bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Nitric Oxide on Anammox Bacteria
Authors: Kartal Boran , Tan Nico C. G. , Van de Biezen Erwin , Kampschreur Marlies J. , Van Loosdrecht Mark C. M. , Jetten Mike S. M. 
Published: July 2010

ABSTRACT
The effects of nitrogen oxides on anammox bacteria are not well known. Therefore, anammox bacteria were exposed to 3,500 ppm nitric oxide (NO) in the gas phase. The anammox bacteria were not inhibited by the high NO concentration but rather used it to oxidize additional ammonium to dinitrogen gas under conditions relevant to wastewater treatment.
Evolutionary Dynamics of Insertion Sequences in Relation to the Evolutionary Histories of the Chromosome and Symbiotic Plasmid Genes of
Rhizobium etli
Populations
Authors: Lozano Luis , Hernández-González Ismael , Bustos Patricia , Santamaría Rosa I. , Souza Valeria , Young J. Peter W. , Dávila Guillermo , González Víctor 
Published: July 2010

ABSTRACT

Insertion sequences (IS) are mobile genetic elements that are distributed in many prokaryotes. In particular, in the genomes of the symbiotic nitrogen-fixing bacteria collectively known as rhizobia, IS are fairly abundant in plasmids or chromosomal islands that carry the genes needed for symbiosis. Here, we report an analysis of the distribution and genetic conservation of the IS found in the genome of
Rhizobium etli
CFN42 in a collection of 87
Rhizobium
strains belonging to populations with different geographical origins. We used PCR to generate presence/absence profiles of the 39 IS found in
R. etli
CFN42 and evaluated whether the IS were located in consistent genomic contexts. We found that the IS from the symbiotic plasmid were frequently present in the analyzed strains, whereas the chromosomal IS were observed less frequently. We then examined the evolutionary dynamics of these strains based on a population genetic analysis of two chromosomal housekeeping genes (
glyA
and
dnaB
) and three symbiotic sequences (
nodC
and the two IS elements). Our results indicate that the IS contained within the symbiotic plasmid have a higher degree of genomic context conservation, lower nucleotide diversity and genetic differentiation, and fewer recombination events than the chromosomal housekeeping genes. These results suggest that the
R. etli
populations diverged recently in Mexico, that the symbiotic plasmid also had a recent origin, and that the IS elements have undergone a process of cyclic infection and expansion.
Prolyl Aminopeptidase from
Streptomyces thermoluteus
subsp.
fuscus
Strain NBRC14270 and Synthesis of Proline-Containing Peptides by Its S144C Variant
Authors: Yamamoto Yukihiro , Usuki Hirokazu , Iwabuchi Masaki , Hatanaka Tadashi 
Published: July 2010

ABSTRACT

We specifically examined an exopeptidase, prolyl aminopeptidase (PAP), as a target for synthesis of proline-containing peptides. A PAP from
Streptomyces thermoluteus
subsp.
fuscus
NBRC14270 (PAP14270) was obtained using sequence-based screening. From PAP14270, 144Ser was replaced by Cys (scPAP14270) to give aminolysis activity. In contrast to wild-type PAP14270, scPAP14270 produced a polymer of proline benzyl ester and cyclo[Pro-Pro]. The product mass was confirmed using liquid chromatography-mass spectrometry (LC/MS). Several factors affecting the reaction, such as the pH, concentration of the substrate, and reaction time, were measured to determine their effects. Furthermore, a correlation was found between substrate specificity in proline peptide synthesis and the log
D
value of acyl acceptors in aminolysis catalyzed by scPAP14270. Results showed that dipeptide synthesis proceeded in a weakly acidic environment and that cyclization and polymerization occurred under alkaline conditions. Furthermore, results suggest that almost all amino acid esters whose log
D
value is greater than 0, except hydroxyproline benzyl ester (Hyp-OBzl), can be recognized as acyl acceptors. These findings support the use of PAPs as a tool for production of physiologically active proline peptides.
Enhanced Production of a Plant Monoterpene by Overexpression of the 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase Catalytic Domain in
Saccharomyces cerevisiae
Authors: Rico Juan , Pardo Ester , Orejas Margarita 
Published: July 2010

