bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Fe(III) Reduction by Chlororespiring
Anaeromxyobacter dehalogenans
Authors: He Qiang , Sanford Robert A. 
Published: May 2003

ABSTRACT

Anaeromyxobacter dehalogenans
strain 2CP-C has been shown to grow by coupling the oxidation of acetate to the reduction of
ortho
-substituted halophenols, oxygen, nitrate, nitrite, or fumarate. In this study, strain 2CP-C was also found to grow by coupling Fe(III) reduction to the oxidation of acetate, making it one of the few isolates capable of growth by both metal reduction and chlororespiration. Doubling times for growth of 9.2 and 10.2 h were determined for Fe(III) and 2-chlorophenol reduction, respectively. These were determined by using the rate of [
14
C]acetate uptake into biomass. Fe(III) compounds used by strain 2CP-C include ferric citrate, ferric pyrophosphate, and amorphous ferric oxyhydroxide. The addition of the humic acid analog anthraquinone 2,6-disulfonate (AQDS) increased the reduction rate of amorphous ferric iron oxide, suggesting AQDS was used as an electron shuttle by strain 2CP-C. The addition of chloramphenicol to fumarate-grown cells did not inhibit Fe(III) reduction, indicating that the latter activity is constitutive. In contrast, the addition of chloramphenicol inhibited dechlorination activity, indicating that chlororespiration is inducible. The presence of insoluble Fe(III) oxyhydroxide did not significantly affect dechlorination, whereas the presence of soluble ferric pyrophosphate inhibited dechlorination. With its ability to respire chlorinated organic compounds and metals such as Fe(III), strain 2CP-C is a promising model organism for the study of the interaction of these potentially competing processes in contaminated environments.
Electrophoretic Analysis of Genetic Variability within
Cryptosporidium parvum
from Imported and Autochthonous Cases of Human Cryptosporidiosis in the United Kingdom
Authors: Gasser R. B. , EL-Osta Y. G. Abs , Chalmers R. M. 
Published: May 2003

ABSTRACT

Cryptosporidium parvum
oocyst DNA samples (
n
= 184) from humans with cryptosporidiosis contracted during foreign travel or during outbreaks in the United Kingdom were characterized genetically and categorized by single-strand conformation polymorphism (SSCP)-based analysis of the small-subunit gene (pSSU) (∼300 bp) and second internal transcribed spacer (pITS-2) (∼230 bp) of nuclear ribosomal DNA. The two recognized genotypes (types 1 and 2) of
C. parvum
could be readily differentiated by a distinct electrophoretic shift in the pSSU SSCP profile, associated with a nucleotide difference of ∼1.3 to 1.7%. Of the 102 samples from cases contracted during foreign travel, 88 (86.3%) were identified as
C. parvum
type 1 and 14 (13.7%) were identified as type 2. For outbreak samples, unequivocal differentiation between type 1 (
n
= 20; one child nursery outbreak) and type 2 (
n
= 62; two waterborne outbreaks) was also achieved. Nucleotide variation in pITS-2 (both within and among samples representing each genotype) was substantially greater (10 to 13 different profiles for each genotype, relating to sequence differences of ∼1 to 42%) than that in pSSU. SSCP analysis of pITS-2 for all samples revealed that some profiles had a broad geographical distribution whereas others were restricted to particular locations, suggesting a link between some subgenotypes and the geographical origin or source. Comparative denaturing polyacrylamide gel electrophoretic analysis revealed the same genotypic identification and a similar subgenotypic classification of samples as SSCP analysis. The findings of this study, particularly the detection of intragenotypic variation by SSCP, should have significant diagnostic implications for investigating transmission patterns and the monitoring of outbreaks.
Identification of New Genes Positively Regulated by
Tri10
and a Regulatory Network for Trichothecene Mycotoxin Production
Authors: Peplow Andrew W. , Tag Andrew G. , Garifullina Gulnara F. , Beremand Marian N. 
Published: May 2003

