bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning and Characterization of the DNA Region Responsible for Megacin A-216 Production in
Bacillus megaterium
216
Authors: Kiss Antal , Balikó Gabriella , Csorba Attila , Chuluunbaatar Tungalag , Medzihradszky Katalin F. , Alföldi Lajos 
Published: August 2008

ABSTRACT

Upon induction,
Bacillus megaterium
216 produces the bacteriocin megacin A-216, which leads to lysis of the producer cell and kills
B. megaterium
and a few other bacterial species. The DNA region responsible for megacinogeny was cloned in
B. megaterium
. The nucleotide sequence of a 5,494-bp-long subfragment was determined, and the function of the genes on this fragment was studied by generating deletions and analyzing their effects on MegA phenotypes. An open reading frame (ORF) encoding a 293-amino-acid protein was identified as the gene (
megA
) coding for megacin A-216. BLAST searches detected sequence similarity between megacin A-216 and proteins with phospholipase A2 activity. Purified biologically active megacin A-216 preparations contained three proteins. Mass spectrometry analysis showed that the largest protein is the full-length translation product of the
megA
gene, whereas the two shorter proteins are fragments of the long protein created by cleavage between Gln-185 and Val-186. The molecular masses of the three polypeptides are 32,855, 21,018, and 11,855 Da, respectively. Comparison of different megacin preparations suggests that the intact chain as well as the two combined fragments can form biologically active megacin. An ORF located next to the
megA
gene and encoding a 91-amino-acid protein was shown to be responsible for the relative immunity displayed by the producer strain against megacin A-216. Besides the
megA
gene, at least two other genes, including a gene encoding a 188-amino-acid protein sharing high sequence similarity with RNA polymerase sigma factors, were shown to be required for induction of megacin A-216 expression.
Surface Spreading Motility Shown by a Group of Phylogenetically Related, Rapidly Growing Pigmented Mycobacteria Suggests that Motility Is a Common Property of Mycobacterial Species but Is Restricted to Smooth Colonies
Authors: Agustí Gemma , Astola Oihane , Rodríguez-Güell Elisabeth , Julián Esther , Luquin Marina 
Published: August 2008

ABSTRACT

Motility in mycobacteria was described for the first time in 1999. It was reported that
Mycobacterium smegmatis
and
Mycobacterium avium
could spread on the surface of solid growth medium by a sliding mechanism and that the presence of cell wall glycopeptidolipids was essential for motility. We recently reported that
Mycobacterium vaccae
can also spread on growth medium surfaces; however, only smooth colonies presented this property. Smooth colonies of
M. vaccae
do not produce glycopeptidolipids but contain a saturated polyester that is absent in rough colonies. Here, we demonstrate that
Mycobacterium chubuense
,
Mycobacterium gilvum
,
Mycobacterium obuense
, and
Mycobacterium parafortuitum
, which are phylogenetically related to
M. vaccae
, are also motile. Such motility is restricted to smooth colonies, since natural rough mutants are nonmotile. Thin-layer chromatography analysis of the content of cell wall lipids confirmed the absence of glycopeptidolipids. However, compounds like the above-mentioned
M. vaccae
polyester were detected in all the strains but only in smooth colonies. Scanning electron microscopy showed great differences in the arrangement of the cells between smooth and rough colonies. The data obtained suggest that motility is a common property of environmental mycobacteria, and this capacity correlates with the smooth colonial morphotype. The species studied in this work do not contain glycopeptidolipids, so cell wall compounds or extracellular materials other than glycopeptidolipids are implicated in mycobacterial motility. Furthermore, both smooth motile and rough nonmotile variants formed biofilms on glass and polystyrene surfaces.
The Two-Component System PhoPR of
Clostridium acetobutylicum
Is Involved in Phosphate-Dependent Gene Regulation
Authors: Fiedler Tomas , Mix Maren , Meyer Uta , Mikkat Stefan , Glocker Michael O. , Bahl Hubert , Fischer Ralf-Jörg 
Published: August 2008

