bluuebunny/crossref_metadata_2025 huggingface dataset:
LysM-Type Mycorrhizal Receptor Recruited for Rhizobium Symbiosis in Nonlegume
Parasponia
Authors: Op den Camp Rik , Streng Arend , De Mita Stéphane , Cao Qingqin , Polone Elisa , Liu Wei , Ammiraju Jetty S. S. , Kudrna Dave , Wing Rod , Untergasser Andreas , Bisseling Ton , Geurts René
Published: December 2010

Parasponia
uses a mycorrhizal signaling receptor essential for arbuscle formation to control rhizobium nodule symbiosis.
Crystal Structure of the Eukaryotic 40
S
Ribosomal Subunit in Complex with Initiation Factor 1
Authors: Rabl Julius , Leibundgut Marc , Ataide Sandro F. , Haag Andrea , Ban Nenad
Published: December 2010

The structure provides insight into how protein synthesis is initiated and into the evolution of the eukaryotic ribosome.
Induction of Colonic Regulatory T Cells by Indigenous
Clostridium
Species
Authors: Atarashi Koji , Tanoue Takeshi , Shima Tatsuichiro , Imaoka Akemi , Kuwahara Tomomi , Momose Yoshika , Cheng Genhong , Yamasaki Sho , Saito Takashi , Ohba Yusuke , Taniguchi Tadatsugu , Takeda Kiyoshi , Hori Shohei , Ivanov Ivaylo I. , Umesaki Yoshinori , Itoh Kikuji , Honda Kenya
Published: December 2010

Bacteria of the genus
Clostridium
promote the induction of suppressor T cells in the colons of mice.
New Insights into the Genetic Organization of the FK228 Biosynthetic Gene Cluster in
Chromobacterium violaceum
No. 968
Authors: Potharla Vishwakanth Y. , Wesener Shane R. , Cheng Yi-Qiang
Published: December 2010

The biosynthetic gene cluster of FK228, an FDA-approved anticancer natural product, was identified and sequenced previously. The genetic organization of this gene cluster has now been delineated through systematic gene deletion and transcriptional analysis. As a result, the gene cluster is redefined to contain 12 genes:
depA
through
depJ
,
depM
, and a newly identified pathway regulatory gene,
depR
.
Reconstitution of the FK228 Biosynthetic Pathway Reveals Cross Talk between Modular Polyketide Synthases and Fatty Acid Synthase
Authors: Wesener Shane R. , Potharla Vishwakanth Y. , Cheng Yi-Qiang
Published: December 2010

Functional cross talk between fatty acid biosynthesis and secondary metabolism has been discovered in several cases in microorganisms; none of them, however, involves a modular biosynthetic enzyme. Previously, we reported a hybrid modular nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) pathway for the biosynthesis of FK228 anticancer depsipeptide in
Chromobacterium violaceum
strain 968. This pathway contains two PKS modules on the DepBC enzymes that lack a functional acyltransferase (AT) domain, and no apparent AT-encoding gene exists within the gene cluster or its vicinity. We report here that, through reconstitution of the FK228 biosynthetic pathway in
Escherichia coli
cells, two essential genes,
fabD1
and
fabD2
, both encoding a putative malonyl coenzyme A (CoA) acyltransferase component of the fatty acid synthase complex, are positively identified to be involved in FK228 biosynthesis. Either gene product appears sufficient to complement the AT-less PKS modules on DepBC for polyketide chain elongation. Concurrently, a gene (
sfp
) encoding a putative Sfp-type phosphopantetheinyltransferase was identified to be necessary for FK228 biosynthesis as well. Most interestingly, engineered
E. coli
strains carrying variable genetic components produced significant levels of FK228 under both aerobic and anaerobic cultivation conditions. Discovery of the
trans
complementation of modular PKSs by housekeeping ATs reveals natural product biosynthesis diversity. Moreover, demonstration of anaerobic production of FK228 by an engineered facultative bacterial strain validates our effort toward the engineering of novel tumor-targeting bioagents.
Development and Application of a Method for Counterselectable In-Frame Deletion in
Clostridium perfringens
Authors: Nariya Hirofumi , Miyata Shigeru , Suzuki Motoo , Tamai Eiji , Okabe Akinobu
Published: December 2010

Many pathogenic clostridial species produce toxins and enzymes. To facilitate genome-wide identification of virulence factors and biotechnological application of their useful products, we have developed a markerless in-frame deletion method for
Clostridium perfringens
which allows efficient counterselection and multiple-gene disruption. The system comprises a
galKT
gene disruptant and a suicide
galK
plasmid into which two fragments of a target gene for in-frame deletion are cloned. The system was shown to be accurate and simple by using it to disrupt the alpha-toxin gene of the organism. It was also used to construct of two different virulence-attenuated strains, ΗΝ1303 and HN1314: the former is a disruptant of the
virRS
operon, which regulates the expression of virulence factors, and the latter is a disruptant of the six genes encoding the α, θ, and κ toxins; a clostripain-like protease; a 190-kDa secretory protein; and a putative cell wall lytic endopeptidase. Comparison of the two disruptants in terms of growth ability and the background levels of secreted proteins showed that HN1314 is more useful than ΗΝ1303 as a host for the large-scale production of recombinant proteins.
Characterization of a Phosphotriesterase-Like Lactonase from
Sulfolobus solfataricus
and Its Immobilization for Disruption of Quorum Sensing
Authors: Ng Filomena S. W. , Wright Daniel M. , Seah Stephen Y. K.
Published: December 2010

