bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome Analysis Suggests that the Soil Oligotrophic Bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) Is a Nitrogen-Fixing Symbiont of Aeschynomene indica
Authors: Okubo Takashi , Fukushima Shohei , Itakura Manabu , Oshima Kenshiro , Longtonglang Aphakorn , Teaumroong Neung , Mitsui Hisayuki , Hattori Masahira , Hattori Reiko , Hattori Tsutomu , Minamisawa Kiwamu
Published: February 2013

Agromonas oligotrophica(Bradyrhizobium oligotrophicum) S58Tis a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lackingnodABCgenes and the typical symbiosis island. The genome showed a high level of similarity to the genomes ofBradyrhizobiumsp. ORS278 andBradyrhizobiumsp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant,Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nifandfix) withA. indicawere well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with fiveA. oligotrophicastrains (S58, S42, S55, S72, and S80). Surprisingly, all five strains ofA. oligotrophicaformed effective nitrogen-fixing nodules on the roots and/or stems ofA. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwellingA. oligotrophicagenerally possesses the ability to establish symbiosis withA. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis withA. indicais a common trait ofnodABC- and symbiosis island-lacking strains within the members of the photosyntheticBradyrhizobiumclade, includingA. oligotrophica.
Distribution and Origin of Oxygen-Dependent and Oxygen-Independent Forms of Mg-Protoporphyrin Monomethylester Cyclase among Phototrophic Proteobacteria
Authors: Boldareva-Nuianzina Ekaterina N. , Bláhová Zuzana , Sobotka Roman , Koblížek Michal
Published: February 2013

Magnesium-protoporphyrin IX monomethylester cyclase is one of the key enzymes of the bacteriochlorophyll biosynthesis pathway. There exist two fundamentally different forms of this enzyme. The oxygen-dependent form, encoded by the gene
acsF
, catalyzes the formation of the bacteriochlorophyll fifth ring using oxygen, whereas the oxygen-independent form encoded by the gene
bchE
utilizes an oxygen atom extracted from water. The presence of
acsF
and
bchE
genes was surveyed in various phototrophic
Proteobacteria
using the available genomic data and newly designed degenerated primers. It was found that while the majority of purple nonsulfur bacteria contained both forms of the cyclase, the purple sulfur bacteria contained only the oxygen-independent form. All tested species of aerobic anoxygenic phototrophs contained
acsF
genes, but some of them also retained the
bchE
gene. In contrast to
bchE
phylogeny, the
acsF
phylogeny was in good agreement with 16S inferred phylogeny. Moreover, the survey of the genome data documented that the
acsF
gene occupies a conserved position inside the photosynthesis gene cluster, whereas the
bchE
location in the genome varied largely between the species. This suggests that the oxygen-dependent cyclase was recruited by purple phototrophic bacteria very early during their evolution. The primary sequence and immunochemical similarity with its cyanobacterial counterparts suggests that
acsF
may have been acquired by
Proteobacteria
via horizontal gene transfer from cyanobacteria. The acquisition of the gene allowed purple nonsulfur phototrophic bacteria to proliferate in the mildly oxygenated conditions of the Proterozoic era.
New Biotransformation Process for Production of the Fragrant Compound γ-Dodecalactone from 10-Hydroxystearate by Permeabilized Waltomyces lipofer Cells
Authors: An Jung-Ung , Joo Young-Chul , Oh Deok-Kun
Published: February 2013

A new biotransformation process for the production of the flavor lactone was developed by using permeabilized
Waltomyces lipofer
, which was selected as an efficient γ-dodecalactone-producing yeast among 10 oleaginous yeast strains. The optimal reaction conditions for γ-dodecalactone production by permeabilized
W. lipofer
cells were pH 6.5, 35°C, 200 rpm, 0.7 M Tris, 60 g/liter of 10-hydroxystearic acid, and 30 g/liter of cells. Under these conditions, nonpermeabilized cells produced 12 g/liter of γ-dodecalactone after 30 h, with a conversion yield of 21% (wt/wt) and a productivity of 0.4 g/liter/h, whereas permeabilized cells obtained after sequential treatments with 50% ethanol and 0.5% Triton X-100 produced 46 g/liter of γ-dodecalactone after 30 h, with a conversion yield of 76% (wt/wt) and a productivity of 1.5 g/liter/h. These values were 3.7- and 3.8-fold higher than those obtained using nonpermeabilized cells. These are the highest reported concentration, conversion yield, and productivity for the production of the bioflavor lactone.
Syringyl-Rich Lignin Renders Poplars More Resistant to Degradation by Wood Decay Fungi
Authors: Skyba Oleksandr , Douglas Carl J. , Mansfield Shawn D.
Published: February 2013