ABSTRACT

Tri10
, a regulatory gene in trichothecene mycotoxin-producing
Fusarium
species, is required for trichothecene biosynthesis and the coordinated expression of four trichothecene pathway-specific genes (
Tri4
,
Tri5
,
Tri6
, and
Tri101
) and the isoprenoid biosynthetic gene for farnesyl pyrophosphate synthetase (
FPPS
). We showed that six more trichothecene genes (
Tri3
,
Tri7
,
Tri8
,
Tri9
,
Tri11
, and
Tri12
) are regulated by
Tri10
. We also constructed a cDNA library from a strain of
Fusarium sporotrichioides
that overexpresses
Tri10
(↑
Tri10
) and used cDNA derived from the ↑
Tri10
strain and a non-
Tri10
-expressing strain (Δ
Tri10
) to differentially screen macroarrays prepared from the cDNA library. This screen identified 15 additional
Tri10
-regulated transcripts. Four of these transcripts represent
Tri1
,
Tri13
, and
Tri14
and a gene designated
Tri15
. Three other sequences are putative orthologs of genes for isoprenoid biosynthesis, the primary metabolic pathway preceding trichothecene biosynthesis. The remaining eight sequences have been designated
Ibt
(influenced by
Tri10
) genes. Of the 26 transcripts now known to be positively regulated by
Tri10
, 22 are positively coregulated by
Tri6
, a gene that encodes a previously characterized trichothecene pathway-specific transcription factor. These 22
Tri10
- and
Tri6
-coregulated sequences include all of the known
Tri
genes (except for
Tri10
), the
FPPS
gene, and the other three putative isoprenoid biosynthetic genes.
Tri6
also regulates a transcript that is not regulated by
Tri10
. Thus,
Tri10
and
Tri6
regulate overlapping sets of genes that include a common group of multiple genes for both primary and secondary metabolism.
Purification and Characterization of Streptin, a Type A1 Lantibiotic Produced by
Streptococcus pyogenes
Authors: Wescombe Philip A. , Tagg John R. 
Published: May 2003

ABSTRACT

Approximately 10% of
Streptococcus pyogenes
strains inhibit the growth of all nine indicators in a standardized streptococcal bacteriocin typing scheme. The present study has shown that this inhibitory profile, referred to as bacteriocin producer (P)-type 777 activity, is due to the type A1 lantibiotic streptin. Two major forms of streptin were purified to homogeneity from 95% acidified (pH 2) methanol extracts of
S. pyogenes
M25 cells by using a series of reversed-phase chromatographic separations. The fully processed form of streptin (streptin 1) is a 23-amino-acid peptide with a mass of 2,424 Da. The 2,821-
M
r
form of the peptide (streptin 2) has three additional amino acids (TPY) at the N terminus. Strain M25 extracts also contained small quantities of the streptin 1 and streptin 2 peptides in various stages of dehydration. Streptin 1 and streptin 2 were each capable of specifically inducing streptin production when added to strain M25 cultures. The streptin gene cluster resembled that of other type A1 lantibiotics but appeared to lack a streptin-specific proteinase gene. Although the streptin structural gene (
srtA
) was widespread within
S. pyogenes
, being detected in 40 of 58 strains, each representing a different M serotype, only 10 of these
srtA
-positive strains produced active streptin. The failure of some strains to express streptin was attributed to an ∼4.5-kb deletion in their streptin loci, encompassing genes putatively encoding proteins involved in streptin processing (
srtB
and
srtC
) and transport (
srtT
). In other strains,
srtA
transcription appeared to be defective. No direct association could be detected between the production of streptin and the production of the lantibiotic-like hemolysin streptolysin S in strain M25.
Homologous
npdGI
Genes in 2,4-Dinitrophenol- and 4-Nitrophenol-Degrading
Rhodococcus
spp
Authors: Heiss Gesche , Trachtmann Natalie , Abe Yoshikatsu , Takeo Masahiro , Knackmuss Hans-Joachim 
Published: May 2003