SsoPox, a bifunctional enzyme with organophosphate hydrolase and
N
-acyl homoserine lactonase activities from the hyperthermophilic archaeon
Sulfolobus solfataricus
, was overexpressed and purified from recombinant
Pseudomonas putida
KT2440 with a yield of 9.4 mg of protein per liter of culture. The enzyme has a preference for
N
-acyl homoserine lactones (AHLs) with acyl chain lengths of at least 8 carbon atoms, mainly due to lower

K
m

values for these substrates. The highest specificity constant obtained was for
N
-3-oxo-decanoyl homoserine lactone (
k
cat
/

K
m

= 5.5 × 10
3
M
−1
·s
−1
), but SsoPox can also degrade
N
-butyryl homoserine lactone (C
4
-HSL) and
N
-oxo-dodecanoyl homoserine lactone (oxo-C
12
-HSL), which are important for quorum sensing in our
Pseudomonas aeruginosa
model system. When
P. aeruginosa
PAO1 cultures were grown in the presence of SsoPox-immobilized membranes, the production of C
4
-HSL- and oxo-C
12
-HSL-regulated virulence factors, elastase, protease, and pyocyanin were significantly reduced. This is the first demonstration that immobilized quorum-quenching enzymes can be used to attenuate the production of virulence factors controlled by quorum-sensing signals.
Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic Bacterium
Pseudoalteromonas haloplanktis
TAC125
Authors: Wilmes Boris , Kock Holger , Glagla Susanne , Albrecht Dirk , Voigt Birgit , Markert Stephanie , Gardebrecht Antje , Bode Rüdiger , Danchin Antoine , Feller Georges , Hecker Michael , Schweder Thomas
Published: December 2010

The psychrophilic model bacterium
Pseudoalteromonas haloplanktis
is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of
P. haloplanktis
strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium
P. haloplanktis
in its natural environments.
Development and Application of a Tool To Assess Laboratory Hygiene in Contained-Use Facilities
Authors: Rutjes S. A. , Lodder-Verschoor F. , Tijssen J. P. , de Roda Husman A. M.
Published: December 2010

To gain information on laboratory hygiene in contained-use laboratories, a method was developed to study the presence of microorganisms on laboratory equipment. Focusing detection on genetically modified organisms (GMOs) containing the universal M13 primer binding sites enabled the detection of a broad range of GMOs using a single PCR. Swabbing surfaces in three different contained-use laboratories led to detection of M13-containing PCR products in 26 out of 34 swabs. Most sequences (up to five per sample) were detected in swabs from the centrifuge and sink, followed by swabs taken from the bin and incubator (up to four sequences per sample). The obtained sequences varied in length from 171 nucleotides (nt) to 878 nt. In most cases, sequences were only partially similar to sequences published in GenBank. The lengths of the regions with high similarity varied from 94 nt to 795 nt, and these similarities ranged from 81% to 100%. Similarities with more than one sequence were commonly found, complicating the identification of detected sequences. Nonetheless, 84% of the detected sequences were actually handled in the laboratory at the time of sampling. This demonstrates that the method may be used as a quality control tool to assess the efficacy of decontamination and cleaning of commonly used surfaces, such as laboratory benches, freezer doors, and centrifuge rotors, without prior knowledge of the identity or characteristics of the GMOs.
Metagenomic Analysis of the Viral Communities in Fermented Foods
Authors: Park Eun-Jin , Kim Kyoung-Ho , Abell Guy C. J. , Kim Min-Soo , Roh Seong Woon , Bae Jin-Woo
Published: December 2010

Viruses are recognized as the most abundant biological components on Earth, and they regulate the structure of microbial communities in many environments. In soil and marine environments, microorganism-infecting phages are the most common type of virus. Although several types of bacteriophage have been isolated from fermented foods, little is known about the overall viral assemblages (viromes) of these environments. In this study, metagenomic analyses were performed on the uncultivated viral communities from three fermented foods, fermented shrimp, kimchi, and sauerkraut. Using a high-throughput pyrosequencing technique, a total of 81,831, 70,591 and 69,464 viral sequences were obtained from fermented shrimp, kimchi and sauerkraut, respectively. Moreover, 37 to 50% of these sequences showed no significant hit against sequences in public databases. There were some discrepancies between the prediction of bacteriophages hosts via homology comparison and bacterial distribution, as determined from 16S rRNA gene sequencing. These discrepancies likely reflect the fact that the viral genomes of fermented foods are poorly represented in public databases. Double-stranded DNA viral communities were amplified from fermented foods by using a linker-amplified shotgun library. These communities were dominated by bacteriophages belonging to the viral order
Caudovirales
(i.e.,
Myoviridae
,
Podoviridae
, and
Siphoviridae
). This study indicates that fermented foods contain less complex viral communities than many other environmental habitats, such as seawater, human feces, marine sediment, and soil.
Genome Sequence and Characterization of the
Tsukamurella
Bacteriophage TPA2
Authors: Petrovski Steve , Seviour Robert J. , Tillett Daniel
Published: December 2010

