bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity of Cultivated Endophytic Bacteria from Sugarcane: Genetic and Biochemical Characterization of
Burkholderia cepacia
Complex Isolates
Authors: Mendes Rodrigo , Pizzirani-Kleiner Aline A. , Araujo Welington L. , Raaijmakers Jos M.
Published: September 2007

Bacteria were isolated from the rhizosphere and from inside the roots and stems of sugarcane plants grown in the field in Brazil. Endophytic bacteria were found in both the roots and the stems of sugarcane plants, with a significantly higher density in the roots. Many of the cultivated endophytic bacteria were shown to produce the plant growth hormone indoleacetic acid, and this trait was more frequently found among bacteria from the stem. 16S rRNA gene sequence analysis revealed that the selected isolates of the endophytic bacterial community of sugarcane belong to the genera of
Burkholderia, Pantoea, Pseudomonas
, and
Microbacterium
. Bacterial isolates belonging to the genus
Burkholderia
were the most predominant among the endophytic bacteria. Many of the
Burkholderia
isolates produced the antifungal metabolite pyrrolnitrin, and all were able to grow at 37°C. Phylogenetic analyses of the 16S rRNA gene and
recA
gene sequences indicated that the endophytic
Burkholderia
isolates from sugarcane are closely related to clinical isolates of the
Burkholderia cepacia
complex and clustered with
B. cenocepacia
(gv. III) isolates from cystic fibrosis patients. These results suggest that isolates of the
B. cepacia
complex are an integral part of the endophytic bacterial community of sugarcane in Brazil and reinforce the hypothesis that plant-associated environments may act as a niche for putative opportunistic human pathogenic bacteria.
Exploration of New Geometries in Cellulosome-Like Chimeras
Authors: Mingardon Florence , Chanal Angélique , Tardif Chantal , Bayer Edward A. , Fierobe Henri-Pierre
Published: September 2007

In this study, novel cellulosome chimeras exhibiting atypical geometries and binding modes, wherein the targeting and proximity functions were directly incorporated as integral parts of the enzyme components, were designed. Two pivotal cellulosomal enzymes (family 48 and 9 cellulases) were thus appended with an efficient cellulose-binding module (CBM) and an optional cohesin and/or dockerin. Compared to the parental enzymes, the chimeric cellulases exhibited improved activity on crystalline cellulose as opposed to their reduced activity on amorphous cellulose. Nevertheless, the various complexes assembled using these engineered enzymes were somewhat less active on crystalline cellulose than the conventional designer cellulosomes containing the parental enzymes. The diminished activity appeared to reflect the number of protein-protein interactions within a given complex, which presumably impeded the mobility of their catalytic modules. The presence of numerous CBMs in a given complex, however, also reduced their performance. Furthermore, a “covalent cellulosome” that combines in a single polypeptide chain a CBM, together with family 48 and family 9 catalytic modules, also exhibited reduced activity. This study also revealed that the cohesin-dockerin interaction may be reversible under specific conditions. Taken together, the data demonstrate that cellulosome components can be used to generate higher-order functional composites and suggest that enzyme mobility is a critical parameter for cellulosome efficiency.
Layered Structure of Bacterial and Archaeal Communities and Their In Situ Activities in Anaerobic Granules
Authors: Satoh Hisashi , Miura Yuki , Tsushima Ikuo , Okabe Satoshi
Published: September 2007

The microbial community structure and spatial distribution of microorganisms and their in situ activities in anaerobic granules were investigated by 16S rRNA gene-based molecular techniques and microsensors for CH
4
, H
2
, pH, and the oxidation-reduction potential (ORP). The 16S rRNA gene-cloning analysis revealed that the clones related to the phyla
Alphaproteobacteria
(detection frequency, 51%),
Firmicutes
(20%),
Chloroflexi
(9%), and
Betaproteobacteria
(8%) dominated the bacterial clone library, and the predominant clones in the archaeal clone library were affiliated with
Methanosaeta
(73%). In situ hybridization with oligonucleotide probes at the phylum level revealed that these microorganisms were numerically abundant in the granule. A layered structure of microorganisms was found in the granule, where
Chloroflexi
and
Betaproteobacteria
were present in the outer shell of the granule,
Firmicutes
were found in the middle layer, and aceticlastic
Archaea
were restricted to the inner layer. Microsensor measurements for CH
4
, H
2
, pH, and ORP revealed that acid and H
2
production occurred in the upper part of the granule, below which H
2
consumption and CH
4
production were detected. Direct comparison of the in situ activity distribution with the spatial distribution of the microorganisms implied that
Chloroflexi
contributed to the degradation of complex organic compounds in the outermost layer, H
2
was produced mainly by
Firmicutes
in the middle layer, and
Methanosaeta
produced CH
4
in the inner layer. We determined the effective diffusion coefficient for H
2
in the anaerobic granules to be 2.66 × 10
−5
cm
2
s
−1
, which was 57% in water.
Caulobacter crescentus
as a Whole-Cell Uranium Biosensor
Authors: Hillson Nathan J. , Hu Ping , Andersen Gary L. , Shapiro Lucy
Published: September 2007

