bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Molecular Analysis of Endoevaporitic Microbial Communities
Authors: Sahl Jason W. , Pace Norman R. , Spear John R. 
Published: August 2008

ABSTRACT
A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity.
Engineering of a Glycerol Utilization Pathway for Amino Acid Production by
Corynebacterium glutamicum
Authors: Rittmann Doris , Lindner Steffen N. , Wendisch Volker F. 
Published: August 2008

ABSTRACT

The amino acid-producing organism
Corynebacterium glutamicum
cannot utilize glycerol, a stoichiometric by-product of biodiesel production. By heterologous expression of
Escherichia coli
glycerol utilization genes,
C. glutamicum
was engineered to grow on glycerol. While expression of the
E. coli
genes for glycerol kinase (
glpK
) and glycerol 3-phosphate dehydrogenase (
glpD
) was sufficient for growth on glycerol as the sole carbon and energy source, additional expression of the aquaglyceroporin gene
glpF
from
E. coli
increased growth rate and biomass formation. Glutamate production from glycerol was enabled by plasmid-borne expression of
E. coli glpF, glpK
, and
glpD
in
C. glutamicum
wild type. In addition, a lysine-producing
C. glutamicum
strain expressing
E. coli glpF, glpK
, and
glpD
was able to produce lysine from glycerol as the sole carbon substrate as well as from glycerol-glucose mixtures.
Heme Uptake by
Microscilla marina
and Evidence for Heme Uptake Systems in the Genomes of Diverse Marine Bacteria
Authors: Hopkinson Brian M. , Roe Kelly L. , Barbeau Katherine A. 
Published: August 2008

ABSTRACT

The ability to acquire diverse and abundant forms of iron would be expected to confer a survival advantage in the marine environment, where iron is scarce. Marine bacteria are known to use siderophores and inorganic iron, but their ability to use heme, an abundant intracellular iron form, has only been examined preliminarily.
Microscilla marina
, a cultured relative of a bacterial group frequently found on marine particulates, was used as a model organism to examine heme uptake. Searches of the genome revealed analogs to known heme transport proteins, and reverse transcription-quantitative PCR analysis of these genes showed that they were expressed and upregulated under iron stress and during growth on heme.
M. marina
was found to take up heme-bound iron and could grow on heme as a sole iron source, supporting the genetic evidence for heme transport. Similar putative heme transport components were identified in the genomes of diverse marine bacteria. These systems were found in the genomes of many bacteria thought to be particle associated but were lacking in known free-living organisms (e.g.,
Pelagibacter ubique
and marine cyanobacteria). This distribution of transporters is consistent with the hydrophobic, light-sensitive nature of heme, suggesting that it is primarily available on phytoplankton or detritus or in nutrient-rich environments.
Identification of Critical Members in a Sulfidogenic Benzene-Degrading Consortium by DNA Stable Isotope Probing
Authors: Oka A. R. , Phelps C. D. , McGuinness L. M. , Mumford A. , Young L. Y. , Kerkhof L. J. 
Published: August 2008

ABSTRACTStable isotope probing (SIP) was used to identify the active members in a benzene-degrading sulfidogenic consortium. SIP-terminal restriction fragment length polymorphism analysis indicated that a 270-bp peak incorporated the majority of the13C label and is a sequence closely related to that of clone SB-21 (GenBank accession no. AF029045). This target may be an important biomarker for anaerobic benzene degradation in the field.
Functional Expression and Subcellular Localization of the Aflatoxin Pathway Enzyme Ver-1 Fused to Enhanced Green Fluorescent Protein
Authors: Hong Sung-Yong , Linz John E. 
Published: August 2008

