bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Cytochrome 579, an Unusual Cytochrome Isolated from an Iron-Oxidizing Microbial Community
Authors: Singer Steven W. , Chan Clara S. , Zemla Adam , VerBerkmoes Nathan C. , Hwang Mona , Hettich Robert L. , Banfield Jillian F. , Thelen Michael P. 
Published: May 2008

ABSTRACT

A novel, soluble cytochrome with an unusual visible spectral signature at 579 nm (Cyt
579
) has been characterized after isolation from several different microbial biofilms collected in an extremely acidic ecosystem. Previous proteogenomic studies of an Fe(II)-oxidizing community indicated that this abundant red cytochrome could be extracted from the biofilms with dilute sulfuric acid. Here, we found that the Fe(II)-dependent reduction of Cyt
579
was thermodynamically favorable at a pH of >3, raising the possibility that Cyt
579
acts as an accessory protein for electron transfer. The results of transmission electron microscopy of immunogold-labeled biofilm indicated that Cyt
579
is localized near the bacterial cell surface, consistent with periplasmic localization. The results of further protein analysis of Cyt
579
, using preparative chromatofocusing and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, revealed three forms of the protein that correspond to different N-terminal truncations of the amino acid sequence. The results of intact-protein analysis corroborated the posttranslational modifications of these forms and identified a genomically uncharacterized Cyt
579
variant. Homology modeling was used to predict the overall cytochrome structure and heme binding site; the positions of nine amino acid substitutions found in three Cyt
579
variants all map to the surface of the protein and away from the heme group. Based on this detailed characterization of Cyt
579
, we propose that Cyt
579
acts as an electron transfer protein, shuttling electrons derived from Fe(II) oxidation to support critical metabolic functions in the acidophilic microbial community.
Surface Plasmon Resonance Assay for Real-Time Monitoring of Somatic Coliphages in Wastewaters
Authors: García-Aljaro Cristina , Muñoz-Berbel Xavier , Jenkins A. Toby A. , Blanch Anicet R. , Muñoz Francesc Xavier 
Published: May 2008

ABSTRACT

The surface plasmon resonance (SPR) technique is a well-established method for the measurement of molecules binding to surfaces and the quantification of binding constants between surface-immobilized proteins and proteins in solution. In this paper we describe an extension of the methodology to study bacteriophage-bacterium interactions. A two-channel microfluidic SPR sensor device was used to detect the presence of somatic coliphages, a group of bacteriophages that have been proposed as fecal pollution indicators in water, using their host,
Escherichia coli
WG5, as a target for their selective detection. The bacterium,
E. coli
WG5, was immobilized on gold sensor chips using avidin-biotin and bacteriophages extracted from wastewater added. The initial binding of the bacteriophage was observed at high concentrations, and a separate, time-delayed cell lysis event also was observed, which was sensitive to bacteriophage at low concentrations. As few as 1 PFU/ml of bacteriophage injected into the chamber could be detected after a phage incubation period of 120 min, which equates to an approximate limit of detection of around 10
2
PFU/ml. The bacteriophage-bacterium interaction appeared to cause a structural change in the surface-bound bacteria, possibly due to collapse of the cell, which was observed as an increase in mass density on the sensor chip. These results suggest that this methodology could be employed for future biosensor technologies and for quantification of the bacteriophage concentration.
Discovery of a Modified Transcription Factor Endowing Yeasts with Organic-Solvent Tolerance and Reconstruction of an Organic-Solvent-Tolerant
Saccharomyces cerevisiae
Strain
Authors: Matsui Ken , Teranishi Shinya , Kamon Shohei , Kuroda Kouichi , Ueda Mitsuyoshi 
Published: May 2008

ABSTRACT

Organic-solvent tolerance in
Saccharomyces cerevisiae
strain KK-211, which was first isolated as an organic-solvent-tolerant strain, depends on point mutation (R821S) of the transcription factor Pdr1p. The integration of the
PDR1
R821S mutation into wild-type yeast results in organic-solvent tolerance, and the
PDR1
R821S mutant can reduce carbonyl compounds in organic solvents.
Direct Interactions between the Paf1 Complex and a Cleavage and Polyadenylation Factor Are Revealed by Dissociation of Paf1 from RNA Polymerase II
Authors: Nordick Kristen , Hoffman Matthew G. , Betz Joan L. , Jaehning Judith A. 
Published: May 2008