We engineered a strain of the bacterium
Caulobacter crescentus
to fluoresce in the presence of micromolar levels of uranium at ambient temperatures when it is exposed to a hand-held UV lamp. Previous microarray experiments revealed that several
Caulobacter
genes are significantly upregulated in response to uranium but not in response to other heavy metals. We designated one of these genes
urcA
(for
u
ranium
r
esponse in
c
aulobacter). We constructed a reporter that utilizes the
urcA
promoter to produce a UV-excitable green fluorescent protein in the presence of the uranyl cation, a soluble form of uranium. This reporter is specific for uranium and has little cross specificity for nitrate (<400 μM), lead (<150 μM), cadmium (<48 μM), or chromium (<41.6 μM). The uranium reporter construct was effective for discriminating contaminated groundwater samples (4.2 μM uranium) from uncontaminated groundwater samples (<0.1 μM uranium) collected at the Oak Ridge Field Research Center. In contrast to other uranium detection methodologies, the
Caulobacter
reporter strain can provide on-demand usability in the field; it requires minimal sample processing and no equipment other than a hand-held UV lamp, and it may be sprayed directly on soil, groundwater, or industrial surfaces.
LambdaSa1 and LambdaSa2 Prophage Lysins of
Streptococcus agalactiae
Authors: Pritchard David G. , Dong Shengli , Kirk Marion C. , Cartee Robert T. , Baker John R.
Published: September 2007

Putative
N
-acetylmuramyl-
l
-alanine amidase genes from LambdaSa1 and LambdaSa2 prophages of
Streptococcus agalactiae
were cloned and expressed in
Escherichia coli
. The purified enzymes lysed the cell walls of
Streptococcus agalactiae
,
Streptococcus pneumoniae
, and
Staphylococcus aureus
. The peptidoglycan digestion products in the cell wall lysates were not consistent with amidase activity. Instead, the structure of the muropeptide digestion fragments indicated that both the LambdaSa1 and LambdaSa2 lysins exhibited γ-
d
-glutaminyl-
l
-lysine endopeptidase activity. The endopeptidase cleavage specificity of the lysins was confirmed using a synthetic peptide substrate corresponding to a portion of the stem peptide and cross bridge of
Streptococcus agalactiae
peptidoglycan. The LambdaSa2 lysin also displayed β-
d
-
N
-acetylglucosaminidase activity.
Activation of Endocytosis as an Adaptation to the Mammalian Host by Trypanosomes
Authors: Natesan Senthil Kumar A. , Peacock Lori , Matthews Keith , Gibson Wendy , Field Mark C.
Published: September 2007

Immune evasion in African trypanosomes is principally mediated by antigenic variation, but rapid internalization of surface-bound immune factors may contribute to survival. Endocytosis is upregulated approximately 10-fold in bloodstream compared to procyclic forms, and surface coat remodeling accompanies transition between these life stages. Here we examined expression of endocytosis markers in tsetse fly stages in vivo and monitored modulation during transition from bloodstream to procyclic forms in vitro. Among bloodstream stages nonproliferative stumpy forms have endocytic activity similar to that seen with rapidly dividing slender forms, while differentiation of stumpy forms to procyclic forms is accompanied by rapid down-regulation of Rab11 and clathrin, suggesting that modulation of endocytic and recycling systems accompanies this differentiation event. Significantly, rapid down-regulation of endocytic markers occurs upon entering the insect midgut and expression of Rab11 and clathrin remains low throughout subsequent development, which suggests that high endocytic activity is not required for remodeling the parasite surface or for survival within the fly. However, salivary gland metacyclic forms dramatically increase expression of clathrin and Rab11, indicating that emergence of mammalian infective forms is coupled to reacquisition of a high-activity endocytic-recycling system. These data suggest that high-level endocytosis in
Trypanosoma brucei
is an adaptation required for viability in the mammalian host.
O
-Mannosyltransferase 1 in
Aspergillus fumigatus
(AfPmt1p) Is Crucial for Cell Wall Integrity and Conidium Morphology, Especially at an Elevated Temperature
Authors: Zhou Hui , Hu Hongyan , Zhang Lijuan , Li Ruoyu , Ouyang Haomiao , Ming Jia , Jin Cheng
Published: September 2007

Protein O-mannosyltransferases initiate O mannosylation of secretory proteins, which are of fundamental importance in eukaryotes. In this study, the
PMT
gene family of the human fungal pathogen
Aspergillus fumigatus
was identified and characterized. Unlike the case in
Saccharomyces cerevisiae
, where the
PMT
family is highly redundant, only one member of each
PMT
subfamily, namely, Af
pmt1
, Af
pmt2
, and Af
pmt4
, is present in
A. fumigatus
. Mutants with a deletion of Af
pmt1
are viable. In vitro and in vivo activity assays confirmed that the protein encoded by Af
pmt1
acts as an O-mannosyltransferase (AfPmt1p). Characterization of the ΔAf
pmt1
mutant showed that a lack of AfPmt1p results in sensitivity to elevated temperature and defects in growth and cell wall integrity, thereby affecting cell morphology, conidium formation, and germination. In a mouse model, Af
pmt1
was not required for the virulence of
A. fumigatus
under the experimental conditions used.
Functional Characterization of the Fission Yeast Phosphatidylserine Synthase Gene,
pps1
, Reveals Novel Cellular Functions for Phosphatidylserine
Authors: Matsuo Yasuhiro , Fisher Edward , Patton-Vogt Jana , Marcus Stevan
Published: September 2007