ABSTRACT

Aflatoxin, a mycotoxin synthesized by
Aspergillus
spp., is among the most potent naturally occurring carcinogens known. Little is known about the subcellular organization of aflatoxin synthesis. Previously, we used transmission electron microscopy and immunogold labeling to demonstrate that the late aflatoxin enzyme OmtA localizes primarily to vacuoles in fungal cells on the substrate surface of colonies. In the present work, we monitored subcellular localization of Ver-1 in real time in living cells.
Aspergillus parasiticus
strain CS10-N2 was transformed with plasmid constructs that express enhanced green fluorescent protein (EGFP) fused to Ver-1. Analysis of transformants demonstrated that EGFP fused to Ver-1 at either the N or C terminus functionally complemented nonfunctional Ver-1 in recipient cells. Western blot analysis detected predominantly full-length Ver-1 fusion proteins in transformants. Confocal laser scanning microscopy demonstrated that Ver-1 fusion proteins localized in the cytoplasm and in the lumen of up to 80% of the vacuoles in hyphae grown for 48 h on solid media. Control EGFP (no Ver-1) expressed in transformants was observed in only 13% of the vacuoles at this time. These data support a model in which middle and late aflatoxin enzymes are synthesized in the cytoplasm and transported to vacuoles, where they participate in aflatoxin synthesis.
Antimicrobial Resistance in
Salmonella enterica
Serovar Heidelberg Isolates from Retail Meats, Including Poultry, from 2002 to 2006
Authors: Zhao S. , White D. G. , Friedman S. L. , Glenn A. , Blickenstaff K. , Ayers S. L. , Abbott J. W. , Hall-Robinson E. , McDermott P. F. 
Published: August 2008

ABSTRACT

Salmonella enterica
serovar Heidelberg frequently causes food-borne illness in humans. There are few data on the prevalence, antimicrobial susceptibility, and genetic diversity of
Salmonella
serovar Heidelberg isolates in retail meats. We compared the prevalences of
Salmonella
serovar Heidelberg in a sampling of 20,295 meats, including chicken breast (
n
= 5,075), ground turkey (
n
= 5,044), ground beef (
n
= 5,100), and pork chops (
n
= 5,076), collected during 2002 to 2006. Isolates were analyzed for antimicrobial susceptibility and compared genetically using pulsed-field gel electrophoresis (PFGE) and PCR for the
bla
CMY
gene. A total of 298
Salmonella
serovar Heidelberg isolates were recovered, representing 21.6% of all
Salmonella
serovars from retail meats. One hundred seventy-eight (59.7%) were from ground turkey, 110 (36.9%) were from chicken breast, and 10 (3.4%) were from pork chops; none was found in ground beef. One hundred ninety-eight isolates (66.4%) were resistant to at least one compound, and 49 (16.4%) were resistant to at least five compounds. Six isolates (2.0%), all from ground turkey, were resistant to at least nine antimicrobials. The highest resistance in poultry isolates was to tetracycline (39.9%), followed by streptomycin (37.8%), sulfamethoxazole (27.7%), gentamicin (25.7%), kanamycin (21.5%), ampicillin (19.8%), amoxicillin-clavulanic acid (10.4%), and ceftiofur (9.0%). All isolates were susceptible to ceftriaxone and ciprofloxacin. All ceftiofur-resistant strains carried
bla
CMY
. PFGE using XbaI and BlnI showed that certain clones were widely dispersed in different types of meats and meat brands from different store chains in all five sampling years. These data indicate that
Salmonella
serovar Heidelberg is a common serovar in retail poultry meats and includes widespread clones of multidrug-resistant strains.
TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets
Authors: Junier Pilar , Junier Thomas , Witzel Karl-Paul 
Published: August 2008

ABSTRACT

We describe TRiFLe, a freely accessible computer program that generates theoretical terminal restriction fragments (T-RFs) from any user-supplied sequence set tailored to a particular group of organisms, sequences from clone libraries, or sequences from specific genes. The program allows a rapid identification of the most polymorphic enzymes, creates a collection of T-RFs for the data set, and can potentially identify specific T-RFs in T-RF length polymorphism (T-RFLP) patterns by comparing theoretical and experimental results. TRiFLE was used for analyzing T-RFLP data generated for the
amoA
and
pmoA
genes. The peaks identified in the T-RFLP patterns show an overlap of ammonia- and methane-oxidizing bacteria in the metalimnion of a subtropical lake.
TaqMan-Based Real-Time PCR Method for Detection of
Yersinia pseudotuberculosis
in Food
Authors: Lambertz S. Thisted , Nilsson C. , Hallanvuo S. 
Published: August 2008

ABSTRACT

A sensitive and specific assay for detection of food-borne pathogenic
Yersinia pseudotuberculosis
was developed. The primer-probe set was designed to target a 157-bp sequence of the chromosomally located gene
ail
. The complete method, including an internal amplification control, was evaluated for several different food items.
ShmR Is Essential for Utilization of Heme as a Nutritional Iron Source inSinorhizobium meliloti
Authors: Amarelle Vanesa , O'Brian Mark R. , Fabiano Elena 
Published: August 2008

