bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatially‐focussed melt formation in aluminous metapelites from Broken Hill, Australia
Authors: WHITE R. W. , POWELL R. , HALPIN J. A. 
Published: January 2005

AbstractLarge garnet poikiloblasts hosted by leucosome in metapelitic gneiss from Broken Hill reflect complex mineral–melt relationships. The spatial relationship between the leucosomes and the garnet poikiloblasts implies that the growth of garnet was strongly linked to the production of melt. The apparent difficulty of garnet to nucleate a large number of grains during the prograde breakdown of coexisting biotite and sillimanite led to the spatial focussing of melting reactions around the few garnet nuclei that formed. Continued reaction of biotite and sillimanite required diffusion of elements from where minerals were reacting to sites of garnet growth. This diffusion was driven by chemical potential gradients between garnet‐bearing and garnet‐absent parts of the rock. As a consequence, melt and peritectic K‐feldspar also preferentially formed around the garnet. The diffusion of elements led to the chemical partitioning of the rock within an overall context in which equilibrium may have been approached. Thus, the garnet‐bearing leucosomes record in situ melt formation around garnet porphyroblasts rather than centimetre‐scale physical melt migration and segregation. The near complete preservation of the high‐grade assemblages in the mesosome and leucosome is consistent with substantial melt loss. Interconnected networks between garnet‐rich leucosomes provide the most likely pathway for melt migration. Decimetre‐scale, coarse‐grained, garnet‐poor leucosomes may represent areas of melt flux through a large‐scale melt transfer network.
Biofilm Formation by
Escherichia coli
O157:H7 on Stainless Steel: Effect of Exopolysaccharide and Curli Production on Its Resistance to Chlorine
Authors: Ryu Jee-Hoon , Beuchat Larry R. 
Published: January 2005

ABSTRACT

The resistance of
Escherichia coli
O157:H7 strains ATCC 43895-, 43895-EPS (an exopolysaccharide [EPS]-overproducing mutant), and ATCC 43895+ (a curli-producing mutant) to chlorine, a sanitizer commonly used in the food industry, was studied. Planktonic cells of strains 43895-EPS and/or ATCC 43895+ grown under conditions supporting EPS and curli production, respectively, showed the highest resistance to chlorine, indicating that EPS and curli afford protection. Planktonic cells (ca. 9 log
10
CFU/ml) of all strains, however, were killed within 10 min by treatment with 50 μg of chlorine/ml. Significantly lower numbers of strain 43895-EPS, compared to those of strain ATCC 43895-, attached to stainless steel coupons, but the growth rate of strain 43895-EPS on coupons was not significantly different from that of strain ATCC 43895-, indicating that EPS production did not affect cell growth during biofilm formation. Curli production did not affect the initial attachment of cells to coupons but did enhance biofilm production. The resistance of
E. coli
O157:H7 to chlorine increased significantly as cells formed biofilm on coupons; strain ATCC 43895+ was the most resistant. Population sizes of strains ATCC 43895+ and ATCC 43895- in biofilm formed at 12°C were not significantly different, but cells of strain ATCC 43895+ showed significantly higher resistance than did cells of strain ATCC 43895-. These observations support the hypothesis that the production of EPS and curli increase the resistance of
E. coli
O157:H7 to chlorine.
Microbial Desulfurization of Gasoline in a
Mycobacterium goodii
X7B Immobilized-Cell System
Authors: Li Fuli , Xu Ping , Feng Jinhui , Meng Ling , Zheng Yuan , Luo Lailong , Ma Cuiqing 
Published: January 2005

ABSTRACT

Mycobacterium goodii
X7B, which had been primarily isolated as a bacterial strain capable of desulfurizing dibenzothiophene to produce 2-hydroxybiphenyl via the 4S pathway, was also found to desulfurize benzothiophene. The desulfurization product was identified as
o
-hydroxystyrene by gas chromatography (GC)-mass spectrometry analysis. This strain appeared to have the ability to remove organic sulfur from a broad range of sulfur species in gasoline. When Dushanzi straight-run gasoline (DSRG227) containing various organic sulfur compounds was treated with immobilized cells of strain X7B for 24 h, the total sulfur content significantly decreased, from 227 to 71 ppm at 40°C. GC flame ionization detection and GC atomic emission detection analysis were used to qualitatively evaluate the effects of
M. goodii
X7B treatment on the contents of gasoline. In addition, when immobilized cells were incubated at 40°C with DSRG275, the sulfur content decreased from 275 to 54 ppm in two consecutive reactions. With this excellent efficiency, strain X7B is considered a good potential candidate for industrial applications for the biodesulfurization of gasoline.
Starch-Binding Domain Affects Catalysis in Two
Lactobacillus
α-Amylases
Authors: Rodríguez-Sanoja R. , Ruiz B. , Guyot J. P. , Sanchez S. 
Published: January 2005

