bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Regulation of
ponA
and
pilMNOPQ
Expression by the MtrR Transcriptional Regulatory Protein in
Neisseria gonorrhoeae
Authors: Folster Jason P. , Dhulipala Vijaya , Nicholas Robert A. , Shafer William M. 
Published: May 2007

ABSTRACT

Neisseria gonorrhoeae
utilizes the
mtrCDE
-encoded efflux pump system to resist not only host-derived, hydrophobic antimicrobials that bathe mucosal surfaces, which likely aids in its ability to colonize and infect numerous sites within the human host, but also antibiotics that have been used clinically to treat infections. Recently, overexpression of the MtrC-MtrD-MtrE efflux pump was shown to be critically involved in the capacity of gonococci to develop chromosomally mediated resistance to penicillin G, which for over 40 years was used to treat gonococcal infections. Mutations in either the promoter or the coding sequence of the
mtrR
gene, which encodes a repressor of the efflux pump operon, decrease gonococcal susceptibility to penicillin. We now describe the capacity of MtrR to directly or indirectly influence the expression of two other loci that are involved in gonococcal susceptibility to penicillin:
ponA
, which encodes penicillin-binding protein 1 (PBP 1), and the
pilMNOPQ
operon, which encodes components of the type IV pilus secretion system, with PilQ acting as a channel for entry for penicillin. We determined that MtrR increases the expression of
ponA
directly or indirectly, resulting in increased levels of PBP 1, while repressing the expression of the divergently transcribed
pilM
gene, the first gene in the
pilMNOPQ
operon. Taken together with other studies, the results presented herein indicate that transcriptional regulation of gonococcal genes by MtrR is centrally involved in determining levels of gonococcal susceptibility to penicillin and provides a framework for understanding how resistance developed over the years.
Differential Expression of the Three Multicopper Oxidases from
Myxococcus xanthus
Authors: Sánchez-Sutil María Celestina , Gómez-Santos Nuria , Moraleda-Muñoz Aurelio , Martins Lígia O. , Pérez Juana , Muñoz-Dorado José 
Published: May 2007

ABSTRACT

Myxococcus xanthus
is a soil bacterium that undergoes a unique life cycle among the prokaryotes upon starvation, which includes the formation of macroscopic structures, the fruiting bodies, and the differentiation of vegetative rods into coccoid myxospores. This peculiarity offers the opportunity to study the copper response in this bacterium in two different stages. In fact,
M. xanthus
vegetative rods exhibit 15-fold-greater resistance against copper than developing cells. However, cells preadapted to this metal reach the same levels of resistance during both stages. Analysis of the
M. xanthus
genome reveals that many of the genes involved in copper resistance are redundant, three of which encode proteins of the multicopper oxidase family (MCO). Each MCO gene exhibits a different expression profile in response to external copper addition. Promoters of
cuoA
and
cuoB
respond to Cu(II) ions during growth and development; however, they show a 10-fold-increased copper sensitivity during development. The promoter of
cuoC
shows copper-independent induction upon starvation, but it is copper up-regulated during growth. Phenotypic analyses of deletion mutants reveal that CuoB is involved in the primary copper-adaptive response; CuoA and CuoC are necessary for the maintenance of copper tolerance; and CuoC is required for normal development. These roles seem to be carried out through cuprous oxidase activity.
Proteomic Identification of a Novel
Anaplasma phagocytophilum
DNA Binding Protein That Regulates a Putative Transcription Factor
Authors: Wang Xueqi , Kikuchi Takane , Rikihisa Yasuko 
Published: May 2007

