bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Caffeate Respiration in the Acetogenic Bacterium
Acetobacterium woodii
Authors: Dilling Sabrina , Imkamp Frank , Schmidt Silke , Müller Volker 
Published: April 2007

ABSTRACT

The anaerobic acetogenic bacterium
Acetobacterium woodii
can conserve energy by oxidation of various substrates coupled to either carbonate or caffeate respiration. We used a cell suspension system to study the regulation and kinetics of induction of caffeate respiration. After addition of caffeate to suspensions of fructose-grown cells, there was a lag phase of about 90 min before caffeate reduction commenced. However, in the presence of tetracycline caffeate was not reduced, indicating that de novo protein synthesis is required for the ability to respire caffeate. Induction also took place in the presence of CO
2
, and once a culture was induced, caffeate and CO
2
were used simultaneously as electron acceptors. Induction of caffeate reduction was also observed with H
2
plus CO
2
as the substrate, but the lag phase was much longer. Again, caffeate and CO
2
were used simultaneously as electron acceptors. In contrast, during oxidation of methyl groups derived from methanol or betaine, acetogenesis was the preferred energy-conserving pathway, and caffeate reduction started only after acetogenesis was completed. The differential flow of reductants was also observed with suspensions of resting cells in which caffeate reduction was induced prior to harvest of the cells. These cell suspensions utilized caffeate and CO
2
simultaneously with fructose or hydrogen as electron donors, but CO
2
was preferred over caffeate during methyl group oxidation. Caffeate-induced resting cells could reduce caffeate and also
p
-coumarate or ferulate with hydrogen as the electron donor.
p
-Coumarate or ferulate also served as an inducer for caffeate reduction. Interestingly, caffeate-induced cells reduced ferulate in the absence of an external reductant, indicating that caffeate also induces the enzymes required for oxidation of the methyl group of ferulate.
Clonothrix fuscaRoze 1896, a Filamentous, Sheathed, Methanotrophic γ-Proteobacterium
Authors: Vigliotta Giovanni , Nutricati Eliana , Carata Elisabetta , Tredici Salvatore M. , De Stefano Mario , Pontieri Paola , Massardo Domenica Rita , Prati Maria Vittoria , De Bellis Luigi , Alifano Pietro 
Published: April 2007

ABSTRACTCrenothrix polysporaCohn 1870 andClonothrix fuscaRoze 1896 are two filamentous, sheathed microorganisms exhibiting complex morphological differentiation, whose phylogeny and physiology have been obscure for a long time due to the inability to cultivate them. Very recently, DNA sequencing data from unculturedC. polyspora-enriched material have suggested thatCrenothrixis a methane-oxidizing γ-proteobacterium (39). In contrast, the possible ecological function ofC. fusca, originally considered a developmental stage ofC. polyspora, is unknown. In this study, temporal succession of two filamentous, sheathed microorganisms resembling Cohn'sCrenothrixand Roze'sClonothrixwas observed by analyzing the microbial community of an artesian well by optical microscopy. Combined culture-based and culture-independent approaches enabled us to assignC. fuscato a novel subgroup of methane-oxidizing γ-proteobacteria distinct from that ofC. polyspora. This assignment was supported by (i) methane uptake and assimilation experiments, (ii) ultrastructural data showing the presence inC. fuscacytoplasm of an elaborate membrane system resembling that of methanotrophic γ-proteobacteria, and (iii) sequencing data demonstrating the presence in its genome of a methanol dehydrogenase α subunit-encoding gene (mxaF) and a conventional particulate methane mono-oxygenase α subunit-encoding gene (pmoA) that is different from the unusualpmoA(u-pmoA) ofC. polyspora.
Chlamydomonas reinhardtii
CNX1E Reconstitutes Molybdenum Cofactor Biosynthesis in
Escherichia coli
Mutants
Authors: Llamas Ángel , Tejada-Jimenez Manuel , González-Ballester David , Higuera José Javier , Schwarz Guenter , Galván Aurora , Fernández Emilio 
Published: April 2007

