bluuebunny/crossref_metadata_2025_split huggingface dataset:
Degradation of a Mixture of Hydrocarbons, Gasoline, and Diesel Oil Additives by
Rhodococcus aetherivorans
and
Rhodococcus wratislaviensis
Authors: Auffret Marc , Labbé Diane , Thouand Gérald , Greer Charles W. , Fayolle-Guichard Françoise 
Published: October 2009

ABSTRACT

Two strains, identified as
Rhodococcus wratislaviensis
IFP 2016 and
Rhodococcus aetherivorans
IFP 2017, were isolated from a microbial consortium that degraded 15 petroleum compounds or additives when provided in a mixture containing 16 compounds (benzene, toluene, ethylbenzene,
m
-xylene,
p
-xylene,
o
-xylene, octane, hexadecane, 2,2,4-trimethylpentane [isooctane], cyclohexane, cyclohexanol, naphthalene, methyl
tert
-butyl ether [MTBE], ethyl
tert
-butyl ether [ETBE],
tert
-butyl alcohol [TBA], and 2-ethylhexyl nitrate [2-EHN]). The strains had broad degradation capacities toward the compounds, including the more recalcitrant ones, MTBE, ETBE, isooctane, cyclohexane, and 2-EHN.
R. wratislaviensis
IFP 2016 degraded and mineralized to different extents 11 of the compounds when provided individually, sometimes requiring 2,2,4,4,6,8,8-heptamethylnonane (HMN) as a cosolvent.
R. aetherivorans
IFP 2017 degraded a reduced spectrum of substrates. The coculture of the two strains degraded completely 13 compounds, isooctane and 2-EHN were partially degraded (30% and 73%, respectively), and only TBA was not degraded. Significant MTBE and ETBE degradation rates, 14.3 and 116.1 μmol of ether degraded h
−1
g
−1
(dry weight), respectively, were measured for
R. aetherivorans
IFP 2017. The presence of benzene, toluene, ethylbenzene, and xylenes (BTEXs) had a detrimental effect on ETBE and MTBE biodegradation, whereas octane had a positive effect on the MTBE biodegradation by
R. wratislaviensis
IFP 2016. BTEXs had either beneficial or detrimental effects on their own degradation by
R. wratislaviensis
IFP 2016. Potential genes involved in hydrocarbon degradation in the two strains were identified and partially sequenced.
Analyses of Current-Generating Mechanisms of
Shewanella loihica
PV-4 and
Shewanella oneidensis
MR-1 in Microbial Fuel Cells
Authors: Newton Gregory J. , Mori Shigeki , Nakamura Ryuhei , Hashimoto Kazuhito , Watanabe Kazuya 
Published: October 2009

ABSTRACT

Although members of the genus
Shewanella
have common features (e.g., the presence of decaheme
c
-type cytochromes [
c
-cyts]), they are widely variable in genetic and physiological features. The present study compared the current-generating ability of
S. loihica
PV-4 in microbial fuel cells (MFCs) with that of well-characterized
S. oneidensis
MR-1 and examined the roles of
c
-cyts in extracellular electron transfer. We found that strains PV-4 and MR-1 exhibited notable differences in current-generating mechanisms. While the MR-1 MFCs maintained a constant current density over time, the PV-4 MFCs continued to increase in current density and finally surpassed the MR-1 MFCs. Coulombic efficiencies reached 26% in the PV-4 MFC but 16% in the MR-1 MFCs. Although both organisms produced quinone-like compounds, anode exchange experiments showed that anode-attached cells of PV-4 produced sevenfold more current than planktonic cells in the same chamber, while planktonic cells of MR-1 produced twice the current of the anode-attached cells. Examination of the genome sequence indicated that PV-4 has more
c
-cyt genes in the metal reductase-containing locus than MR-1. Mutational analysis revealed that PV-4 relied predominantly on a homologue of the decaheme
c
-cyt MtrC in MR-1 for current generation, even though it also possesses two homologues of the decaheme
c
-cyt OmcA in MR-1. These results suggest that current generation in a PV-4 MFC is in large part accomplished by anode-attached cells, in which the MtrC homologue constitutes the main path of electrons toward the anode.
Genetic Features of Resident Biofilms Determine Attachment of
Listeria monocytogenes
Authors: Habimana Olivier , Meyrand Mickael , Meylheuc Thierry , Kulakauskas Saulius , Briandet Romain 
Published: October 2009