ABSTRACT

The Paf1 complex (Paf1, Ctr9, Cdc73, Rtf1, and Leo1) is normally associated with RNA polymerase II (Pol II) throughout the transcription cycle. However, the loss of either Rtf1 or Cdc73 results in the detachment of the Paf1 complex from Pol II and the chromatin form of actively transcribed genes. Using functionally tagged forms of the Paf1 complex factors, we have determined that, except for the more loosely associated Rtf1, the remaining components stay stably associated with one another in an RNase-resistant complex after dissociation from Pol II and chromatin. The loss of Paf1, Ctr9, or to a lesser extent Cdc73 or Rtf1 results in reduced levels of serine 2 phosphorylation of the Pol II C-terminal domain and in increased read through of the
MAK21
polyadenylation site. We found that the cleavage and polyadenylation factor Cft1 requires the Pol II-associated form of the Paf1 complex for full levels of interaction with the serine 5-phosphorylated form of Pol II. When the Paf1 complex is dissociated from Pol II, a direct interaction between Cft1 and the Paf1 complex can be detected. These results are consistent with the Paf1 complex providing a point of contact for recruitment of 3′-end processing factors at an early point in the transcription cycle. The lack of this connection helps to explain the defects in 3′-end formation observed in the absence of Paf1.
TheFrancisellaPathogenicity Island Protein PdpD Is Required for Full Virulence and Associates with Homologues of the Type VI Secretion System
Authors: Ludu Jagjit S. , de Bruin Olle M. , Duplantis Barry N. , Schmerk Crystal L. , Chou Alicia Y. , Elkins Karen L. , Nano Francis E. 
Published: May 2008

ABSTRACTFrancisella tularensisis a highly infectious, facultative intracellular bacterial pathogen that is the causative agent of tularemia. Nearly a century ago, researchers observed that tularemia was often fatal in North America but almost never fatal in Europe and Asia. The chromosomes ofF. tularensisstrains carry two identical copies of theFrancisellapathogenicity island (FPI), and the FPIs of North America-specific biotypes contain two genes,anmKandpdpD, that are not found in biotypes that are distributed over the entire Northern Hemisphere. In this work, we studied the contribution ofanmKandpdpDto virulence by usingF. novicida, which is very closely related toF. tularensisbut which carries only one copy of the FPI. We showed thatanmKandpdpDare necessary for full virulence but not for intracellular growth. This is in sharp contrast to most other FPI genes that have been studied to date, which are required for intracellular growth. We also showed that PdpD is localized to the outer membrane. Further, overexpression of PdpD affects the cellular distribution of FPI-encoded proteins IglA, IglB, and IglC. Finally, deletions of FPI genes encoding proteins that are homologues of known components of type VI secretion systems abolished the altered distribution of IglC and the outer membrane localization of PdpD.
Lipoprotein Signal Peptides Are Processed by Lsp and Eep of
Streptococcus uberis
Authors: Denham E. L. , Ward P. N. , Leigh J. A. 
Published: May 2008

ABSTRACT

Lipoprotein signal peptidase (
lsp
) is responsible for cleaving the signal peptide sequence of lipoproteins in gram-positive bacteria. Investigation of the role of Lsp in
Streptococcus uberis
, a common cause of bovine mastitis, was undertaken using the lipoprotein MtuA (a protein essential for virulence) as a marker. The
S. uberis lsp
mutant phenotype displayed novel lipoprotein processing. Not only was full-length (uncleaved) MtuA detected by Western blotting, but during late log phase, a lower-molecular-weight derivative of MtuA was evident. Similar analysis of an
S. uberis
double mutant containing insertions disrupting both
lsp
and
eep
(a homologue of the
Enterococcus faecalis
“enhanced expression of pheromone” gene) indicated a role for
eep
in cleavage of lipoproteins in the absence of Lsp. Such a function may indicate a role for
eep
in maintenance of secretion pathways during disruption of normal lipoprotein processing.
Switching Control of Expression ofptsGfrom the Mlc Regulon to the NagC Regulon
Authors: El Qaidi Samir , Plumbridge Jacqueline 
Published: May 2008