ABSTRACT

We have isolated and characterized the
Chlamydomonas reinhardtii
genes for molybdenum cofactor biosynthesis, namely,
CNX1G
and
CNX1E
, and expressed them and their chimeric fusions in
Chlamydomonas
and
Escherichia coli
. In all cases, the wild-type phenotype was restored in individual mutants as well as in a
CNX1G CNX1E
double mutant. Therefore, CrCNX1E is the first eukaryotic protein able to complement an
E. coli moeA
mutant.
Barrier Activity in
Candida albicans
Mediates Pheromone Degradation and Promotes Mating
Authors: Schaefer Dana , Côte Pierre , Whiteway Malcolm , Bennett Richard J. 
Published: April 2007

ABSTRACT

Mating in
Candida albicans
and
Saccharomyces cerevisiae
is regulated by the secretion of peptide pheromones that initiate the mating process. An important regulator of pheromone activity in
S. cerevisiae
is barrier activity, involving an extracellular aspartyl protease encoded by the
BAR1
gene that degrades the alpha pheromone. We have characterized an equivalent barrier activity in
C. albicans
and demonstrate that the loss of
C. albicans BAR1
activity results in opaque
a
cells exhibiting hypersensitivity to alpha pheromone. Hypersensitivity to pheromone is clearly seen in halo assays; in response to alpha pheromone, a lawn of
C. albicans
Δ
bar1
mutant cells produces a marked zone in which cell growth is inhibited, whereas wild-type strains fail to show halo formation.
C. albicans
mutants lacking
BAR1
also exhibit a striking mating defect in
a
cells, but not in α cells, due to overstimulation of the response to alpha pheromone. The block to mating occurs prior to cell fusion, as very few mating zygotes were observed in mixes of Δ
bar1
a
and α cells. Finally, in a barrier assay using a highly pheromone-sensitive strain, we were able to demonstrate that barrier activity in
C. albicans
is dependent on Bar1p. These studies reveal that a barrier activity to alpha pheromone exists in
C. albicans
and that the activity is analogous to that caused by Bar1p in
S. cerevisiae
.
Role of SP65 in Assembly of the
Dictyostelium discoideum
Spore Coat
Authors: Metcalf Talibah , van der Wel Hanke , Escalante Ricardo , Sastre Leandro , West Christopher M. 
Published: April 2007

ABSTRACT

Like the cyst walls of other protists, the spore coat of
Dictyostelium discoideum
is formed de novo to protect the enclosed dormant cell from stress. Spore coat assembly is initiated by exocytosis of protein and polysaccharide precursors at the cell surface, followed by the infusion of nascent cellulose fibrils, resulting in an asymmetrical trilaminar sandwich with cellulose filling the middle layer. A molecular complex consisting of cellulose and two proteins, SP85 and SP65, is associated with the inner and middle layers and is required for proper organization of distinct proteins in the outer layer. Here we show that, unlike SP85 and other protein precursors, which are stored in prespore vesicles, SP65 is, like cellulose, synthesized just in time. By tagging the SP65 locus with green fluorescent protein, we find that SP65 is delivered to the cell surface via largely distinct vesicles, suggesting that separate delivery of components of the cellulose-SP85-SP65 complex regulates its formation at the cell surface. In support of previous in vivo studies, recombinant SP65 and SP85 are shown to interact directly. In addition, truncation of SP65 causes a defect of the outer layer permeability barrier as seen previously for SP85 mutants. These observations suggest that assembly of the cellulose-SP85-SP65 triad at the cell surface is biosynthetically regulated both temporally and spatially and that the complex contributes an essential function to outer layer architecture and function.
Flagellar Motility and Structure in the Hyperthermoacidophilic Archaeon
Sulfolobus solfataricus
Authors: Szabó Zalán , Sani Musa , Groeneveld Maarten , Zolghadr Benham , Schelert James , Albers Sonja-Verena , Blum Paul , Boekema Egbert J. , Driessen Arnold J. M. 
Published: April 2007

