bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological and Metabolic Effects of Carbon Monoxide Oxidation in the Model Marine Bacterioplankton Ruegeria pomeroyi DSS-3
Authors: Cunliffe Michael 
Published: November 2012

ABSTRACT

Ruegeria pomeroyi
expresses carbon monoxide (CO) dehydrogenase and oxidizes CO; however, CO has no effect on growth. Nuclear magnetic resonance (NMR) spectra showed that CO has no effect on cellular metabolite profiles. These data support ecosystem models proposing that, even though bacterioplankton CO oxidation is biogeochemically significant, it has an insignificant effect on bacterioplankton productivity.
Heterologous Carotenoid-Biosynthetic Enzymes: Functional Complementation and Effects on Carotenoid Profiles in Escherichia coli
Authors: Song Gyu Hyeon , Kim Se Hyeuk , Choi Bo Hyun , Han Se Jong , Lee Pyung Cheon 
Published: November 2012

ABSTRACT

A limited number of carotenoid pathway genes from microbial sources have been studied for analyzing the pathway complementation in the heterologous host
Escherichia coli
. In order to systematically investigate the functionality of carotenoid pathway enzymes in
E. coli
, the pathway genes of carotenogenic microorganisms (
Brevibacterium linens
,
Corynebacterium glutamicum
,
Rhodobacter sphaeroides
,
Rhodobacter capsulatus
,
Rhodopirellula baltica
, and
Pantoea ananatis
) were modified to form synthetic expression modules and then were complemented with
Pantoea agglomerans
pathway enzymes (CrtE, CrtB, CrtI, CrtY, and CrtZ). The carotenogenic pathway enzymes in the synthetic modules showed unusual activities when complemented with
E. coli
. For example, the expression of heterologous CrtEs of
B. linens
,
C. glutamicum
, and
R. baltica
influenced
P. agglomerans
CrtI to convert its substrate phytoene into a rare product—3,4,3′,4′-tetradehydrolycopene—along with lycopene, which was an expected product, indicating that CrtE, the first enzyme in the carotenoid biosynthesis pathway, can influence carotenoid profiles. In addition, CrtIs of
R. sphaeroides
and
R. capsulatus
converted phytoene into an unusual lycopene as well as into neurosporene. Thus, this study shows that the functional complementation of pathway enzymes from different sources is a useful methodology for diversifying biosynthesis as nature does.
Induction of Nitrate-Dependent Fe(II) Oxidation by Fe(II) in Dechloromonas sp. Strain UWNR4 and Acidovorax sp. Strain 2AN
Authors: Chakraborty Anirban , Picardal Flynn 
Published: November 2012

ABSTRACT

We evaluated the inducibility of nitrate-dependent Fe(II)-EDTA oxidation (NDFO) in non-growth, chloramphenicol-amended, resting-cell suspensions of
Dechloromonas
sp. strain UWNR4 and
Acidovorax
sp. strain 2AN. Cells previously incubated with Fe(II)-EDTA oxidized ca. 6-fold more Fe(II)-EDTA than cells previously incubated with Fe(III)-EDTA. This is the first report of induction of NDFO by Fe(II).
Predation Response of Vibrio fischeri Biofilms to Bacterivorus Protists
Authors: Chavez-Dozal Alba , Gorman Clayton , Erken Martina , Steinberg Peter D. , McDougald Diane , Nishiguchi Michele K. 
Published: November 2012

ABSTRACT

Vibrio fischeri
proliferates in a sessile, stable community known as a biofilm, which is one alternative survival strategy of its life cycle. Although this survival strategy provides adequate protection from abiotic factors, marine biofilms are still susceptible to grazing by bacteria-consuming protozoa. Subsequently, grazing pressure can be controlled by certain defense mechanisms that confer higher biofilm antipredator fitness. In the present work, we hypothesized that
V. fischeri
exhibits an antipredator fitness behavior while forming biofilms. Different predators representing commonly found species in aquatic populations were examined, including the flagellates
Rhynchomonas nasuta
and
Neobodo designis
(early biofilm feeders) and the ciliate
Tetrahymena pyriformis
(late biofilm grazer).
V. fischeri
biofilms included isolates from both seawater and squid hosts (
Euprymna
and
Sepiola
species). Our results demonstrate inhibition of predation by biofilms, specifically, isolates from seawater. Additionally, antiprotozoan behavior was observed to be higher in late biofilms, particularly toward the ciliate
T. pyriformis
; however, inhibitory effects were found to be widespread among all isolates tested. These results provide an alternative explanation for the adaptive advantage and persistence of
V. fischeri
biofilms and provide an important contribution to the understanding of defensive mechanisms that exist in the out-of-host environment.
Clostridium carboxidivorans Strain P7T Recombinant Formate Dehydrogenase Catalyzes Reduction of CO
2
to Formate
Authors: Alissandratos Apostolos , Kim Hye-Kyung , Matthews Hayden , Hennessy James E. , Philbrook Amy , Easton Christopher J. 
Published: November 2012

