bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broad Up-Regulation of Innate Defense Factors during Acute Cholera
Authors: Flach Carl-Fredrik , Qadri Firdausi , Bhuiyan Taufiqur R. , Alam Nur H. , Jennische Eva , Lönnroth Ivar , Holmgren Jan 
Published: February 2007

ABSTRACTWe used a whole-genome microarray screening system (Affymetrix human GeneChips covering 47,000 different transcripts) to examine the gene expression in duodenal mucosa during acute cholera. Biopsies were taken from the duodenal mucosa of seven cholera patients 2 and 30 days after the onset of diarrhea, and the gene expression patterns in the acute- and convalescent-phase samples were compared pairwise. Of about 21,000 transcripts expressed in the intestinal epithelium, 29 were defined as transcripts that were up-regulated and 33 were defined as transcripts that were down-regulated during acute cholera. The majority of the up-regulated genes characterized were found to have an established or possible role in the innate defense against infections; these genes included the LPLUNC1, LF, VCC1, TCN1, CD55, SERPINA3, MMP1, MMP3, IL1B, LCN2, SOCS3, GDF15, SLPI, CXCL13, and MUC1 genes. The results of confirmative PCR correlated well with the microarray data. An immunohistochemical analysis revealed increased expression of lactoferrin in lamina propria cells and increased expression of CD55 in epithelial cells, whereas increased expression of the SERPINA3 protein (α1-antichymotrypsin) was detected in both lamina propria and epithelial cells during acute cholera. The expression pattern of CD55 and SERPINA3 in cholera toxin (CT)-stimulated Caco-2 cells was the same as the pattern found in the intestinal mucosa during acute cholera, indicating that the activation of the CD55 and SERPINA3 genes in intestinal epithelium was induced by CT. In conclusion, during acute cholera infection, innate defense mechanisms are switched on to an extent not described previously. Both direct effects of CT on the epithelial cells and changes in the lamina propria cells contribute to this up-regulation.
Gingival Epithelial Cell Transcriptional Responses to Commensal and Opportunistic Oral Microbial Species
Authors: Hasegawa Yoshiaki , Mans Jeffrey J. , Mao Song , Lopez M. Cecilia , Baker Henry V. , Handfield Martin , Lamont Richard J. 
Published: February 2007

ABSTRACT

Transcriptional profiling and ontology tools were utilized to define the biological pathways of gingival epithelial cells modulated by coculture with the oral commensal
Streptococcus gordonii
and the opportunistic commensal
Fusobacterium nucleatum
. Overall,
F. nucleatum
and
S. gordonii
perturbed the gingival epithelial cell transcriptome much less significantly than the oral pathogens
Porphyromonas gingivalis
and
Aggregatibacter actinomycetemcomitans
perturbed the transcriptome, indicating that there was a greater degree of host adaptation by the commensal species (M. Handfield, J. J. Mans, G. Zheng, M. C. Lopez, S. Mao, A. Progulske-Fox, G. Narasimhan, H. V. Baker, and R. J. Lamont, Cell. Microbiol.
7:
811-823, 2005). The biological pathways significantly impacted by
F. nucleatum
and
S. gordonii
included the mitogen-activated protein kinase (MAPK) and Toll-like receptor signaling pathways. Differential regulation of GADD45 and DUSP4, key components of the MAPK pathway, was confirmed at the protein level by Western blotting. Modulation of the MAPK pathway is likely to affect host cell proliferation and differentiation. In addition, both the MAPK and Toll-like receptor pathways ultimately converge on cytokine gene expression. An enzyme-linked immunosorbent assay of secreted interleukin-6 (IL-6) and IL-8 demonstrated that
F. nucleatum
induced production of these cytokines, whereas
S. gordonii
inhibited secretion from the epithelial cells. Stimulation of secretion of proinflammatory cytokines from epithelial cells may reflect the invasive phenotype of
F. nucleatum
and contribute to the greater pathogenic potential of
F. nucleatum
than of
S. gordonii
.
Proteomic and Immunoblot Analyses of
Bartonella quintana
Total Membrane Proteins Identify Antigens Recognized by Sera from Infected Patients
Authors: Boonjakuakul Jenni K. , Gerns Helen L. , Chen Yu-Ting , Hicks Linda D. , Minnick Michael F. , Dixon Scott E. , Hall Steven C. , Koehler Jane E. 
Published: February 2007

