bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retargeting R-Type Pyocins To Generate Novel Bactericidal Protein Complexes
Authors: Williams Steven R. , Gebhart Dana , Martin David W. , Scholl Dean 
Published: April 2008

ABSTRACT

R-type pyocins are high-molecular-weight bacteriocins that resemble bacteriophage tail structures and are produced by some
Pseudomonas aeruginosa
strains. R-type pyocins kill by dissipating the bacterial membrane potential after binding. The high-potency, single-hit bactericidal kinetics of R-type pyocins suggest that they could be effective antimicrobials. However, the limited antibacterial spectra of natural R-type pyocins would ultimately compromise their clinical utility. The spectra of these protein complexes are determined in large part by their tail fibers. By replacing the pyocin tail fibers with tail fibers of
Pseudomonas
phage PS17, we changed the bactericidal specificity of R2 pyocin particles to a different subset of
P. aeruginosa
strains, including some resistant to PS17 phage. We further extended this idea by fusing parts of R2 tail fibers with parts of tail fibers from phages that infect other bacteria, including
Escherichia coli
and
Yersinia pestis
, changing the killing spectrum of pyocins from
P. aeruginosa
to the bacterial genus, species, or strain that serves as a host for the donor phage. The assembly of active R-type pyocins requires chaperones specific for the C-terminal portion of the tail fiber. Natural and retargeted R-type pyocins exhibit narrow bactericidal spectra and thus can be expected to cause little collateral damage to the healthy microbiotae and not to promote the horizontal spread of multidrug resistance among bacteria. Engineered R-type pyocins may offer a novel alternative to traditional antibiotics in some infections.
Roles of DacB and Spm Proteins in
Clostridium perfringens
Spore Resistance to Moist Heat, Chemicals, and UV Radiation
Authors: Paredes-Sabja Daniel , Sarker Nahid , Setlow Barbara , Setlow Peter , Sarker Mahfuzur R. 
Published: April 2008

ABSTRACT

Clostridium perfringens
food poisoning is caused mainly by enterotoxigenic type A isolates that typically possess high spore heat resistance. Previous studies have shown that α/β-type small, acid-soluble proteins (SASP) play a major role in the resistance of
Bacillus subtilis
and
C. perfringens
spores to moist heat, UV radiation, and some chemicals. Additional major factors in
B. subtilis
spore resistance are the spore's core water content and cortex peptidoglycan (PG) structure, with the latter properties modulated by the
spm
and
dacB
gene products and the sporulation temperature. In the current work, we have shown that the
spm
and
dacB
genes are expressed only during
C. perfringens
sporulation and have examined the effects of
spm
and
dacB
mutations and sporulation temperature on spore core water content and spore resistance to moist heat, UV radiation, and a number of chemicals. The results of these analyses indicate that for
C. perfringens
SM101 (i) core water content and, probably, cortex PG structure have little if any role in spore resistance to UV and formaldehyde, presumably because these spores’ DNA is saturated with α/β-type SASP; (ii) spore resistance to moist heat and nitrous acid is determined to a large extent by core water content and, probably, cortex structure; (iii) core water content and cortex PG cross-linking play little or no role in spore resistance to hydrogen peroxide; (iv) spore core water content decreases with higher sporulation temperatures, resulting in spores that are more resistant to moist heat; and (v) factors in addition to SpmAB, DacB, and sporulation temperature play roles in determining spore core water content and thus, spore resistance to moist heat.
Two Angular Dioxygenases Contribute to the Metabolic Versatility of Dibenzofuran-Degrading
Rhodococcus
sp. Strain HA01
Authors: Aly Hamdy A. H. , Huu Nguyen B. , Wray Victor , Junca Howard , Pieper Dietmar H. 
Published: April 2008

ABSTRACT

Rhodococcus
sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-
p
-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (
dfdA1A2A3A4
and
dbfA1A2
) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from
Terrabacter
sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% ± 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from
Terrabacter
sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus,
Rhodococcus
sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.
Increased Fitness of
Pseudomonas fluorescens
Pf0-1 Leucine Auxotrophs in Soil
Authors: Kim Wook , Levy Stuart B. 
Published: April 2008