The formation of stable foam in activated sludge plants is a global problem for which control is difficult. These foams are often stabilized by hydrophobic mycolic acid-synthesizing
Actinobacteria
, among which are
Tsukamurella
spp. This paper describes the isolation from activated sludge of the novel double-stranded DNA phage TPA2. This polyvalent
Siphoviridae
family phage is lytic for most
Tsukamurella
species. Whole-genome sequencing reveals that the TPA2 genome is circularly permuted (61,440 bp) and that 70% of its sequence is novel. We have identified 78 putative open reading frames, 95 pairs of inverted repeats, and 6 palindromes. The TPA2 genome has a modular gene structure that shares some similarity to those of
Mycobacterium
phages. A number of the genes display a mosaic architecture, suggesting that the TPA2 genome has evolved at least in part from genetic recombination events. The genome sequence reveals many novel genes that should inform any future discussion on
Tsukamurella
phage evolution.
Nationwide Groundwater Surveillance of Noroviruses in South Korea, 2008
Authors: Lee Sung-Geun , Jheong Weon-Hwa , Suh Chang-Il , Kim Sang-Hyun , Lee Joong-Bok , Jeong Yong-Seok , Ko GwangPyo , Jang Kyung Lib , Lee Gyu-Cheol , Paik Soon-Young
Published: December 2010

To inspect the norovirus contamination of groundwater in South Korea, a nationwide study was performed in the summer (June to August) and winter (October to December) of 2008. Three-hundred sites designated by the government ministry were inspected. Water samples were collected for analysis of water quality, microorganism content, and viral content. Water quality was assessed by temperature, pH, turbidity, residual chlorine, and nitrite nitrogen content. Microorganism contents were analyzed bacteria, total coliforms,Escherichia coli, and bacteriophage. Virus analyses included panenterovirus and norovirus. Two primer sets were used for the detection of norovirus genotypes GI and GII, respectively. Of 300 samples, 65 (21.7%) were norovirus positive in the summer and in 52 (17.3%) were norovirus positive in the winter. The genogroup GI noroviruses that were identified were GI-1, GI-2, GI-3, GI-4, GI-5, GI-6, and GI-8 genotypes; those in the GII genogroup were GII-4 and GII-Yuri genotypes. The analytic data showed correlative relationships between the norovirus detection rate and the following parameters: water temperature and turbidity in physical-chemical parameters and somatic phage in microbial parameters. It is necessary to periodically monitor waterborne viruses that frequently cause epidemic food poisoning in South Korea for better public health and sanitary conditions.
Novel Antibacterial Proteins from the Microbial Communities Associated with the Sponge
Cymbastela concentrica
and the Green Alga
Ulva australis
Authors: Yung Pui Yi , Burke Catherine , Lewis Matt , Kjelleberg Staffan , Thomas Torsten
Published: December 2010

The functional metagenomic screening of the microbial communities associated with a temperate marine sponge and a green alga identified three novel hydrolytic enzymes with antibacterial activities. The results suggest that uncultured alpha- and gammaproteobacteria contain new classes of proteins that may be a source of antibacterial agents.
Identification of Candidate Carrier Proteins for Surface Display on
Lactococcus lactis
by Theoretical and Experimental Analyses of the Surface Proteome
Authors: Berlec Aleš , Zadravec Petra , Jevnikar Zala , Štrukelj Borut
Published: December 2010

Lactococcus lactis
is a lactic acid bacterium of proven safety for use in human oral applications. For this purpose, surface display of recombinant proteins is important, and new approaches for it are being sought. Analysis of the bacterial surface proteome is essential in identifying new candidate carrier proteins for surface display. We have made two different predictions of surface-associated proteins of
L. lactis
MG1363 by using Augur and LocateP software, which yielded 666 and 648 proteins, respectively. Surface proteins of
L. lactis
NZ9000, a derivative of MG1363, were identified by using a proteomics approach. The surface proteins were cleaved from intact bacteria, and the resulting peptides were identified by mass spectrometry. The latter approach yielded 80 proteins, 34 of which were not predicted by either software. Of the 80 proteins, 7 were selected for further study. These were cloned in frame with a C-terminal hexahistidine tag and overexpressed in
L. lactis
NZ9000 using nisin-controlled expression. Proteins of correct molecular weight carrying a hexahistidine tag were detected. Their surface localization was confirmed with flow cytometry. Basic membrane protein A (BmpA) was exposed at the highest level. To test BmpA as a candidate carrier protein, the hexahistidine tag was replaced by the B domain of staphylococcal protein A in the genetic construct. The B domain was displayed on the surface with BmpA as a carrier. The advantage of covalent BmpA binding was demonstrated. BmpA was thus shown to be a suitable candidate for a carrier protein in lactococcal surface display.
Bacterial Endosymbiont Localization inHyalesthes obsoletus, the Insect Vector of Bois Noir inVitis vinifera
Authors: Gonella Elena , Negri Ilaria , Marzorati Massimo , Mandrioli Mauro , Sacchi Luciano , Pajoro Massimo , Crotti Elena , Rizzi Aurora , Clementi Emanuela , Tedeschi Rosemarie , Bandi Claudio , Alma Alberto , Daffonchio Daniele
Published: December 2010