ABSTRACT

Bartonella quintana
is a fastidious, gram-negative, rod-shaped bacterium that causes prolonged bacteremia in immunocompetent humans and severe infections in immunocompromised individuals. We sought to define the outer membrane subproteome of
B. quintana
in order to obtain insight into the biology and pathogenesis of this emerging pathogen and to identify the predominant
B. quintana
antigens targeted by the human immune system during infection. We isolated the total membrane proteins of
B. quintana
and identified 60 proteins by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and peptide mass fingerprinting. Using the newly constructed proteome map, we then utilized two-dimensional immunoblotting with sera from 21
B. quintana
-infected patients to identify 24 consistently recognized, immunoreactive
B. quintana
antigens that have potential relevance for pathogenesis and diagnosis. Among the outer membrane proteins, the
v
ariably expressed
o
uter
m
embrane
p
rotein adhesins (VompA and VompB), peptidyl-prolyl
cis-trans
-isomerase (PpI), and
h
emin-
b
inding
p
rotein
E
(HbpE) were recognized most frequently by sera from patients, which is consistent with surface expression of these virulence factors during human infection.
Repression of Intracellular Virulence Factors in
Salmonella
by the Hha and YdgT Nucleoid-Associated Proteins
Authors: Silphaduang Umaporn , Mascarenhas Mariola , Karmali Mohamed , Coombes Brian K. 
Published: February 2007

ABSTRACT

The Hha/YmoA family of nucleoid-associated proteins is involved in gene regulation in enterobacteria. In
Salmonella enterica
serovar Typhimurium, virulence genes required for intracellular growth are induced following host cell invasion but the proteins responsible for repressing these genes prior to host cell entry have not been fully identified. We demonstrate here that Hha is the major repressor responsible for silencing virulence genes carried in
Salmonella
pathogenicity island 2 prior to bacteria sensing an intracellular environmental cue.
A Riboswitch Regulates Expression of the Coenzyme B
12
-Independent Methionine Synthase in
Mycobacterium tuberculosis
: Implications for Differential Methionine Synthase Function in Strains H37Rv and CDC1551
Authors: Warner Digby F. , Savvi Suzana , Mizrahi Valerie , Dawes Stephanie S. 
Published: February 2007

ABSTRACT

We observed vitamin B
12
-mediated growth inhibition of
Mycobacterium tuberculosis
strain CDC1551. The B
12
sensitivity was mapped to a polymorphism in
metH
, encoding a coenzyme B
12
-dependent methionine synthase. Vitamin B
12
-resistant suppressor mutants of CDC1551 containing mutations in a B
12
riboswitch upstream of the
metE
gene, which encodes a B
12
-independent methionine synthase, were isolated. Expression analysis confirmed that the B
12
riboswitch is a transcriptional regulator of
metE
in
M. tuberculosis
.
Role of PBP1 in Cell Division of
Staphylococcus aureus
Authors: Pereira S. F. F. , Henriques A. O. , Pinho M. G. , de Lencastre H. , Tomasz A. 
Published: February 2007

ABSTRACT

We constructed a conditional mutant of
pbpA
in which transcription of the gene was placed under the control of an IPTG (isopropyl-β-
d
-thiogalactopyranoside)-inducible promoter in order to explore the role of PBP1 in growth, cell wall structure, and cell division. A methicillin-resistant strain and an isogenic methicillin-susceptible strain, each carrying the
pbpA
mutation, were unable to grow in the absence of the inducer. Conditional mutants of
pbpA
transferred into IPTG-free medium underwent a four- to fivefold increase in cell mass, which was not accompanied by a proportional increase in viable titer. Examination of thin sections of such cells by transmission electron microscopy or fluorescence microscopy of intact cells with Nile red-stained membranes showed a morphologically heterogeneous population of bacteria with abnormally increased sizes, distorted axial ratios, and a deficit in the number of cells with completed septa. Immunofluorescence with an antibody specific for PBP1 localized the protein to sites of cell division. No alteration in the composition of peptidoglycan was detectable in
pbpA
conditional mutants grown in the presence of a suboptimal concentration of IPTG, which severely restricted the rate of growth, and the essential function of PBP1 could not be replaced by PBP2A present in methicillin-resistant cells. These observations suggest that PBP1 is not a major contributor to the cross-linking of peptidoglycan and that its essential function must be intimately integrated into the mechanism of cell division.
Inactivation of the Mismatch Repair System in
Pseudomonas aeruginosa
Attenuates Virulence but Favors Persistence of Oropharyngeal Colonization in Cystic Fibrosis Mice
Authors: Mena Ana , Maciá María D. , Borrell Nuria , Moya Bartolomé , de Francisco Teresa , Pérez José L. , Oliver Antonio 
Published: February 2007

