses, Corexit 9500 has the potential to alter the aquatic virosphere.
Discovery and Characterization of a 5-Hydroxymethylfurfural Oxidase from Methylovorus sp. Strain MP688
Authors: Dijkman Willem P. , Fraaije Marco W. 
Published: November 2013

ABSTRACT

In the search for useful and renewable chemical building blocks, 5-hydroxymethylfurfural (HMF) has emerged as a very promising candidate, as it can be prepared from sugars. HMF can be oxidized to 2,5-furandicarboxylic acid (FDCA), which is used as a substitute for petroleum-based terephthalate in polymer production. On the basis of a recently identified bacterial degradation pathway for HMF, candidate genes responsible for selective HMF oxidation have been identified. Heterologous expression of a protein from
Methylovorus
sp. strain MP688 in
Escherichia coli
and subsequent enzyme characterization showed that the respective gene indeed encodes an efficient HMF oxidase (HMFO). HMFO is a flavin adenine dinucleotide-containing oxidase and belongs to the glucose-methanol-choline-type flavoprotein oxidase family. Intriguingly, the activity of HMFO is not restricted to HMF, as it is active with a wide range of aromatic primary alcohols and aldehydes. The enzyme was shown to be relatively thermostable and active over a broad pH range. This makes HMFO a promising oxidative biocatalyst that can be used for the production of FDCA from HMF, a reaction involving both alcohol and aldehyde oxidations.
The FtsZ-Like Protein FtsZm of Magnetospirillum gryphiswaldense Likely Interacts with Its Generic Homolog and Is Required for Biomineralization under Nitrate Deprivation
Authors: Müller Frank D. , Raschdorf Oliver , Nudelman Hila , Messerer Maxim , Katzmann Emanuel , Plitzko Jürgen M. , Zarivach Raz , Schüler Dirk 
Published: November 2013

ABSTRACT

Midcell selection, septum formation, and cytokinesis in most bacteria are orchestrated by the eukaryotic tubulin homolog FtsZ. The alphaproteobacterium
Magnetospirillum gryphiswaldense
(MSR-1) septates asymmetrically, and cytokinesis is linked to splitting and segregation of an intracellular chain of membrane-enveloped magnetite crystals (magnetosomes). In addition to a generic, full-length
ftsZ
gene, MSR-1 contains a truncated
ftsZ
homolog (
ftsZm
) which is located adjacent to genes controlling biomineralization and magnetosome chain formation. We analyzed the role of FtsZm in cell division and biomineralization together with the full-length MSR-1 FtsZ protein. Our results indicate that loss of FtsZm has a strong effect on microoxic magnetite biomineralization which, however, could be rescued by the presence of nitrate in the medium. Fluorescence microscopy revealed that FtsZm-mCherry does not colocalize with the magnetosome-related proteins MamC and MamK but is confined to asymmetric spots at midcell and at the cell pole, coinciding with the FtsZ protein position. In
Escherichia coli
, both FtsZ homologs form distinct structures but colocalize when coexpressed, suggesting an FtsZ-dependent recruitment of FtsZm.
In vitro
analyses indicate that FtsZm is able to interact with the FtsZ protein. Together, our data suggest that FtsZm shares key features with its full-length homolog but is involved in redox control for magnetite crystallization.
Repression of Flagellar Genes in Exponential Phase by CsgD and CpxR, Two Crucial Modulators of Escherichia coli Biofilm Formation
Authors: Dudin Omaya , Geiselmann Johannes , Ogasawara Hiroshi , Ishihama Akira , Lacour Stéphan 
Published: November 2013

ABSTRACT

Escherichia coli
adapts its lifestyle to the variations of environmental growth conditions, swapping between swimming motility or biofilm formation. The stationary-phase sigma factor RpoS is an important regulator of this switch, since it stimulates adhesion and represses flagellar biosynthesis. By measuring the dynamics of gene expression, we show that RpoS inhibits the transcription of the flagellar sigma factor, FliA, in exponential growth phase. RpoS also partially controls the expression of CsgD and CpxR, two transcription factors important for bacterial adhesion. We demonstrate that these two regulators repress the transcription of
fliA
,
flgM
, and
tar
and that this regulation is dependent on the growth medium. CsgD binds to the
flgM
and
fliA
promoters around their −10 promoter element, strongly suggesting direct repression. We show that CsgD and CpxR also affect the expression of other known modulators of cell motility. We propose an updated structure of the regulatory network controlling the choice between adhesion and motility.
Cyclic Di-AMP Impairs Potassium Uptake Mediated by a Cyclic Di-AMP Binding Protein in Streptococcus pneumoniae
Authors: Bai Yinlan , Yang Jun , Zarrella Tiffany M. , Zhang Yang , Metzger Dennis W. , Bai Guangchun 
Published: November 2013

ABSTRACT

Cyclic di-AMP (c-di-AMP) has been shown to play important roles as a second messenger in bacterial physiology and infections. However, understanding of how the signal is transduced is still limited. Previously, we have characterized a diadenylate cyclase and two c-di-AMP phosphodiesterases in
Streptococcus pneumoniae
, a Gram-positive pathogen. In this study, we identified a
c
-di-
A
MP
b
inding
p
rotein (CabP) in
S. pneumoniae
using c-di-AMP affinity chromatography. We demonstrated that CabP specifically bound c-di-AMP and that this interaction could not be interrupted by competition with other nucleotides, including ATP, cAMP, AMP, phosphoadenylyl adenosine (pApA), and cyclic di-GMP (c-di-GMP). By using a bacterial two-hybrid system and genetic mutagenesis, we showed that CabP directly interacted with a potassium transporter (SPD_0076) and that both proteins were required for pneumococcal growth in media with low concentrations of potassium. Interestingly, the interaction between CabP and SPD_0076 and the efficiency of potassium uptake were impaired by elevated c-di-AMP in pneumococci. These results establish a direct c-di-AMP-mediated signaling pathway that regulates pneumococcal potassium uptake.