bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lignin-Derived Compounds as Efficient Laccase Mediators for Decolorization of Different Types of Recalcitrant Dyes
Authors: Camarero Susana , Ibarra David , Martínez María Jesús , Martínez Ángel T. 
Published: April 2005

ABSTRACTTen phenols were selected as natural laccase mediators after screening 44 different compounds with a recalcitrant dye (Reactive Black 5) as a substrate. Their performances were evaluated at different mediator/dye ratios and incubation times (up to 6 h) by the use ofPycnoporus cinnabarinusandTrametes villosalaccases and were compared with those of eight known synthetic mediators (including -NOH- compounds). Among the six types of dyes assayed, only Reactive Blue 38 (phthalocyanine) was resistant to laccase-mediator treatment under the conditions used. Acid Blue 74 (indigoid dye), Reactive Blue 19 (anthraquinoid dye), and Aniline Blue (triarylmethane-type dye) were partially decolorized by the laccases alone, although decolorization was much more efficient and rapid with mediators, whereas Reactive Black 5 (diazo dye) and Azure B (heterocyclic dye) could be decolorized only in the presence of mediators. The efficiency of each natural mediator depended on the type of dye to be treated but, with the only exception being Azure B (<50% decolorization), nearly complete decolorization (80 to 100%) was attained in all cases. Similar rates were attained with the best synthetic mediators, but the reactions were significantly slower. Phenolic aldehydes, ketones, acids, and esters related to the three lignin units were among the best mediators, includingp-coumaric acid, vanillin, acetovanillone, methyl vanillate, and above all, syringaldehyde and acetosyringone. The last two compounds are especially promising as ecofriendly (and potentially cheap) mediators for industrial applications since they provided the highest decolorization rates in only 5 to 30 min, depending on the type of dye to be treated.
Azospirillum brasilense
Produces the Auxin-Like Phenylacetic Acid by Using the Key Enzyme for Indole-3-Acetic Acid Biosynthesis
Authors: Somers E. , Ptacek D. , Gysegom P. , Srinivasan M. , Vanderleyden J. 
Published: April 2005

ABSTRACT

An antimicrobial compound was isolated from
Azospirillum brasilense
culture extracts by high-performance liquid chromatography and further identified by gas chromatography-mass spectrometry as the auxin-like molecule, phenylacetic acid (PAA). PAA synthesis was found to be mediated by the indole-3-pyruvate decarboxylase, previously identified as a key enzyme in indole-3-acetic acid (IAA) production in
A. brasilense
. In minimal growth medium, PAA biosynthesis by
A. brasilense
was only observed in the presence of phenylalanine (or precursors thereof). This observation suggests deamination of phenylalanine, decarboxylation of phenylpyruvate, and subsequent oxidation of phenylacetaldehyde as the most likely pathway for PAA synthesis. Expression analysis revealed that transcription of the
ipdC
gene is upregulated by PAA, as was previously described for IAA and synthetic auxins, indicating a positive feedback regulation. The synthesis of PAA by
A. brasilense
is discussed in relation to previously reported biocontrol properties of
A. brasilense
.
Anaerobic Ammonia-Oxidizing Bacteria and Related Activity in Baltimore Inner Harbor Sediment
Authors: Tal Yossi , Watts Joy E. M. , Schreier Harold J. 
Published: April 2005

ABSTRACT

The discovery of bacteria capable of anaerobic ammonia oxidation (anammox) has generated interest in understanding the activity, diversity, and distribution of these bacteria in the environment. In this study anammox activity in sediment samples obtained from the Inner Harbor of Baltimore, Md., was detected by
15
N tracer assays. Anammox-specific oligonucleotide primer sets were used to screen a
Planctomycetales
-specific 16S rRNA gene library generated from sediment DNA preparations, and four new anammox bacterial sequences were identified. Three of these sequences form a cohesive new branch of the anammox group, and the fourth sequence branches separately from this group. Denaturing gradient gel electrophoresis analysis of sediment incubated with anammox-specific media confirmed the presence of the four anammox-related 16S rRNA gene sequences. Evidence for the presence of anammox bacteria in Inner Harbor sediment was also obtained by using an anammox-specific probe in fluorescence in situ hybridization studies. To our knowledge, this is the first report of anammox activity and related bacterial 16S rRNA gene sequences from the Chesapeake Bay basin area, and the results suggest that this pathway plays an important role in the nitrogen cycle of this estuarine environment. Furthermore, the presence of these bacteria and their activity in sediment strengthen the contention that anammox-related
Plactomycetales
are globally distributed.
Rapid Engineering of the Geldanamycin Biosynthesis Pathway by Red/ET Recombination and Gene Complementation
Authors: Vetcher Leandro , Tian Zong-Qiang , McDaniel Robert , Rascher Andreas , Revill W. Peter , Hutchinson C. Richard , Hu Zhihao 
Published: April 2005