ABSTRACT

The inactivation of the mismatch repair (MMR) system of
Pseudomonas aeruginosa
modestly reduced in vitro fitness, attenuated virulence in murine models of acute systemic and respiratory infections, and decreased the initial oropharyngeal colonization potential. In contrast, the inactivation of the MMR system favored long-term persistence of oropharyngeal colonization in cystic fibrosis mice. These results may help in understanding the reasons for the low and high prevalences, respectively, of hypermutable
P. aeruginosa
strains in acute and chronic infections.
Reconstitution of the Biochemical Activities of the AttJ Repressor and the AttK, AttL, and AttM Catabolic Enzymes of
Agrobacterium tumefaciens
Authors: Chai Yunrong , Tsai Ching Sung , Cho Hongbaek , Winans Stephen C. 
Published: February 2007

ABSTRACT

The
attKLM
operon encodes a lactonase (AttM) that hydrolyzes acylhomoserine lactone autoinducers, as well as two putative dehydrogenases (AttK and AttL). Here we show that AttK, AttL, and AttM collectively covert gamma-butyrolactone to succinate. Two metabolic intermediates, gamma-hydroxybutyrate and succinic semialdehyde, inactivated the AttJ repressor in vitro and induced
attKLM
transcription in vivo.
Interaction between Cell Division Proteins FtsE and FtsZ
Authors: Corbin Brian D. , Wang Yipeng , Beuria Tushar K. , Margolin William 
Published: February 2007

ABSTRACT

FtsE and FtsX, which are widely conserved homologs of ABC transporters and interact with each other, have important but unknown functions in bacterial cell division. Coimmunoprecipitation of
Escherichia coli
cell extracts revealed that a functional FLAG-tagged version of FtsE, the putative ATP-binding component, interacts with FtsZ, the bacterial tubulin homolog required to assemble the cytokinetic Z ring and recruit the components of the divisome. This interaction is independent of FtsX, the predicted membrane component of the ABC transporter, which has been shown previously to interact with FtsE. The interaction also occurred independently of FtsA or ZipA, two other
E. coli
cell division proteins that interact with FtsZ. In addition, FtsZ copurified with FLAG-FtsE. Surprisingly, the conserved C-terminal tail of FtsZ, which interacts with other cell division proteins, such as FtsA and ZipA, was dispensable for interaction with FtsE. In support of a direct interaction with FtsZ, targeting of a green fluorescent protein (GFP)-FtsE fusion to Z rings required FtsZ, but not FtsA. Although GFP-FtsE failed to target Z rings in the absence of ZipA, its localization was restored in the presence of the
ftsA
* bypass suppressor, indicating that the requirement for ZipA is indirect. Coexpression of FLAG-FtsE and FtsX under certain conditions resulted in efficient formation of minicells, also consistent with an FtsE-FtsZ interaction and with the idea that FtsE and FtsX regulate the activity of the divisome.
Cross Talk between Type III Secretion and Flagellar Assembly Systems in
Pseudomonas aeruginosa
Authors: Soscia Chantal , Hachani Abderrahman , Bernadac Alain , Filloux Alain , Bleves Sophie 
Published: February 2007

ABSTRACT

Pseudomonas aeruginosa
cytotoxicity is linked to a type III secretion system (T3SS) that delivers effectors into the host cell. We show here that a negative cross-control exists between T3SS and flagellar assembly. We observed that, in a strain lacking flagella, T3SS gene expression, effector secretion, and cytotoxicity were increased. Conversely, we revealed that flagellar-gene expression and motility were decreased in a strain overproducing ExsA, the T3SS master regulator. Interestingly, a nonmotile strain lacking the flagellar filament (Δ
fliC
) presented a hyperefficient T3SS and a nonmotile strain assembling flagella (Δ
motAB
) did not. More intriguingly, a strain lacking
motCD
genes is a flagellated strain with a slight defect in swimming. However, in this strain, T3SS gene expression was up-regulated. These results suggest that flagellar assembly and/or mobility antagonizes the T3SS and that a negative cross talk exists between these two systems. An illustration of this is the visualization by electron microscopy of T3SS needles in a nonmotile
P. aeruginosa
strain, needles which otherwise are not detected. The molecular basis of the cross talk is complex and remains to be elucidated, but proteins like MotCD might have a crucial role in signaling between the two processes. In addition, we found that the GacA response regulator negatively affects the T3SS. In a
gacA
mutant, the T3SS effector ExoS is hypersecreted. Strikingly, GacA was previously reported as a positive regulator for motility. Globally, our data document the idea that some virulence factors are coordinately but inversely regulated, depending on the bacterial colonization phase and infection types.
Transcriptional Regulation of the CO
2
-Concentrating Mechanism in a Euryhaline, Coastal Marine Cyanobacterium,
Synechococcus
sp. Strain PCC 7002: Role of NdhR/CcmR
Authors: Woodger Fiona J. , Bryant Donald A. , Price G. Dean 
Published: February 2007