ABSTRACT

Linalool production was evaluated in different
Saccharomyces cerevisiae
strains expressing the
Clarkia breweri
linalool synthase gene (
LIS
). The wine strain T
73
was shown to produce higher levels of linalool than conventional laboratory strains (i.e., almost three times the amount). The performance of this strain was further enhanced by manipulating the endogenous mevalonate (MVA) pathway: deregulated overexpression of the rate-limiting 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase) doubled linalool production. In a haploid laboratory strain, engineering of this key step also improved linalool yield.
Role of Aspergillus fumigatus DvrA in Host Cell Interactions and Virulence
Authors: Ejzykowicz Daniele E. , Solis Norma V. , Gravelat Fabrice N. , Chabot Josee , Li Xuexian , Sheppard Donald C. , Filler Scott G. 
Published: July 2010

ABSTRACT

The transcription factors that regulate
Aspergillus fumigatus
interactions with host cells and virulence are incompletely defined. We investigated the role of the putative C2H2 transcription factor DvrA in governing these processes. Although DvrA was identified by its limited homology to
Candida albicans
Bcr1, a Δ
dvrA
mutant strain of
A. fumigatus
had wild-type adherence to host constituents
in vitro
. However, it had increased capacity to damage both endothelial cells and a pulmonary epithelial cell line compared to the ability of the wild-type strain and a Δ
dvrA
::
dvrA
-complemented strain. This increase in damage required direct contact between the mutant and host cells. The Δ
dvrA
mutant also stimulated greater CCL20, interleukin-8, and tumor necrosis factor mRNA expression in a pulmonary epithelial cell line compared to levels induced by the control strains. Also, it was resistant to nikkomycin Z, suggesting an altered cell wall composition. As predicted by these
in vitro
results, the Δ
dvrA
mutant had increased virulence and stimulated a greater pulmonary inflammatory response than the wild-type strain and Δ
dvrA
::
dvrA
-complemented strains in the nonneutropenic mouse model of invasive pulmonary aspergillosis. These results indicate that DvrA influences
A. fumigatus
virulence as well as its capacity to damage host cells and stimulate a proinflammatory response.
Sulfate Assimilation Mediates Tellurite Reduction and Toxicity in Saccharomyces cerevisiae
Authors: Ottosson Lars-Göran , Logg Katarina , Ibstedt Sebastian , Sunnerhagen Per , Käll Mikael , Blomberg Anders , Warringer Jonas 
Published: July 2010

ABSTRACT

Despite a century of research and increasing environmental and human health concerns, the mechanistic basis of the toxicity of derivatives of the metalloid tellurium, Te, in particular the oxyanion tellurite, Te(IV), remains unsolved. Here, we provide an unbiased view of the mechanisms of tellurium metabolism in the yeast
Saccharomyces cerevisiae
by measuring deviations in Te-related traits of a complete collection of gene knockout mutants. Reduction of Te(IV) and intracellular accumulation as metallic tellurium strongly correlated with loss of cellular fitness, suggesting that Te(IV) reduction and toxicity are causally linked. The sulfate assimilation pathway upstream of Met17, in particular, the sulfite reductase and its cofactor siroheme, was shown to be central to tellurite toxicity and its reduction to elemental tellurium. Gene knockout mutants with altered Te(IV) tolerance also showed a similar deviation in tolerance to both selenite and, interestingly, selenomethionine, suggesting that the toxicity of these agents stems from a common mechanism. We also show that Te(IV) reduction and toxicity in yeast is partially mediated via a mitochondrial respiratory mechanism that does not encompass the generation of substantial oxidative stress. The results reported here represent a robust base from which to attack the mechanistic details of Te(IV) toxicity and reduction in a eukaryotic organism.
Subtelomeric Silencing of the
MTL3
Locus of Candida glabrata Requires yKu70, yKu80, and Rif1 Proteins
Authors: Ramírez-Zavaleta Candy Y. , Salas-Delgado Griselda E. , De Las Peñas Alejandro , Castaño Irene 
Published: July 2010

