bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outer Membrane Proteins ofFibrobacter succinogeneswith Potential Roles in Adhesion to Cellulose and in Cellulose Digestion
Authors: Jun Hyun-Sik , Qi Meng , Gong Joshua , Egbosimba Emmanuel E. , Forsberg Cecil W. 
Published: July 2007

ABSTRACTComparative analysis of binding of intact glucose-grownFibrobacter succinogenesstrain S85 cells and adhesion-defective mutants AD1 and AD4 to crystalline and acid-swollen (amorphous) cellulose showed that strain S85 bound efficiently to both forms of cellulose while mutant Ad1 bound to acid-swollen cellulose, but not to crystalline cellulose, and mutant Ad4 did not bind to either. One- and two-dimensional electrophoresis (2-DE) of outer membrane cellulose binding proteins and of outer membranes, respectively, of strain S85 and adhesion-defective mutant strains in conjunction with mass spectrometry analysis of tryptic peptides was used to identify proteins with roles in adhesion to and digestion of cellulose. Examination of the binding to cellulose of detergent-solubilized outer membrane proteins from S85 and mutant strains revealed six proteins in S85 that bound to crystalline cellulose that were absent from the mutants and five proteins in Ad1 that bound to acid-swollen cellulose that were absent from Ad4. Twenty-five proteins from the outer membrane fraction of cellulose-grownF. succinogeneswere identified by 2-DE, and 16 of these were up-regulated by growth on cellulose compared to results with growth on glucose. A protein identified as a Cl-stimulated cellobiosidase was repressed in S85 cells growing on glucose and further repressed in the mutants, while a cellulose-binding protein identified as pilin was unchanged in S85 grown on glucose but was not produced by the mutants. The candidate differential cellulose binding proteins of S85 and the mutants and the proteins induced by growth of S85 on cellulose provide the basis for dissecting essential components of the cellulase system ofF. succinogenes.
Origins of Flagellar Gene Operons and Secondary Flagellar Systems
Authors: Liu Renyi , Ochman Howard 
Published: July 2007

ABSTRACTForty-one flagellated species representing 11 bacterial phyla were used to investigate the origin of secondary flagellar systems and the structure and formation of flagellar gene operons over the course of bacterial evolution. Secondary (i.e., lateral) flagellar systems, which are harbored by five of the proteobacterial species considered, originated twice, once in the alphaproteobacterial lineage and again in the common ancestor of theBeta- andGammaproteobacteria. The order and organization of flagellar genes have undergone extensive shuffling and rearrangement among lineages, and based on the phylogenetic distributions of flagellar gene complexes, the flagellar gene operons existed as small, usually two-gene units in the ancestor ofBacteriaand have expanded through the recruitment of new genes and fusion of gene units. In contrast to the evolutionary trend towards larger flagellar gene complexes, operon structures have been highly disrupted through gene disassociation and rearrangements in theEpsilon- andAlphaproteobacteria. These results demonstrate that the genetic basis of this ancient and structurally conserved organelle has been subject to many lineage-specific modifications.
Mycothiol Import by
Mycobacterium smegmatis
and Function as a Resource for Metabolic Precursors and Energy Production
Authors: Bzymek Krzysztof P. , Newton Gerald L. , Ta Philong , Fahey Robert C. 
Published: July 2007

ABSTRACT

Mycothiol ([MSH] AcCys-GlcN-Ins, where Ac is acetyl) is the major thiol produced by
Mycobacterium smegmatis
and other actinomycetes. Mutants deficient in MshA (strain 49) or MshC (transposon mutant Tn
1
) of MSH biosynthesis produce no MSH. However, when stationary phase cultures of these mutants were incubated in medium containing MSH, they actively transported it to generate cellular levels of MSH comparable to or greater than the normal content of the wild-type strain. When these MSH-loaded mutants were transferred to MSH-free preconditioned medium, the cellular MSH was catabolized to generate GlcN-Ins and AcCys. The latter was rapidly converted to Cys by a high deacetylase activity assayed in extracts. The Cys could be converted to pyruvate by a cysteine desulfhydrase or used to regenerate MSH in cells with active MshC. Using MSH labeled with [U-
14
C]cysteine or with [6-
3
H]GlcN, it was shown that these residues are catabolized to generate radiolabeled products that are ultimately lost from the cell, indicating extensive catabolism via the glycolytic and Krebs cycle pathways. These findings, coupled with the fact the
myo
-inositol can serve as a sole carbon source for growth of
M. smegmatis
, indicate that MSH functions not only as a protective cofactor but also as a reservoir of readily available biosynthetic precursors and energy-generating metabolites potentially important under stress conditions. The half-life of MSH was determined in stationary phase cells to be ∼50 h in strains with active MshC and 16 ± 3 h in the MshC-deficient mutant, suggesting that MSH biosynthesis may be a suitable target for drugs to treat dormant tuberculosis.
Investigation of Transcription Repression and Small-Molecule Responsiveness by TetR-Like Transcription Factors Using a HeterologousEscherichia coli-Based Assay
Authors: Ahn Sang Kyun , Tahlan Kapil , Yu Zhou , Nodwell Justin 
Published: July 2007