ABSTRACT

Anaplasma phagocytophilum
, the etiologic agent of human granulocytic anaplasmosis, is an obligatory intracellular bacterium. Little is known about the gene regulatory mechanisms for this bacterium. A gene encoding a putative transcription factor,
tr1
, upstream of three tandem genes encoding outer membrane proteins, including the major outer membrane protein P44, is driven by a strong promoter. In the present study, gel mobility shift assays revealed the presence of
A. phagocytophilum
proteins that interact with the promoter region of
tr1
. These proteins interacting with the
tr1
promoter region were purified by biotin-labeled DNA affinity chromatography from a large amount of host cell-free bacteria. Mass spectrometry identified the major protein as an
A. phagocytophilum
12.5-kDa hypothetical protein, which was named ApxR. In a DNase I protection assay, recombinant ApxR (rApxR) bound cooperatively to four 24- or 25-bp sites within 235 bp upstream of
tr1
: regions III and IV proximal to
tr1
had higher affinity than regions I and II did. Deletion assays showed that regions III and IV were essential for rApxR binding, whereas regions I and II upstream of regions III and IV were not. The primary
cis
-acting region was region IV, since region IV alone was sufficient for rApxR to strongly transactivate the downstream gene in a
lacZ
reporter assay. Addition of regions I, II, and III did not enhance transactivation. These results show that ApxR is a novel transcriptional regulator that directly regulates
tr1
.
Predicted Glycosyl Transferase Genes Located outside the HEP Island Are Required for Formation of Heterocyst Envelope Polysaccharide in
Anabaena
sp. Strain PCC 7120
Authors: Wang Yu , Lechno-Yossef Sigal , Gong Yangmin , Fan Qing , Wolk C. Peter , Xu Xudong 
Published: May 2007

ABSTRACT

During maturation, heterocysts form an envelope layer of polysaccharide, called heterocyst envelope polysaccharide (HEP), whose synthesis depends on a cluster of genes, the HEP island, and on an additional, distant gene,
hepB
, or a gene immediately downstream from
hepB
. We show that HEP formation depends upon the predicted glycosyl transferase genes all4160 at a third locus and alr3699, which is adjacent to
hepB
and is cotranscribed with it. Mutations in the histidine kinase genes
hepN
and
hepK
appear to silence the promoter of
hepB
and incompletely down-regulate all4160.
Global Gene Expression Patterns ofNostoc punctiformein Steady-State Dinitrogen-Grown Heterocyst-Containing Cultures and at Single Time Points during the Differentiation of Akinetes and Hormogonia
Authors: Campbell Elsie L. , Summers Michael L. , Christman Harry , Martin Miriam E. , Meeks John C. 
Published: May 2007

ABSTRACTThe vegetative cells of the filamentous cyanobacteriumNostoc punctiformecan differentiate into three mutually exclusive cell types: nitrogen-fixing heterocysts, spore-like akinetes, and motile hormogomium filaments. A DNA microarray consisting of 6,893N. punctiformegenes was used to identify the global transcription patterns at single time points in the three developmental states, compared to those in ammonium-grown time zero cultures. Analysis of ammonium-grown cultures yielded a transcriptome of 2,935 genes, which is nearly twice the size of a soluble proteome. The NH4+-grown transcriptome was enriched in genes encoding core metabolic functions. A steady-state N2-grown (heterocyst-containing) culture showed differential transcription of 495 genes, 373 of which were up-regulated. The majority of the up-regulated genes were predicted from studies of heterocyst differentiation and N2fixation; other genes are candidates for more detailed genetic analysis. Three days into the developmental process, akinetes showed a similar number of differentially expressed genes (497 genes), which were equally up- and down-regulated. The down-regulated genes were enriched in core metabolic functions, consistent with entry into a nongrowth state. There were relatively few adaptive genes up-regulated in 3-day akinetes, and there was little overlap with putative heterocyst developmental genes. There were 1,827 differentially transcribed genes in 24-h hormogonia, which was nearly fivefold greater than the number in akinete-forming or N2-fixing cultures. The majority of the up-regulated adaptive genes were genes encoding proteins for signal transduction and transcriptional regulation, which is characteristic of a motile filament that is poised to sense and respond to the environment. The greatest fraction of the 883 down-regulated genes was involved in core metabolism, also consistent with entry into a nongrowth state. The differentiation of heterocysts (steady state, N2grown), akinetes, and hormogonia appears to involve the up-regulation of genes distinct for each state.
The Copper-Inducible
cin
Operon Encodes an Unusual Methionine-Rich Azurin-Like Protein and a Pre-Q
0
Reductase in
Pseudomonas putida
KT2440
Authors: Quaranta Davide , McCarty Reid , Bandarian Vahe , Rensing Christopher 
Published: May 2007