ABSTRACT

The annotation process of a newly sequenced bacterial genome is largely based on algorithms derived from databases of previously defined RNA and protein-encoding gene structures. This process generally excludes the possibility that the two strands of a given stretch of DNA can each harbor a gene in an overlapping manner. While the presence of such structures in eukaryotic genomes is considered to be relatively common, their counterparts in prokaryotic genomes are just beginning to be recognized. Application of an in vivo expression technology has previously identified 22 discrete genetic loci in
Pseudomonas fluorescens
Pf0-1 that were specifically activated in the soil environment, of which 10 were present in an antisense orientation relative to previously annotated genes. This observation led to the hypothesis that the physiological role of overlapping genetic structures may be relevant to growth conditions outside artificial laboratory media. Here, we examined the role of one of the overlapping gene pairs,
iiv19
and
leuA2
, in soil. Although
iiv19
was previously demonstrated to be preferentially activated in the soil environment, its absence did not alter the ability of
P. fluorescens
to colonize or survive in soil. Surprisingly, the absence of the
leuA2
gene conferred a fitness advantage in the soil environment when leucine was supplied exogenously. This effect was determined to be independent of the
iiv19
gene, and further analyses revealed that amino acid antagonism was the underlying mechanism behind the observed fitness advantage of the bacterium in soil. Our findings provide a potential mechanism for the frequent occurrence of auxotrophic mutants of
Pseudomonas
spp. in the lungs of cystic fibrosis patients.
Temporal Variations in the Dynamics of Potentially Microcystin-Producing Strains in a Bloom-Forming
Planktothrix agardhii
(Cyanobacterium) Population
Authors: Briand Enora , Gugger Muriel , François Jean-Christophe , Bernard Cécile , Humbert Jean-François , Quiblier Catherine 
Published: April 2008

ABSTRACT

The concentration of microcystins (MCs) produced during blooms depends on variations in both the proportion of strains containing the genes involved in MC production and the MC cell quota (the ratio between the MC concentration and the density of cells with the
mcyA
genotype) for toxic strains. In order to assess the dynamics of MC-producing and non-MC-producing strains and to identify the impact of environmental factors on the relative proportions of these two subpopulations, we performed a 2-year survey of a perennial bloom of
Planktothrix agardhii
(cyanobacteria). Applying quantitative real-time PCR to the
mcyA
and phycocyanin genes, we found that the proportion of cells with the
mcyA
genotype varied considerably over time (ranging from 30 to 80% of the population). The changes in the proportion of cells with the
mcyA
genotype appeared to be inversely correlated to changes in the density of
P. agardhii
cells and also, to a lesser extent, to the availability of certain nutrients and the abundance of cladocerans. Among toxic cells, the MC cell quota varied throughout the survey. However, a negative correlation between the MC cell quota and the
mcyA
cell number during two short periods characterized by marked changes in the cyanobacterial biomass was found. Finally, only 54% of the variation in the MC concentrations measured in the lake can be explained by the dynamics of the density of cells with the MC producer genotype, suggesting that this measurement is not a satisfactory method for use in monitoring programs intended to predict the toxic risk associated with cyanobacterial proliferation.
Alternative Hand Contamination Technique To Compare the Activities of Antimicrobial and Nonantimicrobial Soaps under Different Test Conditions
Authors: Fuls Janice L. , Rodgers Nancy D. , Fischler George E. , Howard Jeanne M. , Patel Monica , Weidner Patrick L. , Duran Melani H. 
Published: April 2008