ABSTRACT

A new starch-binding domain (SBD) was recently described in α-amylases from three lactobacilli (
Lactobacillus amylovorus
,
Lactobacillus plantarum
, and
Lactobacillus manihotivorans
). Usually, the SBD is formed by 100 amino acids, but the SBD sequences of the mentioned lactobacillus α-amylases consist of almost 500 amino acids that are organized in tandem repeats. The three lactobacillus amylase genes share more than 98% sequence identity. In spite of this identity, the SBD structures seem to be quite different. To investigate whether the observed differences in the SBDs have an effect on the hydrolytic capability of the enzymes, a kinetic study of
L. amylovorus
and
L. plantarum
amylases was developed, with both enzymes acting on several starch sources in granular and gelatinized forms. Results showed that the amylolytic capacities of these enzymes are quite different; the
L. amylovorus
α-amylase is, on average, 10 times more efficient than the
L. plantarum
enzyme in hydrolyzing all the tested polymeric starches, with only a minor difference in the adsorption capacities.
Intracellular Butyryl Phosphate and Acetyl Phosphate Concentrations in
Clostridium acetobutylicum
and Their Implications for Solvent Formation
Authors: Zhao Yinsuo , Tomas Christopher A. , Rudolph Fredrick B. , Papoutsakis Eleftherios T. , Bennett George N. 
Published: January 2005

ABSTRACT

It has been suggested (L. H. Harris, R. P. Desai, N. E. Welker, and E. T. Papoutsakis, Biotechnol. Bioeng.
67:
1-11, 2000) that butyryl phosphate (BuP) is a regulator of solventogenesis in
Clostridium acetobutylicum
. Here, we determined BuP and acetyl phosphate (AcP) levels in fermentations of
C. acetobutylicum
wild type (WT), degenerate strain M5, a butyrate kinase (
buk
) mutant, and a phosphotransacetylase (
pta
) mutant. A sensitive method was developed to measure BuP and AcP in the same sample. Compared to the WT, the
buk
mutant had higher levels of BuP and AcP; the BuP levels were high during the early exponential phase, and there was a peak corresponding to solvent production. Consistent with this, solvent formation was initiated significantly earlier and was much stronger in the
buk
mutant than in all other strains. For all strains, initiation of butanol formation corresponded to a BuP peak concentration that was more than 60 to 70 pmol/g (dry weight), and higher and sustained levels corresponded to higher butanol formation fluxes. The BuP levels never exceeded 40 to 50 pmol/g (dry weight) in strain M5, which produces no solvents. The BuP profiles were bimodal, and there was a second peak midway through solventogenesis that corresponded to carboxylic acid reutilization. AcP showed a delayed single peak during late solventogenesis corresponding to acetate reutilization. As expected, in the
pta
mutant the AcP levels were very low, yet this strain exhibited strong butanol production. These data suggest that BuP is a regulatory molecule that may act as a phosphodonor of transcriptional factors. DNA array-based transcriptional analysis of the
buk
and M5 mutants demonstrated that high BuP levels corresponded to downregulation of flagellar genes and upregulation of solvent formation and stress genes.
Starvation for Different Nutrients in
Escherichia coli
Results in Differential Modulation of RpoS Levels and Stability
Authors: Mandel Mark J. , Silhavy Thomas J. 
Published: January 2005

ABSTRACT

Levels of RpoS increase upon glucose starvation in
Escherichia coli
, which leads to the transcription of genes whose products combat a variety of stresses. RpoS stability is a key level of control in this process, as SprE (RssB)-mediated degradation is inhibited under glucose starvation. Starvation for ammonia or phosphate also results in increased stress resistance and induction of RpoS-dependent genes. However, we demonstrate that RpoS levels following ammonia starvation are only slightly increased compared to growing cells and are 10-fold below the levels observed under glucose or phosphate limitation. This difference is largely due to regulated proteolysis of RpoS, as its stability in ammonia-starved cells is intermediate between that in logarithmic-phase cells and glucose-starved cells. Use of an
rpoS
construct that is devoid of the gene's native transcriptional and translational control regions reveals that stability differences are sufficient to explain the different levels of RpoS observed in logarithmic phase, ammonia starvation, and glucose starvation. Under phosphate starvation, however,
rpoS
translation is increased. The cellular response to nutrient limitation is much more complex than previously appreciated, as there is not simply one response that is activated by starvation for any essential nutrient. Our data support the hypothesis that SprE activity is the key level at which ammonia and glucose starvation signals are transmitted to RpoS, and they suggest that carbon source and/or energy limitation are necessary for full inactivation of the SprE pathway.
Interaction between Components of the Type III Secretion System ofChlamydiaceae
Authors: Slepenkin Anatoly , de la Maza Luis M. , Peterson Ellena M. 
Published: January 2005