ABSTRACTThe SCO7222 protein and ActR are two of ∼150 TetR-like transcription factors encoded in theStreptomyces coelicolorgenome. Using bioluminescence as a readout, we have developedEscherichia coli-based biosensors that accurately report the regulatory activity of these proteins and used it to investigate their interactions with DNA and small-molecule ligands. We found that the SCO7222 protein and ActR repress the expression of their putative target genes, SCO7223 andactII-ORF2 (actA), respectively, by interacting with operator sequence in the promoters. The operators recognized by the two proteins are related such thatO7223(an operator for SCO7223) could be bound by both the SCO7222 protein and ActR with similar affinities. In contrast,Oact(an operator foractII-ORF2) was bound tightly by ActR and more weakly by the SCO7222 protein. We demonstrated ligand specificity of these proteins by showing that while TetR (but not ActR or the SCO7222 protein) interacts with tetracyclines, ActR (but not TetR or the SCO7222 protein) interacts with actinorhodin and related molecules. Through operator-targeted mutagenesis, we found that at least two nucleotide changes inO7223were required to disrupt its interaction with SCO7222 protein, while ActR was more sensitive to changes onOact. Most importantly, we found that the interaction of each protein with wild-type and mutant operator sequences in vivo and in vitro correlated perfectly. Our data suggest thatE. coli-based biosensors of this type should be broadly applicable to TetR-like transcription factors.
Specificity and Regulation of Interaction between the P
II
and AmtB
1
Proteins in
Rhodospirillum rubrum
Authors: Wolfe David M. , Zhang Yaoping , Roberts Gary P. 
Published: July 2007

ABSTRACT

The nitrogen regulatory protein P
II
and the ammonia gas channel AmtB are both found in most prokaryotes. Interaction between these two proteins has been observed in several organisms and may regulate the activities of both proteins. The regulation of their interaction is only partially understood, and we show that in
Rhodospirillum rubrum
one P
II
homolog, GlnJ, has higher affinity for an AmtB
1
-containing membrane than the other two P
II
homologs, GlnB and GlnK. This interaction strongly favors the nonuridylylated form of GlnJ and is disrupted by high levels of 2-ketoglutarate (2-KG) in the absence of ATP or low levels of 2-KG in the presence of ATP. ADP inhibits the destabilization of the GlnJ-AmtB
1
complex in the presence of ATP and 2-KG, supporting a role for P
II
as an energy sensor measuring the ratio of ATP to ADP. In the presence of saturating levels of ATP, the estimated

K
d

of 2-KG for GlnJ bound to AmtB
1
is 340 μM, which is higher than that required for uridylylation of GlnJ in vitro, about 5 μM. This supports a model where multiple 2-KG and ATP molecules must bind a P
II
trimer to stimulate release of P
II
from AmtB
1
, in contrast to the lower 2-KG requirement for productive uridylylation of P
II
by GlnD.
MukEF Is Required for Stable Association of MukB with the Chromosome
Authors: She Weifeng , Wang Qinhong , Mordukhova Elena A. , Rybenkov Valentin V. 
Published: July 2007