ABSTRACT

Flagellation in archaea is widespread and is involved in swimming motility. Here, we demonstrate that the structural flagellin gene from the crenarchaeaon
Sulfolobus solfataricus
is highly expressed in stationary-phase-grown cells and under unfavorable nutritional conditions. A mutant in a flagellar auxiliary gene,
flaJ
, was found to be nonmotile. Electron microscopic imaging of the flagellum indicates that the filaments are composed of right-handed helices.
Molecular Interaction between Lipoteichoic Acids and
Lactobacillus delbrueckii
Phages Depends on
d
-Alanyl and α-Glucose Substitution of Poly(Glycerophosphate) Backbones
Authors: Räisänen Liisa , Draing Christian , Pfitzenmaier Markus , Schubert Karin , Jaakonsaari Tiina , von Aulock Sonja , Hartung Thomas , Alatossava Tapani 
Published: April 2007

ABSTRACT

Lipoteichoic acids (LTAs) have been shown to act as bacterial counterparts to the receptor binding proteins of LL-H, LL-H host range mutant LL-H-a21, and JCL1032. Here we have used LTAs purified by hydrophobic interaction chromatography from different phage-resistant and -sensitive strains of
Lactobacillus delbrueckii
subsp.
lactis.
Nuclear magnetic resonance analyses revealed variation in the degree of α-glucosyl and
d
-alanyl substitution of the 1,3-linked poly(glycerophosphate) LTAs between the phage-sensitive and phage-resistant strains. Inactivation of phages was less effective if there was a high level of
d
-alanine residues in the LTA backbones. Prior incubation of the LTAs with α-glucose-specific lectin inhibited the LL-H phage inactivation. The overall level of decoration or the specific spatial combination of α-glucosyl-substituted,
d
-alanyl-substituted, and nonsubstituted glycerol residues may also affect phage adsorption.
Identification of Essential Residues in Apolipoprotein
N
-Acyl Transferase, a Member of the CN Hydrolase Family
Authors: Vidal-Ingigliardi Dominique , Lewenza Shawn , Buddelmeijer Nienke 
Published: April 2007

ABSTRACT

Apolipoprotein
N
-acyl transferase (Lnt) is an essential membrane-bound protein involved in lipid modification of all lipoproteins in gram-negative bacteria. Essential residues in Lnt of
Escherichia coli
were identified by using site-directed mutagenesis and an in vivo complementation assay. Based on sequence conservation and known protein structures, we predict a model for Lnt, which is a member of the CN hydrolase family. Besides the potential catalytic triad E267-K335-C387, four residues that directly affect the modification of Braun's lipoprotein Lpp are absolutely required for Lnt function. Residues Y388 and E389 are part of the hydrophobic pocket that constitutes the active site. Residues W237 and E343 are located on two flexible arms that face away from the active site and are expected to open and close upon the binding and release of phospholipid and/or apolipoprotein. Substitutions causing temperature-dependent effects were located at different positions in the structural model. These mutants were not affected in protein stability. Lnt proteins from other proteobacteria, but not from actinomycetes, were functional in vivo, and the essential residues identified in Lnt of
E. coli
are conserved in these proteins.
Characterization of a Small Mobilizable Transposon, MTnSag1, inStreptococcus agalactiae
Authors: Achard Adeline , Leclercq Roland 
Published: April 2007

ABSTRACTThe transposon MTnSag1 fromStreptococcus agalactiaecarried an IS1-like transposase gene and thelnu(C) gene, which encoded a lincosamide nucleotidyltransferase. MTnSag1 could be mobilized by the conjugative transposon Tn916. An intermediate circular form of MTnSag1 and a putative origin of transfer at the 3′ end of thelnu(C) gene were characterized.
Distribution of Protein A on the Surface ofStaphylococcus aureus
Authors: DeDent Andrea C. , McAdow Molly , Schneewind Olaf 
Published: April 2007