ABSTRACT

Rhodococcus
(
opacus
)
erythropolis
HL PM-1 grows on 2,4,6-trinitrophenol or 2,4-dinitrophenol (2,4-DNP) as a sole nitrogen source. The NADPH-dependent F
420
reductase (NDFR; encoded by
npdG
) and the hydride transferase II (HTII; encoded by
npdI
) of the strain were previously shown to convert both nitrophenols to their respective hydride Meisenheimer complexes. In the present study,
npdG
and
npdI
were amplified from six 2,4-DNP degrading
Rhodococcus
spp. The genes showed sequence similarities of 86 to 99% to the respective
npd
genes of strain HL PM-1. Heterologous expression of the
npdG
and
npdI
genes showed that they were involved in 2,4-DNP degradation. Sequence analyses of both the NDFRs and the HTIIs revealed conserved domains which may be involved in binding of NADPH or F
420
. Phylogenetic analyses of the NDFRs showed that they represent a new group in the family of F
420
-dependent NADPH reductases. Phylogenetic analyses of the HTIIs revealed that they form an additional group in the family of F
420
-dependent glucose-6-phosphate dehydrogenases and F
420
-dependent
N
5
,
N
10
-methylenetetrahydromethanopterin reductases. Thus, the NDFRs and the HTIIs may each represent a novel group of F
420
-dependent enzymes involved in catabolism.
Genome Differences That Distinguish
Bacillus anthracis
from
Bacillus cereus
and
Bacillus thuringiensis
Authors: Radnedge Lyndsay , Agron Peter G. , Hill Karen K. , Jackson Paul J. , Ticknor Lawrence O. , Keim Paul , Andersen Gary L. 
Published: May 2003

ABSTRACT

The three species of the group 1 bacilli,
Bacillus anthracis
,
B. cereus
, and
B. thuringiensis
, are genetically very closely related. All inhabit soil habitats but exhibit different phenotypes.
B. anthracis
is the causative agent of anthrax and is phylogenetically monomorphic, while
B. cereus
and
B. thuringiensis
are genetically more diverse. An amplified fragment length polymorphism analysis described here demonstrates genetic diversity among a collection of non-anthrax-causing
Bacillus
species, some of which show significant similarity to
B. anthracis
. Suppression subtractive hybridization was then used to characterize the genomic differences that distinguish three of the non-anthrax-causing bacilli from
B. anthracis
Ames. Ninety-three DNA sequences that were present in
B. anthracis
but absent from the non-anthrax-causing
Bacillus
genomes were isolated. Furthermore, 28 of these sequences were not found in a collection of 10 non-anthrax-causing
Bacillus
species but were present in all members of a representative collection of
B. anthracis
strains. These sequences map to distinct loci on the
B. anthracis
genome and can be assayed simultaneously in multiplex PCR assays for rapid and highly specific DNA-based detection of
B. anthracis
.
Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin
Authors: Dhillon Ashita , Teske Andreas , Dillon Jesse , Stahl David A. , Sogin Mitchell L. 
Published: May 2003

ABSTRACT

The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (
dsrAB
) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The
dsrAB
sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus
Desulfobacter
and a clade of novel, deeply branching
dsr
sequences related to environmental
dsr
sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other
dsr
clones were affiliated with gram-positive thermophilic sulfate reducers (genus
Desulfotomaculum
) and the delta-proteobacterial species
Desulforhabdus amnigena
and
Thermodesulforhabdus norvegica
. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with
Desulfobacterium niacini
, a member of the acetate-oxidizing, nutritionally versatile genus
Desulfobacterium
, and one clone related to
Desulfobacula toluolica
and
Desulfotignum balticum
. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and
dsrAB
clone libraries resulted in identification of members of the
Desulfobacteriales
in the Guaymas sediments. In addition, the
dsrAB
sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.
Predictability of
Vibrio cholerae
in Chesapeake Bay
Authors: Louis Valérie R. , Russek-Cohen Estelle , Choopun Nipa , Rivera Irma N. G. , Gangle Brian , Jiang Sunny C. , Rubin Andrea , Patz Jonathan A. , Huq Anwar , Colwell Rita R. 
Published: May 2003