To investigate the contributions of phosphatidylserine to the growth and morphogenesis of the rod-shaped fission yeast
Schizosaccharomyces pombe
, we have characterized the single gene in this organism,
pps1
, encoding a predicted phosphatidylserine synthase.
S. pombe pps1
Δ mutants grow slowly in rich medium and are inviable in synthetic minimal medium. They do not produce detectable phosphatidylserine in vivo and possess negligible in vitro phosphatidylserine synthase activity, indicating that
pps1
encodes the major phosphatidylserine synthase activity in
S. pombe
. Supplementation of growth medium with ethanolamine partially suppresses the growth-defective phenotype of
pps1
Δ cells, reflecting the likely importance of phosphatidylserine as a precursor for phosphatidylethanolamine in
S. pombe
. In medium lacking ethanolamine,
pps1
Δ mutants exhibit striking cell morphology, cytokinesis, actin cytoskeleton, and cell wall remodeling and integrity defects. Overexpression of
pps1
likewise leads to defects in cell morphology and cytokinesis, thus implicating phosphatidylserine as a dosage-dependent regulator of these processes. During log-phase growth, green fluorescent protein-Pps1p fusion proteins are concentrated at the cell and nuclear peripheries as well as presumptive endoplasmic reticulum membranes, while in stationary-phase cells, they are redistributed to unusual cytoplasmic structures of unknown origin. Moreover, stationary-phase
pps1
Δ cultures retain very poor viability relative to wild-type
S. pombe
cells, even in medium containing ethanolamine, demonstrating a role for phosphatidylserine in the physiological adaptations required for stationary-phase survival. Our findings reveal novel cellular functions for phosphatidylserine and emphasize the usefulness of
S. pombe
as a model organism for elucidating potentially conserved biological and molecular functions of this phospholipid.
Sexual Pheromone Induces Diffusion of the Pheromone-Homologous Polypeptide in the Extracellular Matrix of
Volvox carteri
Authors: Ishida Koichi
Published: September 2007

The C-terminal domain of pherophorin II is homologous to the sexual pheromone of
Volvox carteri
and is released from other domains during sexual induction. Green fluorescent protein fused to the C terminus of pherophorin II was located at the extracellular matrix directly surrounding the gonidium, the final target of the sexual-induction signal.
Two Iron-Responsive Promoter Elements Control Expression of
FOX1
in
Chlamydomonas reinhardtii
Authors: Deng Xiaodong , Eriksson Mats
Published: September 2007

FOX1
encodes an iron deficiency-induced ferroxidase involved in a high-affinity iron uptake system. Mutagenesis analysis of the
FOX1
promoter identified two separate iron-responsive elements, FeRE1 (CACACG) and FeRE2 (CACGCG), between positions −87 and −82 and between positions −65 and −60, respectively, and both are needed for induced
FOX1
expression under conditions of iron deficiency.
Biochemical Characterization of dTDP-
d
-Qui4N and dTDP-
d
-Qui4NAc Biosynthetic Pathways in
Shigella dysenteriae
Type 7 and
Escherichia coli
O7
Authors: Wang Ying , Xu Yanli , Perepelov Andrei V. , Qi Yuanyuan , Knirel Yuriy A. , Wang Lei , Feng Lu
Published: September 2007

O-antigen variation due to the presence of different types of sugars and sugar linkages is important for the survival of bacteria threatened by host immune systems. The O antigens of
Shigella dysenteriae
type 7 and
Escherichia coli
O7 contain 4-(
N
-acetylglycyl)amino-4,6-dideoxy-
d
-glucose (
d
-Qui4NGlyAc) and 4-acetamido-4,6-dideoxy-
d
-glucose (
d
-Qui4NAc), respectively, which are sugars not often found in studied polysaccharides. In this study, we characterized the biosynthetic pathways for dTDP-
d
-Qui4N and dTDP-
d
-Qui4NAc (the nucleotide-activated precursors of
d
-Qui4NGlyAc and
d
-Qui4NAc in O antigens). Predicted genes involved in the synthesis of the two sugars were cloned, and the gene products were overexpressed and purified as His-tagged fusion proteins. In vitro enzymatic reactions were carried out using the purified proteins, and the reaction products were analyzed by capillary electrophoresis, electrospray ionization-mass spectrometry, and nuclear magnetic resonance spectroscopy. It is shown that in
S. dysenteriae
type 7 and
E. coli
O7, dTDP-
d
-Qui4N is synthesized from α-
d
-glucose-1-phosphate in three reaction steps catalyzed by glucose-1-phosphate thymidyltransferase (RmlA), dTDP-
d
-glucose 4,6-dehydratase (RmlB), and dTDP-4-keto-6-deoxy-
d
-glucose aminotransferase (VioA). An additional acetyltransferase (VioB) catalyzes the conversion of dTDP-
d
-Qui4N into dTDP-
d
-Qui4NAc in
E. coli
O7. Kinetic parameters and some other properties of VioA and VioB are described and differences between VioA proteins from
S. dysenteriae
type 7 (VioA
D7
) and
E. coli
O7 (VioA
O7
) discussed. To our knowledge, this is the first time that functions of VioA and VioB have been biochemically characterized. This study provides valuable enzyme sources for the production of dTDP-
d
-Qui4N and dTDP-
d
-Qui4NAc, which are potentially useful in the pharmaceutical industry for drug development.
Sequencing the Botulinum Neurotoxin Gene and Related Genes in
Clostridium botulinum
Type E Strains Reveals
orfx3
and a Novel Type E Neurotoxin Subtype
Authors: Chen Ying , Korkeala Hannu , Aarnikunnas Johannes , Lindström Miia
Published: September 2007