ABSTRACT

Recombinant formate dehydrogenase from the acetogen
Clostridium carboxidivorans
strain P7
T
, expressed in
Escherichia coli
, shows particular activity towards NADH-dependent carbon dioxide reduction to formate due to the relative binding affinities of the substrates and products. The enzyme retains activity over 2 days at 4°C under oxic conditions.
Multiplex PCR Assay Targeting a Diguanylate Cyclase-Encoding Gene,
cgcA
, To Differentiate Species within the Genus Cronobacter
Authors: Carter L. , Lindsey L. A. , Grim C. J. , Sathyamoorthy V. , Jarvis K. G. , Gopinath G. , Lee C. , Sadowski J. A. , Trach L. , Pava-Ripoll M. , McCardell B. A. , Tall B. D. , Hu L. 
Published: November 2012

ABSTRACT

In a comparison to the widely used
Cronobacter rpoB
PCR assay, a highly specific multiplexed PCR assay based on
cgcA
, a diguanylate cyclase gene, that identified all of the targeted six species among 305
Cronobacter
isolates was designed. This assay will be a valuable tool for identifying suspected
Cronobacter
isolates from food-borne investigations.
An Adenovirus-Based Vaccine with a Double-Stranded RNA Adjuvant Protects Mice and Ferrets against H5N1 Avian Influenza in Oral Delivery Models
Authors: Scallan Ciaran D. , Tingley Debora W. , Lindbloom Jonathan D. , Toomey James S. , Tucker Sean N. 
Published: November 2012

ABSTRACT
An oral gene-based avian influenza vaccine would allow rapid development and simplified distribution, but efficacy has previously been difficult to achieve by the oral route. This study assessed protection against avian influenza virus challenge using a chimeric adenovirus vector expressing hemagglutinin and a double-stranded RNA adjuvant. Immunized ferrets and mice were protected upon lethal challenge. Further, ferrets immunized by the peroral route induced cross-clade neutralizing antibodies, and the antibodies were selective against hemagglutinin, not the vector. Similarly, experiments in mice demonstrated selective immune responses against HA with peroral delivery and the ability to circumvent preexisting vector immunity.
Are There Acyl-Homoserine Lactones within Mammalian Intestines?
Authors: Swearingen Matthew C. , Sabag-Daigle Anice , Ahmer Brian M. M. 
Published: November 2012

ABSTRACTManyProteobacteriaare capable of quorum sensing usingN-acyl-homoserine lactone (acyl-HSL) signaling molecules that are synthesized by LuxI or LuxM homologs and detected by transcription factors of the LuxR family. Most quorum-sensing species have at least one LuxR and one LuxI homolog. However, members of theEscherichia,Salmonella,Klebsiella, andEnterobactergenera possess only a single LuxR homolog, SdiA, and no acyl-HSL synthase. The most obvious hypothesis is that these organisms are eavesdropping on acyl-HSL production within the complex microbial communities of the mammalian intestinal tract. However, there is currently no evidence of acyl-HSLs being produced within normal intestinal communities. A few intestinal pathogens, includingYersinia enterocolitica, do produce acyl-HSLs, andSalmonellacan detect them during infection. Therefore, a more refined hypothesis is that SdiA orthologs are used for eavesdropping on other quorum-sensing pathogens in the host. However, the lack of acyl-HSL signaling among the normal intestinal residents is a surprising finding given the complexity of intestinal communities. In this review, we examine the evidence for and against the possibility of acyl-HSL signaling molecules in the mammalian intestine and discuss the possibility that related signaling molecules might be present and awaiting discovery.
The Nitrogenase Regulatory Enzyme Dinitrogenase Reductase ADP-Ribosyltransferase (DraT) Is Activated by Direct Interaction with the Signal Transduction Protein GlnB
Authors: Moure Vivian R. , Danyal Karamatullah , Yang Zhi-Yong , Wendroth Shannon , Müller-Santos Marcelo , Pedrosa Fabio O. , Scarduelli Marcelo , Gerhardt Edileusa C. M. , Huergo Luciano F. , Souza Emanuel M. , Seefeldt Lance C. 
Published: November 2012