ABSTRACTThe bacteriumSinorhizobium melilotiis able to use heme as a nutritional iron source. Here, we show that the iron-regulatedshmRgene encodes an outer membrane protein required for growth on heme. Furthermore, anshmRmutant is resistant to the toxic heme analog gallium protoporphyrin. Thus, the receptor protein of the heme transport system has been identified inS. meliloti.
Septal Pore Cap Protein SPC18, Isolated from the Basidiomycetous Fungus
Rhizoctonia solani
, Also Resides in Pore Plugs
Authors: van Driel Kenneth G. A. , van Peer Arend F. , Grijpstra Jan , Wösten Han A. B. , Verkleij Arie J. , Müller Wally H. , Boekhout Teun 
Published: August 2008

ABSTRACT

The hyphae of filamentous fungi are compartmentalized by septa that have a central pore. The fungal septa and septum-associated structures play an important role in maintaining cellular and intrahyphal homeostasis. The dolipore septa in the higher
Basidiomycota
(i.e.,
Agaricomycotina
) are associated with septal pore caps. Although the ultrastructure of the septal pore caps has been studied extensively, neither the biochemical composition nor the function of these organelles is known. Here, we report the identification of the glycoprotein SPC18 that was found in the septal pore cap-enriched fraction of the basidiomycetous fungus
Rhizoctonia solani
. Based on its N-terminal sequence, the
SPC18
gene was isolated.
SPC18
encodes a protein of 158 amino acid residues, which contains a hydrophobic signal peptide for targeting to the endoplasmic reticulum and has an N-glycosylation motif. Immunolocalization showed that SPC18 is present in the septal pore caps. Surprisingly, we also observed SPC18 being localized in some plugs. The data reported here strongly support the hypothesis that septal pore caps are derived from endoplasmic reticulum and are involved in dolipore plugging and, thus, contribute to hyphal homeostasis in basidiomycetous fungi.
The Asexual Pathogen
Aspergillus fumigatus
Expresses Functional Determinants of
Aspergillus nidulans
Sexual Development
Authors: Große Verena , Krappmann Sven 
Published: August 2008

ABSTRACT

The major fungal pathogen of humans,
Aspergillus fumigatus
, lacks a defined sexual cycle, although the presence of genes encoding putative mating type idiomorphs and regulators of
Aspergillus
sexual development heightens the potential for cryptic sexuality in this deuteromycete. To test the functionality of these genetic determinants, we transferred the alpha box-encoding
mat1-1
idiomorph from an
A. fumigatus
isolate to the homothallic fertile species
Aspergillus nidulans
. Abundant formation of fruiting bodies (cleistothecia) containing viable ascospores establishes functionality of this mating type gene product in the transgenic strain. Using a similar approach, we also established that the conserved transcriptional regulator from
A. fumigatus
, the
nsdD
gene product, can act as a functional, positively acting factor for
A. nidulans
cleistothecium development; moreover, high-level expression of NsdD in the endogenous host
A. fumigatus
profoundly alters hyphal development by triggering the formation of coiled hyphae. Our findings demonstrate that the presumably asexual pathogen
A. fumigatus
encodes functional regulators of mating and sexual development, thereby potentiating the case for cryptic sexuality in this fungal pathogen.
Detection and Localization of Single LysM-Peptidoglycan Interactions
Authors: Andre Guillaume , Leenhouts Kees , Hols Pascal , Dufrêne Yves F. 
Published: August 2008

ABSTRACT

The lysin motif (LysM) is a ubiquitous protein module that binds peptidoglycan and structurally related molecules. Here, we used single-molecule force spectroscopy (SMFS) to measure and localize individual LysM-peptidoglycan interactions on both model and cellular surfaces. LysM modules of the major autolysin AcmA of
Lactococcus lactis
were bound to gold-coated atomic force microscopy tips, while peptidoglycan was covalently attached onto model supports. Multiple force curves recorded between the LysM tips and peptidoglycan surfaces yielded a bimodal distribution of binding forces, presumably reflecting the occurrence of one and two LysM-peptidoglycan interactions, respectively. The specificity of the measured interaction was confirmed by performing blocking experiments with free peptidoglycan. Next, the LysM tips were used to map single LysM interactions on the surfaces of
L. lactis
cells. Strikingly, native cells showed very poor binding, suggesting that peptidoglycan was hindered by other cell wall constituents. Consistent with this notion, treatment of the cells with trichloroacetic acid, which removes peptidoglycan-associated polymers, resulted in substantial and homogeneous binding of the LysM tip. These results provide novel insight into the binding forces of bacterial LysMs and show that SMFS is a promising tool for studying the heterologous display of proteins or peptides on bacterial surfaces.
Roles and Interactions of
Burkholderia pseudomallei
BpsIR Quorum-Sensing System Determinants
Authors: Kiratisin Pattarachai , Sanmee Sittinee 
Published: August 2008