One emerging disease of grapevine in Europe is Bois noir (BN), a phytoplasmosis caused by “CandidatusPhytoplasma solani” and spread in vineyards by the planthopperHyalesthes obsoletus(Hemiptera: Cixiidae). Here we present the first full characterization of the bacterial community of this important disease vector collected from BN-contaminated areas in Piedmont, Italy. Length heterogeneity PCR and denaturing gradient gel electrophoresis analysis targeting the 16S rRNA gene revealed the presence of a number of bacteria stably associated with the insect vector. In particular, symbiotic bacteria detected by PCR with high infection rates in adult individuals fell within the “CandidatusSulcia muelleri” cluster in theBacteroidetesand in the “CandidatusPurcelliella pentastirinorum” group in theGammaproteobacteria, both previously identified in different leafhoppers and planthoppers. A high infection rate (81%) was also shown for another symbiont belonging to theBetaproteobacteria, designated the HO1-V symbiont. Because of the low level of 16S rRNA gene identity (80%) with the closest relative, an uncharacterized symbiont of the tickHaemaphysalis longicornis, we propose the new name “CandidatusVidania fulgoroideae.” Other bacterial endosymbionts identified inH. obsoletuswere related to the intracellular bacteriaWolbachia pipientis,Rickettsiasp., and “CandidatusCardinium hertigii.” Fluorescentin situhybridization coupled with confocal laser scanning microscopy and transmission electron microscopy showed that these bacteria are localized in the gut, testicles, and oocytes. As “Ca.Sulcia” is usually reported in association with other symbiotic bacteria, we propose that inH. obsoletus, it may occur in a bipartite or even tripartite relationship between “Ca.Sulcia” and “Ca.Purcelliella,” “Ca.Vidania,” or both.
Inactivation of Murine Norovirus 1, Coliphage φX174, andBacillus fragilisPhage B40-8 on Surfaces and Fresh-Cut Iceberg Lettuce by Hydrogen Peroxide and UV Light
Authors: Li Dan , Baert Leen , De Jonghe Maarten , Van Coillie Els , Ryckeboer Jaak , Devlieghere Frank , Uyttendaele Mieke
Published: December 2010

In this study, the inactivating properties of liquid hydrogen peroxide (L-H2O2), vaporized hydrogen peroxide (V-H2O2), UV light, and a combination of V-H2O2and UV light were tested on murine norovirus 1 (MNV-1) and bacteriophages (φX174 and B40-8) as models for human noroviruses. Disinfection of surfaces was examined on stainless steel discs based on European Standard EN 13697 (2001). For fresh-produce decontamination, a mixture of the viruses was inoculated onto shredded iceberg lettuce and treated after overnight incubation at 2°C. According to our results, L-H2O2(2.1%) was able to inactivate MNV-1 and φX174 on stainless steel discs by approximately 4 log10units within 10 min of exposure, whereas for B40-8, 15% of L-H2O2was needed to obtain a similar reduction in 10 min. Only a marginal reduction (≤1 log10unit after 5 min of exposure) by V-H2O2(2.52%) was achieved for the tested model viruses, although in combination with UV light, a 4-log10-unit decrease within 5 min of treatment was observed on stainless steel discs. Similar trends were observed for the decontamination of shredded iceberg lettuce, but the viral decline was reduced. These results demonstrated that both L-H2O2and a combination of V-H2O2and UV light can be used for norovirus inactivation on surfaces; V-H2O2(2.52%) in combination with UV light is promising for decontamination of fresh produce with much less consumption of water and disinfectant.
Influence of Two-Component Signal Transduction Systems of
Lactobacillus casei
BL23 on Tolerance to Stress Conditions
Authors: Alcántara Cristina , Revilla-Guarinos Ainhoa , Zúñiga Manuel
Published: December 2010

Lactobacillus casei
BL23 carries 17 two-component signal transduction systems. Insertional mutations were introduced into each gene encoding the cognate response regulators, and their effects on growth under different conditions were assayed. Inactivation of systems TC01, TC06, and TC12 (LCABL_02080-LCABL_02090, LCABL_12050-LCABL_12060, and LCABL_19600-LCABL_19610, respectively) led to major growth defects under the conditions assayed.
Involvement of an Alkane Hydroxylase System of
Gordonia
sp. Strain SoCg in Degradation of Solid
n
-Alkanes
Authors: Lo Piccolo Luca , De Pasquale Claudio , Fodale Roberta , Puglia Anna Maria , Quatrini Paola
Published: December 2010

Enzymes involved in oxidation of long-chain
n
-alkanes are still not well known, especially those in Gram-positive bacteria. This work describes the alkane degradation system of the
n
-alkane degrader actinobacterium
Gordonia
sp. strain SoCg, which is able to grow on
n
-alkanes from dodecane (C
12
) to hexatriacontane (C
36
) as the sole C source. SoCg harbors in its chromosome a single
alk
locus carrying six open reading frames (ORFs), which shows 78 to 79% identity with the alkane hydroxylase (AH)-encoding systems of other alkane-degrading actinobacteria. Quantitative reverse transcription-PCR showed that the genes encoding AlkB (alkane 1-monooxygenase), RubA3 (rubredoxin), RubA4 (rubredoxin), and RubB (rubredoxin reductase) were induced by both
n
-hexadecane and
n
-triacontane, which were chosen as representative long-chain liquid and solid
n
-alkane molecules, respectively. Biotransformation of
n
-hexadecane into the corresponding 1-hexadecanol was detected by solid-phase microextraction coupled with gas chromatography-mass spectrometry (SPME/GC-MS) analysis. The
Gordonia
SoCg
alkB
was heterologously expressed in
Escherichia coli
BL21 and in
Streptomyces coelicolor
M145, and both hosts acquired the ability to transform
n
-hexadecane into 1-hexadecanol, but the corresponding long-chain alcohol was never detected on
n
-triacontane. However, the recombinant
S. coelicolor
M145-AH, expressing the
Gordonia alkB
gene, was able to grow on
n
-triacontane as the sole C source. A SoCg
alkB
disruption mutant that is completely unable to grow on
n
-triacontane was obtained, demonstrating the role of an AlkB-type AH system in degradation of solid
n
-alkanes.
Longitudinal Evaluation of the Efficacy of Heat Treatment Procedures against
Legionella
spp. in Hospital Water Systems by Using a Flow Cytometric Assay
Authors: Allegra Severine , Grattard Florence , Girardot Françoise , Riffard Serge , Pozzetto Bruno , Berthelot Philippe
Published: December 2010