ABSTRACT

The genome sequences of several pseudomonads have revealed a gene cluster containing genes for a two-component heavy metal histidine sensor kinase and response regulator upstream of
cinA
and
cinQ
, which we show herein to encode a copper-containing azurin-like protein and a pre-Q
0
reductase, respectively. In the presence of copper,
Pseudomonas putida
KT2440 produces the CinA and CinQ proteins from a bicistronic mRNA. UV-visible spectra of CinA show features at 439, 581, and 719 nm, which is typical of the plastocyanin family of proteins. The redox potential of the protein was shown to be 456 ± 4 mV by voltametric titrations. Surprisingly, CinQ is a pyridine nucleotide-dependent nitrile oxidoreductase that catalyzes the conversion of pre-Q
0
to pre-Q
1
in the nucleoside queuosine biosynthetic pathway. Gene disruptions of
cinA
and
cinQ
did not lead to a significant increase in the copper sensitivity of
P. putida
KT2440 under the conditions tested. Possible roles of CinA and CinQ to help pseudomonads adapt and survive under prolonged copper stress are discussed.
The Extracytoplasmic Function-Type Sigma Factor SigM of
Corynebacterium glutamicum
ATCC 13032 Is Involved in Transcription of Disulfide Stress-Related Genes
Authors: Nakunst Diana , Larisch Christof , Hüser Andrea T. , Tauch Andreas , Pühler Alfred , Kalinowski Jörn 
Published: May 2007

ABSTRACT

The gene for the extracytoplasmic function (ECF) sigma factor SigM was deleted from the chromosome of the gram-positive soil bacterium
Corynebacterium glutamicum
to elucidate the role of the SigM protein in the regulation of gene expression. Comparative DNA microarray hybridizations of the
C. glutamicum
wild type and
sigM
-deficient mutant
C. glutamicum
DN1 revealed 23 genes with enhanced expression in the
sigM
-proficient strain, encoding functions in the assembly of iron-sulfur clusters (
suf
operon), thioredoxin reductase (
trxB
), thioredoxins (
trxC
,
trxB1
), chaperones (
groES
,
groEL
,
clpB
), and proteins involved in the heat shock response (
hspR
,
dnaJ
,
grpE
). Deletion of the
sigM
gene rendered the
C. glutamicum
cells more sensitive to heat, cold, and the presence of the thiol oxidant diamide. Transcription of the
sigM
gene increased under different stress conditions, including heat shock, cold shock, and disulfide stress caused by diamide treatment, suggesting a regulatory role for SigM under thiol-oxidative stress conditions. Stress-responsive promoters were determined upstream of the
suf
operon and of the
trxB
,
trxC
, and
trxB1
genes. The deduced SigM consensus promoter is characterized by the −35 hexamer gGGAAT and the −10 hexamer YGTTGR. Transcription of the
sigM
gene is apparently controlled by the ECF sigma factor SigH, since a
sigH
mutant was unable to enhance the expression of
sigM
and the SigM regulon under thiol-oxidative stress conditions. A typical SigH-responsive promoter was mapped upstream of the
sigM
gene. The ECF sigma factor SigM is apparently part of a regulatory cascade, and its transcription is controlled by SigH under conditions of thiol-oxidative stress.
Mutational Analysis of theompAPromoter fromFlavobacterium johnsoniae
Authors: Chen Shicheng , Bagdasarian Michael , Kaufman Michael G. , Bates Adam K. , Walker Edward D. 
Published: May 2007

ABSTRACTSequences that mediate the initiation of transcription inFlavobacteriumspecies are not well known. The majority of identifiedFlavobacteriumpromoter elements show homology to those of other members of the phylumBacteroidetes, but not of proteobacteria, and they function poorly inEscherichia coli. In order to analyze theFlavobacteriumpromoter structure systematically, we investigated the −33 consensus element, −7 consensus element, and spacer length of theFlavobacterium ompApromoter by measuring the effects of site-directed mutations on promoter activity. The nonconserved sequences in the spacer region and in regions close to the consensus motifs were randomized in order to determine their importance for promoter activity. Most of the base substitutions in these regions caused large decreases in promoter activity. The optimal −33/−7 motifs (TTTG/TANNTTTG) were identical toBacteroides fragilisσABfrconsensus −33/−7 promoter elements but lacked similarity to theE. coliσ70promoter elements. The length of the spacer separating the −33 and −7 motifs of theompApromoter also had a pronounced effect on promoter activity, with 19 bp being optimal. In addition to the consensus promoter elements and spacer length, the GC content of the core promoter sequences had a pronounced effect onFlavobacteriumpromoter activity. This information was used to conduct a scan of theFlavobacterium johnsoniaeandB. fragilisgenomes for putative promoters, resulting in 188 hits inB. fragilisand 109 hits inF. johnsoniae.
An Antibiotic-Inducible Cell Wall-Associated Protein That Protects
Bacillus subtilis
from Autolysis
Authors: Salzberg Letal I. , Helmann John D. 
Published: May 2007

