bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen Fixation by
Vibrio parahaemolyticus
and Its Implications for a New Ecological Niche
Authors: Criminger J. D. , Hazen T. H. , Sobecky P. A. , Lovell C. R. 
Published: August 2007

ABSTRACT

A
Vibrio parahaemolyticus
strain isolated from the rhizosphere of the ecosystem dominant estuarine grass,
Spartina alterniflora
, was characterized and shown to carry
nifH
, the gene encoding the nitrogenase iron protein, and to fix N
2
. Nitrogen fixation may contribute substantially to the adaptability, niche breadth, and ecological significance of
V. parahaemolyticus
.
Novel Sensitive High-Throughput Screening Strategy for Nitrilase-Producing Strains
Authors: Zhu Qing , Fan Ao , Wang Yuanshan , Zhu Xiaoqin , Wang Zhao , Wu Minghuo , Zheng Yuguo 
Published: August 2007

ABSTRACT

Nitrilases have found wide use in the pharmaceutical industry for the production of fine chemicals, and it is important to have a method by which to screen libraries of isolated or engineered nitrilase variants (including bacteria and fungi). The conventional methods, such as high-performance liquid chromatography, liquid chromatography-mass spectrometry, capillary electrophoresis, or gas chromatography, are tedious and time-consuming. Therefore, a direct and sensitive readout of the nitrilase's activity has to be considered. In this paper, we report a novel time-resolved luminescent probe:
o
-hydroxybenzonitrile derivatives could be applied to detect the activity of the nitrilases. By the action of nitrilases,
o
-hydroxybenzonitrile derivatives can be transformed to the corresponding salicylic acid derivatives, which, upon binding Tb
3+
, serve as a photon antenna and sensitize Tb
3+
luminescence. Because of the time-resolved property of the luminescence, the background from the other proteins (especially in the fermentation system) in the assay could be reduced and, therefore, the sensitivity was increased. Moreover, because the detection was performed on a 96- or 384-well plate, the activity of the nitrilases from microorganisms could be determined quickly. Based on this strategy, the best fermentation conditions for nitrilase-producing strains were obtained.
IncP-1β Plasmid pGNB1 Isolated from a Bacterial Community from a Wastewater Treatment Plant Mediates Decolorization of Triphenylmethane Dyes
Authors: Schlüter Andreas , Krahn Irene , Kollin Florian , Bönemann Gabriele , Stiens Michael , Szczepanowski Rafael , Schneiker Susanne , Pühler Alfred 
Published: August 2007

ABSTRACT

Plasmid pGNB1 was isolated from bacteria residing in the activated sludge compartment of a wastewater treatment plant by using a transformation-based approach. This 60-kb plasmid confers resistance to the triphenylmethane dye crystal violet and enables its host bacterium to decolorize crystal violet. Partial sequencing of pGNB1 revealed that its backbone is very similar to that of previously sequenced IncP-1β plasmids. The two accessory regions of the plasmid, one located downstream of the replication initiation gene
trfA
and the other located between the conjugative transfer modules Tra and Trb, were completely sequenced. Accessory region L1 contains a transposon related to Tn
5501
and a gene encoding a Cupin 2 conserved barrel protein with an unknown function. The triphenylmethane reductase gene
tmr
and a truncated dihydrolipoamide dehydrogenase gene that is flanked by IS
1071
and another putative insertion element were identified in accessory region L2. Subcloning of the pGNB1
tmr
gene demonstrated that this gene is responsible for the observed crystal violet resistance phenotype and mediates decolorization of the triphenylmethane dyes crystal violet, malachite green, and basic fuchsin. Plasmid pGNB1 and the associated phenotype are transferable to the α-proteobacterium
Sinorhizobium meliloti
and the γ-proteobacterium
Escherichia coli
. This is the first report of a promiscuous IncP-1β plasmid isolated from the bacterial community from a wastewater treatment plant that harbors a triphenylmethane reductase gene. The pGNB1-encoded enzyme activity is discussed with respect to bioremediation of sewage polluted with triphenylmethane dyes.
“
Candidatus
Accumulibacter” Population Structure in Enhanced Biological Phosphorus Removal Sludges as Revealed by Polyphosphate Kinase Genes
Authors: He Shaomei , Gall Daniel L. , McMahon Katherine D. 
Published: August 2007