ABSTRACTSurface proteins ofStaphylococcus aureusfulfill many important roles during the pathogenesis of human infections and are anchored to the cell wall envelope by sortases. Although the chemical linkage of proteins to cell wall cross bridges is known, the mechanisms whereby polypeptides are distributed on the staphylococcal surface have not been revealed. We show here that protein A, the ligand of immunoglobulin, is unevenly distributed over the staphylococcal surface. Upon removal with trypsin, newly synthesized polypeptide is deposited at two to four discrete foci. During subsequent growth, protein A appears to be slowly distributed from these sites. When viewed through multiple focal planes by laser scanning microscopy, protein A foci are arranged in a circle surrounding the bacterial cell. This pattern of distribution requires the LPXTG sorting signal of protein A as well as sortase A, the transpeptidase that anchors polypeptides to cell wall cross bridges. A model is presented whereby protein A deposition at discrete sites coupled with cell wall synthesis enables distribution of protein A on the staphylococcal surface.
Functional Genomics Enables Identification of Genes of the Arginine Transaminase Pathway in
Pseudomonas aeruginosa
Authors: Yang Zhe , Lu Chung-Dar 
Published: April 2007

ABSTRACT

Arginine utilization in
Pseudomonas aeruginosa
with multiple catabolic pathways represents one of the best examples of the metabolic versatility of this organism. To identify genes involved in arginine catabolism, we have employed DNA microarrays to analyze the transcriptional profiles of this organism in response to
l
-arginine. While most of the genes involved in arginine uptake, regulation, and metabolism have been identified as members of the ArgR (arginine-responsive regulatory protein) regulon in our previous study, they did not include any genes of the arginine dehydrogenase (ADH) pathway. In this study, 18 putative transcriptional units of 38 genes, including the two known genes of the ADH pathway,
kauB
and
gbuA
, were found to be inducible by exogenous
l
-arginine in the absence of ArgR. To identify the missing genes that encode enzymes for the initial steps of the ADH pathway, the potential physiological functions of those candidate genes in arginine utilization were studied by growth phenotype analysis of knockout mutants. Expression of these genes was induced by
l
-arginine in an
aruF
mutant strain devoid of a functional arginine succinyltransferase pathway, the major route of arginine utilization. Disruption of
dadA
, a putative catabolic alanine dehydrogenase-encoding gene, in the
aruF
mutant produced no growth on
l
-arginine, suggesting the involvement of
l
-alanine in arginine catabolism. This hypothesis was further supported by the detection of an
l
-arginine-inducible arginine:pyruvate transaminase activity in the
aruF
mutant. Knockout of
aruH
and
aruI
, which encode an arginine:pyruvate transaminase and a 2-ketoarginine decarboxylase in an operon, also abolished the ability of the
aruF
mutant to grow on
l
-arginine. The results of high-performance liquid chromatography analysis demonstrated consumption of 2-ketoarginine and suggested that generation of 4-guanidinobutyraldehyde occurred in the
aruF
mutant but not in the
aruF aruI
mutant. These results led us to propose the arginine transaminase pathway that removes the α-amino group of
l
-arginine via transamination instead of oxidative deamination by dehydrogenase or oxidase as originally proposed. In the same genetic locus, we also identified a two-component system, AruRS, for the regulation of arginine-responsive induction of the arginine transaminase pathway. This work depicted a wider network of arginine metabolism than we previously recognized.
Characterization of an Arginine:Pyruvate Transaminase in Arginine Catabolism of
Pseudomonas aeruginosa
PAO1
Authors: Yang Zhe , Lu Chung-Dar 
Published: April 2007

