bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glutamyl-tRNA Reductase of
Chlorobium vibrioforme
Is a Dissociable Homodimer That Contains One Tightly Bound Heme per Subunit
Authors: Srivastava Alaka , Beale Samuel I. 
Published: June 2005

ABSTRACT

δ-Aminolevulinic acid, the biosynthetic precursor of tetrapyrroles, is synthesized from glutamate via the tRNA-dependent five-carbon pathway in the green sulfur bacterium
Chlorobium vibrioforme
. The enzyme glutamyl-tRNA reductase (GTR), encoded by the
hemA
gene, catalyzes the first committed step in this pathway, which is the reduction of tRNA-bound glutamate to produce glutamate 1-semialdehyde. To characterize the GTR protein, the
hemA
gene from
C. vibrioforme
was cloned into expression plasmids that added an N-terminal His
6
tag to the expressed protein. The His-tagged GTR protein was purified using Ni affinity column chromatography. GTR was observable as a 49-kDa band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels. The native molecular mass, as determined by gel filtration chromatography, appeared to be approximately 40 kDa, indicating that native GTR is a monomer. However, when the protein was mixed with 5% (vol/vol) glycerol, the product had an apparent molecular mass of 95 kDa, indicating that the protein is a dimer under these conditions. Purified His
6
-GTR was catalytically active in vitro when it was incubated with
Escherichia coli
glutamyl-tRNA
Glu
and purified recombinant
Chlamydomonas reinhardtii
glutamate-1-semialdehyde aminotransferase. The expressed GTR contained 1 mol of tightly bound heme per mol of pep tide subunit. The heme remained bound to the protein throughout purification and was not removed by anion- or cation-exchange column chromatography. However, the bound heme was released during SDS-PAGE if the protein was denatured in the presence of β-mercaptoethanol. Added heme did not inhibit the activity of purified expressed GTR in vitro. However, when the GTR was expressed in the presence of 3-amino-2,3- dihydrobenzoic acid (gabaculine), an inhibitor of heme synthesis, the purified GTR had 60 to 70% less bound heme than control GTR, and it was inhibited by hemin in vitro.
Transport and Metabolism of Citrate by
Streptococcus mutans
Authors: Korithoski Bryan , Krastel Kirsten , Cvitkovitch Dennis G. 
Published: June 2005

ABSTRACT

Streptococcus mutans
, a normal inhabitant of dental plaque, is considered a primary etiological agent of dental caries. Two virulence determinants of
S. mutans
are its acidogenicity and aciduricity (the ability to produce acid and the ability to survive and grow at low pH, respectively). Citric acid is ubiquitous in nature; it is a component of fruit juices, bones, and teeth. In lactic acid bacteria citrate transport has been linked to increased survival in acidic conditions. We identified putative citrate transport and metabolism genes in
S. mutans
, which led us to investigate citrate transport and metabolism. Our goals in this study were to determine the mechanisms of citrate transport and metabolism in
S. mutans
and to examine whether citrate modulates
S. mutans
aciduricity. Radiolabeled citrate was used during citrate transport to identify citrate metal ion cofactors, and thin-layer chromatography was used to identify metabolic end products of citrate metabolism.
S. mutans
was grown in medium MM4 with different citrate concentrations and pH values, and the effects on the growth rate and cell survival were monitored. Intracellular citrate inhibited the growth of the bacteria, especially at low pH. The most effective cofactor for citrate uptake by
S. mutans
was Fe
3+
. The metabolic end product of citrate metabolism was aspartate, and a citrate transporter mutant was more citrate tolerant than the parent.
Transposon Mutagenesis in a Marine
Synechococcus
Strain: Isolation of Swimming Motility Mutants
Authors: McCarren J. , Brahamsha B. 
Published: June 2005