ABSTRACT

We investigated the fine-scale population structure of the “
Candidatus
Accumulibacter” lineage in enhanced biological phosphorus removal (EBPR) systems using the polyphosphate kinase 1 gene (
ppk1
) as a genetic marker. We retrieved fragments of “
Candidatus
Accumulibacter” 16S rRNA and
ppk1
genes from one laboratory-scale and several full-scale EBPR systems. Phylogenies reconstructed using 16S rRNA genes and
ppk1
were largely congruent, with
ppk1
granting higher phylogenetic resolution and clearer tree topology and thus serving as a better genetic marker than 16S rRNA for revealing population structure within the “
Candidatus
Accumulibacter” lineage. Sequences from at least five clades of “
Candidatus
Accumulibacter” were recovered by
ppk1
-targeted PCR, and subsequently, specific primer sets were designed to target the
ppk1
gene for each clade. Quantitative real-time PCR (qPCR) assays using “
Candidatus
Accumulibacter”-specific 16S rRNA and “
Candidatus
Accumulibacter” clade-specific
ppk1
primers were developed and conducted on three laboratory-scale and nine full-scale EBPR samples and two full-scale non-EBPR samples to determine the abundance of the total “
Candidatus
Accumulibacter” lineage and the relative distributions and abundances of the five “
Candidatus
Accumulibacter” clades. The qPCR-based estimation of the total “
Candidatus
Accumulibacter” fraction as a proportion of the bacterial community as measured using 16S rRNA genes was not significantly different from the estimation measured using
ppk1
, demonstrating the power of
ppk1
as a genetic marker for detection of all currently defined “
Candidatus
Accumulibacter” clades. The relative distributions of “
Candidatus
Accumulibacter” clades varied among different EBPR systems and also temporally within a system. Our results suggest that the “
Candidatus
Accumulibacter” lineage is more diverse than previously realized and that different clades within the lineage are ecologically distinct.
Bacteria Metabolically Engineered for Enhanced Phytochelatin Production and Cadmium Accumulation
Authors: Kang Seung Hyun , Singh Shailendra , Kim Jae-Young , Lee Wonkyu , Mulchandani Ashok , Chen Wilfred 
Published: August 2007

ABSTRACT

Phytochelatins (PCs) with good binding affinities for a wide range of heavy metals were exploited to develop microbial sorbents for cadmium removal. PC synthase from
Schizosaccharomyces pombe
(SpPCS) was overexpressed in
Escherichia coli
, resulting in PC synthesis and 7.5-times-higher Cd accumulation. The coexpression of a variant γ-glutamylcysteine synthetase desensitized to feedback inhibition (GshI*) increased the supply of the PC precursor glutathione, resulting in further increases of 10- and 2-fold in PC production and Cd accumulation, respectively. A Cd transporter, MntA, was expressed with SpPCS and GshI* to improve Cd uptake, resulting in a further 1.5-fold increase in Cd accumulation. The level of Cd accumulation in this recombinant
E. coli
strain (31.6 μmol/g [dry weight] of cells) was more than 25-fold higher than that in the control strain.
An Sfi1p-Like Centrin-Binding Protein Mediates Centrin-Based Ca
2+
-Dependent Contractility in
Paramecium tetraurelia
Authors: Gogendeau Delphine , Beisson Janine , de Loubresse Nicole Garreau , Le Caer Jean-Pierre , Ruiz Françoise , Cohen Jean , Sperling Linda , Koll France , Klotz Catherine 
Published: August 2007