In order to elucidate the effects of lignin composition on the resistance of wood to degradation by decay fungi, wood specimens from two transgenic poplar lines expressing an
Arabidopsis
gene encoding ferulate 5-hydroxylase (F5H) driven by the cinnimate-4-hydroxylase promoter (C4H::F5H) that increased syringyl/guaiacyl (S/G) monolignol ratios relative to those in the untransformed control wood were incubated with six different wood decay fungi. Alterations in wood weight and chemical composition were monitored over the incubation period. The results showed that transgenic poplar lines extremely rich in syringyl lignin exhibited a drastically improved resistance to degradation by all decay fungi evaluated. Lignin monomer composition and its distribution among cell types and within different cell layers were the sole wood chemistry parameters determining wood durability. Since transgenic poplars with exceedingly high syringyl contents were recalcitrant to degradation, where wood durability is a critical factor, these genotypes may offer improved performance.
Phosphotransferase System-Mediated Glucose Uptake Is Repressed in Phosphoglucoisomerase-Deficient Corynebacterium glutamicum Strains
Authors: Lindner Steffen N. , Petrov Dimitar P. , Hagmann Christian T. , Henrich Alexander , Krämer Reinhard , Eikmanns Bernhard J. , Wendisch Volker F. , Seibold Gerd M.
Published: February 2013

Corynebacterium glutamicumis particularly known for its industrial application in the production of amino acids. Amino acid overproduction comes along with a high NADPH demand, which is covered mainly by the oxidative part of the pentose phosphate pathway (PPP). In previous studies, the complete redirection of the carbon flux toward the PPP by chromosomal inactivation of thepgigene, encoding the phosphoglucoisomerase, has been applied for the improvement ofC. glutamicumamino acid production strains, but this was accompanied by severe negative effects on the growth characteristics. To investigate these effects in a genetically defined background, we deleted thepgigene in the type strainC. glutamicumATCC 13032. The resulting strain,C. glutamicumΔpgi, lacked detectable phosphoglucoisomerase activity and grew poorly with glucose as the sole substrate. Apart from the already reported inhibition of the PPP by NADPH accumulation, we detected a drastic reduction of the phosphotransferase system (PTS)-mediated glucose uptake inC. glutamicumΔpgi. Furthermore, Northern blot analyses revealed that expression ofptsG, which encodes the glucose-specific EII permease of the PTS, was abolished in this mutant. Applying our findings, we optimizedl-lysine production in the model strainC. glutamicumDM1729 by deletion ofpgiand overexpression of plasmid-encodedptsG.l-Lysine yields and productivity withC. glutamicumΔpgi(pBB1-ptsG) were significantly higher than those withC. glutamicumΔpgi(pBB1). These results show thatptsGoverexpression is required to overcome the repressed activity of PTS-mediated glucose uptake inpgi-deficientC. glutamicumstrains, thus enabling efficient as well as fastl-lysine production.
Linking Microbial Community Structure to Function in Representative Simulated Systems
Authors: Marcus Ian M. , Wilder Hailey A. , Quazi Shanin J. , Walker Sharon L.
Published: February 2013

Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with
Escherichia coli
O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of
E. coli
O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with
E. coli
O157:H7 were found to be significantly different from those of
E. coli
O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present.
Environmental Distribution and Seasonal Prevalence of Mycobacterium ulcerans in Southern Louisiana
Authors: Hennigan Caroline E. , Myers Leann , Ferris Michael J.
Published: February 2013

Mycobacterium ulcerans
is an emerging environmental pathogen that causes debilitating, ulcerative disease in humans and other vertebrates. The majority of human cases occur in tropical and temperate regions of Africa and Australia, and outbreaks of piscine mycobacteriosis caused by
M. ulcerans
have been reported in disparate geographic locations spanning the globe. While exposure to a natural body of water is the most common risk factor for human infection, the environmental distribution of
M. ulcerans
in aquatic habitats has not been extensively studied. Although no human cases have been reported in the United States, a strain of
M. ulcerans
has been identified as the cause of a piscine mycobacteriosis in Striped bass (
Morone saxatilis
) within the Chesapeake Bay. Infected fish exhibit bright red ventral and lateral dermal lesions. We observed a possible outbreak causing similar lesions on red drum (
Sciaenops ocellatus
) in wetlands of southern Louisiana and detected
M. ulcerans
-specific genetic markers in lesion samples from these fish. Based on these findings, we studied the geographic and seasonal prevalence of these markers across southern Louisiana.
M. ulcerans
was detected in each of the nine areas sampled across the state.
M. ulcerans
prevalence was significantly lower in the fall samples, and the low prevalence coincided with decreased nutrient levels and an increase in water temperature. To our knowledge, this is the first study of
M. ulcerans
biomarkers in the southern United States.
Effects of the Peptide Pheromone Plantaricin A and Cocultivation with Lactobacillus sanfranciscensis DPPMA174 on the Exoproteome and the Adhesion Capacity of Lactobacillus plantarum DC400
Authors: Calasso Maria , Di Cagno Raffaella , De Angelis Maria , Campanella Daniela , Minervini Fabio , Gobbetti Marco
Published: February 2013