ABSTRACT

Certain marine unicellular cyanobacteria of the genus
Synechococcus
exhibit a unique type of swimming motility characterized by the absence of flagella or any other obvious organelles of motility. While the abundant cell surface-associated 130-kDa glycoprotein SwmA is known to be required for the generation of thrust, identification of other components of the motility apparatus has, until recently, been unsuccessful. Here we report on the development of a transposon mutagenesis system for use with marine
Synechococcus
sp. strain WH8102, a model organism for which the genome has been sequenced. Utilizing this mutagenesis technique, we have isolated 17 independent mutants impaired in swimming motility. These 17 transposon insertions are located in nine open reading frames, which cluster in three separate regions of the genome. Included within these clusters are several multicomponent transport systems as well as a number of glycosyltransferases.
OmcF, a Putative
c
-Type Monoheme Outer Membrane Cytochrome Required for the Expression of Other Outer Membrane Cytochromes in
Geobacter sulfurreducens
Authors: Kim Byoung-Chan , Leang Ching , Ding Yan-Huai R. , Glaven Richard H. , Coppi Maddalena V. , Lovley Derek R. 
Published: June 2005

ABSTRACT

Outer membrane cytochromes are often proposed as likely agents for electron transfer to extracellular electron acceptors, such as Fe(III). The
omcF
gene in the dissimilatory Fe(III)-reducing microorganism
Geobacter sulfurreducens
is predicted to code for a small outer membrane monoheme
c
-type cytochrome. An OmcF-deficient strain was constructed, and its ability to reduce and grow on Fe(III) citrate was found to be impaired. Following a prolonged lag phase (150 h), the OmcF-deficient strain developed the ability to grow in Fe(III) citrate medium with doubling times and yields that were ca. 145% and 70% of those of the wild type, respectively. Comparison of the
c
-type cytochrome contents of outer membrane-enriched fractions prepared from wild-type and OmcF-deficient cultures confirmed the outer membrane association of OmcF and revealed multiple changes in the cytochrome content of the OmcF-deficient strain. These changes included loss of expression of two previously characterized outer membrane cytochromes, OmcB and OmcC, and overexpression of a third previously characterized outer membrane cytochrome, OmcS, during growth on Fe(III) citrate. The
omcB
and
omcC
transcripts could not be detected in the OmcF-deficient mutant by either reverse transcriptase PCR or Northern blot analyses. Expression of the
omcF
gene in
trans
restored both the capacity of the OmcF-deficient mutant to reduce Fe(III) and wild-type levels of
omcB
and
omcC
mRNA and protein. Thus, elimination of OmcF may impair Fe(III) reduction by influencing expression of OmcB, which has previously been demonstrated to play a critical role in Fe(III) reduction.
Mutational Analysis of a Bifunctional Ferrisiderophore Receptor and Signal-Transducing Protein fromPseudomonas aeruginosa
Authors: James H. Ellen , Beare Paul A. , Martin Lois W. , Lamont Iain L. 
Published: June 2005

ABSTRACTThe FpvA protein ofPseudomonas aeruginosastrain PAO1 mediates uptake of a siderophore, ferripyoverdine. It is also a component of a signal transduction pathway that controls production of an exotoxin, a protease, pyoverdine, and FpvA itself. The purpose of the research described here was to dissect these different functions of FpvA. Signaling involves an N-terminal domain of FpvA, and it was shown that this domain is probably located in the periplasm, as expected. Short peptides were inserted at 36 sites within FpvA by linker insertion mutagenesis. The effects of these mutations on the presence of FpvA in the outer membrane, on FpvA-mediated uptake of ferripyoverdine, and on pyoverdine synthesis and gene expression were determined. Five of the mutations resulted in the absence of FpvA from the outer membrane of the bacteria. All of the remaining mutations eliminated either the transport or signaling function of FpvA and most affected both functions. Three mutations prevented transport of ferripyoverdine but had no effect on the signal transduction pathway showing that transport of ferripyoverdine is not required for the trans-membrane signaling process. Conversely, eight mutations affected pyoverdine-mediated signaling but had no effect on transport of ferripyoverdine. These data show that insertions throughout FpvA resulted in loss of function and that signaling and transport are separate and discrete functions of FpvA.
Llama Antibodies against a Lactococcal Protein Located at the Tip of the Phage Tail Prevent Phage Infection
Authors: De Haard Hans J. W. , Bezemer Sandra , Ledeboer Aat M. , Müller Wally H. , Boender Piet J. , Moineau Sylvain , Coppelmans Marie-Cecile , Verkleij Arie J. , Frenken Leon G. J. , Verrips C. Theo 
Published: June 2005