ABSTRACT

Candida glabrata
is a haploid opportunistic fungal pathogen that is phylogenetically related to
Saccharomyces cerevisiae
. Even though
C. glabrata
has no known sexual cycle, it contains, like
S. cerevisiae
, three mating type-like loci (
MTL
) called
MTL1
,
MTL2
, and
MTL3
, as well as most of the genes required for mating, meiosis, and sporulation.
MTL1
is localized at an internal position on chromosome B and is thought to be the locus corresponding to the
MAT
locus in
S. cerevisiae
.
MTL2
and
MTL3
are localized close to two telomeres on different chromosomes (29.4 kb from Chr E-L and 10.5 kb from Chr B-L, respectively). By using
URA3
reporter gene insertions at the three
MTL
loci, we found that in contrast to the case for
S. cerevisiae
, only
MTL3
is subject to transcriptional silencing while
MTL2
is transcriptionally active, and this is in agreement with previously reported data. We found that the silencing of
MTL3
is nucleated primarily at the left telomere of chromosome B and spreads over 12 kb to
MTL3
, rather than nucleating at flanking, closely positioned
cis
-acting silencers, like those flanking
HMR
and
HML
of
S. cerevisiae
. Interestingly, the silencing of
MTL3
absolutely requires the yKu70, yKu80, and Rif1 proteins, in sharp contrast to the silencing of the
HM
loci of
S. cerevisiae
. In addition, we found that several cell type-specific genes are expressed in
C. glabrata
regardless of the presence, or even absence, of mating type information at any of the
MTL
loci.
Comparative Study of the Roles of AhpC and KatE as Respiratory Antioxidants inBrucella abortus2308
Authors: Steele Kendra H. , Baumgartner John E. , Valderas Michelle Wright , Roop R. Martin 
Published: July 2010

ABSTRACTBrucellastrains are exposed to potentially toxic levels of H2O2both as a consequence of their aerobic metabolism and through the respiratory burst of host phagocytes. To evaluate the relative contributions of the sole catalase KatE and the peroxiredoxin AhpC produced by these strains in defense against H2O2-mediated toxicity, isogenickatE,ahpC, andkatE ahpCmutants were constructed and the phenotypic properties of these mutants compared with those of the virulent parental strainB. abortus2308. The results of these studies indicate that AhpC is the primary detoxifier of endogenous H2O2generated by aerobic metabolism. KatE, on the other hand, plays a major role in scavenging exogenous and supraphysiologic levels of H2O2, although this enzyme can play a supporting role in the detoxification of H2O2of endogenous origin if AhpC is absent.B. abortus ahpCandkatEmutants exhibit wild-type virulence in C57BL/6 and BALB/c mice, but theB. abortus ahpC katEdouble mutant is extremely attenuated, and this attenuation is not relieved in derivatives of C57BL/6 mice that lack NADPH oxidase (cybb) or inducible nitric oxide synthase (Nos2) activity. These experimental findings indicate that the generation of endogenous H2O2represents a relevant environmental stress thatB. abortus2308 must deal with during its residence in the host and that AhpC and KatE perform compensatory roles in detoxifying this metabolic H2O2.
A NAC for Regulating Metabolism: the Nitrogen Assimilation Control Protein (NAC) from
Klebsiella pneumoniae
Authors: Bender Robert A. 
Published: July 2010