This study aimed at investigating the extracellular and cell wall-associated proteins (exoproteome) of
Lactobacillus plantarum
DC400 when cultivated on modified chemically defined medium (CDM) supplemented with the chemically synthesized pheromone plantaricin A (PlnA) or cocultured with
L. plantarum
DPPMA20 or
Lactobacillus sanfranciscensis
DPPMA174. Compared to monoculture, two-dimensional gel electrophoresis (2-DE) analysis showed that the exoproteome of
L. plantarum
DC400 was affected by PlnA and cocultivation with strains DPPMA20 and, especially, DPPMA174. The highest similarity of the 2-DE maps was found between DC400 cells cultivated in monoculture and in coculture with strain DPPMA20. Almost all extracellular proteins (22 spots) and cell wall-associated proteins (40 spots) which showed decreased or increased levels of synthesis during growth in CDM supplemented with PlnA and/or in coculture with strain DPPMA20 or DPPMA174 were identified. On the basis of the sequences in the Kyoto Encyclopedia of Genes and Genomes database, changes to the exoproteome concerned proteins involved in quorum sensing (QS), the transport system, stress response, carbohydrate metabolism and glycolysis, oxidation/reduction processes, the proteolytic system, amino acid metabolism, cell wall and catabolic processes, and cell shape, growth, and division. Cultivation with PlnA and cocultivation with strains DPPMA20 and, especially, DPMMA174 markedly increased the capacity of
L. plantarum
DC400 to form biofilms, to adhere to human Caco-2 cells, and to prevent the adhesion of potential intestinal pathogens. These phenotypic traits were in part related to oversynthesized moonlighting proteins (e.g., DnaK and GroEL, pyruvate kinase, enolase, and glyceraldehyde-3-phosphate dehydrogenase) in response to QS mechanisms and interaction with
L. plantarum
DPPMA20 and, especially,
L. sanfranciscensis
DPPMA174.
Development of a Rapid Real-Time PCR Method as a Tool To Quantify Viable Photobacterium phosphoreum Bacteria in Salmon (Salmo salar) Steaks
Authors: Macé Sabrina , Mamlouk Kelthoum , Chipchakova Stoyka , Prévost Hervé , Joffraud Jean-Jacques , Dalgaard Paw , Pilet Marie-France , Dousset Xavier
Published: February 2013

A specific real-time PCR quantification method combined with a propidium monoazide sample treatment step was developed to determine quantitatively the viable population of the
Photobacterium phosphoreum
species group in raw modified-atmosphere-packed salmon. Primers were designed to amplify a 350-bp fragment of the gyrase subunit B gene (
gyrB
) of
P. phosphoreum
. The specificity of the two primers was demonstrated by using purified DNA from 81 strains of 52 different bacterial species. When these primers were used for real-time PCR in pure culture, a good correlation (
R
2
of 0.99) was obtained between this method and conventional enumeration on marine agar (MA). Quantification was linear over 5 log units as confirmed by using inoculated salmon samples. On naturally contaminated fresh salmon, the new real-time PCR method performed successfully with a quantification limit of 3 log CFU/g. A correlation coefficient (
R
2
) of 0.963 was obtained between the PCR method and classic enumeration on MA, followed by identification of colonies (290 isolates identified by real-time PCR or by 16S rRNA gene sequencing). A good correlation with an
R
2
of 0.940 was found between the new PCR method and an available specific conductance method for
P. phosphoreum
. This study presents a rapid tool for producing reliable quantitative data on viable
P. phosphoreum
bacteria in fresh salmon in 6 h. This new culture-independent method will be valuable for future fish inspection, the assessment of raw material quality in fish processing plants, and studies on the ecology of this important specific spoilage microorganism.
Optimization of Magnetosome Production and Growth by the Magnetotactic Vibrio Magnetovibrio blakemorei Strain MV-1 through a Statistics-Based Experimental Design
Authors: Silva Karen T. , Leão Pedro E. , Abreu Fernanda , López Jimmy A. , Gutarra Melissa L. , Farina Marcos , Bazylinski Dennis A. , Freire Denise M. G. , Lins Ulysses
Published: February 2013

The growth and magnetosome production of the marine magnetotactic vibrio
Magnetovibrio blakemorei
strain MV-1 were optimized through a statistics-based experimental factorial design. In the optimized growth medium, maximum magnetite yields of 64.3 mg/liter in batch cultures and 26 mg/liter in a bioreactor were obtained.
Monitoring the Perturbation of Soil and Groundwater Microbial Communities Due to Pig Production Activities
Authors: Hong Pei-Ying , Yannarell Anthony C. , Dai Qinghua , Ekizoglu Melike , Mackie Roderick I.
Published: February 2013