ABSTRACT

Cyanobacterial photosynthesis occurs in radically diverse habitats and utilizes various forms of a CO
2
-concentrating mechanism (CCM) featuring multiple inorganic carbon (C
i
) transporters. Cyanobacteria from dynamic environments can transform CCM activity depending on C
i
availability, and yet the molecular basis for this regulation is unclear, especially in coastal strains. LysR family transcription factors resembling the Calvin cycle regulator CbbR from proteobacteria have been implicated in the expression of C
i
transporter genes in freshwater cyanobacteria. Our survey of related factors revealed a group of divergent CbbR-like sequences confined to freshwater and coastal or offshore cyanobacteria. Inactivation of the single gene (termed
ccmR
) from this variable cluster in the euryhaline (coastal) strain
Synechococcus
sp. strain PCC 7002 led to constitutive expression of a high-affinity CCM. Derepression of HCO
3
−
transporter gene transcription, including that of BicA, a recently discovered HCO
3
−
transporter (G. D. Price et al., Proc. Natl. Acad. Sci. USA
101
:18228-18233, 2004), was observed. A unique CcmR-regulated operon containing
bicA
plus 9 open reading frames encoding likely Na
+
/H
+
antiporters from the CPA1 and Mnh families was defined that is essential for maximal HCO
3
−
-dependent oxygen evolution. The promoter region required for C
i
-regulated transcription of this operon was defined. We propose that CcmR (and its associated regulon) represents a specialization for species inhabiting environments subject to fluctuating C
i
concentrations.
Complete Genome Sequence of the Prototype Lactic Acid Bacterium
Lactococcus lactis
subsp.
cremoris
MG1363
Authors: Wegmann Udo , O'Connell-Motherway Mary , Zomer Aldert , Buist Girbe , Shearman Claire , Canchaya Carlos , Ventura Marco , Goesmann Alexander , Gasson Michael J. , Kuipers Oscar P. , van Sinderen Douwe , Kok Jan 
Published: February 2007

ABSTRACT

Lactococcus lactis
is of great importance for the nutrition of hundreds of millions of people worldwide. This paper describes the genome sequence of
Lactococcus lactis
subsp.
cremoris
MG1363, the lactococcal strain most intensively studied throughout the world. The 2,529,478-bp genome contains 81 pseudogenes and encodes 2,436 proteins. Of the 530 unique proteins, 47 belong to the COG (clusters of orthologous groups) functional category “carbohydrate metabolism and transport,” by far the largest category of novel proteins in comparison with
L. lactis
subsp.
lactis
IL1403. Nearly one-fifth of the 71 insertion elements are concentrated in a specific 56-kb region. This integration hot-spot region carries genes that are typically associated with lactococcal plasmids and a repeat sequence specifically found on plasmids and in the “lateral gene transfer hot spot” in the genome of
Streptococcus thermophilus
. Although the parent of
L. lactis
MG1363 was used to demonstrate lysogeny in
Lactococcus
,
L. lactis
MG1363 carries four remnant/satellite phages and two apparently complete prophages. The availability of the
L. lactis
MG1363 genome sequence will reinforce its status as the prototype among lactic acid bacteria through facilitation of further applied and fundamental research.
Lipolytic Enzymes inMyxococcus xanthus
Authors: Moraleda-Muñoz Aurelio , Shimkets Lawrence J. 
Published: February 2007