Three
Clostridium botulinum
type E strains were sequenced for the botulinum neurotoxin (BoNT) gene cluster, and 11 type E strains, representing a wide biodiversity, were sequenced for the
bont
/E gene. The total length of the BoNT/E gene cluster was 12,908 bp, and a novel gene (partial) designated
orfx3
, together with the complete
orfx2
gene, was identified in the three type E strains for the first time. Apart from
orfx3
, the structure and organization of the neurotoxin gene cluster of the three strains were identical to those of previously published ones. Only minor differences (≤3%) in the nucleotide sequences of the gene cluster components were observed among the three strains and the published BoNT/E-producing clostridia. The
orfx3
,
orfx2
,
orfx1
, and
p47
gene sequences of the three type E strains shared homologies of 81%, 67 to 76%, 78 to 79%, and 79 to 85%, respectively, with published sequences for type A1 and A2
C. botulinum
. Analysis of
bont
/E from the 14 type E strains and 19 previously published BoNT/E-producing clostridia revealed six neurotoxin subtypes, with a new distinct subtype consisting of three Finnish isolates alone. The amino acid sequence of the subtype E6 neurotoxin differed 3 to 6% from the other subtypes, suggesting that these subtype E6 neurotoxins may possess specific antigenic or functional properties.
In Vivo Mutations of Thymidylate Synthase (Encoded by
thyA
) Are Responsible for Thymidine Dependency in Clinical Small-Colony Variants of
Staphylococcus aureus
Authors: Chatterjee Indranil , Kriegeskorte Andre , Fischer Andreas , Deiwick Susanne , Theimann Nadine , Proctor Richard A. , Peters Georg , Herrmann Mathias , Kahl Barbara C.
Published: September 2007

Trimethoprim-sulfamethoxazole (SXT)-resistant
Staphylococcus aureus
thymidine-dependent small-colony variants (TD-SCVs) are frequently isolated from the airways of cystic fibrosis (CF) patients, often in combination with isogenic normal strains if patients were treated with SXT for extended periods. As SXT inhibits the synthesis of tetrahydrofolic acid, which acts as a cofactor for thymidylate synthase (
thyA
), the survival of TD-SCVs depends exclusively on the availability of external thymidine. Since the underlying mechanism for thymidine dependency is unknown, we investigated if alterations in the
thyA
nucleotide sequences were responsible for this phenomenon. Sequence analysis of several clinical TD-SCVs and their isogenic normal strains with reference to previously published
S. aureus thyA
nucleotide sequences was performed. Three clinical TD-SCVs were complemented by transforming TD-SCVs with the vector pCX19 expressing ThyA from
S. aureus
8325-4. Transcriptional analysis of metabolic and virulence genes and regulators (
agr
,
hla
,
spa
,
citB
,
thyA
, and
nupC
) was performed by quantitative reverse transcription-PCR. The previously published sequences of
thyA
and two normal clinical strains were highly conserved, while
thyA
of four normal strains and four SCVs had nonsynonymous point mutations. In 8/10 SCVs, deletions occurred, resulting in stop codons which were located in 4/10 SCVs close to or within the active site of the protein (dUMP binding). Complementation of TD-SCVs with
thyA
almost fully reversed the phenotype, growth characteristics, and transcription patterns. In conclusion, we demonstrated that mutations of the
thyA
gene were responsible for the phenotype of TD-SCVs. Complementation of TD-SCVs with
thyA
revealed that a functional ThyA protein is necessary and sufficient to change the SCV phenotype and behavior back to normal.
A New O-Antigen Gene Cluster Has a Key Role in the Virulence of the
Escherichia coli
Meningitis Clone O45:K1:H7
Authors: Plainvert Céline , Bidet Philippe , Peigne Chantal , Barbe Valérie , Médigue Claudine , Denamur Erick , Bingen Edouard , Bonacorsi Stéphane
Published: September 2007

A new highly pathogenic clone of
Escherichia coli
meningitis strains harboring the unusual serogroup O45 has recently emerged in France. To gain insight into the pathogenicity of this new clone, we investigated the possible role of antigen O45 in the virulence of strain S88 (O45:K1:H7), representative of this emerging clone. We first showed that the S88 O-antigen gene cluster sequence differs from that of O45 in the reference strain
E. coli
96-3285, suggesting that the two O45 polysaccharides, while probably sharing a community of epitopes, represent two different antigens. The unique functional organization of the two O-antigen gene clusters and the low DNA sequence homology of the orthologous genes suggest that the two loci originated from a common ancestor and have since undergone multiple recombination events. Phylogenetic analysis based on the flanking gene
gnd
sequences indicates that the S88 antigen O45 (O45
S88
) gene cluster may have been acquired, at least in part, from another member of the
Enterobacteriaceae
. Mutagenesis of the O45
S88
antigen gene cluster was used for functional analysis of the loci and revealed the crucial role of the O polysaccharide in S88 virulence in a neonatal rat meningitis model. We also developed a PCR method to specifically identify the O45
S88
antigen gene cluster. Together, our findings suggest that horizontal acquisition of a new O-antigen gene cluster, at least partly from another species, may have been a key event in the emergence and virulence of the
E. coli
O45:K1:H7 clone in France.
Response of the Hyperthermophilic ArchaeonSulfolobus solfataricusto UV Damage
Authors: Fröls Sabrina , Gordon Paul M. K. , Panlilio Mayi Arcellana , Duggin Iain G. , Bell Stephen D. , Sensen Christoph W. , Schleper Christa
Published: September 2007

In order to characterize the genome-wide transcriptional response of the hyperthermophilic, aerobic crenarchaeoteSulfolobus solfataricusto UV damage, we used high-density DNA microarrays which covered 3,368 genetic features encoded on the host genome, as well as the genes of several extrachromosomal genetic elements. While no significant up-regulation of genes potentially involved in direct DNA damage reversal was observed, a specific transcriptional UV response involving 55 genes could be dissected. Although flow cytometry showed only modest perturbation of the cell cycle, strong modulation of the transcript levels of the Cdc6 replication initiator genes was observed. Up-regulation of an operon encoding Mre11 and Rad50 homologs pointed to induction of recombinational repair. Consistent with this, DNA double-strand breaks were observed between 2 and 8 h after UV treatment, possibly resulting from replication fork collapse at damaged DNA sites. The strong transcriptional induction of genes which potentially encode functions for pilus formation suggested that conjugational activity might lead to enhanced exchange of genetic material. In support of this, a statistical microscopic analysis demonstrated that large cell aggregates formed upon UV exposure. Together, this provided supporting evidence to a link between recombinational repair and conjugation events.
The Catabolite Control Protein CcpA Binds to P
mga
and Influences Expression of the Virulence Regulator Mga in the Group A Streptococcus
Authors: Almengor Audry C. , Kinkel Traci L. , Day Stephanie J. , McIver Kevin S.
Published: September 2007