ABSTRACT

The
phoPR
gene locus of
Clostridium acetobutylicum
ATCC 824 comprises two genes,
phoP
and
phoR
. Deduced proteins are predicted to represent a response regulator and sensor kinase of a phosphate-dependent two-component regulatory system. We analyzed the expression patterns of
phoPR
in P
i
-limited chemostat cultures and in response to P
i
pulses. A basic transcription level under high-phosphate conditions was shown, and a significant increase in mRNA transcript levels was found when external P
i
concentrations dropped below 0.3 mM. In two-dimensional gel electrophoresis experiments, a 2.5-fold increase in PhoP was observed under P
i
-limiting growth conditions compared to growth with an excess of P
i
. At least three different transcription start points for
phoP
were determined by primer extension analyses. Proteins PhoP and an N-terminally truncated *PhoR were individually expressed heterologously in
Escherichia coli
and purified. Autophosphorylation of *PhoR and phosphorylation of PhoP were shown in vitro. Electromobility shift assays proved that there was a specific binding of PhoP to the promoter region of the phosphate-regulated
pst
operon of
C. acetobutylicum
.
Carbonylated Proteins Are Detectable Only in a Degradation-Resistant Aggregate State in
Escherichia coli
Authors: Maisonneuve Etienne , Fraysse Laetitia , Lignon Sabrina , Capron Laure , Dukan Sam 
Published: August 2008

ABSTRACT

Carbonylation is currently used as a marker for irreversible protein oxidative damage. Several studies indicate that carbonylated proteins are more prone to degradation than their nonoxidized counterparts. In this study, we observed that in
Escherichia coli
, more than 95% of the total carbonyl content consisted of insoluble protein and most were cytosolic proteins. We thereby demonstrate that, in vivo, carbonylated proteins are detectable mainly in an aggregate state. Finally, we show that detectable carbonylated proteins are not degraded in vivo. Here we propose that some carbonylated proteins escape degradation in vivo by forming carbonylated protein aggregates and thus becoming nondegradable. In light of these findings, we provide evidence that the accumulation of nondegradable carbonylated protein presented in an aggregate state contributes to the increases in carbonyl content observed during senescence.
Clp and Lon Proteases Occupy Distinct Subcellular Positions inBacillus subtilis
Authors: Simmons Lyle A. , Grossman Alan D. , Walker Graham C. 
Published: August 2008

ABSTRACTAmong other functions, ATP-dependent proteases degrade misfolded proteins and remove several key regulatory proteins necessary to activate stress responses. InBacillus subtilis, ClpX, ClpE, and ClpC form homohexameric ATPases that couple to the ClpP peptidase. To understand where these peptidases and ATPases localize in living cells, each protein was fused to a fluorescent moiety. We found that ClpX-GFP (green fluorescent protein) and ClpP-GFP localized as focal assemblies in areas that were not occupied by the nucleoid. We found that the percentage of cells with ClpP-GFP foci increased following heat shock independently of protein synthesis. We determined that ClpE-YFP (yellow fluorescent protein) and ClpC-YFP formed foci coincident with nucleoid edges, usually near cell poles. Furthermore, we found that ClpQ-YFP (HslV) localized as small foci, usually positioned near the cell membrane. We found that ClpQ-YFP foci were dependent on the presence of the cognate hexameric ATPase ClpY (HslU). Moreover, we found that LonA-GFP is coincident with the nucleoid during normal growth and that LonA-GFP also localized to the forespore during development. We also investigated LonB-GFP and found that this protein localized to the forespore membrane early in development, followed by localization throughout the forespore later in development. Our comprehensive study has shown that inB. subtilisseveral ATP-fueled proteases occupy distinct subcellular locations. With these data, we suggest that substrate specificity could be determined, in part, by the spatial and temporal organization of proteases in vivo.
Role of the N-Terminal Domain of φC31 Integrase in
attB-attP
Synapsis
Authors: Rowley Paul A. , Smith Margaret C. M. 
Published: August 2008

ABSTRACT
φC31 integrase is a serine recombinase containing an N-terminal domain (NTD) that provides catalytic activity and a large C-terminal domain that controls which pair of DNA substrates is able to synapse. We show here that substitutions in amino acid V129 in the NTD can lead to defects in synapsis and DNA cleavage, indicating that the NTD also has an important role in synapsis.
Role of the
Helicobacter hepaticus
Flagellar Sigma Factor FliA in Gene Regulation and Murine Colonization
Authors: Sterzenbach Torsten , Bartonickova Lucie , Behrens Wiebke , Brenneke Birgit , Schulze Jessika , Kops Friederike , Chin Elaine Y. , Katzowitsch Elena , Schauer David B. , Fox James G. , Suerbaum Sebastian , Josenhans Christine 
Published: August 2008