ABSTRACTMukB is a bacterial SMC(structural maintenance of chromosome) protein required for correct folding of theEscherichia colichromosome. MukB acts in complex with the two non-SMC proteins, MukE and MukF. The role of MukEF is unclear. MukEF disrupts MukB-DNA interactions in vitro. In vivo, however, MukEF stimulates MukB-induced DNA condensation and is required for the assembly of MukB clusters at the quarter positions of the cell length. We report here that MukEF is essential for stable association of MukB with the chromosome. We found that MukBEF forms a stable complex with the chromosome that copurifies with nucleoids following gentle cell lysis. Little MukB could be found with the nucleoids in the absence or upon overproduction of MukEF. Similarly, overproduced MukEF recruited MukB-green fluorescent protein (GFP) from its quarter positions, indicating that formation of MukB-GFP clusters and stable association with the chromosome could be mechanistically related. Finally, we report that MukE-GFP forms foci at the quarter positions of the cell length but not in cells that lack MukB or overproduce MukEF, suggesting that the clusters are formed by MukBEF and not by its individual subunits. These data support the view that MukBEF acts as a macromolecular assembly, a scaffold, in chromosome organization and that MukEF is essential for the assembly of this scaffold.
In Situ Analysis of Sulfur Species in Sulfur Globules Produced from Thiosulfate by
Thermoanaerobacter sulfurigignens
and
Thermoanaerobacterium thermosulfurigenes
Authors: Lee Yong-Jin , Prange Alexander , Lichtenberg Henning , Rohde Manfred , Dashti Mona , Wiegel Juergen 
Published: July 2007

ABSTRACT

The
Firmicutes Thermoanaerobacter sulfurigignens
and
Thermoanaerobacterium thermosulfurigenes
convert thiosulfate, forming sulfur globules inside and outside cells. X-ray absorption near-edge structure analysis revealed that the sulfur consisted mainly of sulfur chains with organic end groups similar to sulfur formed in purple sulfur bacteria, suggesting the possibility that the process of sulfur globule formation by bacteria is an ancient feature.
A Novel Indole Compound That Inhibits
Pseudomonas aeruginosa
Growth by Targeting MreB Is a Substrate for MexAB-OprM
Authors: Robertson Gregory T. , Doyle Timothy B. , Du Qun , Duncan Leonard , Mdluli Khisimuzi E. , Lynch A. Simon 
Published: July 2007

ABSTRACT

Drug efflux systems contribute to the intrinsic resistance of
Pseudomonas aeruginosa
to many antibiotics and biocides and hamper research focused on the discovery and development of new antimicrobial agents targeted against this important opportunistic pathogen. Using a
P. aeruginosa
PAO1 derivative bearing deletions of
opmH
, encoding an outer membrane channel for efflux substrates, and four efflux pumps belonging to the resistance nodulation/cell division class including
mexAB-oprM
, we identified a small-molecule indole-class compound (CBR-4830) that is inhibitory to growth of this efflux-compromised strain. Genetic studies established MexAB-OprM as the principal pump for CBR-4830 and revealed MreB, a prokaryotic actin homolog, as the proximal cellular target of CBR-4830. Additional studies establish MreB as an essential protein in
P. aeruginosa
, and efflux-compromised strains treated with CBR-4830 transition to coccoid shape, consistent with MreB inhibition or depletion. Resistance genetics further suggest that CBR-4830 interacts with the putative ATP-binding pocket in MreB and demonstrate significant cross-resistance with A22, a structurally unrelated compound that has been shown to promote rapid dispersion of MreB filaments in vivo. Interestingly, however, ATP-dependent polymerization of purified recombinant
P. aeruginosa
MreB is blocked in vitro in a dose-dependent manner by CBR-4830 but not by A22. Neither compound exhibits significant inhibitory activity against mutant forms of MreB protein that bear mutations identified in CBR-4830-resistant strains. Finally, employing the strains and reagents prepared and characterized during the course of these studies, we have begun to investigate the ability of analogues of CBR-4830 to inhibit the growth of both efflux-proficient and efflux-compromised
P. aeruginosa
through specific inhibition of MreB function.
The Unusual 23S rRNA Gene of
Coxiella burnetii
: Two Self-Splicing Group I Introns Flank a 34-Base-Pair Exon, and One Element Lacks the Canonical ΩG
Authors: Raghavan Rahul , Miller Scott R. , Hicks Linda D. , Minnick Michael F. 
Published: July 2007