ABSTRACTFe protein (dinitrogenase reductase) activity is reversibly inactivated by dinitrogenase reductase ADP-ribosyltransferase (DraT) in response to an increase in the ammonium concentration or a decrease in cellular energy inAzospirillum brasilense,Rhodospirillum rubrum, andRhodobacter capsulatus. The ADP-ribosyl is removed by the dinitrogenase reductase-activating glycohydrolase (DraG), promoting Fe protein reactivation. The signaling pathway leading to DraT activation by ammonium is still not completely understood, but the available evidence shows the involvement of direct interaction between the enzyme and the nitrogen-signaling PIIproteins. InA. brasilense, two PIIproteins, GlnB and GlnZ, were identified. We used Fe protein fromAzotobacter vinelandiias the substrate to assess the activity ofA. brasilenseDraTin vitrocomplexed or not with PIIproteins. Under our conditions, GlnB was necessary for DraT activity in the presence of Mg-ADP. The PIIeffector 2-oxoglutarate, in the presence of Mg-ATP, inhibited DraT-GlnB activity, possibly by inducing complex dissociation. DraT was also activated by GlnZ and by both uridylylated PIIproteins, but not by a GlnB variant carrying a partial deletion of the T loop. Kinetics studies revealed that theA. brasilenseDraT-GlnB complex was at least 18-fold more efficient than DraT purified fromR. rubrum, but with a similarKmvalue for NAD+. Our results showed that ADP-ribosylation of the Fe protein does not affect the electronic state of its metal cluster and prevents association between the Fe and MoFe proteins, thus inhibiting electron transfer.
Flagellum Density Regulates Proteus mirabilis Swarmer Cell Motility in Viscous Environments
Authors: Tuson Hannah H. , Copeland Matthew F. , Carey Sonia , Sacotte Ryan , Weibel Douglas B. 
Published: November 2012

ABSTRACT

Proteus mirabilis
is an opportunistic pathogen that is frequently associated with urinary tract infections. In the lab,
P. mirabilis
cells become long and multinucleate and increase their number of flagella as they colonize agar surfaces during swarming. Swarming has been implicated in pathogenesis; however, it is unclear how energetically costly changes in
P. mirabilis
cell morphology translate into an advantage for adapting to environmental changes. We investigated two morphological changes that occur during swarming—increases in cell length and flagellum density—and discovered that an increase in the surface density of flagella enabled cells to translate rapidly through fluids of increasing viscosity; in contrast, cell length had a small effect on motility. We found that swarm cells had a surface density of flagella that was ∼5 times larger than that of vegetative cells and were motile in fluids with a viscosity that inhibits vegetative cell motility. To test the relationship between flagellum density and velocity, we overexpressed FlhD
4
C
2
, the master regulator of the flagellar operon, in vegetative cells of
P. mirabilis
and found that increased flagellum density produced an increase in cell velocity. Our results establish a relationship between
P. mirabilis
flagellum density and cell motility in viscous environments that may be relevant to its adaptation during the infection of mammalian urinary tracts and movement in contact with indwelling catheters.
FliW and FliS Function Independently To Control Cytoplasmic Flagellin Levels in Bacillus subtilis
Authors: Mukherjee Sampriti , Babitzke Paul , Kearns Daniel B. 
Published: November 2012

ABSTRACT

The cytoplasmic level of flagellin (called Hag) is homeostatically regulated in the Gram-positive bacterium
Bacillus subtilis
by a partner-switching mechanism between the protein FliW and either the Hag structural protein or CsrA, an RNA binding protein that represses
hag
translation. Here we show that FliW and the putative secretion chaperone FliS bind to Hag simultaneously but control Hag translation by different mechanisms. While FliW directly inhibits CsrA activity, FliS antagonizes CsrA indirectly by binding to Hag, enhancing Hag secretion, and depleting Hag in the cytoplasm to trigger the FliW partner switch. Consistent with a role for FliS in potentiating Hag secretion, the mutation of
fliS
crippled both motility and flagellar filament assembly, and both phenotypes could be partially rescued by artificially increasing the concentration of the Hag substrate through the absence of CsrA. Furthermore, the absence of FliS resulted in an approximately 30-fold reduction in extracellular Hag accumulation in cells mutated for CsrA (to relieve homeostatic control) and the filament cap protein FliD (to secrete flagellin into the supernatant). Thus, we mechanistically discriminate between the FliW regulator and the FliS chaperone to show that secretion disrupts flagellin homeostasis and promotes high-level flagellin synthesis during the period of filament assembly in
B. subtilis
.
High-Mobility-Group A-Like CarD Binds to a DNA Site Optimized for Affinity and Position and to RNA Polymerase To Regulate a Light-Inducible Promoter in Myxococcus xanthus
Authors: García-Heras Francisco , Abellón-Ruiz Javier , Murillo Francisco J. , Padmanabhan S. , Elías-Arnanz Montserrat 
Published: November 2012