Legionella
spp. are frequently isolated in hospital water systems. Heat shock (30 min at 70°C) is recommended by the World Health Organization to control its multiplication. The aim of the study was to evaluate retrospectively the efficacy of heat treatments by using a flow cytometry assay (FCA) able to identify viable but nonculturable (VBNC) cells. The study included
Legionella
strains (
L. pneumophila
[3 clusters] and
L. anisa
[1 cluster]) isolated from four hot water circuits of different hospital buildings in Saint-Etienne, France, during a 20-year prospective surveillance. The strains recovered from the different circuits were not epidemiologically related, but the strains isolated within a same circuit over time exhibited an identical genotypic profile. After an
in vitro
treatment of 30 min at 70°C, the mean percentage of viable cells and VBNC cells varied from 4.6% to 71.7%. The
in vitro
differences in heat sensitivity were in agreement with the observed efficacy of preventive and corrective heating measures used to control water contamination. These results suggest that
Legionella
strains can become heat resistant after heating treatments for a long time and that flow cytometry could be helpful to check the efficacy of heat treatments on
Legionella
spp. and to optimize the decontamination processes applied to water systems for the control of
Legionella
proliferation.
Identification of the Monooxygenase Gene Clusters Responsible for the Regioselective Oxidation of Phenol to Hydroquinone in Mycobacteria
Authors: Furuya Toshiki , Hirose Satomi , Osanai Hisashi , Semba Hisashi , Kino Kuniki
Published: December 2010

Mycobacterium goodii
strain 12523 is an actinomycete that is able to oxidize phenol regioselectively at the
para
position to produce hydroquinone. In this study, we investigated the genes responsible for this unique regioselective oxidation. On the basis of the fact that the oxidation activity of
M. goodii
strain 12523 toward phenol is induced in the presence of acetone, we first identified acetone-induced proteins in this microorganism by two-dimensional electrophoretic analysis. The N-terminal amino acid sequence of one of these acetone-induced proteins shares 100% identity with that of the protein encoded by the open reading frame Msmeg_1971 in
Mycobacterium smegmatis
strain mc
2
155, whose genome sequence has been determined. Since Msmeg_1971, Msmeg_1972, Msmeg_1973, and Msmeg_1974 constitute a putative binuclear iron monooxygenase gene cluster, we cloned this gene cluster of
M. smegmatis
strain mc
2
155 and its homologous gene cluster found in
M. goodii
strain 12523. Sequence analysis of these binuclear iron monooxygenase gene clusters revealed the presence of four genes designated
mimABCD
, which encode an oxygenase large subunit, a reductase, an oxygenase small subunit, and a coupling protein, respectively. When the
mimA
gene (Msmeg_1971) of
M. smegmatis
strain mc
2
155, which was also found to be able to oxidize phenol to hydroquinone, was deleted, this mutant lost the oxidation ability. This ability was restored by introduction of the
mimA
gene of
M. smegmatis
strain mc
2
155 or of
M. goodii
strain 12523 into this mutant. Interestingly, we found that these gene clusters also play essential roles in propane and acetone metabolism in these mycobacteria.
Essential Role of Yl
MPO1
, a Novel
Yarrowia lipolytica
Homologue of
Saccharomyces cerevisiae MNN4
, in Mannosylphosphorylation of N- and O-Linked Glycans
Authors: Park Jeong-Nam , Song Yunkyoung , Cheon Seon Ah , Kwon Ohsuk , Oh Doo-Byoung , Jigami Yoshifumi , Kim Jeong-Yoon , Kang Hyun Ah
Published: December 2010

Mannosylphosphorylation of N- and O-glycans, which confers negative charges on the surfaces of cells, requires the functions of both
MNN4
and
MNN6
in
Saccharomyces cerevisiae
. To identify genes relevant to mannosylphosphorylation in the dimorphic yeast
Yarrowia lipolytica
, the molecular functions of five
Y. lipolytica
genes showing significant sequence homology with
S. cerevisiae MNN4
and
MNN6
were investigated. A set of mutant strains in which
Y. lipolytica MNN4
and
MNN6
homologues were deleted underwent glycan structure analysis. In contrast to
S. cerevisiae MNN4
(Sc
MNN4
), the
Y. lipolytica MNN4
homologue,
MPO1
(Yl
MPO1
), encodes a protein that lacks the long KKKKEEEE repeat domain at its C terminus. Moreover, just a single disruption of Yl
MPO1
resulted in complete disappearance of the acidic sugar moiety in both the N- and O-linked glycan profiles. In contrast, even quadruple disruption of all Sc
MNN6
homologues, designated Yl
KTR1
, Yl
KTR2
, Yl
KTR3
, and Yl
KTR4
, resulted in no apparent reduction in acidic sugar moieties. These findings strongly indicate that YlMpo1p performs a significant role in mannosylphosphorylation in
Y. lipolytica
with no involvement of the Mnn6p homologues. Mutant strains harboring the Yl
MPO1
gene disruption may serve as useful platforms for engineering
Y. lipolytica
glycosylation pathways for humanized glycans without any yeast-specific acidic modifications.
Identification of Enterococci from Broiler Products and a Broiler Processing Plant and Description of
Enterococcus viikkiensis
sp. nov
Authors: Rahkila Riitta , Johansson Per , Säde Elina , Björkroth Johanna
Published: December 2010