Carbon catabolite repression (CCR) allows bacteria to alter metabolism in response to the availability of specific sugar sources, and increasing evidence suggests that CCR is involved in regulating virulence gene expression in many pathogens. A scan of the M1 SF370 group A streptococcus (GAS) genome using a
Bacillus subtilis
consensus identified a number of potential catabolite-responsive elements (
cre
) important for binding by the catabolite control protein A (CcpA), a mediator of CCR in gram-positive bacteria. Intriguingly, a putative
cre
was identified in the promoter region of
mga
upstream of its distal P1 start of transcription. Electrophoretic mobility shift assays showed that a His-CcpA fusion protein was capable of binding specifically to the
cre
in P
mga
in vitro. Deletion analysis of P
mga
using single-copy P
mga
-
gusA
reporter strains found that P
mga
P1 and its upstream
cre
were not required for normal autoregulated
mga
expression from P
mga
P2 as long as Mga was produced from its native locus. In fact, the P
mga
P1 region appeared to show a negative influence on P
mga
P2 in these studies. However, deletion of the
cre
at the native P
mga
resulted in a reduction of total
mga
transcripts as determined by real-time reverse transcription-PCR, supporting a role for CcpA in initial expression. Furthermore, normal transcriptional initiation from the P
mga
P1 start site alone was dependent on the presence of the
cre
. Importantly, inactivation of
ccpA
in the M6 GAS strain JRS4 resulted in a reduction in P
mga
expression and Mga protein levels in late-logarithmic-phase cell growth. These data support a role for CcpA in the early activation of the
mga
promoter and establish a link between CCR and Mga regulation in the GAS.
Identification of Promoters Recognized by RNA Polymerase-σ
E
Holoenzyme from
Thermus thermophilus
HB8
Authors: Shinkai Akeo , Ohbayashi Naomi , Terada Takaho , Shirouzu Mikako , Kuramitsu Seiki , Yokoyama Shigeyuki
Published: September 2007

Thermus thermophilus
σ
E
, an extracytoplasmic function σ factor from the extremely thermophilic bacterium
Thermus thermophilus
HB8, bound to the RNA polymerase core enzyme and showed transcriptional activity. With the combination of in vitro transcription assay and GeneChip technology, we identified three promoters recognized by σ
E
. The predicted consensus promoter sequence for σ
E
is 5′-CA(A/T)(A/C)C(A/C)-N
15
-CCGTA-3′.
Site-Directed Disulfide Cross-Linking Shows that Cleft Flexibility in the Periplasmic Domain Is Needed for the Multidrug Efflux Pump AcrB of
Escherichia coli
Authors: Takatsuka Yumiko , Nikaido Hiroshi
Published: September 2007

Escherichia coli
AcrB is a multidrug efflux transporter that recognizes multiple toxic chemicals having diverse structures. Recent crystallographic studies of the asymmetric trimer of AcrB suggest that each protomer in the trimeric assembly goes through a cycle of conformational changes during drug export. However, biochemical evidence for these conformational changes has not been provided previously. In this study, we took advantage of the observation that the external large cleft in the periplasmic domain of AcrB appears to become closed in the crystal structure of one of the three protomers, and we carried out in vivo cross-linking between cysteine residues introduced by site-directed mutagenesis on both sides of the cleft, as well as at the interface between the periplasmic domains of the AcrB trimer. Double-cysteine mutants with mutations in the cleft or the interface were inactive. The possibility that this was due to the formation of disulfide bonds was suggested by the restoration of transport activity of the cleft mutants in a
dsbA
strain, which had diminished activity to form disulfide bonds in the periplasm. Furthermore, rapidly reacting, sulfhydryl-specific chemical cross-linkers, methanethiosulfonates, inactivated the AcrB transporter with double-cysteine residues in the cleft expressed in
dsbA
cells, and this inactivation could be observed within a few seconds after the addition of a cross-linker in real time by increased ethidium influx into the cells. These observations indicate that conformational changes, including the closure of the external cleft in the periplasmic domain, are required for drug transport by AcrB.
Resistance to Bacitracin in
Bacillus subtilis
: Unexpected Requirement of the BceAB ABC Transporter in the Control of Expression of Its Own Structural Genes
Authors: Bernard Remi , Guiseppi Annick , Chippaux Marc , Foglino Maryline , Denizot François
Published: September 2007

The
Bacillus subtilis
BceAB ABC transporter involved in a defense mechanism against bacitracin is composed of a membrane-spanning domain and a nucleotide-binding domain. Induction of the structural
bceAB
genes requires the BceR response regulator and the BceS histidine kinase of a signal transduction system. However, despite the presence of such a transduction system and of bacitracin, no transcription from an unaltered
bceA
promoter is observed in cells lacking the BceAB transporter. Expression in
trans
of the BceAB transporter in these
bceAB
cells restores the transcription from the
bceA
promoter. Cells possessing a mutated nucleotide-binding domain of the transporter are also no longer able to trigger transcription from the
bceA
promoter in the presence of bacitracin, although the mutated ABC transporter is still bound to the membrane. In these cells, expression of the
bceA
promoter can no longer be detected, indicating that the ABC transporter not only must be present in the cell membrane, but also must be expressed in a native form for the induction of the
bceAB
genes. Several hypotheses are discussed to explain the simultaneous need for bacitracin, a native signal transduction system, and an active BceAB ABC transporter to trigger transcription from the
bceA
promoter.
Essai de corrélation entre l'humidité du sol et les anomalies chromosomiques dans une population de Claytonia caroliniana var. caroliniana
Authors: Gervais Camille , Grandtner Miroslav M.
Published: October 2007