ABSTRACT

Vibrio cholerae
is autochthonous to natural waters and can pose a health risk when it is consumed via untreated water or contaminated shellfish. The correlation between the occurrence of
V. cholerae
in Chesapeake Bay and environmental factors was investigated over a 3-year period. Water and plankton samples were collected monthly from five shore sampling sites in northern Chesapeake Bay (January 1998 to February 2000) and from research cruise stations on a north-south transect (summers of 1999 and 2000). Enrichment was used to detect culturable
V. cholerae
, and 21.1% (
n
= 427) of the samples were positive. As determined by serology tests, the isolates, did not belong to serogroup O1 or O139 associated with cholera epidemics. A direct fluorescent-antibody assay was used to detect
V. cholerae
O1, and 23.8% (
n
= 412) of the samples were positive.
V. cholerae
was more frequently detected during the warmer months and in northern Chesapeake Bay, where the salinity is lower. Statistical models successfully predicted the presence of
V. cholerae
as a function of water temperature and salinity. Temperatures above 19°C and salinities between 2 and 14 ppt yielded at least a fourfold increase in the number of detectable
V. cholerae
. The results suggest that salinity variation in Chesapeake Bay or other parameters associated with Susquehanna River inflow contribute to the variability in the occurrence of
V. cholerae
and that salinity is a useful indicator. Under scenarios of global climate change, increased climate variability, accompanied by higher stream flow rates and warmer temperatures, could favor conditions that increase the occurrence of
V. cholerae
in Chesapeake Bay.
Bacterial Conversion of Hydroxylamino Aromatic Compounds by both Lyase and Mutase Enzymes Involves Intramolecular Transfer of Hydroxyl Groups
Authors: Nadeau Lloyd J. , He Zhongqi , Spain Jim C. 
Published: May 2003

ABSTRACT

Hydroxylamino aromatic compounds are converted to either the corresponding aminophenols or protocatechuate during the bacterial degradation of nitroaromatic compounds. The origin of the hydroxyl group of the products could be the substrate itself (intramolecular transfer mechanism) or the solvent water (intermolecular transfer mechanism). The conversion of hydroxylaminobenzene to 2-aminophenol catalyzed by a mutase from
Pseudomonas pseudoalcaligenes
JS45 proceeds by an intramolecular hydroxyl transfer. The conversions of hydroxylaminobenzene to 2- and 4-aminophenol by a mutase from
Ralstonia eutropha
JMP134 and to 4-hydroxylaminobenzoate to protocatechuate by a lyase from
Comamonas acidovorans
NBA-10 and
Pseudomonas
sp. strain 4NT were proposed, but not experimentally proved, to proceed by the intermolecular transfer mechanism. GC-MS analysis of the reaction products formed in H
2
18
O did not indicate any
18
O-label incorporation during the conversion of hydroxylaminobenzene to 2- and 4-aminophenols catalyzed by the mutase from
R. eutropha
JMP134. During the conversion of 4-hydroxylaminobenzoate catalyzed by the hydroxylaminolyase from
Pseudomonas
sp. strain 4NT, only one of the two hydroxyl groups in the product, protocatechuate, was
18
O labeled. The other hydroxyl group in the product must have come from the substrate. The mutase in strain JS45 converted 4-hydroxylaminobenzoate to 4-amino-3-hydroxybenzoate, and the lyase in
Pseudomonas
strain 4NT converted hydroxylaminobenzene to aniline and 2-aminophenol but not to catechol. The results indicate that all three types of enzyme-catalyzed rearrangements of hydroxylamino aromatic compounds proceed via intramolecular transfer of hydroxyl groups.
Origin of Contamination and Genetic Diversity of
Escherichia coli
in Beef Cattle
Authors: Aslam Mueen , Nattress Frances , Greer Gordon , Yost Chris , Gill Colin , McMullen Lynn 
Published: May 2003

ABSTRACT

The possible origin of beef contamination and genetic diversity of
Escherichia coli
populations in beef cattle, on carcasses and ground beef, was examined by using random amplification of polymorphic DNA (RAPD) and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the
fliC
gene.
E. coli
was recovered from the feces of 10 beef cattle during pasture grazing and feedlot finishing and from hides, carcasses, and ground beef after slaughter. The 1,403
E. coli
isolates (855 fecal, 320 hide, 153 carcass, and 75 ground beef) were grouped into 121 genetic subtypes by using the RAPD method. Some of the genetic subtypes in cattle feces were also recovered from hides, prechilled carcasses, chilled carcasses, and ground beef.
E. coli
genetic subtypes were shared among cattle at all sample times, but a number of transient types were unique to individual animals. The genetic diversity of the
E. coli
population changed over time within individual animals grazing on pasture and in the feedlot. Isolates from one animal (59 fecal, 30 hide, 19 carcass, and 12 ground beef) were characterized by the PCR-RFLP analysis of the
fliC
gene and were grouped into eight genotypes. There was good agreement between the results obtained with the RAPD and PCR-RFLP techniques. In conclusion, the
E. coli
contaminating meat can originate from cattle feces, and the
E. coli
population in beef cattle was highly diverse. Also, genetic subtypes can be shared among animals or can be unique to an animal, and they are constantly changing.
The
ars
Detoxification System Is Advantageous but Not Required for As(V) Respiration by the Genetically Tractable
Shewanella
Species Strain ANA-3
Authors: Saltikov Chad W. , Cifuentes Ana , Venkateswaran Kasthuri , Newman Dianne K. 
Published: May 2003