ABSTRACT

Bacteriophage p2 belongs to the most prevalent lactococcal phage group (936) responsible for considerable losses in industrial production of cheese. Immunization of a llama with bacteriophage p2 led to higher titers of neutralizing heavy-chain antibodies (i.e., devoid of light chains) than of the classical type of immunoglobulins. A panel of p2-specific single-domain antibody fragments was obtained using phage display technology, from which a group of potent neutralizing antibodies were identified. The antigen bound by these antibodies was identified as a protein with a molecular mass of 30 kDa, homologous to open reading frame 18 (ORF18) of phage sk1, another 936-like phage for which the complete genomic sequence is available. By the use of immunoelectron microscopy, the protein is located at the tip of the tail of the phage particle. The addition of purified ORF18 protein to a bacterial culture suppressed phage infection. This result and the inhibition of cell lysis by anti-ORF18 protein antibodies support the conclusion that the ORF18 protein plays a crucial role in the interaction of bacteriophage p2 with the surface receptors of
Lactococcus lactis
.
Genetic Evidence that GTP Is Required for Transposition of IS
903
and Tn
552
in
Escherichia coli
Authors: Coros Abbie M. , Twiss Erin , Tavakoli Norma P. , Derbyshire Keith M. 
Published: June 2005

ABSTRACT

Surprisingly little is known about the role of host factors in regulating transposition, despite the potentially deleterious rearrangements caused by the movement of transposons. An extensive mutant screen was therefore conducted to identify
Escherichia coli
host factors that regulate transposition. An
E. coli
mutant library was screened using a papillation assay that allows detection of IS
903
transposition events by the formation of blue papillae on a colony. Several host mutants were identified that exhibited a unique papillation pattern: a predominant ring of papillae just inside the edge of the colony, implying that transposition was triggered within these cells based on their spatial location within the colony. These mutants were found to be in
pur
genes, whose products are involved in the purine biosynthetic pathway. The transposition ring phenotype was also observed with Tn
552
, but not Tn
10
, establishing that this was not unique to IS
903
and that it was not an artifact of the assay. Further genetic analyses of purine biosynthetic mutants indicated that the ring of transposition was consistent with a GTP requirement for IS
903
and Tn
552
transposition. Together, our observations suggest that transposition occurs during late stages of colony growth and that transposition occurs inside the colony edge in response to both a gradient of exogenous purines across the colony and the developmental stage of the cells.
Bacillus anthracis
Sortase A (SrtA) Anchors LPXTG Motif-Containing Surface Proteins to the Cell Wall Envelope
Authors: Gaspar Andrew H. , Marraffini Luciano A. , Glass Elizabeth M. , DeBord Kristin L. , Ton-That Hung , Schneewind Olaf 
Published: June 2005

ABSTRACT

Cell wall-anchored surface proteins of gram-positive pathogens play important roles during the establishment of many infectious diseases, but the contributions of surface proteins to the pathogenesis of anthrax have not yet been revealed. Cell wall anchoring in
Staphylococcus aureus
occurs by a transpeptidation mechanism requiring surface proteins with C-terminal sorting signals as well as sortase enzymes. The genome sequence of
Bacillus anthracis
encodes three sortase genes and eleven surface proteins with different types of cell wall sorting signals. Purified
B. anthracis
sortase A cleaved peptides encompassing LPXTG motif-type sorting signals between the threonine (T) and the glycine (G) residues in vitro. Sortase A activity could be inhibited by thiol-reactive reagents, similar to staphylococcal sortases.
B. anthracis
parent strain Sterne 34F
2
, but not variants lacking the
srtA
gene, anchored the collagen-binding MSCRAMM (microbial surface components recognizing adhesive matrix molecules) BasC (BA5258/BAS4884) to the bacterial cell wall. These results suggest that
B. anthracis
SrtA anchors surface proteins bearing LPXTG motif sorting signals to the cell wall envelope of vegetative bacilli.
Breeding activity patterns, reproductive modes, and habitat use by anurans (Amphibia) in a seasonal environment in the Pantanal, Brazil
Authors: Prado Cynthia , Uetanabaro Masao , Haddad Célio 
Published: June 2005