ABSTRACT

Antimicrobial hand soaps provide a greater bacterial reduction than nonantimicrobial soaps. However, the link between greater bacterial reduction and a reduction of disease has not been definitively demonstrated. Confounding factors, such as compliance, soap volume, and wash time, may all influence the outcomes of studies. The aim of this work was to examine the effects of wash time and soap volume on the relative activities and the subsequent transfer of bacteria to inanimate objects for antimicrobial and nonantimicrobial soaps. Increasing the wash time from 15 to 30 seconds increased reduction of
Shigella flexneri
from 2.90 to 3.33 log
10
counts (
P
= 0.086) for the antimicrobial soap, while nonantimicrobial soap achieved reductions of 1.72 and 1.67 log
10
counts (
P
> 0.6). Increasing soap volume increased bacterial reductions for both the antimicrobial and the nonantimicrobial soaps. When the soap volume was normalized based on weight (∼3 g), nonantimicrobial soap reduced
Serratia marcescens
by 1.08 log
10
counts, compared to the 3.83-log
10
reduction caused by the antimicrobial soap (
P
< 0.001). The transfer of
Escherichia coli
to plastic balls following a 15-second hand wash with antimicrobial soap resulted in a bacterial recovery of 2.49 log
10
counts, compared to the 4.22-log
10
(
P
< 0.001) bacterial recovery on balls handled by hands washed with nonantimicrobial soap. This indicates that nonantimicrobial soap was less active and that the effectiveness of antimicrobial soaps can be improved with longer wash time and greater soap volume. The transfer of bacteria to objects was significantly reduced due to greater reduction in bacteria following the use of antimicrobial soap.
Assembly of Viral Metagenomes from Yellowstone Hot Springs
Authors: Schoenfeld Thomas , Patterson Melodee , Richardson Paul M. , Wommack K. Eric , Young Mark , Mead David 
Published: April 2008

ABSTRACT

Thermophilic viruses were reported decades ago; however, knowledge of their diversity, biology, and ecological impact is limited. Previous research on thermophilic viruses focused on cultivated strains. This study examined metagenomic profiles of viruses directly isolated from two mildly alkaline hot springs, Bear Paw (74°C) and Octopus (93°C). Using a new method for constructing libraries from picograms of DNA, nearly 30 Mb of viral DNA sequence was determined. In contrast to previous studies, sequences were assembled at 50% and 95% identity, creating composite contigs up to 35 kb and facilitating analysis of the inherent heterogeneity in the populations. Lowering the assembly identity reduced the estimated number of viral types from 1,440 and 1,310 to 548 and 283, respectively. Surprisingly, the diversity of viral species in these springs approaches that in moderate-temperature environments. While most known thermophilic viruses have a chronic, nonlytic infection lifestyle, analysis of coding sequences suggests lytic viruses are more common in geothermal environments than previously thought. The 50% assembly included one contig with high similarity and perfect synteny to nine genes from
Pyrobaculum spherical virus
(PSV). In fact, nearly all the genes of the 28-kb genome of PSV have apparent homologs in the metagenomes. Similarities to thermoacidophilic viruses isolated on other continents were limited to specific open reading frames but were equally strong. Nearly 25% of the reads showed significant similarity between the hot springs, suggesting a common subterranean source. To our knowledge, this is the first application of metagenomics to viruses of geothermal origin.
Morphological and Genetic Evidence that the Cyanobacterium
Lyngbya wollei
(Farlow ex Gomont) Speziale and Dyck Encompasses at Least Two Species
Authors: Joyner Jennifer J. , Litaker R. Wayne , Paerl Hans W. 
Published: April 2008

ABSTRACT

Dense blooms of the cyanobacterium
Lyngbya wollei
are increasingly responsible for declining water quality and habitat degradation in numerous springs, rivers, and reservoirs. This research represents the first molecular phylogenetic analysis of
L. wollei
in comparison with the traditional morphological characterization of this species. Specimens were collected from several springs in Florida and a reservoir in North Carolina. Segments of the small-subunit (SSU) rRNA and
nifH
genes were PCR amplified, cloned, and sequenced. The phylogenetic analysis of the SSU rRNA gene revealed sequences that fell into three distinct subclusters, each with >97% sequence similarity. These were designated operational taxonomic unit 1 (OTU1), OTU2, and OTU3. Similarly, the
nifH
sequences fell into three distinct subclusters named S1, S2, and S3. When either bulk samples or individual filaments were analyzed, we recovered OTU1 with S1, OTU2 with S2, and OTU3 with S3. The coherence between the three SSU rRNA gene and
nifH
subclusters was consistent with genetically distinct strains or species. Cells associated with subclusters OTU3 and S3 were significantly wider and longer than those associated with other subclusters. The combined molecular and morphological data indicate that the species commonly identified as
L. wollei
in the literature represents two or possibly more species. Springs containing OTU3 and S3 demonstrated lower ion concentrations than other collection sites. Geographical locations of
Lyngbya
subclusters did not correlate with residual dissolved inorganic nitrogen or phosphorus concentrations. This study emphasizes the need to complement traditional identification with molecular characterization to more definitively detect and characterize harmful cyanobacterial species or strains.
Comparison of Broth Microdilution, Etest, and Agar Disk Diffusion Methods for Antimicrobial Susceptibility Testing of
Lactobacillus acidophilus
Group Members
Authors: Mayrhofer Sigrid , Domig Konrad J. , Mair Christiane , Zitz Ulrike , Huys Geert , Kneifel Wolfgang 
Published: April 2008