ABSTRACT

Genetic manipulation of antibiotic producers, such as
Streptomyces
species, is a rational approach to improve the properties of biologically active molecules. However, this can be a slow and sometimes problematic process. Red/ET recombination in an
Escherichia coli
host has permitted rapid and more versatile engineering of geldanamycin biosynthetic genes in a complementation plasmid, which can then be readily transferred into the
Streptomyces
host from which the corresponding wild type gene(s) has been removed. With this rapid Red/ET recombination and gene complementation approach, efficient gene disruptions and gene replacements in the geldanamycin biosynthetic gene cluster have been successfully achieved. As an example, we describe here the creation of a ketoreductase 6 null mutation in an
E. coli
high-copy-number plasmid carrying
gdmA2A3
from
Streptomyces hygroscopicus
NRRL3602 and the subsequent complementation of a
gdmA2A3
deletion host with this plasmid to generate a novel geldanamycin analog.
Biotinylation Facilitates the Uptake of Large Peptides by
Escherichia coli
and Other Gram-Negative Bacteria
Authors: Walker Jennifer R. , Altman Elliot 
Published: April 2005

ABSTRACT

Gram-negative bacteria such as
Escherichia coli
can normally only take up small peptides less than 650 Da, or five to six amino acids, in size. We have found that biotinylated peptides up to 31 amino acids in length can be taken up by
E. coli
and that uptake is dependent on the biotin transporter. Uptake could be competitively inhibited by free biotin or avidin and blocked by the protonophore carbonyl
m
-chlorophenylhydrazone and was abolished in
E. coli
mutants that lacked the biotin transporter. Biotinylated peptides could be used to supplement the growth of a biotin auxotroph, and the transported peptides were shown to be localized to the cytoplasm in cell fractionation experiments. The uptake of biotinylated peptides was also demonstrated for two other gram-negative bacteria,
Salmonella enterica
serovar Typhimurium and
Pseudomonas aeruginosa
. This finding may make it possible to create new peptide antibiotics that can be used against gram-negative pathogens. Researchers have used various moieties to cause the illicit transport of compounds in bacteria, and this study demonstrates the illicit transport of the largest known compound to date.
Nutrient Effects on Biocontrol of
Penicillium roqueforti
by
Pichia anomala
J121 during Airtight Storage of Wheat
Authors: Druvefors Ulrika Ädel , Passoth Volkmar , Schnürer Johan 
Published: April 2005

ABSTRACT

The biocontrol yeast
Pichia anomala
inhibits the growth of a variety of mold species. We examined the mechanism underlying the inhibition of the grain spoilage mold
Penicillium roqueforti
by the biocontrol yeast
P. anomala
J121 during airtight storage. The biocontrol effect in a model grain silo with moist wheat (water activity of 0.96) was enhanced when complex medium, maltose, or glucose was added. Supplementation with additional nitrogen or vitamin sources did not affect the biocontrol activity of the yeast. The addition of complex medium or glucose did not significantly influence the yeast cell numbers in the silos, whether in the presence or absence of
P. roqueforti
. Mold growth was not influenced by the addition of nutrients, if cultivated without yeast. The products of glucose metabolism, mainly ethanol and ethyl acetate, increased after glucose addition to
P. anomala
-inoculated treatments. Our results suggest that neither competition for nutrients nor production of a glucose-repressible cell wall lytic enzyme is the main mode of action of biocontrol by
P. anomala
in this grain system. Instead, the mold-inhibiting effect probably is due to the antifungal action of metabolites, most likely a combination of ethyl acetate and ethanol, derived from glycolysis. The discovery that sugar amendments enhance the biocontrol effect of
P. anomala
suggests novel ways of formulating biocontrol yeasts.
Folate Cross-Feeding Supports Symbiotic Homoacetogenic Spirochetes
Authors: Graber Joseph R. , Breznak John A. 
Published: April 2005