ABSTRACT

The previous characterization and structural analyses of Sfi1p, a
Saccharomyces cerevisiae
centrin-binding protein essential for spindle pole body duplication, have suggested molecular models to account for centrin-mediated, Ca
2+
-dependent contractility processes (S. Li, A. M. Sandercock, P. Conduit, C. V. Robinson, R. L. Williams, and J. V. Kilmartin, J. Cell Biol. 173:867-877, 2006). Such processes can be analyzed by using
Paramecium tetraurelia
, which harbors a large Ca
2+
-dependent contractile cytoskeletal network, the infraciliary lattice (ICL). Previous biochemical and genetic studies have shown that the ICL is composed of diverse centrin isoforms and a high-molecular-mass centrin-associated protein, whose reduced size in the démaillé (dem1) mutant correlates with defective organization of the ICL. Using sequences derived from the high-molecular-mass protein to probe the
Paramecium
genome sequence, we characterized the Pt
CenBP1
gene, which encodes a 460-kDa protein. PtCenBP1p displays six almost perfect repeats of ca. 427 amino acids (aa) and harbors 89 potential centrin-binding sites with the consensus motif LLX
11
F/LX
2
WK/R, similar to the centrin-binding sites of ScSfi1p. The smaller (260-kDa) protein encoded by the dem1 mutant Pt
CenBP1
allele comprises only two repeats of 427 aa and 46 centrin-binding sites. By using RNA interference and green fluorescent protein fusion experiments, we showed that PtCenBP1p forms the backbone of the ICL and plays an essential role in its assembly and contractility. This study provides the first in vivo demonstration of the role of Sfi1p-like proteins in centrin-mediated Ca
2+
-dependent contractile processes.
Plasmids pMOL28 and pMOL30 of
Cupriavidus metallidurans
Are Specialized in the Maximal Viable Response to Heavy Metals
Authors: Monchy Sébastien , Benotmane Mohammed A. , Janssen Paul , Vallaeys Tatiana , Taghavi Safiyh , van der Lelie Daniel , Mergeay Max 
Published: August 2007

ABSTRACT

We fully annotated two large plasmids, pMOL28 (164 open reading frames [ORFs]; 171,459 bp) and pMOL30 (247 ORFs; 233,720 bp), in the genome of
Cupriavidus metallidurans
CH34. pMOL28 contains a backbone of maintenance and transfer genes resembling those found in plasmid pSym of
C. taiwanensis
and plasmid pHG1 of
C. eutrophus
, suggesting that they belong to a new class of plasmids. Genes involved in resistance to the heavy metals Co(II), Cr(VI), Hg(II), and Ni(II) are concentrated in a 34-kb region on pMOL28, and genes involved in resistance to Ag(I), Cd(II), Co(II), Cu(II), Hg(II), Pb(II), and Zn(II) occur in a 132-kb region on pMOL30. We identified three putative genomic islands containing metal resistance operons flanked by mobile genetic elements, one on pMOL28 and two on pMOL30. Transcriptomic analysis using quantitative PCR and microarrays revealed metal-mediated up-regulation of 83 genes on pMOL28 and 143 genes on pMOL30 that coded for all known heavy metal resistance proteins, some new heavy metal resistance proteins (
czcJ
,
mmrQ
, and
pbrU
), membrane proteins, truncated transposases, conjugative transfer proteins, and many unknown proteins. Five genes on each plasmid were down-regulated; for one of them,
chrI
localized on pMOL28, the down-regulation occurred in the presence of five cations. We observed multiple cross-responses (induction of specific metal resistance by other metals), suggesting that the cellular defense of
C. metallidurans
against heavy metal stress involves various regulons and probably has multiple stages, including a more general response and a more metal-specific response.
Control of Methionine Synthesis and Uptake by MetR and Homocysteine in
Streptococcus mutans
Authors: Sperandio Brice , Gautier Céline , McGovern Stephen , Ehrlich Dusko S. , Renault Pierre , Martin-Verstraete Isabelle , Guédon Eric 
Published: August 2007