ABSTRACT

The nitrogen assimilation control protein (NAC) is a LysR-type transcriptional regulator (LTTR) that is made under conditions of nitrogen-limited growth. NAC's synthesis is entirely dependent on phosphorylated NtrC from the two-component Ntr system and requires the unusual sigma factor σ54 for transcription of the
nac
gene. NAC activates the transcription of σ70-dependent genes whose products provide the cell with ammonia or glutamate. NAC represses genes whose products use ammonia and also represses its own transcription. In addition, NAC also subtly adjusts other cellular functions to keep pace with the supply of biosynthetically available nitrogen.
Dual Biosynthesis Pathway for Longer-Chain Polyamines in the Hyperthermophilic Archaeon
Thermococcus kodakarensis
Authors: Morimoto Nanako , Fukuda Wakao , Nakajima Nanami , Masuda Takeaki , Terui Yusuke , Kanai Tamotsu , Oshima Tairo , Imanaka Tadayuki , Fujiwara Shinsuke 
Published: July 2010

ABSTRACT

Long-chain and/or branched-chain polyamines are unique polycations found in thermophiles. Cytoplasmic polyamines were analyzed for cells cultivated at various growth temperatures in the hyperthermophilic archaeon
Thermococcus kodakarensis.
Spermidine [34] and
N
4
-aminopropylspermine [3(3)43] were identified as major polyamines at 60°C, and the amounts of
N
4
-aminopropylspermine [3(3)43] increased as the growth temperature rose. To identify genes involved in polyamine biosynthesis, a gene disruption study was performed. The open reading frames (ORFs) TK0240, TK0474, and TK0882, annotated as agmatine ureohydrolase genes, were disrupted. Only the TK0882 gene disruptant showed a growth defect at 85°C and 93°C, and the growth was partially retrieved by the addition of spermidine. In the TK0882 gene disruptant, agmatine and
N
1
-aminopropylagmatine accumulated in the cytoplasm. Recombinant TK0882 was purified to homogeneity, and its ureohydrolase characteristics were examined. It possessed a 43-fold-higher
k
cat
/

K
m

value for
N
1
-aminopropylagmatine than for agmatine, suggesting that TK0882 functions mainly as
N
1
-aminopropylagmatine ureohydrolase to produce spermidine. TK0147, annotated as spermidine/spermine synthase, was also studied. The TK0147 gene disruptant showed a remarkable growth defect at 85°C and 93°C. Moreover, large amounts of agmatine but smaller amounts of putrescine accumulated in the disruptant. Purified recombinant TK0147 possessed a 78-fold-higher
k
cat
/

K
m

value for agmatine than for putrescine, suggesting that TK0147 functions primarily as an aminopropyl transferase to produce
N
1
-aminopropylagmatine. In
T. kodakarensis
, spermidine is produced mainly from agmatine via
N
1
-aminopropylagmatine. Furthermore, spermine and
N
4
-aminopropylspermine were detected in the TK0147 disruptant, indicating that TK0147 does not function to produce spermine and long-chain polyamines.
Toxicity of the Colicin M Catalytic Domain Exported to the Periplasm Is FkpA Independent
Authors: Barnéoud-Arnoulet Aurélie , Barreteau Hélène , Touzé Thierry , Mengin-Lecreulx Dominique , Lloubès Roland , Duché Denis 
Published: July 2010