Soil moisture and chromosome numbers were determined in a population of Claytonia caroliniana var. caroliniana from Stoneham mountain, Québec, where a previous study had indicated a large proportion of chromosomal anomalies. Soil moisture is significantly related (F = 44.92*) to topography, namely in early May (F = 36.86**) but does not present obvious correlations with the percentages of chromosomal anomalies. The topography and the percentages of chromosomal anomalies, however, are slightly correlated (r = 0.54). The total percentage of observed abnormal chromosome numbers in the population is about the same (45% compared with 50% in 1979) and, as already suggested, seems to be due mainly to the presence of B chromosomes. The existence of diverging chromosome numbers in the root tissues, on the one hand, and in the pedicels and flowers, on the other hand, has been confirmed in two cases. As the anomalies are already observed in the somatic tissues of the young pedicels, they may originate with the formation of the primordia that possibly appear in summer, when the soil seems to be less humid.
Pollen morphology and development of the pollination mechanism in Tsuga heterophylla and T. mertensiana
Authors: Owens John N. , Blake Margaret Dianne
Published: October 2007

Pollen of Tsuga heterophylla (Raf.) Sarg. (western hemlock) is nonsaccate and bears spines, whereas pollen of Tsuga mertensiana (Bong.) Carr. (mountain hemlock) is saccate and lacks spines. The pollination mechanism in western hemlock consists of a short funnel-like integument tip with a large micropyle. Pollen may enter the micropyle or germinate on the bract or ovuliferous scale and form long pollen tubes. The pollination mechanism in mountain hemlock consists of two large micropylar flaps which secrete minute droplets to which pollen adheres. A pollination drop is not formed in either species. These features are discussed in relation to the taxonomy of the genus and the reproductive biology of these two species.
Composition of an isolated prairie in central Ontario
Authors: Reznicek A. A. , Maycock P. F.
Published: October 2007

A remarkable prairie outlier was recently discovered in central Ontario. The site had about 1.6 ha of open prairie surrounded by 11 ha of Quercus rubra – Pinus strobus savanna. The savanna had a density of about 27 huge, open-grown trees per hectare (11 per acre). The vegetation of the prairie opening comprised four zones ranging from a dry sand barrens to a mesic to wet-mesic prairie arrayed on a gentle slope. The major dominants overall were Sorghastrum nutans, Andropogon scoparius, Danthonia spicata, Lespedeza capitata, Desmodium canadense, Aster azureus, Monarda fistulosa, Solidago nemoralis, Aster sagittifolius, Equisetum hyemale, Car ex rugosperma, and Panicum linearifolium. The site had a rich flora of 115 species, of which more than one-third were listed as prevalent or modal species of Wisconsin prairies and related communities, occurring more than 800 km to the west. In addition, about 15% of the species in the prairie opening were regionally rare and three, Carex richardsonii, Lespedeza intermedia, and Scirpus clintonii, were considered rare in Ontario.
A natural auxotroph of a nematode-trapping fungus
Authors: Zachariah K. , Victor J. R.
Published: October 2007

The nutritional requirements of a unique predatory fungus are described. The strain of Arthrobotrys dactyloides was isolated from forest soil and has an absolute requirement for histidine and methionine with a partial requirement for several other amino acids. In common with many other fungi it requires glucose and one or more of the B vitamins.
Studies of gametophytes of Matteuccia struthiopteris (ostrich fern) in nature and in culture
Authors: Aderkas P. von
Published: October 2007

The sex expression of gametophytes of Matteuccia struthiopteris (L.) Todaro was compared in nature and in culture. Plants raised from multispore cultures (100 spores/cm2) exhibited the most variety in sexual–morphological types. Individually raised plants were slower to develop and showed less variety of sexual types than was found in the multispore cultures. There appeared to be a density effect on development. Field-collected gametophytes showed the least diversity, the populations being largely composed of poorly developed male and neuter plants. The experimental and field data are considered in relation to antheridiogen and population density studies.
Genetics of Gibberella fujikuroi. II. Natural occurrence and significance of heterokaryosis in sorghum isolates
Authors: Sidhu Gurmel S.
Published: October 2007

Of all the stalk rot fungi, Gibberella fujikuroi (Sawada) Wollenw. (anamorph stage Fusarium moniliforme Sheld.) was most frequently isolated from naturally infected, symptomless sorghum plants. Phenotypically distinct isolates of G. fujikuroi were recovered. This variability is ascribed to heterokaryosis. The homokaryotic components of the most frequently recovered heterokaryons found at a given growth stage were identified on the basis of colony color, texture, growth rate, and sporulation. Nuclear ratios were determined to confirm the presence and stability of heterokaryons. Natural and laboratory-induced heterokaryons were compared on synthetic and natural media, prepared from plant tissue, for stability and other attributes. The occurrence of different heterokaryons at different growth stages suggests genetic adaptation and a possible role of heterokaryosis in generating and maintaining natural variability in this fungus.
Effects of simulated acidic, metal-containing precipitation on coniferous litter decomposition
Authors: Moloney Kirk A. , Stratton Lori J. , Klein Richard M.
Published: October 2007