This study aimed to determine if biotic contaminants originating from pig production farms are disseminated into soil and groundwater microbial communities. A spatial and temporal sampling of soil and groundwater in proximity to pig production farms was conducted, and quantitative PCR (Q-PCR) was utilized to determine the abundances of tetracycline resistance genes (i.e.,
tetQ
and
tetZ
) and integrase genes (i.e.,
intI1
and
intI2
). We observed that the abundances of
tetZ
,
tetQ
,
intI1
, and
intI2
in the soils increased at least 6-fold after manure application, and their abundances remained elevated above the background for up to 16 months. Q-PCR further determined total abundances of up to 5.88 × 10
9
copies/ng DNA for
tetZ
,
tetQ
,
intI1
, and
intI2
in some of the groundwater wells that were situated next to the manure lagoon and in the facility well used to supply water for one of the farms. We further utilized 16S rRNA-based pyrosequencing to assess the microbial communities, and our comparative analyses suggest that most of the soil samples collected before and after manure application did not change significantly, sharing a high Bray-Curtis similarity of 78.5%. In contrast, an increase in
Bacteroidetes
and sulfur-oxidizing bacterial populations was observed in the groundwaters collected from lagoon-associated groundwater wells. Genera associated with opportunistic human and animal pathogens, such as
Acinetobacter
,
Arcobacter
,
Yersinia
, and
Coxiella
, were detected in some of the manure-treated soils and affected groundwater wells. Feces-associated bacteria such as
Streptococcus
,
Erysipelothrix
, and
Bacteroides
were detected in the manure, soil, and groundwater ecosystems, suggesting a perturbation of the soil and groundwater environments by invader species from pig production activities.
Characterization of a Novel Panton-Valentine Leukocidin (PVL)-Encoding Staphylococcal Phage and Its Naturally PVL-Lacking Variant
Authors: El Haddad Lynn , Moineau Sylvain
Published: February 2013

A new siphophage (LH1) was isolated from raw milk using a
Staphylococcus aureus
ST352 host. Its genome (46,048 bp, 57 open reading frames) includes the two genes encoding Panton-Valentine leukocidin (PVL), a virulence factor usually harbored by
S. aureus
prophages. Nine structural proteins were identified, including a tail protein generated through a +1 frameshift. A phage lytic mutant was isolated, and its analysis revealed the deletion of genes coding for the PVL and an integrase. The deletion likely occurred through recombination between direct repeats.
Shewanella spp. Use Acetate as an Electron Donor for Denitrification but Not Ferric Iron or Fumarate Reduction
Authors: Yoon Sukhwan , Sanford Robert A. , Löffler Frank E.
Published: February 2013

Lactate but not acetate oxidation was reported to support electron acceptor reduction by
Shewanella
spp. under anoxic conditions. We demonstrate that the denitrifiers
Shewanella loihica
strain PV-4 and
Shewanella denitrificans
OS217 utilize acetate as an electron donor for denitrification but not for fumarate or ferric iron reduction.
Cross-Sectional Study Reveals High Prevalence of Clostridium difficile Non-PCR Ribotype 078 Strains in Australian Veal Calves at Slaughter
Authors: Knight Daniel R. , Thean Sara , Putsathit Papanin , Fenwick Stan , Riley Thomas V.
Published: February 2013

Recent reports in North America and Europe of
Clostridium difficile
being isolated from livestock and retail meats of bovine origin have raised concerns about the risk to public health. To assess the situation in Australia, we investigated the prevalence and genetic diversity of
C. difficile
in adult cattle and calves at slaughter. Carcass washings, gastrointestinal contents, and feces were collected from abattoirs across five Australian states. Selective culture, toxin profiling, and PCR ribotyping were performed. The prevalence of
C. difficile
was 56% (203/360 samples) in feces from <7-day-old calves, 3.8% (1/26) in 2- to 6-month-old calves, and 1.8% (5/280) in adult cattle. Three PCR ribotypes (RTs), RT127, RT033, and RT126, predominated in <7-day-old calves and comprised 77.8% (158/203 samples) of isolates. RT056, which has not been reported in cattle before, was found in 16 <7-day-old calves (7.7%). Surprisingly, RT078 strains, which dominate production animal carriage studies in the Northern Hemisphere, were not isolated.
Transcriptional Regulation of the Copper Transporter Mfc1 in Meiotic Cells
Authors: Beaudoin Jude , Ioannoni Raphaël , Mailloux Stéphane , Plante Samuel , Labbé Simon
Published: February 2013

Mfc1 is a meiosis-specific protein that mediates copper transport during the meiotic program in
Schizosaccharomyces pombe
. Although the
mfc1
+
gene is induced at the transcriptional level in response to copper deprivation, the molecular determinants that are required for its copper starvation-dependent induction are unknown. Promoter deletion and site-directed mutagenesis have allowed identification of a new
cis
-regulatory element in the promoter region of the
mfc1
+
gene. This
cis
-acting regulatory sequence containing the sequence TCGGCG is responsible for transcriptional activation of
mfc1
+
under low-copper conditions. The TCGGCG sequence contains a CGG triplet known to serve as a binding site for members of the Zn
(2)
Cys
(6)
binuclear cluster transcriptional regulator family. In agreement with this fact, one member of this group of regulators, denoted Mca1, was found to be required for maximum induction of
mfc1
+
gene expression. Analysis of Mca1 cellular distribution during meiosis revealed that it colocalizes with both chromosomes and sister chromatids during early, middle, and late phases of the meiotic program. Cells lacking Mca1 exhibited a meiotic arrest at metaphase I under low-copper conditions. Binding studies revealed that the N-terminal 150-residue segment of Mca1 expressed as a fusion protein in
Escherichia coli
specifically interacts with the TCGGCG sequence of the
mfc1
+
promoter. Taken together, these results identify the
cis
-regulatory TCGGCG sequence and the transcription factor Mca1 as critical components for activation of the meiotic copper transport
mfc1
+
gene in response to copper starvation.
Cysteine Protease Inhibitor (AcStefin) Is Required for Complete Cyst Formation of Acanthamoeba
Authors: Lee Jung-Yub , Song Su-Min , Moon Eun-Kyung , Lee Yu-Ran , Jha Bijay Kumar , Danne Dinzouna-Boutamba Sylvatrie , Cha Hee-Jae , Yu Hak Sun , Kong Hyun-Hee , Chung Dong-Il , Hong Yeonchul
Published: February 2013