ABSTRACT

The
Burkholderia pseudomallei
quorum-sensing system (QSS), designated BpsIR, is encoded by five
bpsR
genes and three
bpsI
genes. This study investigated the roles and interactions of the QSS determinants in terms of gene regulation and protein interaction. We report two novel findings, that BpsR can function as an activator and a repressor for
bpsI
expression and that BpsR may form homodimers and heterodimers.
Abundance Changes of the Response Regulator RcaC Require Specific Aspartate and Histidine Residues and Are Necessary for Normal Light Color Responsiveness
Authors: Li Lina , Kehoe David M. 
Published: August 2008

ABSTRACT

RcaC is a large, complex response regulator that controls transcriptional responses to changes in ambient light color in the cyanobacterium
Fremyella diplosiphon
. The regulation of RcaC activity has been shown previously to require aspartate 51 and histidine 316, which appear to be phosphorylation sites that control the DNA binding activity of RcaC. All available data suggest that during growth in red light, RcaC is phosphorylated and has relatively high DNA binding activity, while during growth in green light RcaC is not phosphorylated and has less DNA binding activity. RcaC has also been found to be approximately sixfold more abundant in red light than in green light. Here we demonstrate that the light-controlled abundance changes of RcaC are necessary, but not sufficient, to direct normal light color responses. RcaC abundance changes are regulated at both the RNA and protein levels. The RcaC protein is significantly less stable in green light than in red light, suggesting that the abundance of this response regulator is controlled at least in part by light color-dependent proteolysis. We provide evidence that the regulation of RcaC abundance does not depend on any RcaC-controlled process but rather depends on the presence of the aspartate 51 and histidine 316 residues that have previously been shown to control the activity of this protein. We propose that the combination of RcaC abundance changes and modification of RcaC by phosphorylation may be necessary to provide the dynamic range required for transcriptional control of RcaC-regulated genes.
Aromatic Amino Acid-Dependent Expression of Indole-3-Pyruvate Decarboxylase Is Regulated by TyrR inEnterobacter cloacaeUW5
Authors: Ryu R. Julie , Patten Cheryl L. 
Published: August 2008

ABSTRACTThe plant growth-promoting rhizobacteriumEnterobacter cloacaeUW5 synthesizes the plant growth hormone indole-3-acetic acid (IAA) via the indole-3-pyruvate pathway utilizing the enzyme indole-3-pyruvate decarboxylase that is encoded byipdC. In this bacterium,ipdCexpression and IAA production occur in stationary phase and are induced by an exogenous source of tryptophan, conditions that are present in the rhizosphere. The aim of this study was to identify the regulatory protein that controls the expression ofipdC. We identified a sequence in the promoter region ofipdCthat is highly similar to the recognition sequence for theEscherichia coliregulatory protein TyrR that regulates genes involved in aromatic amino acid transport and metabolism. Using atyrRinsertional mutant, we demonstrate that TyrR is required for IAA production and for induction ofipdCtranscription. TyrR directly inducesipdCexpression, as was determined by real-time quantitative reverse transcription-PCR, byipdCpromoter-driven reporter gene activity, and by electrophoretic mobility shift assays. Expression increases in response to tryptophan, phenylalanine, and tyrosine. This suggests that, in addition to its function in plant growth promotion, indolepyruvate decarboxylase may be important for aromatic amino acid uptake and/or metabolism.
Box C/D RNA-Guided 2′-O Methylations and the Intron of tRNA
Trp
Are Not Essential for the Viability of
Haloferax volcanii
Authors: Joardar Archi , Gurha Priyatansh , Skariah Geena , Gupta Ramesh 
Published: August 2008

ABSTRACT

Deleting the box C/D RNA-containing intron in the
Haloferax volcanii
tRNA
Trp
gene abolishes RNA-guided 2′-O methylations of C34 and U39 residues of tRNA
Trp
. However, this deletion does not affect growth under standard conditions.
Carbon Catabolite Repression in
Bacillus subtilis
: Quantitative Analysis of Repression Exerted by Different Carbon Sources
Authors: Singh Kalpana D. , Schmalisch Matthias H. , Stülke Jörg , Görke Boris 
Published: August 2008