ABSTRACT

In recent years, the absence of acquired antimicrobial resistance has become an important criterion to evaluate the biosafety of lactobacilli used as industrial starter or probiotic cultures. At present, however, standards for susceptibility testing of
Lactobacillus
strains or approved guidelines for interpreting the test results are not available. Hence, this study was carried out to contribute to the establishment of a standardized procedure for antimicrobial susceptibility testing of lactobacilli. The results obtained by testing 104 strains of the
Lactobacillus acidophilus
group were compared based on broth microdilution, disk diffusion, and Etest. Except for some specific agent-related effects, agreement between MICs resulting from the broth microdilution method and the Etest was good. In addition, inhibition zone diameters determined with disk diffusion correlated well with MICs from Etest and broth microdilution.
Nodulation Gene Regulation and Quorum Sensing Control Density-Dependent Suppression and Restriction of Nodulation in theBradyrhizobium japonicum-Soybean Symbiosis
Authors: Jitacksorn Siriluck , Sadowsky Michael J. 
Published: April 2008

ABSTRACTThe nodulation ofGlycine maxcv. Lambert and the nodulation-restricting plant introduction (PI) genotype PI 417566 by wild-typeBradyrhizobium japonicumUSDA110 is regulated in a population-density-dependent manner. Nodulation on both plant genotypes was suppressed (inhibited) when plants received a high-density inoculum (109cells/ml) of strain USDA110 grown in complex medium, and more nodules were produced on plants receiving a low-cell-density inoculum (105cells/ml). Since cell-free supernatants from strain USDA110 grown to high cell density in complex medium decreased the expression of annodY-lacZfusion, this phenomenon was attributed to bradyoxetin-induced repression ofnodgene expression. Inoculation of either the permissive soybean genotype (cv. Lambert) or PI 417566 with 109cells/ml of thenodD2,nolA,nodW, andnwsBmutants of USDA110 enhanced nodulation (up to 24%) relative to that seen with inoculations done with 105cells/ml of the mutants or the wild-type strain, indicating that these genes are involved in population-density-dependent nodulation of soybeans. In contrast, the number of nodules produced by annodD1mutant on either soybean genotype was less than those seen with the wild-type strain inoculated at a low inoculum density. ThenodD2mutant outcompetedB. japonicumstrain USDA123 for nodulation ofG. maxcv. Lambert at a high or low inoculum density, and the results of root-tip-marking and time-to-nodulate studies indicated that thenolAandnodD2mutants nodulated this soybean genotype faster than wild-type USDA110. Taken together, the results from these studies indicate that thenodD2mutant ofB. japonicummay be useful to enhance soybean nodulation at high inoculum densities and that NodD2 is a key repressor influencing host-controlled restriction of nodulation, density-dependent suppression of nodulation, perception of bradyoxetin, and competitiveness in the soybean-B. japonicumsymbiosis.
Loss of Regulators of Vacuolar ATPase Function and Ceramide Synthesis Results in Multidrug Sensitivity in
Schizosaccharomyces pombe
Authors: Dawson Keren , Toone W. Mark , Jones Nic , Wilkinson Caroline R. M. 
Published: April 2008