ABSTRACTThe CarD-CarG complex controls various cellular processes in the bacteriumMyxococcus xanthusincluding fruiting body development and light-induced carotenogenesis. The CarD N-terminal domain, which defines the large CarD_CdnL_TRCF protein family, binds to CarG, a zinc-associated protein that does not bind DNA. The CarD C-terminal domain resembles eukaryotic high-mobility-group A (HMGA) proteins, and its DNA binding AT hooks specifically recognize the minor groove of appropriately spaced AT-rich tracts. Here, we investigate the determinants of the only known CarD binding site, the one crucial in CarD-CarG regulation of the promoter of thecarQRSoperon (PQRS), a light-inducible promoter dependent on the extracytoplasmic function (ECF) σ factor CarQ.In vitro, mutating either of the 3-bp AT tracts of this CarD recognition site (TTTCCAGAGCTTT) impaired DNA binding, shifting the AT tracts relative to PQRShad no effect or marginally lowered DNA binding, and replacing the native site by the HMGA1a binding one at the human beta interferon promoter (with longer AT tracts) markedly enhanced DNA binding.In vivo, however, all of these changes deterred PQRSactivation in wild-typeM. xanthus, as well as in a strain with the CarD-CarG pair replaced by theAnaeromyxobacter dehalogenansCarD-CarG (CarDAd-CarGAd). CarDAd-CarGAdis functionally equivalent to CarD-CarG despite the lower DNA binding affinityin vitroof CarDAd, whose C-terminal domain resembles histone H1 rather than HMGA. We show that CarD physically associates with RNA polymerase (RNAP) specifically via interactions with the RNAP β subunit. Our findings suggest that CarD regulates a light-inducible, ECF σ-dependent promoter by coupling RNAP recruitment and binding to a specific DNA site optimized for affinity and position.
Cloning, Expression, and Functional Characterization of Secondary Amino Acid Transporters of Lactococcus lactis
Authors: Trip Hein , Mulder Niels L. , Lolkema Juke S. 
Published: November 2012

ABSTRACT

Fourteen genes encoding putative secondary amino acid transporters were identified in the genomes of
Lactococcus lactis
subsp.
cremoris
strains MG1363 and SK11 and
L. lactis
subsp
. lactis
strains IL1403 and KF147, 12 of which were common to all four strains. Amino acid uptake in
L. lactis
cells overexpressing the genes revealed transporters specific for histidine, lysine, arginine, agmatine, putrescine, aromatic amino acids, acidic amino acids, serine, and branched-chain amino acids. Substrate specificities were demonstrated by inhibition profiles determined in the presence of excesses of the other amino acids. Four knockout mutants, lacking the lysine transporter LysP, the histidine transporter HisP (formerly LysQ), the acidic amino acid transporter AcaP (YlcA), or the aromatic amino acid transporter FywP (YsjA), were constructed. The LysP, HisP, and FywP deletion mutants showed drastically decreased rates of uptake of the corresponding substrates at low concentrations. The same was observed for the AcaP mutant with aspartate but not with glutamate. In rich M17 medium, the deletion of none of the transporters affected growth. In contrast, the deletion of the HisP, AcaP, and FywP transporters did affect growth in a defined medium with free amino acids as the sole amino acid source. HisP was essential at low histidine concentrations, and AcaP was essential in the absence of glutamine. FywP appeared to play a role in retaining intracellularly synthesized aromatic amino acids when these were not added to the medium. Finally, HisP, AcaP, and FywP did not play a role in the excretion of accumulated histidine, glutamate, or phenylalanine, respectively, indicating the involvement of other transporters.
The Francisella tularensis FabI Enoyl-Acyl Carrier Protein Reductase Gene Is Essential to Bacterial Viability and Is Expressed during Infection
Authors: Kingry Luke C. , Cummings Jason E. , Brookman Kerry W. , Bommineni Gopal R. , Tonge Peter J. , Slayden Richard A. 
Published: November 2012