ABSTRACT

MetR (formerly Smu.1225), a regulator of the LysR family, controls key genes for methionine supply in
Streptococcus mutans
. An
S. mutans metR
mutant is unable to transport
l
-methionine and to grow in the absence of this amino acid. Accordingly, MetR activates transcription by binding to the promoter regions of two gene clusters and smu.1487, whose products are involved in methionine biosynthesis (MetEF and Smu.1487) and uptake (AtmBDE). Transcriptional activation by MetR requires the presence of a 17-bp palindromic sequence, the Met box. Base substitutions in the Met box hinder the formation of a MetR-DNA complex and abolish MetR-dependent activation, showing that Met boxes correspond to MetR recognition sites. Activation by MetR occurs in methionine-depleted medium and is rapidly triggered under nonactivating conditions by the addition of homocysteine. This intermediate of methionine biosynthesis increases the affinity of MetR for DNA in vitro and appears to be the MetR coeffector in vivo. Homocysteine plays a crucial role in methionine metabolic gene regulation by controlling MetR activity. A similar mechanism of homocysteine- and MetR-dependent control of methionine biosynthetic genes operates in
S. thermophilus
. These data suggest a common mechanism for the regulation of the methionine supply in streptococci. However, some streptococcal species are unable to synthesize the homocysteine coeffector. This intriguing feature is discussed in the light of comparative genomics and streptococcal ecology.
Characterization of IsaA and SceD, Two Putative Lytic Transglycosylases of
Staphylococcus aureus
Authors: Stapleton Melanie R. , Horsburgh Malcolm J. , Hayhurst Emma J. , Wright Lynda , Jonsson Ing-Marie , Tarkowski Andrej , Kokai-Kun John F. , Mond James J. , Foster Simon J. 
Published: August 2007

ABSTRACT

Bacterial cell wall peptidoglycan is a dynamic structure requiring hydrolysis to allow cell wall growth and division.
Staphylococcus aureus
has many known and putative peptidoglycan hydrolases, including two likely lytic transglycosylases. These two proteins, IsaA and SceD, were both found to have autolytic activity. Regulatory studies showed that the
isaA
and
sceD
genes are partially mutually compensatory and that the production of SceD is upregulated in an
isaA
mutant. The expression of
sceD
is also greatly upregulated by the presence of NaCl. Several regulators of
isaA
and
sceD
expression were identified. Inactivation of
sceD
resulted in impaired cell separation, as shown by light microscopy, and “clumping” of bacterial cultures. An
isaA sceD
mutant is attenuated for virulence, while SceD is essential for nasal colonization in cotton rats, thus demonstrating the importance of cell wall dynamics in host-pathogen interactions.
Correlation between Growth Rates, EIIA
Crr
Phosphorylation, and Intracellular Cyclic AMP Levels in
Escherichia coli
K-12
Authors: Bettenbrock Katja , Sauter Thomas , Jahreis Knut , Kremling Andreas , Lengeler Joseph W. , Gilles Ernst-Dieter 
Published: August 2007