In two previous studies dealing with lactic acid bacteria (LAB) from modified-atmosphere-packaged (MAP) broiler products and a broiler processing plant, several isolates remained unidentified. According to 16S rRNA gene sequence analysis, 36 isolates were assigned to the genus
Enterococcus.
Numerical analysis of combined HindIII and EcoRI ribopatterns of these isolates resulted in species-specific clusters that were congruent with the clusters obtained by both DNA-directed RNA polymerase subunit A (
rpoA
) and phenylalanyl-tRNA synthetase α chain (
pheS
) housekeeping gene analyses. In the analyses, a group of five isolates distinct from any known enterococcal species clustered together. The five isolates were positioned in the
Enterococcus avium
group, with
E. devriesei
being the closest phylogenetic neighbor. The DNA-DNA hybridization levels with
E. devriesei
ranged from 28.8 to 54.3% and indicated that these strains represented a novel species. The name
Enterococcus viikkiensis
sp. nov. is proposed, with strain DSM 24043
T
(LMG 26075
T
) being the type strain. Our study demonstrated that the identification of enterococci within the
E. avium
phylogenetic group demands polyphasic taxonomic approaches. The
rpoA
and
pheS
gene similarities (99.0 to 99.2% and 94.3 to 95.4%, respectively) between
E. viikkiensis
and its closest phylogenetic neighbor,
E. devriesei
, were higher than those previously reported within the enterococci. In addition, the phenotypic profiles of the species in the
E. avium
group were also highly similar, and some traits were found to be misleading for enterococci, such as
E. viikkiensis
does not grow at 45°C. The numerical analysis of combined HindIII and EcoRI ribopatterns was of considerable assistance in distinguishing enterococcal species within the
E. avium
group.
Novel Structural Elements within the Nonproteolytic
Clostridium botulinum
Type F Toxin Gene Cluster
Authors: Dover N. , Barash J. R. , Hill K. K. , Detter J. C. , Arnon S. S.
Published: December 2010

We sequenced for the first time the complete neurotoxin gene cluster of a nonproteolytic
Clostridium botulinum
type F. The neurotoxin gene cluster contained a novel gene arrangement that, compared to other
C. botulinum
neurotoxin gene clusters, lacked the regulatory
botR
gene and contained an intergenic
is
element between its
orfX2
and
orfX3
genes.
Involvement of an Alternative Oxidase in Oxidative Stress and Mycelium-to-Yeast Differentiation in Paracoccidioides brasiliensis
Authors: Martins Vicente P. , Dinamarco Taisa M. , Soriani Frederico M. , Tudella Valéria G. , Oliveira Sergio C. , Goldman Gustavo H. , Curti Carlos , Uyemura Sérgio A.
Published: December 2010

Paracoccidioides brasiliensis
is a thermodimorphic human pathogenic fungus that causes paracoccidioidomycosis (PCM), which is the most prevalent systemic mycosis in Latin America. Differentiation from the mycelial to the yeast form (M-to-Y) is an essential step for the establishment of PCM. We evaluated the involvement of mitochondria and intracellular oxidative stress in M-to-Y differentiation. M-to-Y transition was delayed by the inhibition of mitochondrial complexes III and IV or alternative oxidase (AOX) and was blocked by the association of AOX with complex III or IV inhibitors. The expression of
P. brasiliensis
aox
(
Pbaox
) was developmentally regulated through M-to-Y differentiation, wherein the highest levels were achieved in the first 24 h and during the yeast exponential growth phase;
Pbaox
was upregulated by oxidative stress.
Pbaox
was cloned, and its heterologous expression conferred cyanide-resistant respiration in
Saccharomyces cerevisiae
and
Escherichia coli
and reduced oxidative stress in
S. cerevisiae
cells. These results reinforce the role of
Pb
AOX in intracellular redox balancing and demonstrate its involvement, as well as that of other components of the mitochondrial respiratory chain complexes, in the early stages of the M-to-Y differentiation of
P. brasiliensis
.
The Small GTPase RacA Mediates Intracellular Reactive Oxygen Species Production, Polarized Growth, and Virulence in the Human Fungal Pathogen Aspergillus fumigatus
Authors: Li Haiyan , Barker Bridget M. , Grahl Nora , Puttikamonkul Srisombat , Bell Jeremey D. , Craven Kelly D. , Cramer Robert A.
Published: December 2010

Aspergillus fumigatusis the predominant mold pathogen in immunocompromised patients. In this study, we present the first characterization of the small GTPase RacA inA. fumigatus. To gain insight into the function ofracAin the growth and pathogenesis ofA. fumigatus, we constructed a strain that lacks a functionalracAgene. The ΔracAstrain showed significant morphological defects, including a reduced growth rate and abnormal conidiogenesis on glucose minimal medium. In the ΔracAstrain, apical dominance in the leading hyphae is lost and, instead, multiple axes of polarity emerge. Intriguingly, superoxide production at the hyphal tips was reduced by 25% in the ΔracAstrain. Treatment of wild-type hyphae with diphenylene iodonium, an inhibitor of NADPH oxidase, resulted in phenotypes similar to that of the ΔracAstrain. These data suggest that ΔracAstrain phenotypes may be due to a reduction or alteration in the production of reactive oxygen species. Most surprisingly, despite these developmental and growth abnormalities, the ΔracAstrain retained at least wild-type virulence in both an insect model and two immunologically distinct murine models of invasive pulmonary aspergillosis. These results demonstrate thatin vitrogrowth phenotypes do not always correlate within vivovirulence and raise intriguing questions about the role of RacA inAspergillusvirulence.
PigS and PigP Regulate Prodigiosin Biosynthesis inSerratiavia Differential Control of Divergent Operons, Which Include Predicted Transporters of Sulfur-Containing Molecules
Authors: Gristwood Tamzin , McNeil Matthew B. , Clulow James S. , Salmond George P. C. , Fineran Peter C.
Published: December 2010