The encystation of
Acanthamoeba
leads to the formation of resilient cysts from vegetative trophozoites. This process is essential for parasite survival under unfavorable conditions, such as those associated with starvation, low temperatures, and biocides. Furthermore, cysteine proteases have been implicated in the massive turnover of intracellular components required for encystation. Thus, strict modulation of the activities of cysteine proteases is required to protect
Acanthamoeba
from intracellular damage. However, mechanisms underlying the control of protease activity during encystation have not been established in
Acanthamoeba
. In the present study, we identified and characterized
Acanthamoeba
cysteine protease inhibitor (AcStefin), which was found to be highly expressed during encystation and to be associated with lysosomes by fluorescence microscopy. Recombinant AcStefin inhibited various cysteine proteases, including human cathepsin B, human cathepsin L, and papain. Transfection with small interfering RNA against AcStefin increased cysteine protease activity during encystation and resulted in incomplete cyst formation, reduced excystation efficiency, and a significant reduction in cytoplasmic area. Taken together, these results indicate that AcStefin is involved in the modulation of cysteine proteases and that it plays an essential role during the encystation of
Acanthamoeba
.
Adhesins in Human Fungal Pathogens: Glue with Plenty of Stick
Authors: de Groot Piet W. J. , Bader Oliver , de Boer Albert D. , Weig Michael , Chauhan Neeraj
Published: February 2013

Understanding the pathogenesis of an infectious disease is critical for developing new methods to prevent infection and diagnose or cure disease. Adherence of microorganisms to host tissue is a prerequisite for tissue invasion and infection. Fungal cell wall adhesins involved in adherence to host tissue or abiotic medical devices are critical for colonization leading to invasion and damage of host tissue. Here, with a main focus on pathogenic
Candida
species, we summarize recent progress made in the field of adhesins in human fungal pathogens and underscore the importance of these proteins in establishment of fungal diseases.
Identification and Characterization of MalA in the Maltose/Maltodextrin Operon of Sulfolobus acidocaldarius DSM639
Authors: Choi Kyoung-Hwa , Hwang Sungmin , Cha Jaeho
Published: February 2013

A putative maltose/maltodextrin operon was found in the
Sulfolobus acidocaldarius
DSM639 genome. The gene cluster consisted of 7 genes (
malA
,
trmB
,
amyA
,
malG
,
malF
,
malE
, and
malK
). Here, we report the identification of MalA, which is responsible for the hydrolysis of maltose or maltodextrin to glucose in
S. acidocaldarius
. The transcription level of
malA
was increased 3-fold upon the addition of maltose or starch to the medium. Moreover, the α-glucosidase activity for maltose as a substrate in cell extracts of
S. acidocaldarius
DSM639 was also 11- and 10-fold higher during growth in YT medium (Brock's mineral salts, 0.1% [wt/vol] tryptone, and 0.005% [wt/vol] yeast extract) containing maltose or starch, respectively, than during growth on other sugars. The gene encoding MalA was cloned and expressed in
S. acidocaldarius
. The enzyme purified from the organism was a dodecamer in its active state and showed strong maltose-hydrolyzing activity at 100°C and pH 5.0. MalA was remarkably thermostable, with half-lives of 33.8 h, 10.6 h, and 1.8 h at 95°C, 100°C, and 105°C, respectively. Substrate specificity and kinetic studies of MalA with maltooligosaccharides indicated that MalA efficiently hydrolyzed maltose to maltopentaose, which is a typical characteristic of GH31-type α-glucosidases. However, glycogen or starch was not hydrolyzed. Reverse transcription-PCR, sugar uptake, and growth studies of the wild-type DSM639 and Δ
malEFG
mutant on different sugars demonstrated that MalA located in the
mal
operon gene cluster is involved in maltose and starch metabolism in
S. acidocaldarius
.
Interplay between Type 1A Topoisomerases and Gyrase in Chromosome Segregation in Escherichia coli
Authors: Usongo Valentine , Tanguay Cynthia , Nolent Flora , Bessong Jill Egbe , Drolet Marc
Published: February 2013