ABSTRACT

In many bacteria glucose is the preferred carbon source and represses the utilization of secondary substrates. In
Bacillus subtilis
, this carbon catabolite repression (CCR) is achieved by the global transcription regulator CcpA, whose activity is triggered by the availability of its phosphorylated cofactors, HPr(Ser46-P) and Crh(Ser46-P). Phosphorylation of these proteins is catalyzed by the metabolite-controlled kinase HPrK/P. Recent studies have focused on glucose as a repressing substrate. Here, we show that many carbohydrates cause CCR. The substrates form a hierarchy in their ability to exert repression via the CcpA-mediated CCR pathway. Of the two cofactors, HPr is sufficient for complete CCR. In contrast, Crh cannot substitute for HPr on substrates that cause a strong repression. Determination of the phosphorylation state of HPr in vivo revealed a correlation between the strength of repression and the degree of phosphorylation of HPr at Ser46. Sugars transported by the phosphotransferase system (PTS) cause the strongest repression. However, the phosphorylation state of HPr at its His15 residue and PTS transport activity have no impact on the global CCR mechanism, which is a major difference compared to the mechanism operative in
Escherichia coli
. Our data suggest that the hierarchy in CCR exerted by the different substrates is exclusively determined by the activity of HPrK/P.
Kingella kingae
Expresses Type IV Pili That Mediate Adherence to Respiratory Epithelial and Synovial Cells
Authors: Kehl-Fie Thomas E. , Miller Sara E. , St. Geme Joseph W. 
Published: August 2008

ABSTRACT

Kingella kingae
is a gram-negative bacterium that colonizes the respiratory tract and is a common cause of septic arthritis and osteomyelitis. Despite the increasing frequency of
K. kingae
disease, little is known about the mechanism by which this organism adheres to respiratory epithelium and seeds joints and bones. Previous work showed that
K. kingae
expresses long surface fibers that vary in surface density. In the current study, we found that these fibers are type IV pili and are necessary for efficient adherence to respiratory epithelial and synovial cells and that the number of pili expressed by the bacterium correlates with the level of adherence to synovial cells but not with the level of adherence to respiratory cells. In addition, we established that the major pilin subunit is encoded by a
pilA
homolog in a conserved region of the chromosome that also contains a second pilin gene and a type IV pilus accessory gene, both of which are dispensable for pilus assembly and pilus-mediated adherence. Upon examination of the
K. kingae
genome, we identified two genes in physically separate locations on the chromosome that encode homologs of the
Neisseria
PilC proteins and that have only a low level homology to each other. Examination of mutant strains revealed that both of the
K. kingae
PilC homologs are essential for a wild-type level of adherence to both respiratory epithelial and synovial cells. Taken together, these results demonstrate that type IV pili and the two PilC homologs play important roles in mediating
K. kingae
adherence.
The Extracellular Nuclease Dns and Its Role in Natural Transformation of
Vibrio cholerae
Authors: Blokesch Melanie , Schoolnik Gary K. 
Published: August 2008

ABSTRACT

Free extracellular DNA is abundant in many aquatic environments. While much of this DNA will be degraded by nucleases secreted by the surrounding microbial community, some is available as transforming material that can be taken up by naturally competent bacteria. One such species is
Vibrio cholerae
, an autochthonous member of estuarine, riverine, and marine habitats and the causative agent of cholera, whose competence program is induced after colonization of chitin surfaces. In this study, we investigate how
Vibrio cholerae
's two extracellular nucleases, Xds and Dns, influence its natural transformability. We show that in the absence of Dns, transformation frequencies are significantly higher than in its presence. During growth on a chitin surface, an increase in transformation efficiency was found to correspond in time with increasing cell density and the repression of
dns
expression by the quorum-sensing regulator HapR. In contrast, at low cell density, the absence of HapR relieves
dns
repression, leading to the degradation of free DNA and to the abrogation of the transformation phenotype. Thus, as cell density increases,
Vibrio cholerae
undergoes a switch from nuclease-mediated degradation of extracellular DNA to the uptake of DNA by bacteria induced to a state of competence by chitin. Taken together, these results suggest the following model: nuclease production by low-density populations of
V. cholerae
might foster rapid growth by providing a source of nucleotides for the repletion of nucleotide pools. In contrast, the termination of nuclease production by static, high-density populations allows the uptake of intact DNA and coincides with a phase of potential genome diversification.