ABSTRACTThe Mlc and NagC transcriptional repressors bind to similar 23-bp operators. The sequences are weakly palindromic, with just four positions totally conserved. There is no cross regulation observed between the repressors in vivo, but there are no obvious bases which could be responsible for operator site discrimination. To investigate the basis for operator recognition and to try to understand what differentiates NagC sites from Mlc sites, we have undertaken mutagenesis experiments to convertptsGfrom a gene regulated by Mlc into a gene regulated by NagC. There are two Mlc operators upstream ofptsG, and to switchptsGto the NagC regulon, it was necessary to change two different characteristics of both operators. Firstly, we replaced the AT base pair at position +/−11 from the center of symmetry of the operators with a GC base pair. Secondly, we changed the sequence of the CG base pairs in the central region of the operator (positions −4 to +4 around the center of symmetry). Our results show that changes at either of these locations are sufficient to lose regulation by Mlc but that both types of changes in both operators are necessary to convertptsGto a gene regulated by NagC. In addition, these experiments confirmed that two operators are necessary for regulation by NagC. We also show that regulation ofptsGby Mlc involves some cooperative binding of Mlc to the two operators.
SO-LAAO, a Novell-Amino Acid Oxidase That EnablesStreptococcus oligofermentansTo OutcompeteStreptococcus mutansby Generating H2O2from Peptone
Authors: Tong Huichun , Chen Wei , Shi Wenyuan , Qi Fengxia , Dong Xiuzhu 
Published: May 2008

ABSTRACTWe previously demonstrated thatStreptococcus oligofermentanssuppressed the growth ofStreptococcus mutans, the primary cariogenic pathogen, by producing hydrogen peroxide (H2O2) through lactate oxidase activity. In this study, we found that theloxmutant ofS. oligofermentansregained the inhibition while growing on peptone-rich plates. Further studies demonstrated that the H2O2produced on peptone byS. oligofermentanswas mainly derived from sevenl-amino acids, i.e.,l-aspartic acid,l-tryptophan,l-lysine,l-isoleucine,l-arginine,l-asparagine, andl-glutamine, indicating the possible existence ofl-amino acid oxidase (LAAO) that can produce H2O2froml-amino acids. Through searching theS. oligofermentansgenome for open reading frames with a conserved flavin adenine dinucleotide binding motif that exists in the known LAAOs, including those of snake venom, fungi, and bacteria, a putative LAAO gene, assigned asaaoSo, was cloned and overexpressed inEscherichia coli. The purified protein, SO-LAAO, showed a molecular mass of 43 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis and catalyzed H2O2formation from the sevenl-amino acids determined above, thus confirming its LAAO activity. The SO-LAAO identified inS. oligofermentansdiffered evidently from the known LAAOs in both substrate profile and sequence, suggesting that it could represent a novel LAAO. AnaaoSomutant ofS. oligofermentansdid lose H2O2formation from the sevenl-amino acids, further verifying its function as an LAAO. Furthermore, the inhibition byS. oligofermentansofS. mutansin a peptone-rich mixed-species biofilm was greatly reduced for theaaoSomutant, indicating the gene's importance in interspecies competition.
Release of Small Molecules during Germination of Spores of
Bacillus
Species
Authors: Setlow Barbara , Wahome Paul G. , Setlow Peter 
Published: May 2008

ABSTRACT

Free amino acids, dipicolinic acid, and unidentified small molecules were released early in
Bacillus
spore germination before hydrolysis of the peptidoglycan cortex, but adenine nucleotides and 3-phosphoglycerate were not. These results indicate that early in germination there is a major selective change in the permeability of the spore's inner membrane.
VirB3 to VirB6 and VirB8 to VirB11, but Not VirB7, Are Essential for Mediating Persistence ofBrucellain the Reticuloendothelial System
Authors: den Hartigh Andreas B. , Rolán Hortensia G. , de Jong Maarten F. , Tsolis Renée M. 
Published: May 2008

ABSTRACTTheBrucella abortus virBlocus contains 12 open reading frames, termedvirB1throughvirB12, which encode a type IV secretion system. Polar mutations in thevirBlocus markedly reduce the ability ofB. abortusto survive in cultured macrophages or to persist in organs of mice. While a nonpolar deletion of thevirB2gene reduces survival in cultured macrophages and in organs of mice, a nonpolar deletion ofvirB1only reduces survival in macrophages, whereasvirB12is dispensable for either virulence trait. Here we investigated the role of the remaining genes in thevirBlocus during survival in macrophages and virulence in mice. Mutants carrying nonpolar deletions of thevirB3,virB4,virB5,virB6,virB7,virB8,virB9,virB10, orvirB11gene were constructed and characterized. All mutations reduced the ability ofB. abortusto survive in J774A.1 mouse macrophage-like cells to a degree similar to that caused by a deletion of the entirevirBlocus. Deletion ofvirB3,virB4,virB5,virB6,virB8,virB9,virB10, orvirB11markedly reduced the ability ofB. abortusto persist in the spleens of mice at 8 weeks after infection. Interestingly, deletion ofvirB7did not reduce the ability ofB. abortusto persist in spleens of mice. We conclude thatvirB2,virB3,virB4,virB5,virB6,virB8,virB9,virB10, andvirB11are essential for virulence ofB. abortusin mice, while functions encoded by thevirB1,virB7, andvirB12genes are not required for persistence in organs with this animal model.
Involvement of a Novel Efflux System in Biofilm-Specific Resistance to Antibiotics
Authors: Zhang Li , Mah Thien-Fah 
Published: May 2008