ABSTRACT

Treponema primitia
, an H
2
-consuming CO
2
-reducing homoacetogenic spirochete in termite hindguts, requires an exogenous source of folate for growth. Tetrahydrofolate (THF) acts as a C
1
carrier in CO
2
-reductive acetogenesis, a microbially mediated process important to the carbon and energy requirements of termites. To examine the hypothesis that other termite gut microbes probably supply some form of folate to
T. primitia
in situ, we used a bioassay to screen for and isolate folate-secreting bacteria from hindguts of
Zootermopsis angusticollis
, which is the host of
T. primitia
. Based on morphology, physiology, and 16S rRNA gene sequences, the major folate secretors were identified as strains of
Lactococcus lactis
and
Serratia grimesii
. During growth, these isolates secreted 5-formyl-THF at levels up to 146 ng/ml, and their cell-free culture fluids satisfied the folate requirement of
T. primitia
strains in vitro. Analysis of
Z. angusticollis
hindgut fluid revealed that 5-formyl-THF was the only detectable folate compound and occurred at an in situ concentration (1.3 μg/ml) which was more than sufficient to support the growth of
T. primitia
. These results imply that cross-feeding of 5-formyl-THF by other community members is important for growth of symbiotic hindgut spirochetes and thus termite nutrition and survival.
Cytotoxicity Potential and Genotypic Characterization of
Escherichia coli
Isolates from Environmental and Food Sources
Authors: Maldonado Yadilka , Fiser Jennifer C. , Nakatsu Cindy H. , Bhunia Arun K. 
Published: April 2005

ABSTRACT

The presence of
Escherichia coli
isolates in the environment is a potential source of contamination of food and water supplies. Moreover, these isolates may harbor virulence genes that can be a source of new forms of pathogenic strains. Here, using multiplex PCR, we examined the presence of virulence gene markers (
stx
1
,
stx
2
,
eaeA
,
hlyA
) in 1,698 environmental isolates of
E. coli
and 81 isolates from food and clinical sources. The PCR analysis showed that ∼5% (79 of 1,698) of the total environmental isolates and 96% (79 of 81) of the food and clinical isolates were positive for at least one of the genes. Of the food and clinical isolates, 84% (68 of 81 isolates) were positive for all four genes. Of the subset of environmental isolates chosen for further analysis, 16% (13 of 79 isolates) were positive for
stx
2
and 84% (66 of 79 isolates) were positive for
eaeA
; 16 of the latter strains were also positive for
hlyA
. The pathogenic potentials of 174 isolates (81 isolates from food and clinical sources and 93 isolates from environmental sources) were tested by using a cytotoxicity assay based on lactate dehydrogenase release from Vero cells. In general, 97% (79 of 81) of the food and clinical isolates and 41% (39 of 93) of the environmental isolates exhibited positive cytotoxicity. High cytotoxicity values correlated to the presence of
stx
genes. The majority of
hly
-positive but
stx
-negative environmental isolates also exhibited a certain degree of cytotoxicity. Isolates were also tested for sorbitol utilization and were genotyped by ribotyping and by repetitive extragenic palindromic PCR (REP-PCR) as potential means of quickly identifying virulent strains from the environment, but none of these methods could be used to distinguish cytotoxic environmental isolates. Only 31% of the isolates were negative for sorbitol fermentation, and none of the isolates had common ribotypes or REP-PCR fingerprints. This study suggests that overall higher cytotoxicity values correlated with the production of
stx
genes, and the majority of
hly
-positive but
stx
-negative environmental isolates also exhibited a certain degree of cytotoxicity. This study demonstrated that there is widespread distribution of potentially virulent
E. coli
strains in the environment that may be a cause of concern for human health.
Genes Involved in SkfA Killing Factor Production Protect a
Bacillus subtilis
Lipase against Proteolysis
Authors: Westers Helga , Braun Peter G. , Westers Lidia , Antelmann Haike , Hecker Michael , Jongbloed Jan D. H. , Yoshikawa Hirofumi , Tanaka Teruo , van Dijl Jan Maarten , Quax Wim J. 
Published: April 2005