ABSTRACT

Planktonic
Listeria monocytogenes
cells in food-processing environments tend most frequently to adhere to solid surfaces. Under these conditions, they are likely to encounter resident biofilms rather than a raw solid surface. Although metabolic interactions between
L. monocytogenes
and resident microflora have been widely studied, little is known about the biofilm properties that influence the initial fixation of
L. monocytogenes
to the biofilm interface. To study these properties, we created a set of model resident
Lactococcus lactis
biofilms with various architectures, types of matrices, and individual cell surface properties. This was achieved using cell wall mutants that affect bacterial chain formation, exopolysaccharide (EPS) synthesis and surface hydrophobicity. The dynamics of the formation of these biofilm structures were analyzed in flow cell chambers using in situ time course confocal laser scanning microscopy imaging. All the
L. lactis
biofilms tested reduced the initial immobilization of
L. monocytogenes
compared to the glass substratum of the flow cell. Significant differences were seen in
L. monocytogenes
settlement as a function of the genetic background of resident lactococcal biofilm cells. In particular, biofilms of the
L. lactis
chain-forming mutant resulted in a marked increase in
L. monocytogenes
settlement, while biofilms of the EPS-secreting mutant efficiently prevented pathogen fixation. These results offer new insights into the role of resident biofilms in governing the settlement of pathogens on food chain surfaces and could be of relevance in the field of food safety controls.
Microbial Production of Glyceric Acid, an Organic Acid That Can Be Mass Produced from Glycerol
Authors: Habe Hiroshi , Shimada Yuko , Yakushi Toshiharu , Hattori Hiromi , Ano Yoshitaka , Fukuoka Tokuma , Kitamoto Dai , Itagaki Masayuki , Watanabe Kunihiro , Yanagishita Hiroshi , Matsushita Kazunobu , Sakaki Keiji 
Published: October 2009

ABSTRACT

Glyceric acid (GA), an unfamiliar biotechnological product, is currently produced as a small by-product of dihydroxyacetone production from glycerol by
Gluconobacter oxydans
. We developed a method for the efficient biotechnological production of GA as a target compound for new surplus glycerol applications in the biodiesel and oleochemical industries. We investigated the ability of 162 acetic acid bacterial strains to produce GA from glycerol and found that the patterns of productivity and enantiomeric GA compositions obtained from several strains differed significantly. The growth parameters of two different strain types,
Gluconobacter frateurii
NBRC103465 and
Acetobacter tropicalis
NBRC16470, were optimized using a jar fermentor.
G. frateurii
accumulated 136.5 g/liter of GA with a 72%
d
-GA enantiomeric excess (ee) in the culture broth, whereas
A. tropicalis
produced 101.8 g/liter of
d
-GA with a 99% ee. The 136.5 g/liter of glycerate in the culture broth was concentrated to 236.5 g/liter by desalting electrodialysis during the 140-min operating time, and then, from 50 ml of the concentrated solution, 9.35 g of GA calcium salt was obtained by crystallization. Gene disruption analysis using
G. oxydans
IFO12528 revealed that the membrane-bound alcohol dehydrogenase (mADH)-encoding gene (
adhA
) is required for GA production, and purified mADH from
G. oxydans
IFO12528 catalyzed the oxidation of glycerol. These results strongly suggest that mADH is involved in GA production by acetic acid bacteria. We propose that GA is potentially mass producible from glycerol feedstock by a biotechnological process.
Importance of Polyphosphate Kinase 1 for
Campylobacter jejuni
Viable-but-Nonculturable Cell Formation, Natural Transformation, and Antimicrobial Resistance
Authors: Gangaiah Dharanesh , Kassem Issmat I. , Liu Zhe , Rajashekara Gireesh 
Published: October 2009

ABSTRACT

Campylobacter jejuni
, a gram-negative, microaerophilic bacterium, is a predominant cause of bacterial gastroenteritis in humans. Although considered fragile and fastidious and lacking many classical stress response mechanisms,
C
.
jejuni
exhibits a remarkable capacity for survival and adaptation, successfully infecting humans and persisting in the environment. Consequently, understanding the physiological and genetic properties that allow
C
.
jejuni
to survive and adapt to various stress conditions is crucial for therapeutic interventions. Of importance is polyphosphate (poly-P) kinase 1 (PPK1), which is a key enzyme mediating the synthesis of poly-P, an essential molecule for survival, mediating stress responses, host colonization, and virulence in many bacteria. Therefore, we investigated the role of PPK1 in
C
.
jejuni
pathogenesis, stress survival, and adaptation. Our findings demonstrate that a
C
.
jejuni
Δ
ppk1
mutant was deficient in poly-P accumulation, which was associated with a decreased ability to form viable-but-nonculturable cells under acid stress. The Δ
ppk1
mutant also showed a decreased frequency of natural transformation and an increased susceptibility to various antimicrobials. Furthermore, the Δ
ppk1
mutant was characterized by a dose-dependent deficiency in chicken colonization. Complementation of the Δ
ppk
1 mutant with the wild-type copy of
ppk1
restored the deficient phenotypes to levels similar to those of the wild type. Our results suggest that poly-P plays an important role in stress survival and adaptation and might contribute to genome plasticity and the spread and development of antimicrobial resistance in
C
.
jejuni
. These findings highlight the potential of PPK1 as a novel target for therapeutic interventions.
In Vivo Display of a Multisubunit Enzyme Complex on Biogenic Magnetic Nanoparticles
Authors: Ohuchi Shoji , Schüler Dirk 
Published: October 2009