ABSTRACT

The enterohepatic
Helicobacter
species
Helicobacter hepaticus
colonizes the murine intestinal and hepatobiliary tract and is associated with chronic intestinal inflammation, gall stone formation, hepatitis, and hepatocellular carcinoma. Thus far, the role of
H. hepaticus
motility and flagella in intestinal colonization is unknown. In other, closely related bacteria, late flagellar genes are mainly regulated by the sigma factor FliA (σ
28
). We investigated the function of the
H. hepaticus
FliA in gene regulation, flagellar biosynthesis, motility, and murine colonization. Competitive microarray analysis of the wild type versus an isogenic
fliA
mutant revealed that 11 genes were significantly more highly expressed in wild-type bacteria and 2 genes were significantly more highly expressed in the
fliA
mutant. Most of these were flagellar genes, but four novel FliA-regulated genes of unknown function were identified.
H. hepaticus
possesses two identical copies of the gene encoding the FliA-dependent major flagellin subunit FlaA (open reading frames HH1364 and HH1653). We characterized the phenotypes of mutants in which
fliA
or one or both copies of the
flaA
gene were knocked out.
flaA
_
1 flaA
_
2
double mutants and
fliA
mutants did not synthesize detectable amounts of FlaA and possessed severely truncated flagella. Also, both mutants were nonmotile and unable to colonize mice. Mutants with either
flaA
gene knocked out produced flagella morphologically similar to those of wild-type bacteria and expressed FlaA and FlaB.
flaA
_
1
mutants which had flagella but displayed reduced motility did not colonize mice, indicating that motility is required for intestinal colonization by
H. hepaticus
and that the presence of flagella alone is not sufficient.
Chemoreceptors in
Caulobacter crescentus
: Trimers of Receptor Dimers in a Partially Ordered Hexagonally Packed Array
Authors: Khursigara Cezar M. , Wu Xiongwu , Subramaniam Sriram 
Published: August 2008

ABSTRACT

Chemoreceptor arrays are macromolecular complexes that form extended assemblies primarily at the poles of bacterial cells and mediate chemotaxis signal transduction, ultimately controlling cellular motility. We have used cryo-electron tomography to determine the spatial distribution and molecular architecture of signaling molecules that comprise chemoreceptor arrays in wild-type
Caulobacter crescentus
cells. We demonstrate that chemoreceptors are organized as trimers of receptor dimers, forming partially ordered hexagonally packed arrays of signaling complexes in the cytoplasmic membrane. This novel organization at the threshold between order and disorder suggests how chemoreceptors and associated molecules are arranged in signaling assemblies to respond dynamically in the activation and adaptation steps of bacterial chemotaxis.
The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in
Rhodobacter sphaeroides
2.4.1
Authors: Bruscella Patrice , Eraso Jesus M. , Roh Jung Hyeob , Kaplan Samuel 
Published: August 2008

ABSTRACT

The expression of genes involved in photosystem development in
Rhodobacter sphaeroides
is dependent upon three major regulatory networks: FnrL, the PrrBA (RegBA) two-component system, and the transcriptional repressor/antirepressor PpsR/AppA. Of the three regulators, PpsR appears to have the narrowest range of physiological effects, which are limited to effects on the structural and pigment biosynthetic activities involved in photosynthetic membrane function. Although a PrrA
−
mutant is unable to grow under photosynthetic conditions, when a
ppsR
mutation was present, photosynthetic growth occurred. An examination of the double mutant under anaerobic-dark-dimethyl sulfoxide conditions using microarray analysis revealed the existence of an “extended” PpsR regulon and new physiological roles. To characterize the PpsR regulon and to better ascertain the significance of degeneracy within the PpsR binding sequence in vivo, we adapted the chromatin immunoprecipitation technique to
R. sphaeroides
. We demonstrated that in vivo there was direct and significant binding by PpsR to newly identified genes involved in microaerobic respiration and periplasmic stress resistance, as well as to photosynthesis genes. The new members of the PpsR regulon are located outside the photosynthesis gene cluster and have degenerate PpsR binding sequences. The possible interaction under physiologic conditions with degenerate binding sequences in the presence of other biologically relevant molecules is discussed with respect to its importance in physiological processes and to the existence of complex phenotypes associated with regulatory mutants. This study further defines the DNA structure necessary for PpsR binding in situ.
Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK2-FixK1Cascade inBradyrhizobium japonicum
Authors: Mesa Socorro , Hauser Felix , Friberg Markus , Malaguti Emmanuelle , Fischer Hans-Martin , Hennecke Hauke 
Published: August 2008