ABSTRACTMembers of the familyChlamydiaceaepossess at least 13 genes, distributed throughout the chromosome, that are homologous with genes of known type III secretion systems (TTS). The aim of this study was to use putative TTS proteins ofChlamydophila pneumoniae, whose equivalents in other bacterial TTS function as chaperones, to identify interactions between chlamydial proteins. Using the BacterioMatch Two-Hybrid Vector system (Stratagene, La Jolla, Calif.),lcrH-2andsycE, positions 1021 and 0325, respectively, fromC. pneumoniaeCM-1 were used as “bait” to identify target genes (positions 0324, 0705, 0708, 0808 to 0810, 1016 to 1020, and 1022) in close proximity on the chromosome. Interaction between the products of thelcrH-2(1021) andlcrE(copN) (0324) genes was detected and confirmed by pull-down experiments and enzyme immunoassays using recombinant LcrH-2 and LcrE. As further confirmation of this interaction, the homologous genes fromChlamydia trachomatis, serovar E, andChlamydophila psittaci, Texas turkey, were also cloned in the two-hybrid system to determine if LcrH-2 and LcrE would interact with their orthologs in other species. Consistent with their genetic relatedness, LcrH-2 fromC. pneumoniaeinteracted with LcrE produced from the three species ofChlamydiaceae; LcrH-2 fromC. psittacireacted with LcrE fromC. pneumoniaebut not fromC. trachomatis; andC. trachomatisLcrH-2 did not react with LcrE from the other two species. Deletions from the N and C termini of LcrE fromC. pneumoniaeidentified the 50 C-terminal amino acids as essential for the interaction with LcrH-2. Thus, it appears that in theChlamydiaceaeTTS, LcrH-2 interacts with LcrE, and therefore it may serve as a chaperone for this protein.
Nature of the Promoter Activated by C.PvuII, an Unusual Regulatory Protein Conserved among Restriction-Modification Systems
Authors: Knowle Dieter , Lintner Robert E. , Touma Yara M. , Blumenthal Robert M. 
Published: January 2005

ABSTRACTA widely distributed family of small regulators, called C proteins, controls a subset of restriction-modification systems. The C proteins studied to date activate transcription of their own genes and that of downstream endonuclease genes; this arrangement appears to delay endonuclease expression relative to that of the protective methyltransferase when the genes enter a new cell. C proteins bind to conserved sequences called C boxes. In the PvuII system, the C boxes have been reported to extend from −23 to +3 relative to the transcription start for the gene for the C protein, an unexpected starting position relative to a bound activator. This study suggests that transcript initiation within the C boxes represents initial, C-independent transcription ofpvuIICR. The major C protein-dependent transcript appears to be a leaderless mRNA starting farther downstream, at the initiation codon for thepvuIICgene. This conclusion is based on nuclease S1 transcript mapping and the effects of a series of nested deletions in the promoter region. Furthermore, replacing the region upstream of thepvuIICinitiation codon with a library of random oligonucleotides, followed by selection for C-dependent transcription, yielded clones having sequences that resemble −10 promoter hexamers. The −35 hexamer of this promoter would lie within the C boxes. However, the spacing between C boxes/−35 and the apparent −10 hexamer can be varied by ±4 bp with little effect. This suggests that, like some other activator-dependent promoters, PpvuIICRmay not require a −35 hexamer. Features of this transcription activation system suggest explanations for its broad host range.
The
N
5
-Glutamine
S
-Adenosyl-
l
-Methionine-Dependent Methyltransferase PrmC/HemK in
Chlamydia trachomatis
Methylates Class 1 Release Factors
Authors: Pannekoek Yvonne , Heurgué-Hamard Valérie , Langerak Ankie A. J. , Speijer Dave , Buckingham Richard H. , van der Ende Arie 
Published: January 2005