ABSTRACT

Francisella tularensis
is classified as a category A priority pathogen and causes fatal disseminated disease in humans upon inhalation of less than 50 bacteria. Although drugs are available for treatment, they are not ideal because of toxicity and route of delivery, and in some cases patients relapse upon withdrawal. We have an ongoing program to develop novel FAS-II FabI enoyl-ACP reductase enzyme inhibitors for
Francisella
and other select agents. To establish
F. tularensis
FabI (FtFabI) as a clinically relevant drug target, we demonstrated that fatty acid biosynthesis and FabI activity are essential for growth even in the presence of exogenous long-chain lipids and that Ft
fabI
is not transcriptionally altered in the presence of exogenous long-chain lipids. Inhibition of FtFabI or fatty acid synthesis results in loss of viability that is not rescued by exogenous long-chain lipid supplementation. Importantly, whole-genome transcriptional profiling of
F. tularensis
with DNA microarrays from infected tissues revealed that Ft
fabI
and
de novo
fatty acid biosynthetic genes are transcriptionally active during infection. This is the first demonstration that the FabI enoyl-ACP-reductase enzyme encoded by
F. tularensis
is essential and not bypassed by exogenous fatty acids and that
de novo
fatty acid biosynthetic components encoded in
F. tularensis
are transcriptionally active during infection in the mouse model of tularemia.
Detection of Campylobacter Species and Arcobacter butzleri in Stool Samples by Use of Real-Time Multiplex PCR
Authors: de Boer Richard F. , Ott Alewijn , Güren Pınar , van Zanten Evert , van Belkum Alex , Kooistra-Smid Anna M. D. 
Published: November 2012

ABSTRACT

The presence of
Campylobacter
(or
Campylobacter
-like) species in stools from patients suspected of infectious gastroenteritis (
n
= 493) was investigated using real-time PCR for detection of
Arcobacter butzleri
(
hsp60
gene),
Campylobacter coli
(
ceuE
gene),
Campylobacter jejuni
(
mapA
), five acknowledged pathogenic
Campylobacter
spp. (C16S_Lund assay), and the
Campylobacter
genus (C16S_LvI assay). In total, 71.4% of the samples were positive for
Campylobacter
DNA (
n
= 352) by a
Campylobacter
genus-specific (C16S_LvI) assay. A total of 23 samples (4.7%) were positive in the C16S_Lund assay, used for detection of
C. jejuni
,
C. coli
,
C. lari
,
C. upsaliensis
, and
C. hyointestinalis
. Subsequent identification of these samples yielded detection frequencies (DF) of 4.1% (
C. jejuni
), 0.4% (
C. coli
), and 0.4% (
C. upsaliensis
). The DF of
A. butzleri
was 0.4%. Interestingly, sequencing of a subgroup (
n
= 46) of C16S_LvI PCR-positive samples resulted in a considerable number of
Campylobacter concisus
-positive samples (
n
= 20). PCR-positive findings with the C16S_Lund and
C. jejuni
/
C. coli
-specific assays were associated with more serious clinical symptoms (diarrhea and blood). Threshold cycle (

C
T

) values of
C. jejuni
/
C. coli
PCR-positive samples were comparable to those of the C16S_Lund PCR (
P
= 0.21).

C
T

values for both assays were significantly lower than those of the C16S_LvI assay (
P
< 0.001 and
P
< 0.00001, respectively). In conclusion, this study demonstrated that in combination, the
C. jejuni
/
C coli
-specific assays and the C16S_Lund assay are both useful for routine screening purposes. Furthermore, the DF of the emerging pathogen
C. concisus
was at least similar to the DF of
C. jejuni
.
Trimeric Glycosylphosphatidylinositol-Anchored HCDR3 of Broadly Neutralizing Antibody PG16 Is a Potent HIV-1 Entry Inhibitor
Authors: Liu Lihong , Wang Weiming , Yang Lifei , Ren Huanhuan , Kimata Jason T. , Zhou Paul 
Published: November 2012

ABSTRACT
PG9 and PG16 are two quaternary-structure-specific broadly neutralizing antibodies with unique HCDR3 subdomains. Previously, we showed that glycosylphosphatidylinositol (GPI)-anchored HCDR3 subdomains (GPI-HCDR3) can be targeted to lipid rafts of the plasma membrane, bind to the epitope recognized by HCDR3 of PG16, and neutralize diverse HIV-1 isolates. In this study, we further developed trimeric GPI-HCDR3s and demonstrated that trimeric GPI-HCDR3 (PG16) dramatically improves anti-HIV-1 neutralization, suggesting that a stoichiometry of recognition of 3 or 2 HCDR3 molecules (PG16) to 1 viral spike is possible.