ABSTRACT

Magnetosomes are unique bacterial organelles comprising membrane-enveloped magnetic crystals produced by magnetotactic bacteria. Because of several desirable chemical and physical properties, magnetosomes would be ideal scaffolds on which to display highly complicated biological complexes artificially. As a model experiment for the functional expression of a multisubunit complex on magnetosomes, we examined the display of a chimeric bacterial RNase P enzyme composed of the protein subunit (C5) of
Escherichia coli
RNase P and the endogenous RNA subunit by expressing a translational fusion of C5 with MamC, a known magnetosome protein, in the magnetotactic bacterium
Magnetospirillum gryphiswaldense
. As intended, the purified C5 fusion magnetosomes, but not wild-type magnetosomes, showed apparent RNase P activity and the association of a typical bacterial RNase P RNA. Our results demonstrate for the first time that magnetosomes can be employed as scaffolds for the display of multisubunit complexes.
Reengineering
Escherichia coli
for Succinate Production in Mineral Salts Medium
Authors: Zhang X. , Jantama K. , Shanmugam K. T. , Ingram L. O. 
Published: October 2009

ABSTRACT

The fermentative metabolism of glucose was redirected to succinate as the primary product without mutating any genes encoding the native mixed-acid fermentation pathway or redox reactions. Two changes in peripheral pathways were together found to increase succinate yield fivefold: (i) increased expression of phosphoenolpyruvate carboxykinase and (ii) inactivation of the glucose phosphoenolpyruvate-dependent phosphotransferase system. These two changes increased net ATP production, increased the pool of phosphoenolpyruvate available for carboxylation, and increased succinate production. Modest further improvements in succinate yield were made by inactivating the
pflB
gene, encoding pyruvate formate lyase, resulting in an
E
scherichia coli
pathway that is functionally similar to the native pathway in
Actinobacillus succinogenes
and other succinate-producing rumen bacteria.
Periplasmic Electron Transfer via the
c
-Type Cytochromes MtrA and FccA of
Shewanella oneidensis
MR-1
Authors: Schuetz Bjoern , Schicklberger Marcus , Kuermann Johannes , Spormann Alfred M. , Gescher Johannes 
Published: October 2009

ABSTRACT

Dissimilatory microbial reduction of insoluble Fe(III) oxides is a geochemically and ecologically important process which involves the transfer of cellular, respiratory electrons from the cytoplasmic membrane to insoluble, extracellular, mineral-phase electron acceptors. In this paper evidence is provided for the function of the periplasmic fumarate reductase FccA and the decaheme
c
-type cytochrome MtrA in periplasmic electron transfer reactions in the gammaproteobacterium
Shewanella oneidensis
. Both proteins are abundant in the periplasm of ferric citrate-reducing
S. oneidensis
cells. In vitro fumarate reductase FccA and
c
-type cytochrome MtrA were reduced by the cytoplasmic membrane-bound protein CymA. Electron transfer between CymA and MtrA was 1.4-fold faster than the CymA-catalyzed reduction of FccA. Further experiments showing a bidirectional electron transfer between FccA and MtrA provided evidence for an electron transfer network in the periplasmic space of
S. oneidensis
. Hence, FccA could function in both the electron transport to fumarate and via MtrA to mineral-phase Fe(III). Growth experiments with a Δ
fccA
deletion mutant suggest a role of FccA as a transient electron storage protein.
Functional Genomic Analysis of Two
Staphylococcus aureus
Phages Isolated from the Dairy Environment
Authors: García Pilar , Martínez Beatriz , Obeso José María , Lavigne Rob , Lurz Rudi , Rodríguez Ana 
Published: October 2009