ABSTRACT

Bacteria growing in biofilms are more resistant to antibiotics than their planktonic counterparts. How this transition occurs is unclear, but it is likely there are multiple mechanisms of resistance that act together in order to provide an increased overall level of resistance to the biofilm. We have identified a novel efflux pump in
Pseudomonas aeruginosa
that is important for biofilm-specific resistance to a subset of antibiotics. Complete deletion of the genes encoding this pump, PA1874 to PA1877 (PA1874-1877) genes, in an
P. aeruginosa
PA14 background results in an increase in sensitivity to tobramycin, gentamicin, and ciprofloxacin, specifically when this mutant strain is growing in a biofilm. This efflux pump is more highly expressed in biofilm cells than in planktonic cells, providing an explanation for why these genes are important for biofilm but not planktonic resistance to antibiotics. Furthermore, expression of these genes in planktonic cells increases their resistance to antibiotics. We have previously shown that
ndvB
is important for biofilm-specific resistance (T. F. Mah, B. Pitts, B. Pellock, G. C. Walker, P. S. Stewart, and G. A. O'Toole, Nature 426:306-310, 2003). Our discovery that combining the
ndvB
mutation with the PA1874-1877 gene deletion results in a mutant strain that is more sensitive to antibiotics than either single mutant strain suggests that
ndvB
and PA1874-1877 contribute to two different mechanisms of biofilm-specific resistance to antibiotics.
Modulation ofcovRExpression inStreptococcus mutansUA159
Authors: Chong Patrick , Drake Laura , Biswas Indranil 
Published: May 2008

ABSTRACTThe biofilm-formingStreptococcus mutansis a gram-positive bacterium that resides in the human oral cavity and is considered to be the primary etiological agent in the formation of dental caries. The global response regulator CovR, which lacks a cognate sensor kinase, is essential for the pathogenesis and biofilm formation of this bacterium, but it is not clear howcovRexpression is regulated inS. mutans. In this communication, we present the results of our studies examining various factors that regulate the expression ofcovRinS. mutansUA159. The results of Southern hybridization and PCR analysis indicated that CovR is an orphan response regulator in various isolates ofS. mutans. The transcriptional start site forcovRwas found to be 221 base pairs upstream of the ATG start codon, and site-directed mutagenesis of the upstream TATAAT box confirmed our findings. The expression ofcovRis growth phase dependent, with maximal expression observed during exponential-growth phase. While changes to the growth temperature did not significantly affect the expression ofcovR, increasing the pH or the concentration of Mg2+in the growth medium leads to an increase incovRexpression. The results of semiquantitative reverse transcriptase PCR analysis and in vivo transcriptional-fusion reporter assays indicated that CovR autoregulates its own expression; this was verified by the results of electrophoretic mobility shift assays and DNase I protection assays, which demonstrated direct binding of CovR to the promoter region. Apparently, regulation by Mg2+and the autoregulation ofcovRare not linked. A detailed analysis of the regulation of CovR may lead to a better understanding of the pathogenesis ofS. mutans, as well as providing further insight into the prevention of dental caries.
FliZ Is a Posttranslational Activator of FlhD
4
C
2
-Dependent Flagellar Gene Expression
Authors: Saini Supreet , Brown Jonathon D. , Aldridge Phillip D. , Rao Christopher V. 
Published: May 2008