ABSTRACT

In
Bacillus subtilis
, antibiotics that impair cell wall synthesis induce a characteristic stress response including the σ
W
and σ
M
regulons and the previously uncharacterized
yoeB
gene. Here we demonstrate that YoeB is a cell wall-associated protein with weak sequence similarity to a noncatalytic domain of class B penicillin-binding proteins. A
yoeB
-null mutant exhibits an increased rate of autolysis in response to cell wall-targeting antibiotics or nutrient depletion. This phenotype does not appear to be correlated with gross alterations in peptidoglycan structure or levels of autolysins. Promoter dissection experiments define a minimal region necessary for antibiotic-mediated induction of
yoeB
, and this region is highly conserved preceding
yoeB
homologs in close relatives of
B. subtilis
. These results support a model in which induction of YoeB in response to cell envelope stress decreases the activity of autolysins and thereby reduces the rate of antibiotic-dependent cell death.
Contribution of the Mannan Backbone of Cryptococcal Glucuronoxylomannan and a Glycolytic Enzyme ofStaphylococcus aureusto Contact-Mediated Killing ofCryptococcus neoformans
Authors: Ikeda Reiko , Saito Fumito , Matsuo Miki , Kurokawa Kenji , Sekimizu Kazuhisa , Yamaguchi Masashi , Kawamoto Susumu 
Published: May 2007

ABSTRACTThe fungal pathogenCryptococcus neoformansis killed by the bacteriumStaphylococcus aureus, and the killing is inhibited by soluble capsular polysaccharides. To investigate the mechanism of killing, cells in coculture were examined by scanning and transmission electron microscopy.S. aureusattached to the capsule ofC. neoformans, and the ultrastructure of the attachedC. neoformanscells was characteristic of dead cells. To identify the molecules that contributed to the fungal-bacterial interaction, we treated each with NaIO4or protease. Treatment ofC. neoformanswith NaIO4promoted adherence. It was inferred that cleavage of xylose and glucuronic acid side chains of glucuronoxylomannan (GXM) allowedS. aureusto recognize mannose residues in the backbone, which resisted periodate oxidation. On the other hand, treatment ofS. aureuswith protease decreased adherence, suggesting that protein contributed to attachment inS. aureus. In confirmation, side chain-cleaved polysaccharide or defined α-(1→3)-mannan inhibited the killing at lower concentrations than native GXM did. Also, these polysaccharides reduced the adherence of the two species and induced clumping of pureS. aureuscells. α-(1→3)-Mannooligosaccharides with a degree of polymerization (DP) of ≥3 induced cluster formation ofS. aureusin a dose-dependent manner. Surface plasmon resonance analyses showed interaction of GXM and surface protein fromS. aureus; the interaction was inhibited by oligosaccharides with a DP of ≥3. Conformations of α-(1→3) oligosaccharides were predicted. The three-dimensional structures of mannooligosaccharides larger than triose appeared curved and could be imagined to be recognized by a hypothetical staphylococcal lectin. Native polyacrylamide gel electrophoresis of staphylococcal protein followed by electroblotting, enzyme-linked immunolectin assay, protein staining, and N-terminal amino acid sequencing suggested that the candidate protein was triosephosphate isomerase (TPI). The enzymatic activities were confirmed by using whole cells ofS. aureus. TPI point mutants ofS. aureusdecreased the ability to interact withC. neoformans. Thus, TPI onS. aureusadheres to the capsule ofC. neoformansby recognizing the structure of mannotriose units in the backbone of GXM; we suggest that this contact is required for killing ofC. neoformans.
Role of Peptidoglycan Amidases in the Development and Morphology of the Division Septum in
Escherichia coli
Authors: Priyadarshini Richa , de Pedro Miguel A. , Young Kevin D. 
Published: May 2007