ABSTRACT

In
Escherichia coli
K-12, components of the phosphoenolpyruvate-dependent phosphotransferase systems (PTSs) represent a signal transduction system involved in the global control of carbon catabolism through inducer exclusion mediated by phosphoenolpyruvate-dependent protein kinase enzyme IIA
Crr
(EIIA
Crr
) (= EIIA
Glc
) and catabolite repression mediated by the global regulator cyclic AMP (cAMP)-cAMP receptor protein (CRP). We measured in a systematic way the relation between cellular growth rates and the key parameters of catabolite repression, i.e., the phosphorylated EIIA
Crr
(EIIA
Crr
∼P) level and the cAMP level, using in vitro and in vivo assays. Different growth rates were obtained by using either various carbon sources or by growing the cells with limited concentrations of glucose, sucrose, and mannitol in continuous bioreactor experiments. The ratio of EIIA
Crr
to EIIA
Crr
∼P and the intracellular cAMP concentrations, deduced from the activity of a cAMP-CRP-dependent promoter, correlated well with specific growth rates between 0.3 h
−1
and 0.7 h
−1
, corresponding to generation times of about 138 and 60 min, respectively. Below and above this range, these parameters were increasingly uncoupled from the growth rate, which perhaps indicates an increasing role executed by other global control systems, in particular the stringent-relaxed response system.
ASerratia marcescensOxyR Homolog Mediates Surface Attachment and Biofilm Formation
Authors: Shanks Robert M. Q. , Stella Nicholas A. , Kalivoda Eric J. , Doe Megan R. , O'Dee Dawn M. , Lathrop Kira L. , Guo Feng Li , Nau Gerard J. 
Published: August 2007

ABSTRACTOxyR is a conserved bacterial transcription factor with a regulatory role in oxidative stress response. From a genetic screen for genes that modulate biofilm formation in the opportunistic pathogenSerratia marcescens, mutations in anoxyRhomolog and predicted fimbria structural genes were identified.S. marcescens oxyRmutants were severely impaired in biofilm formation, in contrast to the hyperbiofilm phenotype exhibited byoxyRmutants ofEscherichia coliandBurkholderia pseudomallei. Further analysis revealed that OxyR plays a role in the primary attachment of cells to a surface. Similar to what is observed in other bacterial species,S. marcescensOxyR is required for oxidative stress resistance. Mutations inoxyRand type I fimbrial genes resulted in severe defects in fimbria-associated phenotypes, revealing roles in cell-cell and cell-biotic surface interactions. Transmission electron microscopy revealed the absence of fimbria-like surface structures on an OxyR-deficient strain and an enhanced fimbrial phenotype in strains bearingoxyRon a multicopy plasmid. The hyperfimbriated phenotype conferred by the multicopyoxyRplasmid was absent in a type I fimbrial mutant background. Real-time reverse transcriptase PCR indicated an absence of transcripts from a fimbrial operon in anoxyRmutant that were present in the wild type and a complementedoxyRmutant strain. Lastly, chromosomalPlac-mediated expression offimABCDwas sufficient to restore wild-type levels of yeast agglutination and biofilm formation to anoxyRmutant. Together, these data support a model in which OxyR contributes to early stages ofS. marcescensbiofilm formation by influencing fimbrial gene expression.
An Extremely Oligotrophic Bacterium,
Rhodococcus erythropolis
N9T-4, Isolated from Crude Oil
Authors: Ohhata Naoko , Yoshida Nobuyuki , Egami Hiroshi , Katsuragi Tohoru , Tani Yoshiki , Takagi Hiroshi 
Published: August 2007

ABSTRACT

Rhodococcus erythropolis
N9T-4, which was isolated from crude oil, showed extremely oligotrophic growth and formed its colonies on a minimal salt medium solidified using agar or silica gel without any additional carbon source. N9T-4 did not grow under CO
2
-limiting conditions but could grow on a medium containing NaHCO
3
under the same conditions, suggesting that the oligotrophic growth of N9T-4 depends on CO
2
. Proteomic analysis of N9T-4 revealed that two proteins, with molecular masses of 45 and 55 kDa, were highly induced under the oligotrophic conditions. The primary structures of these proteins exhibited striking similarities to those of methanol:
N
,
N
′-dimethyl-4-nitrosoaniline oxidoreductase and an aldehyde dehydrogenase from
Rhodococcus
sp. These enzyme activities were three times higher under oligotrophic conditions than under
n
-tetradecane-containing heterotrophic conditions, and gene disruption for the aldehyde dehydrogenase caused a lack of growth on the minimal salt medium. Furthermore, 3-hexulose 6-phosphate synthase and phospho-3-hexuloisomerase activities, which are key enzymes in the ribulose monophosphate pathway in methylotrophic bacteria, were detected specifically in the cell extract of oligotrophically grown N9T-4. These results suggest that CO
2
fixation involves methanol (formaldehyde) metabolism in the oligotrophic growth of
R. erythropolis
N9T-4.
MarR-Like Transcriptional Regulator Involved in Detoxification of Aromatic Compounds in
Sulfolobus solfataricus
Authors: Fiorentino Gabriella , Ronca Raffaele , Cannio Raffaele , Rossi Mosè , Bartolucci Simonetta 
Published: August 2007