ABSTRACT

Colicin M (ColM) is a bactericidal protein that kills sensitive cells by hydrolyzing lipid II, involved in the biosynthesis of cell wall peptidoglycan. It recognizes FhuA on the outer leaflet, and its translocation through the outer membrane depends on the energized Ton complex in the inner membrane. To be active in the periplasm, ColM must be translocated through the outer membrane and then interact with FkpA, a periplasmic protein that exhibits both
cis
- and
trans
-peptidylprolyl isomerase (PPiase) and chaperon activities. In an attempt to directly target ColM to the periplasm of the producing bacteria, we fused the presequence of OmpA to ColM (sp-ColM). We found that expression of this hybrid protein in an
Escherichia coli
strain devoid of ColM immunity protein (Cmi) was bactericidal. We showed that sp-ColM was correctly expressed, processed, and associated with the inner membrane. sp-ColM toxicity was related to its enzymatic activity and did not rely on the TonB import proteins or the FhuA receptor. The presence of both activity domains of FkpA was still required for sp-ColM activity. Analyses of deletion mutants of sp-ColM show that the domain required for toxicity corresponds to the C-terminal last 153 amino acids of ColM. Like the full-length protein, this domain is not active in the presence of the immunity protein Cmi. On the other hand, it does not require FkpA for toxic activity.
Human Hypervirulent
Clostridium difficile
Strains Exhibit Increased Sporulation as Well as Robust Toxin Production
Authors: Merrigan Michelle , Venugopal Anilrudh , Mallozzi Michael , Roxas Bryan , Viswanathan V. K. , Johnson Stuart , Gerding Dale N. , Vedantam Gayatri 
Published: July 2010

ABSTRACT

Toxigenic
Clostridium difficile
strains produce two toxins (TcdA and TcdB) during the stationary phase of growth and are the leading cause of antibiotic-associated diarrhea.
C. difficile
isolates of the molecular type NAP1/027/BI have been associated with severe disease and hospital outbreaks worldwide. It has been suggested that these “hypervirulent” strains produce larger amounts of toxin and that a mutation in a putative negative regulator (TcdC) allows toxin production at all growth phases. To rigorously explore this possibility, we conducted a quantitative examination of the toxin production of multiple hypervirulent and nonhypervirulent
C. difficile
strains. Toxin gene (
tcdA
and
tcdB
) and toxin gene regulator (
tcdR
and
tcdC
) expression was also monitored. To obtain additional correlates for the hypervirulence phenotype, sporulation kinetics and efficiency were measured. In the exponential phase, low basal levels of
tcdA
,
tcdB
, and
tcdR
expression were evident in both hypervirulent and nonhypervirulent strains, but contrary to previous assumptions, toxin levels were below the detectable thresholds. While hypervirulent strains displayed robust toxin production during the stationary phase of growth, the amounts were not significantly different from those of the nonhypervirulent strains tested; further, total toxin amounts were directly proportional to
tcdA
,
tcdB
, and
tcdR
gene expression. Interestingly,
tcdC
expression did not diminish in stationary phase, suggesting that TcdC may have a modulatory rather than a strictly repressive role. Comparative genomic analyses of the closely related nonhypervirulent strains VPI 10463 (the highest toxin producer) and 630 (the lowest toxin producer) revealed polymorphisms in the
tcdR
ribosome binding site and the
tcdR-tcdB
intergenic region, suggesting that a mechanistic basis for increased toxin production in VPI 10463 could be increased TcdR translation and read-through transcription of the
tcdA
and
tcdB
genes. Hypervirulent isolates produced significantly more spores, and did so earlier, than all other isolates. Increased sporulation, potentially in synergy with robust toxin production, may therefore contribute to the widespread disease now associated with hypervirulent
C. difficile
strains.
Antimicrobial Peptides Activate the Rcs Regulon through the Outer Membrane Lipoprotein RcsF
Authors: Farris Carol , Sanowar Sarah , Bader Martin W. , Pfuetzner Richard , Miller Samuel I. 
Published: July 2010