ABSTRACT

Small lipases of
Bacillus
species, such as LipA from
Bacillus subtilis
, have a high potential for industrial applications. Recent studies showed that deletion of six AT-rich islands from the
B. subtilis
genome results in reduced amounts of extracellular LipA. Here we demonstrate that the reduced LipA levels are due to the absence of four genes,
skfABCD
, located in the prophage 1 region. Intact
skfABCD
genes are required not only for LipA production at wild-type levels by
B. subtilis
168 but also under conditions of LipA overproduction. Notably, SkfA has bactericidal activity and, probably, requires the SkfB to SkfD proteins for its production. The present results show that LipA is more prone to proteolytic degradation in the absence of SkfA and that high-level LipA production can be improved significantly by employing multiple protease-deficient
B. subtilis
strains. In conclusion, our findings imply that SkfA protects LipA, directly or indirectly, against proteolytic degradation. Conceivably, SkfA could act as a modulator in LipA folding or as a protease inhibitor.
Cloning, Expression, and Site-Directed Mutagenesis of the Propene Monooxygenase Genes fromMycobacteriumsp. Strain M156
Authors: Chan Kwo Chion Chan K. , Askew Sarah E. , Leak David J. 
Published: April 2005

ABSTRACTPropene monooxygenase has been cloned fromMycobacteriumsp. strain M156, based on hybridization with theamoABCDgenes ofRhodococcus corallinusB276. Sequencing indicated that the mycobacterial enzyme is a member of the binuclear nonheme iron monooxygenase family and, in gene order and sequence, is most similar to that fromR. corallinusB-276. Attempts were made to express thepmoABCDoperon inEscherichia coliandMycobacterium smegmatismc2155. In the former, there appeared to be a problem resolving overlapping reading frames betweenpmoAand -Band betweenpmoCand -D, while in the latter, problems were encountered with plasmid instability when thepmoABCDgenes were placed under the control of thehsp60heat shock promoter in the pNBV1 vector. Fortuitously, constructs with the opposite orientation were constitutively expressed at a level sufficient to allow preliminary mutational analysis. Two PMO active-site residues (A94 and V188) were targeted by site-directed mutagenesis to alter their stereoselectivity. The results suggest that changing the volume occupied by the side chain at V188 leads to a systematic alteration in the stereoselectivity of styrene oxidation, presumably by producing different orientations for substrate binding during catalysis. Changing the volume occupied by the side chain at A94 produced a nonsystematic change in stereoselectivity, which may be attributable to the role of this residue in expansion of the binding site during substrate binding. Neither set of mutations changed the enzyme's specificity for epoxidation.
Formation of
trans
Fatty Acids Is Not Involved in Growth-Linked Membrane Adaptation of
Pseudomonas putida
Authors: Härtig Claus , Loffhagen Norbert , Harms Hauke 
Published: April 2005

ABSTRACT

Fatty acid compositions in growing and resting cells of several strains of
Pseudomonas putida
(P8, NCTC 10936, and KT 2440) were studied, with a focus on alterations of the saturation degree,
cis-trans
isomerization, and cyclopropane formation. The fatty acid compositions of the strains were very similar under comparable growth conditions, but surprisingly, and contrary to earlier reports,
trans
fatty acids were not found in either exponentially growing cells or stationary-phase cells. During the transition from growth to the starvation state, cyclopropane fatty acids were preferentially formed, an increase in the saturation degree of fatty acids was observed, and larger amounts of hydroxy fatty acids were detected. A lowered saturation degree and concomitant higher membrane fluidity seemed to be optimal for substrate uptake and growth. The incubation of cells under nongrowth conditions rapidly led to the formation of
trans
fatty acids. We show that harvesting and sample preparation for analysis could provoke the enzyme-catalyzed formation of
trans
fatty acids. Freeze-thawing of resting cells and increased temperatures accelerated the formation of
trans
fatty acids. We demonstrate that
cis-trans
isomerization only occurred in cells that were subjected to an abrupt disturbance without having the possibility of adapting to the changed conditions by the de novo synthesis of fatty acids. The
cis-trans
isomerization reaction was in competition with the
cis
-to-cyclopropane fatty acid conversion. The potential for the formation of
trans
fatty acids depended on the cyclopropane content that was already present.
Diversity and Phylogenetic Affiliations of Morphologically Conspicuous Large Filamentous Bacteria Occurring in the Pelagic Zones of a Broad Spectrum of Freshwater Habitats
Authors: Schauer Michael , Hahn Martin W. 
Published: April 2005