ABSTRACT

Arsenate [As(V); HAsO
4
2−
] respiration by bacteria is poorly understood at the molecular level largely due to a paucity of genetically tractable organisms with this metabolic capability. We report here the isolation of a new As(V)-respiring strain (ANA-3) that is phylogenetically related to members of the genus
Shewanella
and that also provides a useful model system with which to explore the molecular basis of As(V) respiration. This gram-negative strain stoichiometrically couples the oxidation of lactate to acetate with the reduction of As(V) to arsenite [As(III); HAsO
2
]. The generation time and lactate molar growth yield (Y
lactate
) are 2.8 h and 10.0 g of cells mol of lactate
−1
, respectively, when it is grown anaerobically on lactate and As(V). ANA-3 uses a wide variety of terminal electron acceptors, including oxygen, soluble ferric iron, oxides of iron and manganese, nitrate, fumarate, the humic acid functional analog 2,6-anthraquinone disulfonate, and thiosulfate. ANA-3 also reduces As(V) to As(III) in the presence of oxygen and resists high concentrations of As(III) (up to 10 mM) when grown under either aerobic or anaerobic conditions. ANA-3 possesses an
ars
operon (
arsDABC
) that allows it to resist high levels of As(III); this operon also confers resistance to the As-sensitive strains
Shewanella oneidensis
MR-1 and
Escherichia coli
AW3110. When the gene encoding the As(III) efflux pump,
arsB
, is inactivated in ANA-3 by a polar mutation that also eliminates the expression of
arsC
, which encodes an As(V) reductase, the resulting As(III)-sensitive strain still respires As(V); however, the generation time and the Y
lactate
value are two- and threefold lower, respectively, than those of the wild type. These results suggest that ArsB and ArsC may be useful for As(V)-respiring bacteria in environments where As concentrations are high, but that neither is required for respiration.
Purification and Characterization of an Inverting Stereo- and Enantioselective
sec
-Alkylsulfatase from the Gram-Positive Bacterium
Rhodococcus ruber
DSM 44541
Authors: Pogorevc Mateja , Faber Kurt 
Published: May 2003

ABSTRACT

Whole cells of
Rhodococcus ruber
DSM 44541 were found to hydrolyze (±)-2-octyl sulfate in a stereo- and enantiospecific fashion. When growing on a complex medium, the cells produced two
sec
-alkylsulfatases and (at least) one
prim
-alkylsulfatase in the absence of an inducer, such as a
sec
-alkyl sulfate or a
sec
-alcohol. From the crude cell-free lysate, two proteins responsible for sulfate ester hydrolysis (designated RS1 and RS2) were separated from each other based on their different hydrophobicities and were subjected to further chromatographic purification. In contrast to sulfatase RS1, enzyme RS2 proved to be reasonably stable and thus could be purified to homogeneity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single band at a molecular mass of 43 kDa. Maximal enzyme activity was observed at 30°C and at pH 7.5. Sulfatase RS2 showed a clear preference for the hydrolysis of linear secondary alkyl sulfates, such as 2-, 3-, or 4-octyl sulfate, with remarkable enantioselectivity (an enantiomeric ratio of up to 21 [23]). Enzymatic hydrolysis of (
R
)-2-octyl sulfate furnished (
S
)-2-octanol without racemization, which revealed that the enzymatic hydrolysis proceeded through inversion of the configuration at the stereogenic carbon atom. Screening of a broad palette of potential substrates showed that the enzyme exhibited limited substrate tolerance; while simple linear
sec
-alkyl sulfates (C
7
to C
10
) were freely accepted, no activity was found with branched and mixed aryl-alkyl
sec
-sulfates. Due to the fact that
prim
-sulfates were not accepted, the enzyme was classified as
sec-
alkylsulfatase (EC 3.1.6.X).