AbstractAnnual patterns of breeding activity, reproductive modes, and habitat use are described for a frog community in a seasonal environment, in the southern Pantanal, Mato Grosso do Sul, Brazil. Data were collected monthly between January 1995 and December 1998. A total of 24 species from four families; Bufonidae (3 species), Hylidae (10 species), Leptodactylidae (9 species), and Microhylidae (2 species) were registered. Three reproductive activity patterns are recognized among these species: continuous, explosive, and prolonged; 50% of the species were explosive breeders. Seasonal pattern of reproduction was verified for three analyzed years (1995-1997); most species reproduced during the rainy season (Nov-Jan). The reproduction was aseasonal in 1998; unexpected rains in the dry season lead to an unusual breeding activity. Five reproductive modes were noted — 62.5% of the species have the generalized aquatic mode, and 33.3% deposit eggs embedded in foam nests. Many species used the same sites for reproduction, although temporal partitioning and calling site segregation was observed. The occurrence of many species that exhibit explosive breeding early in the rainy season is common in seasonal and open environments with variable and unpredictable rainfall, as is the case in the Pantanal.
Sexual dimorphism in the Neotropical lizard, Tropidurus torquatus (Squamata, Tropiduridae)
Authors: Pinto Adriana C.S. , Wiederhecker Helga C. , Colli Guarino R. 
Published: June 2005

Abstract
We describe the sexual dimorphism in coloration, body shape, and body size in
Tropidurus torquatus, a widely distributed lizard species in central Brazil.
Adult males have colored patches varying from yellow to yellow-and-black,
and black on the abdomen, ventral aspect of the thighs, and pre-cloacal
flap. Adult females lack ventral colored patches. During ontogeny, there is
a gradual darkening of the patches, but no modification either in patch size
or color is associated with the reproductive cycle. Adult males have wider
heads and thinner bodies than females of the same body size. Males and
females grow at the same rate prior to sexual maturity, but males take
longer to reach sexual maturity, maturing at a larger body size than
females.
Food availability induces geographic variation in reproductive timing of an aquatic oviparous snake (Natrix maura)
Authors: Santos X. , Llorente G.A. , Feriche M. , Pleguezuelos J.M. , Casals F. , de Sostoa A. 
Published: June 2005

Abstract
The viperine snake Natrix maura is a common water snake, which forages on
aquatic prey such as fish and frogs in Western Mediterranean water bodies.
Female viperine snakes collected from three populations at the Iberian
Peninsula during the vitellogenesis period were compared. Mean clutch size
and range, as well as the slope of the regression between body size and
clutch size, did not show differences between populations. In contrast, mean
size of enlarged follicles of females collected in May from the Ebro Delta
proved significantly smaller than those of females from the Matarranya River
(50 km far) and the Granada Depression (500 km far). There were no
differences in climatic conditions between areas. However, seasonal
variation in food availability was significantly different in the Ebro
Delta. In this area, the rice fields are dry in early spring as men control
the water flow, and prey are not available. This energetic constraint
induced female viperine snakes to adjust reproductive timing according to
seasonal availability and to delay vitellogenesis for at least one month. By
contrast, other Mediterranean populations exhibited a rather high prey
availability from early spring (e.g. Matarranya River), females being in
good condition in this season and consequently vitellogenesis starting
earlier than in the Ebro Delta. This study illustrates a new case of
reproductive plasticity in snakes.
Protein polymorphism in populations of Boa constrictor occidentalis (Boidae) from Córdoba province, Argentina
Authors: Rivera Paula C. , Chiaraviglio Margarita , Pérez Gabriela , Gardenal Cristina N. 
Published: June 2005

Abstract
Boa constrictor occidentalis, the only subspecies of the genus Boa present in
Argentina, is endangered because of the strong hunting pressure due to the
skin and pet-shop trade and the destruction and fragmentation of its
habitat. We estimated levels of protein polymorphism and determined the
degree of genetic differentiation between two populations of B. c.
occidentalis in Córdoba province, Argentina. We obtained blood samples from
93 specimens in two sampling sites 200 km apart. A total of 17 proteins
affording information on 25 presumptive loci were studied by gel
electrophoresis techniques. Only four loci were polymorphic: 6-Pgdh-1,
Cat-1, Ldh and Hp. The mean heterozygosity per locus was low (0.06 and
0.07). Life history and ecological traits of this snake may explain the low
levels of polymorphism found. No evidence of inbreeding was detected. The
average genetic differentiation between the two sampled areas was not
significant ( = 0.004). These results would indicate a relatively recent
fragmentation of an original gene pool.
Age, size and growth of the southern crested newt Triturus karelinii (Strauch 1870) in a population from Bozdag (Western Turkey)
Authors: Olgun Kurtulus , Uzum Nazan , Avci Azız , Miaud Claude 
Published: June 2005