ABSTRACT

Filamentous bacteria with a conspicuous morphology were found in the majority of the bacterioplankton samples from a variety of freshwater habitats that were studied. These heterotrophic filaments typically account for <1 to 11% of the total number of bacteria. The biovolume of this morphotype can exceed 40% of the biovolume for all bacteria. Surprisingly, we found hardly any data on these morphologically conspicuous filaments in the literature. Mixed cultures containing these filamentous bacteria were established by cultivation and isolation experiments with samples from different freshwater lakes. Nearly full-length 16S rRNA gene sequences were obtained from several mixed cultures and environmental samples from habitats in Europe, Africa, China, Australia, and New Zealand. Phylogenetic analysis of the sequences showed that three groups form a single monophyletic cluster, the SOL cluster, in the family
Saprospiraceae
. We developed a set of six nested probes for fluorescence in situ hybridization. Of the six probes, one probe was specific for
Haliscomenobacter hydrossis
, three probes were specific for the three subclusters (each probe was specific for one subcluster), one probe was specific for the entire SOL cluster, and another probe targeted almost the entire
Saprospiraceae
family. Specific hybridization of environmental samples and enrichments showed that the members of the three subclusters exhibited the same filamentous morphology. So far, using the subcluster-specific probes, we have not been able to detect any bacteria with a differing morphology. We conclude that the SOL cluster bacteria are an integral part of bacterioplankton in many freshwater habitats. They potentially account for a large fraction of the total bacterial biomass but have been underrepresented in molecular diversity studies so far.
Identification and Molecular Epidemiology of
Campylobacter coli
Isolates from Human Gastroenteritis, Food, and Animal Sources by Amplified Fragment Length Polymorphism Analysis and Penner Serotyping
Authors: Siemer B. L. , Nielsen E. M. , On S. L. W. 
Published: April 2005

ABSTRACT

Campylobacter coli
is an infrequently studied but important food-borne pathogen with a wide natural distribution. We investigated its molecular epidemiology by use of amplified fragment length polymorphism (AFLP)-based genotyping and Penner serotyping. Serotype reference strains and 177 Danish isolates of diverse origin identified by routine phenotyping as
C. coli
were examined. Molecular tools identified some 12% of field isolates as
Campylobacter jejuni
, emphasizing the need for improved identification methods in routine laboratories. Cluster analysis of AFLP profiles of 174 confirmed
C. coli
isolates revealed a difference in the distribution of isolates from pig and poultry (chicken, duck, turkey, and ostrich) species and indicated the various poultry species, but not pigs, to be likely sources of human
C. coli
infection. A poor correlation was observed between serotyping and AFLP profiling, suggesting that the former method has limited value in epidemiological studies of this species.
Sec-Mediated Secretion of Bacteriocin Enterocin P by
Lactococcus lactis
Authors: Herranz Carmen , Driessen Arnold J. M. 
Published: April 2005

ABSTRACT

Most lactic acid bacterium bacteriocins utilize specific leader peptides and dedicated machineries for secretion. In contrast, the enterococcal bacteriocin enterocin P (EntP) contains a typical signal peptide that directs its secretion when heterologously expressed in
Lactococcus lactis
. Signal peptide mutations and the SecA inhibitor azide blocked secretion. These observations demonstrate that EntP is secreted by the Sec translocase.
Culture-Dependent and -Independent Methods To Investigate the Microbial Ecology of Italian Fermented Sausages
Authors: Rantsiou Kalliopi , Urso Rosalinda , Iacumin Lucilla , Cantoni Carlo , Cattaneo Patrizia , Comi Giuseppe , Cocolin Luca 
Published: April 2005

ABSTRACT

In this study, the microbial ecology of three naturally fermented sausages produced in northeast Italy was studied by culture-dependent and -independent methods. By plating analysis, the predominance of lactic acid bacteria populations was pointed out, as well as the importance of coagulase-negative cocci. Also in the case of one fermentation, the fecal enterocci reached significant counts, highlighting their contribution to the particular transformation process. Yeast counts were higher than the detection limit (>100 CFU/g) in only one fermented sausage. Analysis of the denaturing gradient gel electrophoresis (DGGE) patterns and sequencing of the bands allowed profiling of the microbial populations present in the sausages during fermentation. The bacterial ecology was mainly characterized by the stable presence of
Lactobacillus curvatus
and
Lactobacillus sakei
, but
Lactobacillus paracasei
was also repeatedly detected. An important piece of evidence was the presence of
Lactococcus garvieae
, which clearly contributed in two fermentations. Several species of
Staphylococcus
were also detected. Regarding other bacterial groups,
Bacillus
sp.,
Ruminococcus
sp., and
Macrococcus caseolyticus
were also identified at the beginning of the transformations. In addition, yeast species belonging to
Debaryomyces hansenii
, several
Candida
species, and
Willopsis saturnus
were observed in the DGGE gels. Finally, cluster analysis of the bacterial and yeast DGGE profiles highlighted the uniqueness of the fermentation processes studied.