ABSTRACT

A DNA binding protein, BldR, was identified in the crenarchaeon
Sulfolobus solfataricus
as a protein 5- to 10-fold more abundant in cells grown in the presence of toxic aldehydes; it binds to regulatory sequences located upstream of an alcohol dehydrogenase gene (Sso2536). BldR is homologous to bacterial representatives of the MarR (multiple antibiotic resistance) family of transcriptional regulators that mediate response to multiple environmental stresses. Transcriptional analysis revealed that the
bldR
gene was transcribed in a bicistronic unit composed of the genes encoding the transcriptional regulator (Sso1352) and a putative multidrug transporter (Sso1351) upstream. By homology to bacterial counterparts, the bicistron was named the
mar
-like operon. The level of
mar
-like operon expression was found to be increased at least 10-fold in response to chemical stress by aromatic aldehydes. Under the same growth conditions, similar enhanced in vivo levels of Sso2536 gene transcript were also measured. The gene encoding BldR was expressed in
E. coli
, and the recombinant protein was purified to homogeneity. DNA binding assays demonstrated that the protein is indeed a transcription factor able to recognize site specifically both the Sso2536 and
mar
-like promoters at sites containing palindromic consensus sequences. Benzaldehyde, the substrate of ADH
Ss
, stimulates DNA binding of BldR at both promoters. The role of BldR in the auto-activation as well as in the regulation of the Sso2536 gene, together with results of increased operon and gene expression under conditions of exposure to aromatic aldehydes, indicates a novel coordinate regulatory mechanism in cell defense against stress by aromatic compounds.
The Archaeon
Methanosarcina acetivorans
Contains a Protein Disulfide Reductase with an Iron-Sulfur Cluster
Authors: Lessner Daniel J. , Ferry James G. 
Published: August 2007

ABSTRACT

Methanosarcina acetivorans
, a strictly anaerobic methane-producing species belonging to the domain
Archaea
, contains a gene cluster annotated with homologs encoding oxidative stress proteins. One of the genes (MA3736) is annotated as a gene encoding an uncharacterized carboxymuconolactone decarboxylase, an enzyme required for aerobic growth with aromatic compounds by species in the domain
Bacteria
. Methane-producing species are not known to utilize aromatic compounds, suggesting that MA3736 is incorrectly annotated. The product of MA3736, overproduced in
Escherichia coli
, had protein disulfide reductase activity dependent on a C
67
XXC
70
motif not found in carboxymuconolactone decarboxylase. We propose that MA3736 be renamed
mdrA
(
m
ethanosarcina
d
isulfide
r
eductase). Further, unlike carboxymuconolactone decarboxylase, MdrA contained an Fe-S cluster. Binding of the Fe-S cluster was dependent on essential cysteines C
67
and C
70
, while cysteines C
39
and C
107
were not required. Loss of the Fe-S cluster resulted in conversion of MdrA from an inactive hexamer to a trimer with protein disulfide reductase activity. The data suggest that MdrA is the prototype of a previously unrecognized protein disulfide reductase family which contains an intermolecular Fe-S cluster that controls oligomerization as a mechanism to regulate protein disulfide reductase activity.