ABSTRACT

The gene
prmC
, encoding the putative
S
-adenosyl-
l
-methionine (AdoMet)-dependent methyltransferase (MTase) of release factors (RFs) of the obligate intracellular pathogen
Chlamydia trachomatis
, was functionally analyzed. Chlamydial PrmC expression suppresses the growth defect of a
prmC
knockout strain of
Escherichia coli
K-12, suggesting an interaction of chlamydial PrmC with
E. coli
RFs in vivo. In vivo methylation assays carried out with recombinant PrmC and RFs of chlamydial origin demonstrated that PrmC methylates RFs within the tryptic fragment containing the universally conserved sequence motif Gly-Gly-Gln. This is consistent with the enzymatic properties of PrmC of
E. coli
origin. We conclude that
C. trachomatis
PrmC functions as an
N
5
-glutamine AdoMet-dependent MTase, involved in methylation of RFs.
Comparative Genomics of
Staphylococcus aureus
Musculoskeletal Isolates
Authors: Cassat James E. , Dunman Paul M. , McAleese Fionnuala , Murphy Ellen , Projan Steven J. , Smeltzer Mark S. 
Published: January 2005

ABSTRACT

Much of the research aimed at defining the pathogenesis of
Staphylococcus aureus
has been done with a limited number of strains, most notably the 8325-4 derivative RN6390. Several lines of evidence indicate that this strain is unique by comparison to clinical isolates of
S. aureus
. Based on this, we have focused our efforts on two clinical isolates (UAMS-1 and UAMS-601), both of which are hypervirulent in our animal models of musculoskeletal infection. In this study, we used comparative genomic hybridization to assess the genome content of these two isolates relative to RN6390 and each of seven sequenced
S. aureus
isolates. Our comparisons were done by using an amplicon-based microarray from the Pathogen Functional Genomics Resource Center and an Affymetrix GeneChip that collectively represent the genomes of all seven sequenced strains. Our results confirmed that UAMS-1 and UAMS-601 share specific attributes that distinguish them from RN6390. Potentially important differences included the presence of
cna
and the absence of
isaB, sarT, sarU
, and
sasG
in the UAMS isolates. Among the sequenced strains, the UAMS isolates were most closely related to the dominant European clone EMRSA-16. In contrast, RN6390, NCTC 8325, and COL formed a distinct cluster that, by comparison to the other four sequenced strains (Mu50, N315, MW2, and SANGER-476), was the most distantly related to the UAMS isolates and EMRSA-16.
Functional Dissection of a Conserved Motif within the Pilus Retraction Protein PilT
Authors: Aukema Kelly G. , Kron Erin M. , Herdendorf Timothy J. , Forest Katrina T. 
Published: January 2005

ABSTRACT

PilT is a hexameric ATPase required for type IV pilus retraction in gram-negative bacteria. Retraction of type IV pili mediates intimate attachment to and signaling in host cells, surface motility, biofilm formation, natural transformation, and phage sensitivity. We investigated the in vivo and in vitro roles of each amino acid of the distinct, highly conserved C-terminal AIRNLIRE motif in PilT. Substitution of amino acids A288, I289, L292, and I293 as well as a double substitution of R290 and R294 abolished
Pseudomonas
aeruginosa
PilT function in vivo, as measured by a loss of surface motility and phage sensitivity. When introduced into purified
Aquifex
aeolicus
PilT, substitutions in the AIRNLIRE motif did not disrupt ATPase activity or oligomerization. In contrast, a K136Q substitution in the broadly conserved nucleotide binding motif prevented PilT function in vivo as well as in vitro. We propose that the AIRNLIRE motif forms an amphipathic α helix which transmits signals between a surface-exposed protein interaction site and the ATPase core of PilT, and we recognize a potential functional homology in other type II secretion ATPases.
Evolutionary Genetics of a New Pathogenic
Escherichia
Species:
Escherichia
albertii
and Related
Shigella
boydii
Strains
Authors: Hyma Katie E. , Lacher David W. , Nelson Adam M. , Bumbaugh Alyssa C. , Janda J. Michael , Strockbine Nancy A. , Young Vincent B. , Whittam Thomas S. 
Published: January 2005