Escherichia colipossesses two type 1A topoisomerases, Topo I (topA) and Topo III (topB). Topo I relaxes excess negative supercoiling, andtopAmutants can grow only in the presence of compensatory mechanisms, such as gyrase mutations.topBmutants grow as well as wild-type cells.In vitro, Topo III, but not Topo I, can efficiently decatenate DNA during replication. However,in vivo, a chromosome segregation defect is seen only when both type 1A topoisomerases are absent. Here we present experimental evidence for an interplay between gyrase and type 1A topoisomerases in chromosome segregation. We found that both the growth defect and the Par−phenotypes of agyrB(Ts) mutant at nonpermissive temperatures were significantly corrected by deletingtopA, but only whentopBwas present. Overproducing Topo IV, the major cellular decatenase, could not substitute fortopB. We also show that overproducing Topo III at a very high level could suppress the Par−phenotype. We previously found that the growth and chromosome segregation defects of a tripletopA rnhA gyrB(Ts) mutant in which gyrase supercoiling activity was strongly inhibited could be corrected by overproducing Topo III (V. Usongo, F. Nolent, P. Sanscartier, C. Tanguay, S. Broccoli, I. Baaklini, K. Drlica, and M. Drolet, Mol. Microbiol.69:968-981, 2008). We show here that this overproduction could be bypassed by substituting thegyrB(Ts) allele for agyrB+one or by growing cells in a minimal medium, conditions that reduced bothtopA- andrnhA-dependent unregulated replication. Altogether, our data point to a role for Topo III in chromosome segregation when gyrase is inefficient and suggest that Topo I plays an indirect role via supercoiling regulation.
Structural and Functional Roles of Carotenoids in Chlorosomes
Authors: Pšenčík Jakub , Arellano Juan B. , Collins Aaron M. , Laurinmäki Pasi , Torkkeli Mika , Löflund Benita , Serimaa Ritva E. , Blankenship Robert E. , Tuma Roman , Butcher Sarah J.
Published: February 2013

Chlorosomes are large light-harvesting complexes found in three phyla of anoxygenic photosynthetic bacteria. Chlorosomes are primarily composed of self-assembling pigment aggregates. In addition to the main pigment, bacteriochlorophyll
c
,
d
, or
e
, chlorosomes also contain variable amounts of carotenoids. Here, we use X-ray scattering and electron cryomicroscopy, complemented with absorption spectroscopy and pigment analysis, to compare the morphologies, structures, and pigment compositions of chlorosomes from
Chloroflexus aurantiacus
grown under two different light conditions and
Chlorobaculum tepidum
. High-purity chlorosomes from
C. aurantiacus
contain about 20% more carotenoid per bacteriochlorophyll
c
molecule when grown under low light than when grown under high light. This accentuates the light-harvesting function of carotenoids, in addition to their photoprotective role. The low-light chlorosomes are thicker due to the overall greater content of pigments and contain domains of lamellar aggregates. Experiments where carotenoids were selectively extracted from intact chlorosomes using hexane proved that they are located in the interlamellar space, as observed previously for species belonging to the phylum
Chlorobi
. A fraction of the carotenoids are localized in the baseplate, where they are bound differently and cannot be removed by hexane. In
C. tepidum
, carotenoids cannot be extracted by hexane even from the chlorosome interior. The chemical structure of the pigments in
C. tepidum
may lead to π-π interactions between carotenoids and bacteriochlorophylls, preventing carotenoid extraction. The results provide information about the nature of interactions between bacteriochlorophylls and carotenoids in the protein-free environment of the chlorosome interior.
Regulation of Lipid Biosynthesis, Sliding Motility, and Biofilm Formation by a Membrane-Anchored Nucleoid-Associated Protein of Mycobacterium tuberculosis
Authors: Ghosh Soumitra , Indi Shantinath S. , Nagaraja Valakunja
Published: February 2013

Bacteria use a number of small basic proteins for organization and compaction of their genomes. By their interaction with DNA, these nucleoid-associated proteins (NAPs) also influence gene expression. Rv3852, a NAP of
Mycobacterium tuberculosis
, is conserved among the pathogenic and slow-growing species of mycobacteria. Here, we show that the protein predominantly localizes in the cell membrane and that the carboxy-terminal region with the propensity to form a transmembrane helix is necessary for its membrane localization. The protein is involved in genome organization, and its ectopic expression in
Mycobacterium smegmatis
resulted in altered nucleoid morphology, defects in biofilm formation, sliding motility, and change in apolar lipid profile. We demonstrate its crucial role in regulating the expression of KasA, KasB, and GroEL1 proteins, which are in turn involved in controlling the surface phenotypes in mycobacteria.
Crystallographic Study To Determine the Substrate Specificity of an
l
-Serine-Acetylating Enzyme Found in the
d
-Cycloserine Biosynthetic Pathway
Authors: Oda Kosuke , Matoba Yasuyuki , Kumagai Takanori , Noda Masafumi , Sugiyama Masanori
Published: February 2013