ABSTRACT

We describe the presence and characteristics of two self-splicing group I introns in the sole 23S rRNA gene of
Coxiella burnetii
. The two group I introns, Cbu.L1917 and Cbu.L1951, are inserted at sites 1917 and 1951 (
Escherichia coli
numbering), respectively, in the 23S rRNA gene of
C. burnetii
. Both introns were found to be self-splicing in vivo and in vitro even though the terminal nucleotide of Cbu.L1917 is adenine and not the canonical conserved guanine, termed ΩG, found in Cbu.L1951 and all other group I introns described to date. Predicted secondary structures for both introns were constructed and revealed that Cbu.L1917 and Cbu.L1951 were group IB2 and group IA3 introns, respectively. We analyzed strains belonging to eight genomic groups of
C. burnetii
to determine sequence variation and the presence or absence of the elements and found both introns to be highly conserved (≥99%) among them. Although phylogenetic analysis did not identify the specific identities of donors, it indicates that the introns were likely acquired independently; Cbu.L1917 was acquired from other bacteria like
Thermotoga subterranea
and Cbu.L1951 from lower eukaryotes like
Acanthamoeba castellanii
. We also confirmed the fragmented nature of mature 23S rRNA in
C. burnetii
due to the presence of an intervening sequence. The presence of three selfish elements in
C. burnetii
's 23S rRNA gene is very unusual for an obligate intracellular bacterium and suggests a recent shift to its current lifestyle from a previous niche with greater opportunities for lateral gene transfer.
Characterization of the
Erwinia chrysanthemi gan
Locus, Involved in Galactan Catabolism
Authors: Delangle Aurélie , Prouvost Anne-France , Cogez Virginie , Bohin Jean-Pierre , Lacroix Jean-Marie , Cotte-Pattat Nicole Hugouvieux 
Published: July 2007

ABSTRACT

β-1,4-Galactan is a major component of the ramified regions of pectin. Analysis of the genome of the plant pathogenic bacteria
Erwinia chrysanthemi
revealed the presence of a cluster of eight genes encoding proteins potentially involved in galactan utilization. The predicted transport system would comprise a specific porin GanL and an ABC transporter made of four proteins, GanFGK
2
. Degradation of galactans would be catalyzed by the periplasmic 1,4-β-endogalactanase GanA, which released oligogalactans from trimer to hexamer. After their transport through the inner membrane, oligogalactans would be degraded into galactose by the cytoplasmic 1,4-β-exogalactanase GanB. Mutants affected for the porin or endogalactanase were unable to grow on galactans, but they grew on galactose and on a mixture of galactotriose, galactotetraose, galactopentaose, and galactohexaose. Mutants affected for the periplasmic galactan binding protein, the transporter ATPase, or the exogalactanase were only able to grow on galactose. Thus, the phenotypes of these mutants confirmed the functionality of the
gan
locus in transport and catabolism of galactans. These mutations did not affect the virulence of
E. chrysanthemi
on chicory leaves, potato tubers, or
Saintpaulia ionantha
, suggesting an accessory role of galactan utilization in the bacterial pathogeny.
Flavobacterium johnsoniae
SprA Is a Cell Surface Protein Involved in Gliding Motility
Authors: Nelson Shawn S. , Glocka Padden P. , Agarwal Sarika , Grimm David P. , McBride Mark J. 
Published: July 2007

ABSTRACT

Flavobacterium johnsoniae
cells glide rapidly over surfaces by an unknown mechanism. Transposon-induced
sprA
mutants formed nonspreading colonies on agar, and the cells examined in wet mounts were deficient in attachment to surfaces and were almost completely nonmotile. Exposure of intact cells to proteinase K cleaved the 270-kDa SprA into several large peptides, suggesting that it is partially exposed on the cell surface.
Injuries in female football players in top-level international tournaments
Authors: Junge Astrid , Dvorak Jiri 
Published: July 2007

Background:Despite the growing popularity of women’s football and the increasing number of female players, there has been little research on injuries sustained by female football players.Purpose:Analysis of the incidence, characteristics and circumstances of injury in elite female football players in top-level international tournaments.Study design:Prospective survey.Methods:Injuries incurred in seven international football tournaments were analysed using an established injury report system. Doctors of all participating teams reported all injuries after each match on a standardised injury reporting form. The mean response rate was 95%.Results:387 injuries were reported from 174 matches, equivalent to an incidence of 67.4 injuries/1000 player hours (95% CI 60.7 to 74.1) or 2.2 injuries/match (95% CI 2.0 to 2.4). Most injuries (84%; 317/378) were caused by contact with another player. The injuries most commonly involved the lower extremity (n = 248; 65%), followed by injuries of the head and neck (n = 67, 18%), trunk (n = 33, 9%) and upper extremity (n = 32, 8%). Contusions (n = 166; 45%) were the most frequent type of injury, followed by sprains or ligament rupture (n = 96; 26%) and strains or muscle fibre ruptures (n = 31; 8%). The most common diagnosis was an ankle sprain. There were 7 ligament ruptures and 15 sprains of the knee. On average 1 injury/match (95% CI 0.8 to 1.2) was expected to result in absence from a match or training.Conclusion:The injury rate in women’s top-level tournaments was within the range reported previously for match injuries in elite male and female players. However, the diagnoses and mechanisms of injury among the female players differed substantially from those previously reported in male football players.
The influence of host and temperature on the vertical migration of Pratylenchus penetrans
Authors: Pudasaini Mahesh P. , Viaene Nicole , Moens Maurice 
Published: July 2007