ABSTRACT

A bacterium originally described as
Hafnia
alvei
induces diarrhea in rabbits and causes epithelial damage similar to the attachment and effacement associated with enteropathogenic
Escherichia
coli
. Subsequent studies identified similar
H. alvei
-like strains that are positive for an intimin gene (
eae
) probe and, based on DNA relatedness, are classified as a distinct
Escherichia
species,
Escherichia
albertii
. We determined sequences for multiple housekeeping genes in five
E. albertii
strains and compared these sequences to those of strains representing the major groups of pathogenic
E. coli
and
Shigella
. A comparison of 2,484 codon positions in 14 genes revealed that
E. albertii
strains differ, on average, at ∼7.4% of the nucleotide sites from pathogenic
E. coli
strains and at 15.7% from
Salmonella
enterica
serotype Typhimurium. Interestingly,
E. albertii
strains were found to be closely related to strains of
Shigella
boydii
serotype 13 (
Shigella
B13), a distant relative of
E. coli
representing a divergent lineage in the genus
Escherichia
. Analysis of homologues of intimin (
eae
) revealed that the central conserved domains are similar in
E. albertii
and
Shigella
B13 and distinct from those of
eae
variants found in pathogenic
E. coli
. Sequence analysis of the cytolethal distending toxin gene cluster (
cdt
) also disclosed three allelic groups corresponding to
E. albertii
,
Shigella
B13, and a nontypeable isolate serologically related to
S. boydii
serotype 7. Based on the synonymous substitution rate, the
E. albertii
-
Shigella
B13 lineage is estimated to have split from an
E. coli
-like ancestor ∼28 million years ago and formed a distinct evolutionary branch of enteric pathogens that has radiated into groups with distinct virulence properties.
TheErwinia chrysanthemiType III Secretion System Is Required for Multicellular Behavior
Authors: Mee-Ngan Yap , Yang Ching-Hong , Barak Jeri D. , Jahn Courtney E. , Charkowski Amy O. 
Published: January 2005

ABSTRACTEnterobacterial animal pathogens exhibit aggregative multicellular behavior, which is manifested as pellicles on the culture surface and biofilms at the surface-liquid-air interface. Pellicle formation behavior requires production of extracellular polysaccharide, cellulose, and protein filaments, known as curli. Protein filaments analogous to curli are formed by many protein secretion systems, including the type III secretion system (TTSS). Here, we demonstrate thatErwinia chrysanthemi, which does not carry curli genes, requires the TTSS for pellicle formation. These data support a model where cellulose and generic protein filaments, which consist of either curli or TTSS-secreted proteins, are required for enterobacterial aggregative multicellular behavior. Using this assay, we found thathrpY, which encodes a two-component system response regulator homolog, is required for activity ofhrpS, which encodes a σ54-dependent enhancer-binding protein homolog. In turn,hrpSis required for activity of the sigma factor homologhrpL, which activates genes encoding TTSS structural and secreted proteins. Pellicle formation was temperature dependent and pellicles did not form at 36°C, even though TTSS genes were expressed at this temperature. We found that cellulose is a component of theE. chrysanthemipellicle but that pellicle formation still occurs in a strain with an insertion in a cellulose synthase subunit homolog. Since the TTSS, but not the cellulose synthase subunit, is required forE. chrysanthemipellicle formation, this inexpensive assay can be used as a high throughput screen for TTSS mutants or inhibitors.
The
hrpK
Operon of
Pseudomonas syringae
pv. tomato DC3000 Encodes Two Proteins Secreted by the Type III (Hrp) Protein Secretion System: HopB1 and HrpK, a Putative Type III Translocator
Authors: Petnicki-Ocwieja Tanja , van Dijk Karin , Alfano James R. 
Published: January 2005

ABSTRACT

Pseudomonas syringae
is a gram-negative bacterial plant pathogen that is dependent on a type III protein secretion system (TTSS) and the effector proteins it translocates into plant cells for pathogenicity. The
P. syringae
TTSS is encoded by
hrp-hrc
genes that reside in a central region of a pathogenicity island (Pai). Flanking one side of this Pai is the exchangeable effector locus (EEL). We characterized the transcriptional expression of the open reading frames (ORFs) within the EEL of
P. syringae
pv. tomato DC3000. One of these ORFs, PSPTO1406 (
hopB1
) is expressed in the same transcriptional unit as
hrpK
. Both HopB1 and HrpK were secreted in culture and translocated into plant cells via the TTSS. However, the translocation of HrpK required its C-terminal half. HrpK shares low similarity with a putative translocator, HrpF, from
Xanthomonas campestris
pv. vesicatoria. DC3000 mutants lacking HrpK were significantly reduced in disease symptoms and multiplication in planta, whereas DC3000
hopB1
mutants produced phenotypes similar to the wild type. Additionally,
hrpK
mutants were reduced in their ability to elicit the hypersensitive response (HR), a programmed cell death associated with plant defense. The reduced HR phenotype exhibited by
hrpK
mutants was complemented by
hrpK
expressed in bacteria but not by HrpK transgenically expressed in tobacco, suggesting that HrpK does not function inside plant cells. Further experiments identified a C-terminal transmembrane domain within HrpK that is required for HrpK translocation. Taken together, HopB1 is a type III effector and HrpK plays an important role in the TTSS and is a putative type III translocator.