ABSTRACTSymbiotic N2fixation inBradyrhizobium japonicumis controlled by a complex transcription factor network. Part of it is a hierarchically arranged cascade in which the two-component regulatory system FixLJ, in response to a moderate decrease in oxygen concentration, activates thefixK2gene. The FixK2protein then activates not only a number of genes essential for microoxic respiration in symbiosis (fixNOQPandfixGHIS) but also further regulatory genes (rpoN1,nnrR, andfixK1). The results of transcriptome analyses described here have led to a comprehensive and expanded definition of the FixJ, FixK2, and FixK1regulons, which, respectively, consist of 26, 204, and 29 genes specifically regulated in microoxically grown cells. Most of these genes are subject to positive control. Particular attention was addressed to the FixK2-dependent genes, which included a bioinformatics search for putative FixK2binding sites on DNA (FixK2boxes). Using an in vitro transcription assay with RNA polymerase holoenzyme and purified FixK2as the activator, we validated as direct targets eight new genes. Interestingly, the adjacent but divergently orientedfixK1andcycSgenes shared the same FixK2box for the activation of transcription in both directions. This recognition site may also be a direct target for the FixK1protein, because activation of thecycSpromoter required an intactfixK1gene and either microoxic or anoxic, denitrifying conditions. We present evidence thatcycScodes for ac-type cytochrome which is important, but not essential, for nitrate respiration. Two other, unexpected results emerged from this study: (i) specifically FixK1seemed to exert a negative control on genes that are normally activated by the N2fixation-specific transcription factor NifA, and (ii) a larger number of genes are expressed in a FixK2-dependent manner in endosymbiotic bacteroids than in culture-grown cells, pointing to a possible symbiosis-specific control.
Role of the
Campylobacter jejuni
Cj1461 DNA Methyltransferase in Regulating Virulence Characteristics
Authors: Kim Joo-Sung , Li Jiaqi , Barnes If H. A. , Baltzegar David A. , Pajaniappan Mohanasundari , Cullen Thomas W. , Trent M. Stephen , Burns Christopher M. , Thompson Stuart A. 
Published: August 2008

ABSTRACT

Mutation of the cj1461 predicted methyltransferase gene reduced the motility of
Campylobacter jejuni
81-176. Electron microscopy revealed that the mutant strain had flagella but with aberrant structure. The Δcj1461 mutant was sevenfold more adherent to but 50-fold less invasive of INT-407 human epithelial cells than the wild type.
A Singular Case of Prophage Complementation in Mutational Activation of
recET
Orthologs in
Salmonella enterica
Serovar Typhimurium
Authors: Lemire Sebastien , Figueroa-Bossi Nara , Bossi Lionello 
Published: August 2008

ABSTRACT

A class of mutations that suppress the recombination defects of
recB
mutants in
Salmonella enterica
serovar Typhimurium strain LT2 activates the normally silent
recET
module of the Gifsy-1 prophage. Allele
sbcE21
is a 794-bp deletion within the immunity region of the prophage. Concomitant with activating
recET
,
sbcE21
stimulates Gifsy-1 excision, resulting in unstable suppression. Early studies found both
recB
suppression and its instability to depend on the presence of the related Gifsy-2 prophage elsewhere in the chromosome. In cells lacking Gifsy-2, the
sbcE21
allele became stable but no longer corrected
recB
defects. Here, we show that a single Gifsy-2 gene is required for Gifsy-1
recET
activation in the
sbcE21
background. This gene encodes GtgR, the Gifsy-2 repressor. Significantly, the
sbcE21
deletion has one end point within the corresponding gene in the Gifsy-1 genome,
gogR
, which in strain LT2 is a perfect duplicate of
gtgR
. The deletion truncates
gogR
and places the Gifsy-1 left operon, including the
recET
and
xis
genes, under the control of the
gogR
promoter. The ability of GtgR to
trans
-activate this promoter therefore implies that GtgR and GogR normally activate the transcription of their own genes. Consistent with the symmetry of the system, a similar deletion in Gifsy-2 results in a Gifsy-1-dependent
sbc
phenotype (
sbcF24
). Two additional Gifsy-1 deletions (
sbcE23
and
sbcE25
) were characterized, as well. The latter causes all but the last codon of the
gogR
gene to fuse, in frame, to the second half of
recE
. The resulting hybrid protein appears to function as both a transcriptional regulator and a recombination enzyme.
Paerucumarin, a New Metabolite Produced by the
pvc
Gene Cluster from
Pseudomonas aeruginosa
Authors: Clarke-Pearson Michael F. , Brady Sean F. 
Published: August 2008