ABSTRACT

The arginine transaminase (ATA) pathway represents one of the multiple pathways for
l
-arginine catabolism in
Pseudomonas aeruginosa
. The AruH protein was proposed to catalyze the first step in the ATA pathway, converting the substrates
l
-arginine and pyruvate into 2-ketoarginine and
l
-alanine. Here we report the initial biochemical characterization of this enzyme. The
aruH
gene was overexpressed in
Escherichia coli
, and its product was purified to homogeneity. High-performance liquid chromatography and mass spectrometry (MS) analyses were employed to detect the presence of the transamination products 2-ketoarginine and
l
-alanine, thus demonstrating the proposed biochemical reaction catalyzed by AruH. The enzymatic properties and kinetic parameters of dimeric recombinant AruH were determined by a coupled reaction with NAD
+
and
l
-alanine dehydrogenase. The optimal activity of AruH was found at pH 9.0, and it has a novel substrate specificity with an order of preference of Arg > Lys > Met > Leu > Orn > Gln. With
l
-arginine and pyruvate as the substrates, Lineweaver-Burk plots of the data revealed a series of parallel lines characteristic of a ping-pong kinetic mechanism with calculated
V
max
and
k
cat
values of 54.6 ± 2.5 μmol/min/mg and 38.6 ± 1.8 s
−1
. The apparent

K
m

and catalytic efficiency (
k
cat
/

K
m

) were 1.6 ± 0.1 mM and 24.1 mM
−1
s
−1
for pyruvate and 13.9 ± 0.8 mM and 2.8 mM
−1
s
−1
for
l
-arginine. When
l
-lysine was used as the substrate, MS analysis suggested Δ
1
-piperideine-2-carboxylate as its transamination product. These results implied that AruH may have a broader physiological function in amino acid catabolism.
Eukaryotic-Type Serine/Threonine Protein Kinase StkP Is a Global Regulator of Gene Expression inStreptococcus pneumoniae
Authors: Sasková Lenka , Nováková Linda , Basler Marek , Branny Pavel 
Published: April 2007

ABSTRACTSignal transduction pathways in both prokaryotes and eukaryotes utilize protein phosphorylation as a key regulatory mechanism. Recent studies have proven that eukaryotic-type serine/threonine protein kinases (Hank's type) are widespread in many bacteria, although little is known regarding the cellular processes they control. In this study, we have attempted to establish the role of a single eukaryotic-type protein kinase, StkP ofStreptococcus pneumoniae, in bacterial survival. Our results indicate that the expression of StkP is important for the resistance ofS. pneumoniaeto various stress conditions. To investigate the impact of StkP on this phenotype, we compared the whole-genome expression profiles of the wild-type and ΔstkPmutant strains by microarray technology. This analysis revealed that StkP positively controls the transcription of a set of genes encoding functions involved in cell wall metabolism, pyrimidine biosynthesis, DNA repair, iron uptake, and oxidative stress response. Despite the reduced transformability of thestkPmutant, we found that the competence regulon was derepressed in thestkPmutant under conditions that normally repress natural competence development. Furthermore, the competence regulon was expressed independently of exogenous competence-stimulating peptide. In summary, our studies show that a eukaryotic-type serine/threonine protein kinase functions as a global regulator of gene expression inS. pneumoniae.
Interspecies DNA Microarray Analysis Identifies WblA as a Pleiotropic Down-Regulator of Antibiotic Biosynthesis in
Streptomyces
Authors: Kang Seung-Hoon , Huang Jianqiang , Lee Han-Na , Hur Yoon-Ah , Cohen Stanley N. , Kim Eung-Soo 
Published: April 2007