Serratiasp. strain ATCC 39006 produces the red-pigmented antibiotic prodigiosin. Regulation of prodigiosin biosynthesis involves a complex hierarchy, with PigP a master transcriptional regulator of multiple genes involved in prodigiosin production. The focus of this study was a member of the PigP regulon,pigS, which encodes an ArsR/SmtB family transcriptional repressor. Mutations inpigSreduced production of prodigiosin by decreasing the transcription of the biosynthetic operon. ThepigSgene is the first in a four-gene operon, which also encodes three membrane proteins (pmpABC) of the COG2391 (DUF395; YedE/YeeE) and COG0730 (DUF81; TauE/SafE) families that we propose constitute transport components for sulfur-containing compounds. We provide the first experimental evidence confirming the membrane localization of a COG2391 protein, that of PmpB. Divergently transcribed frompigS-pmpABCis a bicistronic operon (blhA-orfY), which encodes a metallo-β-lactamase and a coenzyme A-disulfide reductase containing a rhodanese homology domain, both of which may participate in reactions with sulfur-containing compounds. The overproduction of the BlhA and OrfY enzymes and the PmpABC membrane proteins differentially affected pigmentation. We have dissected the contributions of these various proteins and determined their importance in the control of prodigiosin production. PigS-mediated control of prodigiosin occurred via binding directly to a short inverted repeat sequence in the intergenic region overlapping the predicted −10 regions of bothpigSandblhApromoters and repressing transcription. PigP was required for the activation of these promoters, but only in the absence of PigS-mediated repression.
Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting EndophyteVariovorax paradoxusS110
Authors: Han Jong-In , Choi Hong-Kyu , Lee Seung-Won , Orwin Paul M. , Kim Jina , LaRoe Sarah L. , Kim Tae-gyu , O'Neil Jennifer , Leadbetter Jared R. , Lee Sang Yup , Hur Cheol-Goo , Spain Jim C. , Ovchinnikova Galina , Goodwin Lynne , Han Cliff
Published: December 2010

Variovorax paradoxusis a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants.V. paradoxusalso engages in mutually beneficial interactions with both bacteria and plants. The complete genome sequence ofV. paradoxusS110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle. Consequently, S110 appears to have evolved into a superbly adaptable microorganism that is able to survive in ever-changing environmental conditions. Based on our findings, we suggestV. paradoxusS110 as a potential candidate for agrobiotechnological applications, such as biofertilizer and biopesticide. Because it has many associations with other biota, it is also suited to serve as an additional model system for studies of microbe-plant and microbe-microbe interactions.
The Chromosomal
mazEF
Locus of
Streptococcus mutans
Encodes a Functional Type II Toxin-Antitoxin Addiction System
Authors: Syed Mohammad Adnan , Koyanagi Stephanie , Sharma Eesha , Jobin Marie-Claude , Yakunin Alexander F. , Lévesque Céline M.
Published: December 2010

Type II chromosomal toxin-antitoxin (TA) modules consist of a pair of genes that encode two components: a stable toxin and a labile antitoxin interfering with the lethal action of the toxin through protein complex formation. Bioinformatic analysis of
Streptococcus mutans
UA159 genome identified a pair of linked genes encoding a MazEF-like TA. Our results show that
S. mutans mazEF
genes form a bicistronic operon that is cotranscribed from a σ70-like promoter. Overproduction of
S. mutans
MazF toxin had a toxic effect on
S. mutans
which can be neutralized by coexpression of its cognate antitoxin,
S. mutans
MazE. Although
mazF
expression inhibited cell growth, no cell lysis of
S. mutans
cultures was observed under the conditions tested. The MazEF TA is also functional in
E. coli
, where
S. mutans
MazF did not kill the cells but rather caused reversible cell growth arrest. Recombinant
S. mutans
MazE and MazF proteins were purified and were shown to interact with each other
in vivo
, confirming the nature of this TA as a type II addiction system. Our data indicate that MazF is a toxic nuclease arresting cell growth through the mechanism of RNA cleavage and that MazE inhibits the RNase activity of MazF by forming a complex. Our results suggest that the MazEF TA module might represent a cell growth modulator facilitating the persistence of
S. mutans
under the harsh conditions of the oral cavity.
Complete Genome of the Plant Growth-Promoting RhizobacteriumPseudomonas putidaBIRD-1
Authors: Matilla Miguel A. , Pizarro-Tobias Paloma , Roca Amalia , Fernández Matilde , Duque Estrella , Molina Lázaro , Wu Xiao , van der Lelie Daniel , Gómez Manuel J. , Segura Ana , Ramos Juan-Luis
Published: December 2010

We report the complete sequence of the 5.7-Mbp genome ofPseudomonas putidaBIRD-1, a metabolically versatile plant growth-promoting rhizobacterium that is highly tolerant to desiccation and capable of solubilizing inorganic phosphate and iron and of synthesizing phytohormones that stimulate seed germination and plant growth.
Draft Genome Sequence ofTuricibacter sanguinisPC909, Isolated from Human Feces
Authors: Cuív Páraic Ó , Klaassens Eline S. , Durkin A. Scott , Harkins Derek M. , Foster Les , McCorrison Jamison , Torralba Manolito , Nelson Karen E. , Morrison Mark
Published: December 2010