ABSTRACT

The
pvc
gene cluster from
Pseudomonas aeruginosa
has been linked to the biosynthesis of both the pyoverdine chromophore and pseudoverdine. Our reinvestigation of the role this gene cluster plays in
P. aeruginosa
secondary metabolite biosynthesis shows that its major product is actually paerucumarin, a novel isonitrile functionalized cumarin.
Regulation of the
Rhodobacter sphaeroides
2.4.1
hemA
Gene by PrrA and FnrL
Authors: Ranson-Olson Britton , Zeilstra-Ryalls Jill H. 
Published: August 2008

ABSTRACT

Part of the oxygen responsiveness of
Rhodobacter sphaeroides
2.4.1 tetrapyrrole production involves changes in transcription of the
hemA
gene, which codes for one of two isoenzymes catalyzing 5-aminolevulinic acid synthesis. Regulation of
hemA
transcription from its two promoters is mediated by the DNA binding proteins FnrL and PrrA. The two PrrA binding sites, binding sites I and II, which are located upstream of the more-5′
hemA
promoter (P1), are equally important to transcription under aerobic conditions, while binding site II is more important under anaerobic conditions. By using phosphoprotein affinity chromatography and immunoblot analyses, we showed that the phosphorylated PrrA levels in the cell increase with decreasing oxygen tensions. Then, using both in vivo and in vitro methods, we demonstrated that the relative affinities of phosphorylated and unphosphorylated PrrA for the two binding sites differ and that phosphorylated PrrA has greater affinity for site II. We also showed that PrrA regulation is directed toward the P1 promoter. We propose that the PrrA component of anaerobic induction of P1 transcription is attributable to higher affinity of phosphorylated PrrA than of unphosphorylated PrrA for binding site II. Anaerobic activation of the more-3′
hemA
promoter (P2) is thought to involve FnrL binding to an FNR consensuslike sequence located upstream of the P2 promoter, but the contribution of FnrL to P1 induction may be indirect since the P1 transcription start is within the putative FnrL binding site. We present evidence suggesting that the indirect action of FnrL works through PrrA and discuss possible mechanisms.
Nitrogen Control in
Mycobacterium smegmatis
: Nitrogen-Dependent Expression of Ammonium Transport and Assimilation Proteins Depends on the OmpR-Type Regulator GlnR
Authors: Amon Johannes , Bräu Tanja , Grimrath Aletta , Hänβler Eva , Hasselt Kristin , Höller Martina , Jeβberger Nadja , Ott Lisa , Szököl Juraj , Titgemeyer Fritz , Burkovski Andreas 
Published: August 2008

ABSTRACT

The effect of nitrogen regulation on the level of transcriptional control has been investigated in a variety of bacteria, such as
Bacillus subtilis, Corynebacterium glutamicum, Escherichia coli
, and
Streptomyces coelicolor
; however, until now there have been no data for mycobacteria. In this study, we found that the OmpR-type regulator protein GlnR controls nitrogen-dependent transcription regulation in
Mycobacterium smegmatis
. Based on RNA hybridization experiments with a wild-type strain and a corresponding mutant strain, real-time reverse transcription-PCR analyses, and DNA binding studies using cell extract and purified protein, the
glnA
(msmeg_4290) gene, which codes for glutamine synthetase, and the
amtB
(msmeg_2425) and
amt1
(msmeg_6259) genes, which encode ammonium permeases, are controlled by GlnR. Furthermore, since
glnK
(msmeg_2426), encoding a PII-type signal transduction protein, and
glnD
(msmeg_2427), coding for a putative uridylyltransferase, are in an operon together with
amtB
, these genes are part of the GlnR regulon as well. The GlnR protein binds specifically to the corresponding promoter sequences and functions as an activator of transcription when cells are subjected to nitrogen starvation.
Role of Phosphopantetheinyl Transferase Genes in Antibiotic Production by
Streptomyces coelicolor
Authors: Lu Ya-Wen , San Roman Adrianna K. , Gehring Amy M. 
Published: August 2008

ABSTRACT

The phosphopantetheinyl transferase genes SCO5883 (
redU
) and SCO6673 were disrupted in
Streptomyces coelicolor
. The
redU
mutants did not synthesize undecylprodigiosin, while SCO6673 mutants failed to produce calcium-dependent antibiotic. Neither gene was essential for actinorhodin production or morphological development in
S. coelicolor
, although their mutation could influence these processes.