ABSTRACT

Using
Streptomyces coelicolor
microarrays to discover regulators of gene expression in other
Streptomyces
species, we identified
wblA
, a
whiB
-like gene encoding a putative transcription factor, as a down-regulator of doxorubicin biosynthesis in
Streptomyces peucetius
. Further analysis revealed that
wblA
functions pleiotropically to control antibiotic production and morphological differentiation in streptomycetes. Our results reveal a novel biological role for
wblA
and show the utility of interspecies microarray analysis for the investigation of streptomycete gene expression.
The Zinc-Responsive Regulator Zur Controls a Zinc Uptake System and Some Ribosomal Proteins inStreptomyces coelicolorA3(2)
Authors: Shin Jung-Ho , Oh So-Young , Kim Soon-Jong , Roe Jung-Hye 
Published: April 2007

ABSTRACTIn various bacteria, Zur, a zinc-specific regulator of the Fur family, regulates genes for zinc transport systems to maintain zinc homeostasis. It has also been suggested that Zur controls zinc mobilization by regulating some ribosomal proteins. The antibiotic-producing soil bacteriumStreptomyces coelicolorcontains four genes for Fur family regulators, and one (namedzur) is located downstream of theznuACBoperon encoding a putative zinc uptake transporter. We found that zinc specifically repressed the level ofznuAtranscripts and that this level was derepressed in a Δzurmutant. Purified Zur existing as homodimers bound to theznuApromoter region in the presence of zinc, confirming the role of Zur as a zinc-responsive repressor. We analyzed transcripts for paralogous forms of ribosomal proteins L31 (RpmE1 and RpmE2) and L33 (RpmG2 and RpmG3) for their dependence on Zur and found that RpmE2 and RpmG2 with no zinc-binding motif of conserved cysteines (C's) were negatively regulated by Zur. C-negative RpmG3 and C-positive RpmE1 were not regulated by Zur. Instead, they were regulated by the sigma factor σRas predicted from their promoter sequences. TherpmE1andrpmG3genes were partially induced by EDTA in a manner dependent on σR, suggesting that zinc depletion may stimulate the σRregulatory system. This finding reflects a link between thiol-oxidizing stress and zinc depletion. We determined the Zur-binding sites withinznuAandrpmG2promoter regions by footprinting analyses and identified a consensus inverted repeat sequence (TGaaAatgatTttCA, where uppercase letters represent the nucleotides common to all sites analyzed). This sequence closely matches that for mycobacterial Zur and allows the prediction of more genes in the Zur regulon.
Characterization of a Novel Bifunctional Dihydropteroate Synthase/Dihydropteroate Reductase Enzyme from
Helicobacter pylori
Authors: Levin Itay , Mevarech Moshe , Palfey Bruce A. 
Published: April 2007

ABSTRACT

Tetrahydrofolate is a ubiquitous C
1
carrier in many biosynthetic pathways in bacteria, importantly, in the biosynthesis of formylmethionyl tRNA
fMet
, which is essential for the initiation of translation. The final step in the biosynthesis of tetrahydrofolate is carried out by the enzyme dihydrofolate reductase (DHFR). A search of the complete genome sequence of
Helicobacter pylori
failed to reveal any sequence that encodes DHFR. Previous studies demonstrated that the
H. pylori
dihydropteroate synthase gene
folP
can complement an
Escherichia coli
strain in which
folA
and
folM
, encoding two distinct DHFRs, are deleted. It was also shown that
H. pylori
FolP possesses an additional N-terminal domain that binds flavin mononucleotide (FMN). Homologous domains are found in FolP proteins of other microorganisms that do not possess DHFR. In this study, we demonstrated that
H. pylori
FolP is also a dihydropteroate reductase that derives its reducing power from soluble flavins, reduced FMN and reduced flavin adenine dinucleotide. We also determined the stoichiometry of the enzyme-bound flavin and showed that half of the bound flavin is exchangeable with the soluble flavins. Finally, site-directed mutagenesis of the most conserved amino acid residues in the N-terminal domain indicated the importance of these residues for the activity of the enzyme as a dihydropteroate reductase.