ABSTRACT

Escherichia coli
contains multiple peptidoglycan-specific hydrolases, but their physiological purposes are poorly understood. Several mutants lacking combinations of hydrolases grow as chains of unseparated cells, indicating that these enzymes help cleave the septum to separate daughter cells after cell division. Here, we confirm previous observations that in the absence of two or more amidases, thickened and dark bands, which we term septal peptidoglycan (SP) rings, appear at division sites in isolated sacculi. The formation of SP rings depends on active cell division, and they apparently represent a cell division structure that accumulates because septal synthesis and hydrolysis are uncoupled. Even though septal constriction was incomplete, SP rings exhibited two properties of mature cell poles: they behaved as though composed of inert peptidoglycan, and they attracted the IcsA protein. Despite not being separated by a completed peptidoglycan wall, adjacent cells in these chains were often compartmentalized by the inner membrane, indicating that cytokinesis could occur in the absence of invagination of the entire cell envelope. Finally, deletion of penicillin-binding protein 5 from amidase mutants exacerbated the formation of twisted chains, producing numerous cells having septa with abnormal placements and geometries. The results suggest that the amidases are necessary for continued peptidoglycan synthesis during cell division, that their activities help create a septum having the appropriate geometry, and that they may contribute to the development of inert peptidoglycan.
Release of the Lipopolysaccharide Deacylase PagL from Latency Compensates for a Lack of Lipopolysaccharide Aminoarabinose Modification-Dependent Resistance to the Antimicrobial Peptide Polymyxin B inSalmonella enterica
Authors: Kawasaki Kiyoshi , China Kotaro , Nishijima Masahiro 
Published: May 2007

ABSTRACTSalmonella entericamodifies its lipopolysaccharide (LPS), including the lipid A portion, to adapt to its environments. The lipid A 3-O-deacylase PagL exhibits latency; deacylation of lipid A is not usually observed in vivo despite the expression of PagL, which is under the control of a two-component regulatory system, PhoP-PhoQ. In contrast, PagL is released from latency inpmrAandpmrEmutants, both of which are deficient in aminoarabinose-modified lipid A, although the biological significance of this is not clear. The attachment of aminoarabinose to lipid A decreases the net anionic charge at the membrane's surface and reduces electrostatic repulsion between neighboring LPS molecules, leading to increases in bacterial resistance to cationic antimicrobial peptides, including polymyxin B. Here we examined the effects of the release of PagL from latency on resistance to polymyxin B. ThepmrA pagLandpmrE pagLdouble mutants were more susceptible to polymyxin B than were the parentalpmrAandpmrEmutants, respectively. Furthermore, introduction of the PagL expression plasmid into thepmrA pagLdouble mutant increased the resistance to polymyxin B. In addition, PagL-dependent deacylation of lipid A was observed in a mutant in which lipid A could not be modified with phosphoethanolamine, which partly contributes to the PmrA-dependent resistance to polymyxin B. These results, taken together, suggest that the release of PagL from latency compensates for the loss of resistance to polymyxin B that is due to a lack of other modifications to LPS.
Additive Effects of SbcCD and PolX Deficiencies in the In Vivo Repair of DNA Double-Strand Breaks inDeinococcus radiodurans
Authors: Bentchikou Esma , Servant Pascale , Coste Geneviève , Sommer Suzanne 
Published: May 2007

ABSTRACTOrthologs of proteins SbcD (Mre11) and SbcC (Rad50) exist in all kingdoms of life and are involved in a wide variety of DNA repair and maintenance functions, including homologous recombination and nonhomologous end joining. Here, we have inactivated thesbcCand/orsbcDgenes ofDeinococcus radiodurans, a highly radioresistant bacterium able to mend hundreds of radiation-induced DNA double-strand breaks (DSB). Mutants devoid of the SbcC and/or SbcD proteins displayed reduced survival and presented a delay in kinetics of DSB repair and cell division following γ-irradiation. It has been recently reported thatD. radioduransDNA polymerase X (PolX) possesses a structure-modulated 3′-to-5′ exonuclease activity reminiscent of specific nuclease activities displayed by the SbcCD complex fromEscherichia coli. We constructed a double mutant devoid of SbcCD and PolX proteins. The double-mutant ΔsbcCDΔpolXDr(whereDrindicatesD. radiodurans) bacteria are much more sensitive to γ-irradiation than the single mutants, suggesting that the deinococcal SbcCD and PolX proteins may play important complementary roles in processing damaged DNA ends. We propose that they are part of a backup repair system acting to rescue cells containing DNA lesions that are excessively numerous or difficult to repair.