Depths of undegraded litter in hardwood and boreal forest ecosystems of Camels Hump Mountain in the Green Mountains of Vermont doubled between 1965 and 1982. Simulations of litter leaching by acidic and nonacidic snowmelt, fog water, or rain showed that hydrogen ions were retained by coniferous-needle litter and both cations and anions were leached. In vitro studies on litter degradation showed that acidic conditions reduced microbial CO2 evolution from litter. CO2 evolution was further repressed by the presence of Pb and Zn, but not by Al or Cu. Cellulose breakdown was unaffected in acidic, metal-containing soils treated with water acidified to pH 3.8. Reduction in litter decomposition, which could adversely alter the rates of mineral cycling in natural ecosystems, may be due to repression of the metabolism of litter-degrading microflora by precipitation acidity and metals present in soils and introduced by polluted rain.
Basic fuchsin: a vascular dye in studies of Verticillium-infected chrysanthemum and tomato
Authors: Robb Jane , Street P. F. S. , Busch L. V.
Published: October 2007

Because basic fuchsin is water soluble and easily detectable, it has been used as a vascular dye to trace movement in plants. The following experiments using stained and unstained chrysanthemum and tomato plants showed that decolorized basic fuchsin can also be used as a readily transportable vascular tracer in conjunction with ultrastructural analysis. (i) Localization of dye movement, cytological observation of freehand sections, and measurement of potassium ion concentration in xylem fluid of healthy stems indicated that the degree of dye toxicity varied and was related to its formulation and age, and also to plant species. Decolorized basic fuchsin could be rendered nontoxic to the plant with restricted use of aged dye. (ii) Preparation of dye-infused plant tissue for electron microscopy using standard fixation and embedding techniques showed that, in plants infected with Verticillium dahliae, the dye was permanent, detectable in 1.0-μm thick plastic sections and apparently caused no changes in cytological structure. Using the above techniques to study the fine structure of functional and nonfunctional veins in the leaves of Verticillium-infected chrysanthemum we showed that necrosis of parenchyma cells adjacent to colonized xylem vessels was the result of infection rather than of leakage of basic fuchsin into the cytoplasm. The data also supported the hypothesis that smooth vascular coating materials play a major role in the restriction of water movement in chrysanthemums with Verticillium-induced wilt disease.
A comparative study of the changes of peroxidase patterns during wheat, rye, and triticale germination
Authors: Asíns M. J. , Benito C. , Vega M. Pérez de la
Published: October 2007

A comparative study on the electrophoretic peroxidase patterns of rye (Secale cereale L.), tetraploid wheat (Triticum turgidum L. durum), hexaploid wheat (Triticum aestivum L.), and hexaploid Triticale during kernel germination has been carried out. Endosperm, embryo, coleoptile, and the first leaf have been analyzed. A drastic change in peroxidase patterns was observed during the first hours of germination in all the materials studied. The triticale peroxidase patterns were similar to tetraploid wheat female parent patterns. The chromosomal locations of two leaf peroxidase isozymes of hexaploid wheat 'Chinese Spring' are also reported. These two isozymes, C9 and C10, are associated with chromosome arms 3DS and 7DS, respectively.
Internal gas atmospheres, ethanol, and leakage of electrolytes from a flood-tolerant and a flood-susceptible sweet potato cultivar as influenced by anaerobiosis
Authors: Chang Ling A. , Hammett Larry K. , Pharr David M.
Published: October 2007

The postanaerobic behavior of sweet potato roots from a flood-tolerant cultivar, 'Centennial,' and a flood-susceptible cultivar, 'Caromex,' was studied. High concentrations of CO2 and low concentrations of O2 were present in the internal atmosphere of 'Caromex' roots even after the anaerobically pretreated roots were restored to air for a few days, whereas in 'Centennial,' the internal gas atmosphere was less affected by anoxia. Ethanol accumulation in 'Caromex' was consistently higher than in 'Centennial,' and the postanaerobic changes were different between cultivars. An inducation of electrolyte leakage was observed from both cultivars immediately after roots were exposed to a CO2-enriched environment for 48 h. The leakage became greater in 'Caromex' after a 3-day aerobic exposure. In 'Centennial,' leakage of electrolytes due to CO2 treatment diminished at the end of 3 days. Application of ethanol to the discs had no immediate effect on electrolyte leakage in either cultivar under a N2 environment. However, anaerobiosis alone resulted in higher electrolyte leakage. It remains to be determined that the postanaerobic patterns of 'Caromex' and 'Centennial' are characteristic of flood-susceptible and flood-tolerant sweet potato cultivars in general.
Isolation from root and shoot surfaces of agglutinins that show specificity for saprophytic Pseudomonads
Authors: Anderson Anne J.
Published: October 2007

Washes of healthy intact roots and shoots of the bean Phaseolus vulgaris caused agglutination of cells of certain saprophytic pseudomonads, notably P. putida isolates. The agglutinin structures in the root and shoot washes were high molecular weight, heat-stable complexes of carbohydrate and protein which required Mg2+ for activity. The ratios of the predominant neutral sugar components, galactose and arabinose, differ in root and shoot agglutinin preparations. Cells of bacteria classified as P. putida were agglutinated to a greater extent than cells of P. fluorescens and P. aeruginosa. Some of the bacterial isolates agglutinated by the plant surface structures were beneficial to plant growth.
Plastes cotylédonaires et activités hydrolytiques dans des plantules de Raphanus sativus (Crucifères) soumises à diverses conditions d'éclairement et de température
Authors: Geneves Louis , Rutin Jacques
Published: October 2007

not available
Ultrastructure of conidial and microconidial ontogeny of Marssonina species pathogenic to poplars
Authors: Spiers A. G. , Hopcroft D. H.
Published: October 2007