ABSTRACTThe genome ofMyxococcus xanthusencodes lipolytic enzymes in three different families: patatin lipases, α/β hydrolases, and GDSL lipases. One member of each family was characterized. The protein encoded by MXAN_3852 contains motifs characteristic of patatins. MXAN_5522 encodes a protein with the G-X-S-X-G motif characteristic of the lipase subfamily of α/β hydrolases. MXAN_4569 encodes a member of the GDSL family of lipolytic enzymes. Strains with deletions of MXAN_5522 and MXAN_4569 undergo faster development and earlier myxospore formation than the wild-type strain. The MXAN_5522 mutation results in spore yields substantially higher than those seen for wild-type cells. Gene expression analysis using translationallacZfusions indicates that while all three genes are expressed during development, only MXAN_5522 and MXAN_4569 are expressed during vegetative growth. The proteins encoded by these genes were overexpressed using a T7 RNA polymerase transcription (pET102/D-TOPO) system inEscherichia coliBL21 Star (DE3) cells. The substrate specificities of the purified enzymes were investigated usingp-nitrophenyl esters with chain lengths from C2to C16. These enzymes preferentially hydrolyzed esters of short-chain fatty acids, yielding the highest activity withp-nitrophenyl acetate.
H-NS Antagonism inShigella flexneriby VirB, a Virulence Gene Transcription Regulator That Is Closely Related to Plasmid Partition Factors
Authors: Turner Elizebeth C. , Dorman Charles J. 
Published: February 2007

ABSTRACTThe VirB protein ofShigella flexneriis a positive regulator of the major virulence operons of this enteroinvasive intracellular pathogen. VirB resembles no other transcription factor but is strongly homologous to plasmid partition proteins. We found that the binding of the VirB protein to the promoter region of theicsBvirulence gene induced hypersensitivity to cleavage by DNase I over a region to which the H-NS repressor protein binds and completely abolished the protection of this sequence from DNase I by H-NS. In the absence of H-NS, the VirB protein had no additive effect on the ability of theicsBpromoter to form an open transcription complex, indicating that VirB is not involved in the recruitment of RNA polymerase to the promoter or in open complex formation. Similarly, VirB did not stimulate promoter function in an in vitro transcription assay but acted as an antagonist of H-NS-mediated repression. A sequence located upstream of theicsBpromoter and related tocis-acting elements involved in plasmid partitioning was required for promoter derepression by VirB. Alterations to one heptameric motif within this DNA sequence attenuated VirB binding and derepression oficsBtranscription.
Mycoplasma hyopneumoniae
mhp379 Is a Ca
2+
-Dependent, Sugar-Nonspecific Exonuclease Exposed on the Cell Surface
Authors: Schmidt Jonathan A. , Browning Glenn F. , Markham Philip F. 
Published: February 2007

ABSTRACT

Mycoplasma hyopneumoniae
mhp379 is a putative lipoprotein that shares significant amino acid sequence similarity with a family of bacterial thermostable nucleases. To examine the nuclease activity of mhp379, the gene was cloned and expressed in
Escherichia coli
following the deletion of the amino-terminal signal sequence and prokaryotic lipoprotein cleavage site and mutagenesis of the mycoplasma TGA tryptophan codons to TGG. The recombinant fusion protein yielded a 33-kDa thrombin cleavage product, corresponding in size to the mature mhp379 protein. Exonuclease activity was indicated by agarose gel electrophoresis analysis of the reaction products that were released when different nucleic acid substrates were used. Endonuclease activity was also indicated by the digestion of closed circular plasmid DNA. The recombinant mhp379 fusion protein completely digested single-stranded DNA, double-stranded DNA (dsDNA), and RNA. The optimal reaction conditions were determined with a novel nuclease assay based on the enhancement of fluorescence of SYBR green I bound to dsDNA. Optimal activity was observed in the presence of calcium ions at a concentration of 15 mM and a pH of 9.5. No nuclease activity was observed in the absence of calcium ions. Mycoplasmas do not have the ability to synthesize nucleic acid precursors, and thus, nucleases are likely to be important in the acquisition of precursors for the synthesis of nucleic acids. Homologs of an ATP-binding cassette (ABC) transport system were identified immediately downstream of the gene encoding mhp379, and two homologs of
M. pneumoniae
lipoprotein multigene family 2 were also identified immediately upstream. Homologs of mhp379 were identified in the sequenced genomes of a number of mycoplasma species, and in most cases the homologous ABC transport system was identified immediately downstream of the homologous gene; in several cases a homolog of
M. pneumoniae
lipoprotein multigene family 2 was also identified immediately upstream. These observations suggest that mhp379 comprises part of a conserved ABC transport operon in mycoplasmas and that the exonuclease activity of mhp379 may be associated with the conserved function of the ABC transport system in the import of nucleic acid precursors. This is the first study to identify the gene and characterize the activity of a mycoplasma exonuclease.