ABSTRACT

The genomes of the two lytic mutant
Staphylococcus aureus
bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (
cos
) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analyses, and functional analyses enabled the assignment of putative functions to 58 gene products, including DNA packaging proteins, morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, modification, and replication. Point mutations in their lysogeny control-associated genes explain their strictly lytic behavior. Muralytic activity associated with other structural components has been detected in virions of both phages. Comparative analysis of phiIPLA35 and phiIPLA88 genome structures shows that they resemble those of φ12 and φ11, respectively, both representatives of large genomic groupings within the
S. aureus
-infecting phages.
Bacterial Polyester Inclusions Engineered To Display Vaccine Candidate Antigens for Use as a Novel Class of Safe and Efficient Vaccine Delivery Agents
Authors: Parlane Natalie A. , Wedlock D. Neil , Buddle Bryce M. , Rehm Bernd H. A. 
Published: October 2009

ABSTRACTBioengineered bacterial polyester inclusions have the potential to be used as a vaccine delivery system. The biopolyester beads were engineered to display a fusion protein of the polyester synthase PhaC and the two key antigens involved in immune response to the infectious agent that causes tuberculosis,Mycobacterium tuberculosis, notably antigen 85A (Ag85A) and the 6-kDa early secreted antigenic target (ESAT-6) fromMycobacterium tuberculosis. Polyester beads displaying the respective fusion protein at a high density were successfully produced (henceforth called Ag85A-ESAT-6 beads) by recombinantEscherichia coli. The ability of the Ag85A-ESAT-6 beads to enhance mouse immunity to the displayed antigens was investigated. The beads were not toxic to the animals, as determined by weight gain and absence of lesions at the inoculation site in immunized animals. In vivo injection of the Ag85A-ESAT-6 beads in mice induced significant humoral and cell-mediated immune responses to both Ag85A and ESAT-6. Vaccination with Ag85A-ESAT-6 beads was efficient at stimulating immunity on their own, and this ability was enhanced by administration of the beads in an oil-in-water emulsion. In addition, vaccination with the Ag85A-ESAT-6 beads induced significantly stronger humoral and cell-mediated immune responses than vaccination with an equivalent dose of the fusion protein Ag85A-ESAT-6 alone. The immune response induced by the beads was of a mixed Th1/Th2 nature, as assessed from the induction of the cytokine gamma interferon (Th1 immune response) and increased levels of immunoglobulin G1 (Th2 immune response). Hence, engineered biopolyester beads displaying foreign antigens represent a new class of versatile, safe, and biocompatible vaccines.
Hwp1 and Related Adhesins Contribute to both Mating and Biofilm Formation in
Candida albicans
Authors: Ene Iuliana V. , Bennett Richard J. 
Published: October 2009

ABSTRACT

Candida albicans
Hwp1, Hwp2, and Rbt1 are related cell wall proteins expressed during the programs of sexual differentiation and filamentous growth. In this study, we compare strains lacking either single factors or a combination of these genes, and we demonstrate distinct but overlapping roles in mating and biofilm formation.
The InhA Metalloproteases ofBacillus cereusContribute Concomitantly to Virulence
Authors: Guillemet Elisabeth , Cadot Céline , Tran Seav-Ly , Guinebretière Marie-Hélène , Lereclus Didier , Ramarao Nalini 
Published: October 2009

ABSTRACTThe virulence ofBacillus cereusrequires that bacteria have the capacity to colonize their host, degrade specific tissues, and circumvent the host immune system. To study this aspect of pathogenesis, we focused on three metalloproteases, InhA1, InhA2, and InhA3, which share more than 66% identity. The expression of these metalloprotease genes was assessed by transcriptional fusions with alacZreporter gene. The expression profiles suggest a complementary time course of InhA production. Indeed, the genes are simultaneously expressed but are oppositely controlled during stationary phase. We constructed single and multipleinhAmutants and assessed the bacterial locations of the proteins as well as their individual or additive roles in macrophage escape and toxicity, antibacterial-peptide cleavage, and virulence. InhA1, a major component of the spore exosporium, is the only InhA metalloprotease involved in bacterial escape from macrophages. A mutant lackinginhA1,inhA2, andinhA3shows a strong decrease in the level of virulence for insects. Taken together, these results show that the InhA metalloproteases ofB. cereusare important virulence factors that may allow the bacteria to counteract the host immune system.
Outer Membrane Machinery and Alginate Synthesis Regulators Control Membrane Vesicle Production inPseudomonas aeruginosa
Authors: Tashiro Yosuke , Sakai Ryosuke , Toyofuku Masanori , Sawada Isao , Nakajima-Kambe Toshiaki , Uchiyama Hiroo , Nomura Nobuhiko 
Published: October 2009