Conidial and microconidial ontogeny of Marssonina brunnea, M. castagnei, and M. populi was annellidic. The primary conidium and microconidium developed holoblastically and a new slightly higher conidiogenous locus was formed with each percurrent vegetative proliferation through the annellophore apex. Delimiting septa were perforate with Woronin bodies and electron-dense septal pore plugs were observed in the bases of seceded conidia and microconidia.
Seed Biology Canadian Botanical Association and Canadian Society of Plant Physiologists Joint Symposium June 21 and 26, 1982 University of Regina, Regina, Saskatchewan
Authors: Quick W. A. , Raju M. V. S.
Published: October 2007

not available
Studies on the genetic control of some physiological processes in seeds
Authors: Naylor J. M.
Published: October 2007

Evidence is presented that genetic variability affecting duration of seed dormancy and seed viability exists in field populations of Avena fatua L. and that this variability is an important factor in the persistence of this weed species in allowing populations to adapt to particular cultural weed-control practices. Duration of seed dormancy is controlled by several or many genes, the effects of which are manifested in at least two physiologically distinct physiological blocks. Expression of genotypes which confer long-term seed dormancy is highly sensitive to temperature and drought stress experienced by maternal plants during seed development. Naturally inbreeding families characterized by long-term dormancy also exhibit rigorous hormonal control of the synthesis of at least one hydrolase in endosperm (α-amylase). This association of physiological traits apparently is not due to pleiotropy but rather to coadaptive multilocus organization.
Immunoreactive detection of four mammalian steroids in plants
Authors: Simons R. G. , Grinwich D. L.
Published: October 2007

Steroids have been detected in a range of plant species. To investigate the prevalence of four steroids in plants, radioimmunoassay was used to detect the presence of androstenone (boar taint), androgen, estrogen, and progesterone. Androstenone is known only from pigs and humans, but the others are widespread in mammals. A total of 128 species from over 50 families was sampled. All four steroids were widespread, with androstenone and progesterone being found in more than 80% of species, androgen in 70%, and estrogen in 50%. All seed samples contained androgen but none contained androstenone. In three species, androgen was more abundant in male flowers than female flowers, but progesterone and estrogen, when present, were at higher level in female flowers. The function of these steroids in plants is not known.
Morphology, histochemistry, and germination of conidia of Sporidesmium sclerotivorum
Authors: Bullock Suzanne , Willetts H. J. , Adams P. B.
Published: October 2007

Sporidesmium sclerotivorum, a mycoparasite of sclerotia of Sclerotinia spp., produces two types of asexual spore, macroconidia and microconidia of the Selenosporella type. Macroconidia developed by dilation of the conidiophore apex, which then divided to form up to eight cells. The outer layers of the thick spore walls were heavily pigmented and contained phenolic compounds. The cytoplasm of mature spores contained polysaccharides and proteins but there were no specialized storage bodies. Germ tubes emerged through a pore in the wall of the distal cell of the macroconidia. They grew over the surface of host sclerotia and entered between rind cells without formation of specialized infection structures. Microconidia of the Selenosporella state of S. sclerotivorum formed on simple or branched conidiophores. Sympodial conidiogenous cells bearing the microconidia were arranged in a verticil at the tips of these conidiophores.
Ion behavior in plant cell walls. I. Characterization of the Sphagnum russowii cell wall ion exchanger
Authors: Richter Conrad , Dainty Jack
Published: October 2007

The ion-exchange properties of Sphagnum russowii cell wall material were studied in the context of the Donnan weak acid model. Titrations in the presence of Na+, Ca2+, or La3+ revealed two classes of weak acid binding sites, one with a low pK between 2 and 4 and the other with a high pK > 5. The total cation-exchange capacities of the low and high pK species were 1071 and 545 μequiv./g dry wt. wall material, respectively, and were related to the uronic, amino, and phenolic acid contents of the walls. Differences in pK estimates obtained in the presence of the different cations (pKNa > pKCa > pKLa) could not be explained by our semiarbitrary choice (1 mL/dry wt. wall material), for the effective volume (Donnan free space) bathing the exchange sites. It was concluded that valence-dependent reductions in cation activities in the wall phase are an important contributor to the differences in the pK estimates. Key words: cation exchange, cell wall, titration, Donnan model, weak acid.
Interaction of geographic isolates of Melampsora medusae and Populus: effect of temperature
Authors: Prakash C. S. , Thielges B. A.
Published: October 2007

Twelve isolates of the leaf rust pathogen Melampsora medusae Thüm., collected from six locations across the eastern U.S.A., were tested for their reaction on 18 poplar genotypes at two temperatures of incubation (16 and 26 °C). All isolates were recognized as distinct physiologic races, based on the qualitative and quantitative reaction of the isolates on the cultivars. Temperature was an important factor in determining the level and type of disease expression in most cultivar – isolate combinations. The results support the hypothesis that the physical environment may have an important role in the regulation of this "wild" pathosystem. The high degree of race specificity observed in the Populus genotypes and the polymorphism for virulence in the M. medusae population emphasize the importance of maintaining host diversity to manage this disease.
Polymorphisme pollinique et polymorphisme génétique
Authors: Till I. , Valdeyron G. , Gouyon P. H.
Published: October 2007

The polymorphism of the exine of pollen grains was studied in different species to determine if it has a genetic component at the intraspecific level. For some species, the results show that significant differences exist between individuals and that the composition of populations can also vary. The authors conclude that the study of pollen polymorphism could increase our understanding of pollen evolution and the mechanisms of pollen – stigma interactions. Key words: polymorphism, pollen, ash, Rumex, iris.