DcsE, one of the enzymes found in the
d
-cycloserine biosynthetic pathway, displays a high sequence homology to
l
-homoserine
O
-acetyltransferase (HAT), but it prefers
l
-serine over
l
-homoserine as the substrate. To clarify the substrate specificity, in the present study we determined the crystal structure of DcsE at a 1.81-Å resolution, showing that the overall structure of DcsE is similar to that of HAT, whereas a turn region to form an oxyanion hole is obviously different between DcsE and HAT: in detail, the first and last residues in the turn of DcsE are Gly
52
and Pro
55
, respectively, but those of HAT are Ala and Gly, respectively. In addition, more water molecules were laid on one side of the turn region of DcsE than on that of HAT, and a robust hydrogen-bonding network was formed only in DcsE. We created a HAT-like mutant of DcsE in which Gly
52
and Pro
55
were replaced by Ala and Gly, respectively, showing that the mutant acetylates
l
-homoserine but scarcely acetylates
l
-serine. The crystal structure of the mutant DcsE shows that the active site, including the turn and its surrounding waters, is similar to that of HAT. These findings suggest that a methyl group of the first residue in the turn of HAT plays a role in excluding the binding of
l
-serine to the substrate-binding pocket. In contrast, the side chain of the last residue in the turn of DcsE may need to form an extensive hydrogen-bonding network on the turn, which interferes with the binding of
l
-homoserine.
Extracellular Life Cycle of ComS, the Competence-Stimulating Peptide of Streptococcus thermophilus
Authors: Gardan Rozenn , Besset Colette , Gitton Christophe , Guillot Alain , Fontaine Laetitia , Hols Pascal , Monnet Véronique
Published: February 2013

In streptococci, ComX is the alternative sigma factor controlling the transcription of the genes encoding the genetic transformation machinery. In
Streptococcus thermophilus
,
comX
transcription is controlled by a complex consisting of a transcriptional regulator of the Rgg family, ComR, and a signaling peptide, ComS, which controls ComR activity. Following its initial production, ComS is processed, secreted, and imported back into the cell by the Ami oligopeptide transporter. We characterized these steps and the partners interacting with ComS during its extracellular circuit in more detail. We identified the mature form of ComS and demonstrated the involvement of the membrane protease Eep in ComS processing. We found that ComS was secreted but probably not released into the extracellular medium. Natural competence was first discovered in a chemically defined medium without peptides. We show here that the presence of a high concentration of nutritional peptides in the medium prevents the triggering of competence. In milk, the ecological niche of
S. thermophilus
, competence was found to be functional, suggesting that the concentration of nutritional peptides was too low to interfere with ComR activation. The kinetics of expression of the
comS
,
comR
, and
comX
genes and of a late competence gene,
dprA
, in cultures inoculated at different initial densities revealed that the activation mechanism of ComR by ComS is more a timing device than a quorum-sensing mechanism sensu stricto. We concluded that the ComS extracellular circuit facilitates tight control over the triggering of competence in
S. thermophilus
.
Expression Level of Bacillus subtilis Germinant Receptors Determines the Average Rate but Not the Heterogeneity of Spore Germination
Authors: Zhang Jing-qiao , Griffiths Keren K. , Cowan Ann , Setlow Peter , Yu Ji
Published: February 2013

Germination of
Bacillus subtilis
spores can be triggered by the binding of specific nutrients, called germinants, to germinant receptors (GRs) in the spore's inner membrane. This interaction eventually initiates, with variable time delays, the release of dipicolinic acid and cations from the spore core—a key step in spore germination. The kinetics of this process are highly heterogeneous for individual spores. In this work, we sought to investigate how the germination heterogeneity was controlled. In particular, we tested whether the rates of germination were determined by GR levels, which vary from spore to spore due to stochastic gene expression. Both the expression levels of GRs and the germination rate were measured in single spores, and the experimental results were compared to theoretical predictions. Our results indicated that the variation in the expression levels of GRs was not the primary factor that controls spore germination heterogeneity. Two alternative hypotheses are discussed in light of this experimental discovery.
Protein Kinase/Phosphatase Function Correlates with Gliding Motility in Mycoplasma pneumoniae
Authors: Page Clinton A. , Krause Duncan C.
Published: February 2013

Mycoplasma pneumoniae
exhibits a novel form of gliding motility that is mediated by the terminal organelle, a differentiated polar structure. Given that genes known to be involved in gliding in other organisms are absent in
M. pneumoniae
, random transposon mutagenesis was employed to generate mutants with gliding-deficient phenotypes. Transposon insertions in the only annotated Ser/Thr protein kinase gene (
prkC
; MPN248) and its cognate phosphatase gene (
prpC
; MPN247) in
M. pneumoniae
resulted in significant and contrasting effects on gliding frequencies.
prkC
mutant cells glided at approximately half the frequency of wild-type cells, while
prpC
mutant cells glided more than twice as frequently as wild-type cells. Phosphoprotein staining confirmed the association between phosphorylation of the cytoskeletal proteins HMW1 and HMW2 and membrane protein P1 and the gliding phenotype. When the
prpC
mutant was complemented by transposon delivery of a wild-type copy of the
prpC
allele, gliding frequencies and phosphorylation levels returned to the wild-type standard. Surprisingly, delivery of the recombinant wild-type
prkC
allele dramatically increased gliding frequency to a level approximately 3-fold greater than that of wild-type in the
prkC
mutant. Collectively, these data suggest that PrkC and PrpC work in opposition in
M. pneumoniae
to influence gliding frequency.
Tacrolimus-associated thrombotic microangiopathy in a lung transplant recipient
Authors: Boyer Nathan Lewis , Niven Alexander , Edelman Jeffery
Published: February 2013