ABSTRACT

Flagellar assembly proceeds in a sequential manner, beginning at the base and concluding with the filament. A critical aspect of assembly is that gene expression is coupled to assembly. When cells transition from a nonflagellated to a flagellated state, gene expression is sequential, reflecting the manner in which the flagellum is made. A key mechanism for establishing this temporal hierarchy is the σ
28
-FlgM checkpoint, which couples the expression of late flagellar (P
class3
) genes to the completion of the hook-basal body. In this work, we investigated the role of FliZ in coupling middle flagellar (P
class2
) gene expression to assembly in
Salmonella enterica
serovar Typhimurium. We demonstrate that FliZ is an FlhD
4
C
2
-dependent activator of P
class2
/middle gene expression. Our results suggest that FliZ regulates the concentration of FlhD
4
C
2
posttranslationally. We also demonstrate that FliZ functions independently of the flagellum-specific sigma factor σ
28
and the filament-cap chaperone/FlhD
4
C
2
inhibitor FliT. Furthermore, we show that the previously described ability of σ
28
to activate P
class2
/middle gene expression is, in fact, due to FliZ, as both are expressed from the same overlapping P
class2
and P
class3
promoters at the
fliAZY
locus. We conclude by discussing the role of FliZ regulation with respect to flagellar biosynthesis based on our characterization of gene expression and FliZ's role in swimming and swarming motility.
Revision of some species of the genus Paralongidorus sensu Siddiqi et al. (1993), with a discussion on the relationships within the family Longidoridae (Nematoda: Dorylaimida)
Authors: Decraemer Wilfrida , Coomans August 
Published: May 2008

Abstract
A study of type material of several longidorid species revealed
misinterpretations of the amphid structure with respect to shape of the
amphidial fovea and amphidial aperture. A standardised terminology of the
amphid structure within the Longidoridae is proposed. Former and recent
hypotheses on phylogenetic relationships within the family based,
respectively, on morphological and on molecular data are discussed, as well
as possible implications for the systematics of the family Longidoridae. As
a result of this study the following new combinations are proposed:
Longidorus boshi n. comb. (syn. Paralongidorus boshi); Longidorus
monegrensis n. comb. (syn. P. monegrensis); Longidorus spiralis n. comb.
(syn. P. spiralis) and Longidorus cedari n. comb. (syn. Longidoroides
cedari). Additional information is provided for Longidoroides bikanerensis,
Paralongidorus buchae and P. zenobiae.
Effect of endophytic Fusarium oxysporum on root penetration and reproduction of Radopholus similis in tissue culture-derived banana (Musa spp.) plants
Authors: Viljoen Altus , Labuschagne Nico , Dubois Thomas , Athman Shahasi , Coyne Daniel , S. Gold Clifford 
Published: May 2008

AbstractIn Uganda, banana (Musa spp.) production is constrained by the burrowing nematode Radopholus similis. Non-pathogenic, endophytic Fusarium oxysporum has been isolated from healthy banana plants, and several strains have shown potential as biological control agents against R. similis. Plant infection by R. similis can be characterised in three steps: host searching, root penetration and reproduction. In this study, we investigated the effects of three endophytic F. oxysporum strains (Eny1.31i, Eny7.11o and V5w2) on root penetration and reproduction of R. similis in tissue culture-derived banana plants. The number of R. similis that penetrated roots of endophyte-inoculated and untreated plants was not influenced by the endophytes in either laboratory or screenhouse experiments. However, R. similis reproduction was reduced by endophytes. Strain V5w2 gave the greatest suppression of R. similis reproduction. The results of this study imply that antagonism of endophytic F. oxysporum against R. similis in banana plants is post-infectional and mediated through disruption of nematode reproduction.
The role of flavonoids produced in response to cyst nematode infection of Arabidopsis thaliana
Authors: Jones John T. , Furlanetto Cleber , Phillips Mark S. 
Published: May 2008

Abstract
Flavonoids have diverse roles in plants, including defence against plant
pathogens and regulation of local auxin transport. Flavonoids have been
shown to be produced in feeding sites of root-knot nematodes induced in a
leguminous plant, and it has previously been suggested that they may be
responsible for manipulation of local auxin levels that underlie early
feeding site development. Here we show that flavonoids are also produced in
developing syncytia induced by Heterodera schachtii and in galls induced by
Xiphinema diversicaudatum in a non-leguminous plant, Arabidopsis thaliana.
We further investigated whether flavonoids are required for normal feeding
site development by screening mutant lines of A. thaliana, defective in
various parts of the flavonoid biosynthetic pathway, with H. schachtii. None
of the lines showed a reduced capacity to support nematode infection and
some showed a statistically significant increase in the numbers of female
nematodes that developed. These data suggest that flavonoids are produced as
part of the defence response to nematode infection rather than being an
integral component of the mechanisms used by nematodes to induce feeding
sites.