ABSTRACTThe opportunistic human bacterial pathogenPseudomonas aeruginosaproduces membrane vesicles (MVs) in its surrounding environment. Several features of theP. aeruginosaMV production mechanism are still unknown. We previously observed that depletion of Opr86, which has a role in outer membrane protein (OMP) assembly, resulted in hypervesiculation. In this study, we showed that the outer membrane machinery and alginate synthesis regulatory machinery are closely related to MV production inP. aeruginosa. Depletion of Opr86 resulted in increased expression of the periplasmic serine protease MucD, suggesting that the accumulation of misfolded OMPs in the periplasm is related to MV production. Indeed, themucDmutant showed a mucoid phenotype and themucDmutation caused increased MV production. Strains with the gene encoding alginate synthetic regulator AlgU, MucA, or MucB deleted also caused altered MV production. Overexpression of either MucD or AlgW serine proteases resulted in decreased MV production, suggesting that proteases localized in the periplasm repress MV production inP. aeruginosa. Deletion ofmucDresulted in increased MV proteins, even in strains with mutations in thePseudomonasquinolone signal (PQS), which serves as a positive regulator of MV production. This study suggests that misfolded OMPs may be important for MV production, in addition to PQS, and that these regulators act in independent pathways.
Diamide Triggers Mainly S Thiolations in the Cytoplasmic Proteomes of
Bacillus subtilis
and
Staphylococcus aureus
Authors: Pöther Dierk-Christoph , Liebeke Manuel , Hochgräfe Falko , Antelmann Haike , Becher Dörte , Lalk Michael , Lindequist Ulrike , Borovok Ilya , Cohen Gerald , Aharonowitz Yair , Hecker Michael 
Published: October 2009

ABSTRACT

Glutathione constitutes a key player in the thiol redox buffer in many organisms. However, the gram-positive bacteria
Bacillus subtilis
and
Staphylococcus aureus
lack this low-molecular-weight thiol. Recently, we identified S-cysteinylated proteins in
B. subtilis
after treatment of cells with the disulfide-generating electrophile diamide. S cysteinylation is thought to protect protein thiols against irreversible oxidation to sulfinic and sulfonic acids. Here we show that S thiolation occurs also in
S. aureus
proteins after exposure to diamide. We further analyzed the formation of inter- and intramolecular disulfide bonds in cytoplasmic proteins using diagonal nonreducing/reducing sodium dodecyl sulfate gel electrophoresis. However, only a few proteins were identified that form inter- or intramolecular disulfide bonds under control and diamide stress conditions in
B. subtilis
and
S. aureus
. Depletion of the cysteine pool was concomitantly measured in
B. subtilis
using a metabolomics approach. Thus, the majority of reversible thiol modifications that were previously detected by two-dimensional gel fluorescence-based thiol modification assay are most likely based on S thiolations. Finally, we found that a glutathione-producing
B. subtilis
strain which expresses the
Listeria monocytogenes gshF
gene did not show enhanced oxidative stress resistance compared to the wild type.
An SOS-Regulated Type 2 Toxin-Antitoxin System
Authors: Singletary Larissa A. , Gibson Janet L. , Tanner Elizabeth J. , McKenzie Gregory J. , Lee Peter L. , Gonzalez Caleb , Rosenberg Susan M. 
Published: October 2009

ABSTRACTTheEscherichia colichromosome encodes seven demonstrated type 2 toxin-antitoxin (TA) systems: cassettes of two or three cotranscribed genes, one encoding a stable toxin protein that can cause cell stasis or death, another encoding a labile antitoxin protein, and sometimes a third regulatory protein. We demonstrate that theyafNOgenes constitute an additional chromosomal type 2 TA system that is upregulated during the SOS DNA damage response. TheyafNOPgenes are part of thedinBoperon, of whichdinBunderlies stress-induced mutagenesis mechanisms.yafNwas identified as a putative antitoxin by homology to known antitoxins, implicatingyafO(and/oryafP) as a putative toxin. Using phage-mediated cotransduction assays for linkage disruption, we show first thatyafNis an essential gene and second that it is essential only whenyafOis present. Third,yafPis not a necessary part of either the toxin or the antitoxin. Fourth, although DinB is required, theyafNOPgenes are not required for stress-induced mutagenesis in theEscherichia coliLac assay. These results imply thatyafNencodes an antitoxin that protects cells against ayafO-encoded toxin and show a protein-based TA system upregulated by the SOS response.