Abstract
We studied the characteristics of bone growth assessed by skeletochronology
in a southern crested newt Triturus karelinii (Urodela) population from
Western Turkey. The timing and patterns of bone arrested growth were
observed using the phalanges of juveniles and adults that were caught in
spring at a breeding site. A metamorphosis line was found in the juveniles.
In some adults, a classical succession of single lines of arrested growth
was observed in about 50% of the cross sections. However, the other adults
exhibited a succession of double lines of arrested growth in their
phalanges. Due to the arid summer and cold winter climate in the Bozdag
region (1200 m a.s.l.), we argue that in this last case, the lines of
arrested growth were deposited during both the summer (aestivation) and
winter (wintering). Body length, age and growth were similar in males and
females. The age of maturity was 3 to 4 years old and longevity was 8 and 11
years in males and females respectively. Body length and age among
taxonomically related large bodied newts of the T. cristatus complex were
reported from populations experiencing various environmental conditions.
Body length and age at maturity were similar to that observed in other newt
species. However, longevity seems to be lower than expected in the T.
karelinii studied population. We hypothesized that the arid climate of
Bozdag could cause a higher mortality risk during the terrestrial phase of
the life cycle. Studying more populations exposed to various conditions is
clearly needed to assess interpopulational variation of these life-history
traits in this newt species.
Mixing and Entrainment in the Red Sea Outflow Plume. Part I: Plume Structure
Authors: Peters Hartmut , Johns William E. , Bower Amy S. , Fratantoni David M. 
Published: June 2005

Abstract
When the salty and heavy water of the Red Sea exits from the Strait of Bab el Mandeb, it continues downslope into the Gulf of Aden mainly along two channels. The 130-km-long “Northern Channel” (NC) is topographically confined and is typically only 5 km wide. In it, the Red Sea plume shows unanticipated patterns of vertical structure, turbulent mixing, and entrainment. Above the seafloor a 25–120-m-thick weakly stratified layer shows little dilution along the channel. Hence this bottom layer undergoes only weak entrainment. In contrast, a 35–285-m-thick interfacial layer shows stronger entrainment and is shown in a companion paper to undergo vigorous turbulent mixing. It is thus the interface that exhibits the bulk of entrainment of the Red Sea plume in the NC. The interfacial layer also carries most of the overall plume transport, increasingly so with downstream distance. The “Southern Channel” (SC) is wider than the NC and is accessed from the latter by a sill about 33 m above the floor of the NC. Entrainment into the bottom layer of the SC is diagnosed to be strong near the entry into the SC such that the near-bottom density and salinity are smaller in the SC than in the NC at the same distance from Bab el Mandeb. In comparison with winter conditions, the authors encountered weaker outflow with shallower equilibration depths during the summer cruise. Bulk Froude numbers computed for the whole plume varied within the range 0.2–1. Local maxima occurred in relatively steep channel sections and coincided with locations of significant entrainment.
Fall–Winter Current Reversals on the Texas–Louisiana Continental Shelf
Authors: Chu Peter P. , Ivanov Leonid M. , Melnichenko Oleg V. 
Published: June 2005

Abstract
Fall–winter recurrence of current reversal from westward to eastward is identified on the Texas–Louisiana continental shelf using the current-meter [Texas–Louisiana Shelf Physical Oceanography Program (LATEX-A)] and near-surface drifting buoy [Surface Current and Lagrangian Drift Program (SCULP-1)] observations in 1993 and 1994. Reversal events roughly satisfy the Poisson distribution with one current reversal nearly every 12 days. Synoptic winds seem responsible for the current reversal events. Other processes such as offshore eddies shed from the Loop Current and river runoff are less important to change alongshore flow direction at synoptic scales. A statistical model is established to predict the synoptic current reversal using the surface wind observations.