ABSTRACT

Salmonella enterica
species are exposed to envelope stresses due to their environmental and infectious lifestyles. Such stresses include amphipathic cationic antimicrobial peptides (CAMPs), and resistance to these peptides is an important property for microbial virulence for animals. Bacterial mechanisms used to sense and respond to CAMP-induced envelope stress include the RcsFCDB phosphorelay, which contributes to survival from polymyxin B exposure. The Rcs phosphorelay includes two inner membrane (IM) proteins, RcsC and RcsD; the response regulator RcsB; the accessory coregulator RcsA; and an outer membrane bound lipoprotein, RcsF. Transcriptional activation of the Rcs regulon occurred within minutes of exposure to CAMP and during the first detectable signs of CAMP-induced membrane disorder. Rcs transcriptional activation by CAMPs required RcsF and preservation of its two internal disulfide linkages. The rerouting of RcsF to the inner membrane or its synthesis as an unanchored periplasmic protein resulted in constitutive activation of the Rcs regulon and RcsCD-dependent phosphorylation. These findings suggest that RcsFCDB activation in response to CAMP-induced membrane disorder is a result of a change in structure or availability of RcsF to the IM signaling constituents of the Rcs phosphorelay.
Different Roles of DosS and DosT in the Hypoxic Adaptation of Mycobacteria
Authors: Kim Min-Ju , Park Kwang-Jin , Ko In-Jeong , Kim Young Min , Oh Jeong-Il 
Published: July 2010

ABSTRACT

The DosS (DevS) and DosT histidine kinases form a two-component system together with the DosR (DevR) response regulator in
Mycobacterium tuberculosis.
DosS and DosT, which have high sequence similarity to each other over the length of their amino acid sequences, contain two GAF domains (GAF-A and GAF-B) in their N-terminal sensory domains. Complementation tests in conjunction with phylogenetic analysis showed that DevS of
Mycobacterium smegmatis
is more closely related to DosT than DosS. We also demonstrated
in vivo
that DosS and DosT of
M. tuberculosis
play a differential role in hypoxic adaptation. DosT responds to a decrease in oxygen tension more sensitively and strongly than DosS, which might be attributable to their different autooxidation rates. The different responsiveness of DosS and DosT to hypoxia is due to the difference in their GAF-A domains accommodating the hemes. Multiple alignment analysis of the GAF-A domains of mycobacterial DosS (DosT) homologs and subsequent site-directed mutagenesis revealed that just one substitution of E87, D90, H97, L118, or T169 of DosS with the corresponding residue of DosT is sufficient to convert DosS to DosT with regard to the responsiveness to changes in oxygen tension.
Characterization of the Enzymes Encoded by the Anthrose Biosynthetic Operon of
Bacillus anthracis
Authors: Dong Shengli , McPherson Sylvia A. , Wang Yun , Li Mei , Wang Pengfei , Turnbough Charles L. , Pritchard David G. 
Published: July 2010

ABSTRACT

Bacillus anthracis
spores, the etiological agents of anthrax, possess a loosely fitting outer layer called the exosporium that is composed of a basal layer and an external hairlike nap. The filaments of the nap are formed by trimers of the collagenlike glycoprotein BclA. Multiple pentasaccharide and trisaccharide side chains are O linked to BclA. The nonreducing terminal residue of the pentasaccharide side chain is the unusual sugar anthrose. A plausible biosynthetic pathway for anthrose biosynthesis has been proposed, and an
antABCD
operon encoding four putative anthrose biosynthetic enzymes has been identified. In this study, we genetically and biochemically characterized the activities of these enzymes. We also used mutant
B. anthracis
strains to determine the effects on BclA glycosylation of individually inactivating the genes of the anthrose operon. The inactivation of
antA
resulted in the appearance of BclA pentasaccharides containing anthrose analogs possessing shorter side chains linked to the amino group of the sugar. The inactivation of
antB
resulted in BclA being replaced with only trisaccharides, suggesting that the enzyme encoded by the gene is a dTDP-β-
l
-rhamnose α-1,3-
l
-rhamnosyl transferase that attaches the fourth residue of the pentasaccharide side chain. The inactivation of
antC
and
antD
resulted in the disappearance of BclA pentasaccharides and the appearance of a tetrasaccharide lacking anthrose. These phenotypes are entirely consistent with the proposed roles for the
antABCD
-encoded enzymes in anthrose biosynthesis. Purified AntA was then shown to exhibit β-methylcrotonyl-coenzyme A (CoA) hydratase activity, as we predicted. Similarly, we confirmed that purified AntC had aminotransferase activity and that purified AntD displayed
N
-acyltransferase activity.