Abstract
The influence of both host and temperature on the vertical migration of
Pratylenchus penetrans was examined in a series of experiments using maize,
carrot, black salsify, pea, bean and potato. Plants were grown in a pot
placed on top of a plastic pipe of variable length in a growth chamber. This
pipe was planted into a second pot to maintain the humidity in the pipe.
Nematodes were inoculated at the bottom of the pipe and were allowed to
migrate upwards for 14 days after which the pipe was cut into 5 cm sectors
from which the nematodes were extracted and counted. More nematodes migrated
at 21°C than at 16 or 11°C. Migration of P. penetrans towards a host
decreased with increasing distance between the nematodes and all hosts, with
maize and bean eliciting the most attraction. They were the only hosts able
to stimulate nematode migration up to the distal end of 31 cm pipes. Potato
and carrot were the least influential hosts. Hosts differently influenced
the migration only of second-stage juveniles (J2), with a greater percentage
of J2 moving under maize and bean than under carrot. Under all hosts, adults
migrated in greater proportions with increasing distance than did other
stages. The attractiveness of hosts was age dependent. Generally,
infectivity decreased with distance travelled by the nematode.
Diversity and evolutionary relationships of entomopathogenic nematodes (Steinernematidae and Heterorhabditidae) from the Central Andean region of Colombia
Authors: López-Núñez Juan Carlos , Cano Liliana , Góngora-B. Carmenza , Stock S. Patricia 
Published: July 2007

Abstract
A survey of entomopathogenic nematodes (EPN) was conducted in the Central
Andean region of Colombia. Out of a total of 945 soil samples, 28 (3%) were
positive for entomopathogenic nematodes. Of them, 26 samples (92.8%)
contained Steinernema and two (7.2%) harboured Heterorhabditis isolates.
Characterisation of the recovered isolates was done by analysis of rDNA
sequences. The large subunit of rDNA (28S) was considered for diagnosis of
Steinernema species whereas the internal transcribed spacer region (ITS) of
rDNA was used to identify Heterorhabditis isolates recovered in this study.
Five Steinernema spp. were isolated and identified as S. websteri and four
new, undescribed species. Steinernema websteri was isolated from two sites:
Naranjal and Paraguaicito stations. At Naranjal, this species was recovered
from a coffee plantation and a forest habitat surrounding these plantations.
At Paraguaicito, the same species was recovered from a coffee-guamo habitat.
Steinernema sp. 1 was collected from nogal cafetero (Cordia allaidora)
groves and forest habitats at Paraguaicito station. Steinernema sp. 2 was
found in coffee-guamo habitats both at Naranjal and Paraguaicito stations.
Steinernema sp. 3 was the only EPN species recovered at Santa Barbara
station in association with plantain. This species was also found at La
Catalina station in association with forest habitats and also from soil
samples taken from a landscaped area with Heliconia sp. and grass cover
(Arachis pintoi) at Cenicafé La Granja station and a coffee-guamo habitat at
Naranjal station. Steinernema sp. 4 was found at La Catalina in a forest
habitat, also associated with Steinernema sp. 3 (isolate JCL002) and
Heterorhabditis sp. 1 (isolate JCL 003). The Heterorhabditis isolates were
identified as two undescribed Heterorhabditis spp. Heterorhabditis sp. 1
(isolate JCL003) was recovered at La Catalina station associated with a
forest habitat. Heterorhabditis sp. 2 (isolate JCL040) was collected from a
coffee-guamo habitat at Naranjal station. Although limited to one geographic
region, this study suggests entomopathogenic nematodes in Colombia are quite
diverse and are perhaps widely distributed in this country. A more intensive
survey covering all geographic regions is currently underway.