While the microbiota resident in the human gut is now known to provide a range of functions relevant to host health, many of the microbial members of the community have not yet been cultured or are represented by a limited number of isolates. We describe here the draft genome sequence ofTuricibacter sanguinisPC909, isolated from a pooled healthy human fecal sample as part of the Australian Human Gut Microbiome Project.
Genome Sequence of
Bacillus subtilis
subsp.
spizizenii
gtP20b, Isolated from the Indian Ocean
Authors: Fan Longjiang , Bo Shiping , Chen Huan , Ye Wanzhi , Kleinschmidt Katrin , Baumann Heike I. , Imhoff Johannes F. , Kleine Michael , Cai Daguang
Published: December 2010

Bacillus subtilis
is an aerobic spore-forming Gram-positive bacterium that is a model organism and of great industrial significance as the source of diverse novel functional molecules. Here we present, to our knowledge, the first genome sequence of
Bacillus subtilis
strain gtP20b isolated from the marine environment. A subset of candidate genes and gene clusters were identified, which are potentially involved in production of diverse functional molecules, like novel ribosomal and nonribosomal antimicrobial peptides. The genome sequence described in this paper is due to its high strain specificity of great importance for basic as well as applied researches on marine organisms.
Genome Sequence of the Zoonotic Pathogen
Chlamydophila psittaci
Authors: Seth-Smith Helena M. B. , Harris Simon R. , Rance Richard , West Anthony P. , Severin Juliette A. , Ossewaarde Jacobus M. , Cutcliffe Lesley T. , Skilton Rachel J. , Marsh Pete , Parkhill Julian , Clarke Ian N. , Thomson Nicholas R.
Published: December 2010

We present the first genome sequence of
Chlamydophila psittaci
, an intracellular pathogen of birds and a human zoonotic pathogen. A comparison with previously sequenced
Chlamydophila
genomes shows that, as in other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The
C. psittaci
plasmid was also sequenced.
Genome Sequence of Poultry Pathogen
Riemerella anatipestifer
Strain RA-YM
Authors: Zhou Zutao , Peng Xiaoya , Xiao Yuncai , Wang Xiliang , Guo Zisheng , Zhu Lei , Liu Mei , Jin Hui , Bi Dingren , Li Zili , Sun Ming
Published: December 2010

Riemerella anatipestifer
is a Gram-negative, rod-shaped bacterium associated with epizootic infections in poultry.
R. anatipestifer
strain RA-YM, belonging to the serotype 1 prevalent in China, is a clinically isolated strain with high-level virulence. Here, we report the first genome sequence of this species.
Genome Sequence of
Leuconostoc inhae
KCTC 3774, Isolated from Kimchi
Authors: Kim Dae-Soo , Choi Sang-Haeng , Kim Dong-Wook , Kim Ryong Nam , Nam Seong-Hyeuk , Kang Aram , Kim Aeri , Park Hong-Seog
Published: December 2010

Leuconostoc inhae
strain KCTC 3774 is a Gram-positive, non-spore-forming, heterofermentative, spherical or lenticular lactic acid bacterium. Here we announce the draft genome sequence of
Leuconostoc inhae
KCTC 3774, isolated from traditional Korean kimchi, and describe major findings from its annotation.
Genome Sequence of
Lactobacillus animalis
KCTC 3501
Authors: Nam Seong-Hyeuk , Choi Sang-Haeng , Kang Aram , Kim Dong-Wook , Kim Ryong Nam , Kim Aeri , Kim Dae-Soo , Park Hong-Seog
Published: December 2010

Lactobacillus animalis
is one of the most prevalent lactic acid bacteria present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of
Lactobacillus animalis
type strain KCTC 3501 (1,882,795 bp, with a G+C content of 41.1%), which consists of 7 scaffolds.
Helminths: an unrecognised disease burden prevalent among migrants in the gastroenterology clinic
Authors: Smith P J , Theis B , McCartney S , Brown M
Published: December 2010

Objective

To estimate the prevalence of, and implement a diagnostic strategy for, imported helminth infection in the gastroenterology clinic.

Design

A retrospective study of eosinophil count and probable tropical exposure (phase I) followed by a prospective study of parasitological investigation (phase II).

Setting

Gastroenterology service of an inner London hospital.

Patients

Adult patients newly attending general gastroenterology and inflammatory bowel disease clinics.

Interventions

In phase I, evidence of undiagnosed helminth infection was sought by analysing patient records for associations between eosinophil count and ethnicity. In phase II, a UK guideline for investigation of eosinophilia in migrants was implemented and diagnostic yield determined.

Main outcome measures

In phase I, prevalence of eosinophilia was determined; in phase II, helminth prevalence and degree of eosinophilia before and after treatment were reported. Information on symptomatic response to treatment was recorded. Ethnicity was used as a proxy measure for tropical exposure.

Results

426 new patients attended in a 12 month period. Eosinophilia was present in 27 (6.3%). 10/27 (37.0%) patients with eosinophilia were of African or Asian ethnicity whereas only 20% (85/426) of patients overall were from these ethnic groups (χ2=5.27, p=0.02). Following implementation of the protocol, 25/36 migrants with eosinophilia attended for parasitological investigations. Helminth infection was diagnosed in 10/25 (40%). Strongyloidiasis (six patients) and schistosomiasis (three patients) were the most common diagnoses. Median eosinophil count was 1.06×109/l in those with helminths and 0.58×109/l in those without (p=0.004). Eosinophil counts normalised in, and symptomatic improvement was reported by, most patients after treatment.

Conclusions

Eosinophilia is associated with African or Asian ethnicity in an inner city gastroenterology service. This association is probably explained by imported helminths, which are prevalent in this setting, may be a cause of gastrointestinal symptoms and is easily diagnosed and treated by standard protocols.