ABSTRACT

We undertook a screen to isolate determinants of drug resistance in fission yeast and identified two genes that, when mutated, result in sensitivity to a range of structurally unrelated compounds, some of them commonly used in the clinic. One gene,
rav1
, encodes the homologue of a budding yeast protein which regulates the assembly of the vacuolar ATPase. The second gene,
lac1
, encodes a homologue of genes that are required for ceramide synthesis. Both mutants are sensitive to the chemotherapeutic agent doxorubicin, and using the naturally fluorescent properties of this compound, we found that both
rav1
and
lac1
mutations result in an increased accumulation of the drug in cells. The multidrug-sensitive phenotype of
rav1
mutants can be rescued by up-regulation of the
lag1
gene which encodes a homologue of
lac1
, whereas overexpression of either
lac1
or
lag1
confers multidrug resistance on wild-type cells. These data suggest that changing the amount of ceramide synthase activity in cells can influence innate drug resistance. The function of Rav1 appears to be conserved, as we show that SpRav1 is part of a RAVE-like complex in fission yeast and that loss of
rav1
results in defects in vacuolar (H
+
)-ATPase activity. Thus, we conclude that loss of normal V-ATPase function results in an increased sensitivity of
Schizosaccharomyces pombe
cells to drugs. The
rav1
and
lac1
genes are conserved in both higher eukaryotes and various pathogenic fungi. Thus, our data could provide the basis for strategies to sensitize tumor cells or drug-resistant pathogenic fungi to drugs.
Genomewide Recruitment Analysis of Rpb4, a Subunit of Polymerase II in
Saccharomyces cerevisiae
, Reveals Its Involvement in Transcription Elongation
Authors: Verma-Gaur Jiyoti , Rao Sudha Narayana , Taya Toshiki , Sadhale Parag 
Published: April 2008

ABSTRACT

The Rpb4/Rpb7 subcomplex of yeast RNA polymerase II (Pol II) has counterparts in all multisubunit RNA polymerases from archaebacteria to higher eukaryotes. The Rpb4/7 subcomplex in
Saccharomyces cerevisiae
is unique in that it easily dissociates from the core, unlike the case in other organisms. The relative levels of Rpb4 and Rpb7 in yeasts affect the differential gene expression and stress response. Rpb4 is nonessential in
S. cerevisiae
and affects expression of a small number of genes under normal growth conditions. Here, using a chromatin immunoprecipitation (“ChIP on-chip”) technique, we compared genomewide binding of Rpb4 to that of a core Pol II subunit, Rpb3. Our results showed that in spite of being nonessential for survival, Rpb4 was recruited on coding regions of most transcriptionally active genes, similar to the case with the core Pol II subunit, Rpb3, albeit to a lesser extent. The extent of Rpb4 recruitment increased with increasing gene length. We also observed Pol II lacking Rpb4 to be defective in transcribing long, GC-rich transcription units, suggesting a role for Rpb4 in transcription elongation. This role in transcription elongation was supported by the observed 6-azauracil (6AU) sensitivity of the
rpb4
Δ mutant. Unlike most phenotypes of
rpb4
Δ, the 6AU sensitivity of the
rpb4
Δ strain was not rescued by overexpression of
RPB7
. This report provides the first instance of a distinct role for Rpb4 in transcription, which is independent of its interacting partner, Rpb7.
Functional Characterization of a Redundant
Plasmodium
TRAP Family Invasin, TRAP-Like Protein, by Aldolase Binding and a Genetic Complementation Test
Authors: Heiss Kirsten , Nie Hui , Kumar Sumit , Daly Thomas M. , Bergman Lawrence W. , Matuschewski Kai 
Published: April 2008

ABSTRACT

Efficient and specific host cell entry is of exquisite importance for intracellular pathogens. Parasites of the phylum
Apicomplexa
are highly motile and actively enter host cells. These functions are mediated by type I transmembrane invasins of the TRAP family that link an extracellular recognition event to the parasite actin-myosin motor machinery. We systematically tested potential parasite invasins for binding to the actin bridging molecule aldolase and complementation of the vital cytoplasmic domain of the sporozoite invasin TRAP. We show that the ookinete invasin CTRP and a novel, structurally related protein, termed TRAP-like protein (TLP), are functional members of the TRAP family. Although
TLP
is expressed in invasive stages, targeted gene disruption revealed a nonvital role during life cycle progression. This is the first genetic analysis of
TLP
, encoding a redundant TRAP family invasin, in the malaria parasite.