A 25-year-old woman with a history of bilateral lung transplant secondary to cystic fibrosis presented with non-specific abdominal complaints and was found to have acute kidney injury, thrombocytopaenia and laboratory findings consistent with a microangiopathic haemolytic anaemia. Her thrombotic microangiopathy (TMA) was attributed to tacrolimus, which was discontinued and replaced with cyclosporine with resolution of her TMA and no subsequent complications. This is the fifth reported case of TMA associated with tacrolimus use in a lung transplant patient, and the third to be successfully managed with cyclosporine substitution. Clinicians must be aware of this uncommon, but likely under-reported complication of tacrolimus therapy in lung transplant recipients. Cyclosporine replacement may be used as a successful therapy to treat tacrolimus-associated TMA without increasing the risk of acute rejection that may be associated with other treatment strategies.
Psoriasis aggravation due to lapatinib
Authors: Selam Meltem
Published: February 2013

Our patient was a 35-year-old woman, who had undergone right radically modified mastectomy and axillary-lymph-nodes dissection in June 2004. The stage of the patient was T2N0M0. She was treated with six cycles of FAC (5-fluorouracil, doxorubicin, cyclofosfamid), tamoxifen after chemotherapy. In June 2008, right axillary lymphadenopathy progressed and was treated with docetaxel and capecitabine after a hand–foot reaction was observed in the patient as an adverse reaction to capacitabine; the treatment was continued with only trastuzmab between February 2009 and April 2010. The addition of vinoralbine was needed due to the newly developed right paratracheal lymphadenopthy in April 2010. After six cycles of chemotherapy we achieved stable disease; she received only trastuzumab; later on, in control thorax CT, multiple metastatic models were observed in April 2011 and thus lapatinip plus capecitabine treatment was started. After one cycle of chemotherapy her psoriatic lesions were aggravated and we had to stop the treatment.
Group B streptococci as an unusual cause of septic arthritis of the hip: association with childbirth
Authors: Kumar Vishwajeet , Desai A , Alva Avinash , Board T N
Published: February 2013

Group B streptococci (GBS) birth canal colonisation in pregnant women and women of child-bearing age is well known. The recognition and incidence of infections caused by these organisms in non-pregnant and elderly adults are increasing. Clinical manifestations of GBS infections can range from simple skin and soft tissue infections to fatal meningitis in newborns. GBS as a cause of septic arthritis of the hip associated with pregnancy is previously unreported. We report a case of septic arthritis of the hip joint caused by GBS in a 30-year-old woman with a history of recent childbirth. Delay in recognition and lack of timely appropriate treatment of this condition henceforth led to severe destruction of the joint, requiring ultimate reconstruction of the joint with cemented total hip arthroplasty. This case report highlights the atypical presentation and rapidly destructive nature of this infection with catastrophic consequences.
Bilateral facial palsy: a form of neuroborreliosis presentation in paediatric age
Authors: Francisco Telma , Marques Marília , Vieira José Pedro , Brito Maria João
Published: February 2013

Bilateral facial palsy (BFP) is a very uncommon entity, particularly in the paediatric age group. Despite its several aetiologies, neuroborreliosis should be suspected, especially in children from endemic areas presenting with acute neurological disease of unknown cause. We present two cases of BFPs as the presenting forms of neuroborreliosis.
Online follow-up after total hip replacement: a first case
Authors: Dexter Caroline , Bradley Benjamin , Williams Daniel H
Published: February 2013

With the current challenging financial climate in the NHS there is an increasing drive to reduce the number of postoperative follow-up appointments. We report on a patient who has successfully used a new online platform,www.myclinicaloutcomes.co.uk, to record condition-specific and generic wellbeing scores following total hip replacement. This case highlights the potential for remote follow-up of routine postoperative patients.
Chemotherapy-induced cerebrospinal fluid malabsorption in a shunted child: case report and review of the literature
Authors: O'Halloran Philip J , Kaliaperumal Chandrasekaran , Caird John
Published: February 2013

Ventriculoperitoneal (VP) shunt insertion is one of the most common neurosurgical procedures for the treatment of chronic hydrocephalus. Although regarded as a relatively benign procedure, several complications including obstruction, infection and mechanical failure can be seen during the postoperative stage. Symptomatic sterile cerebrospinal fluid (CSF) ascites and hydrothoracies are rare complications of VP shunt surgery. The paucity of cases makes identifying the aetiological factors difficult, particularly without catheter tip migration. It is most likely that several factors interact to reduce the absorption of CSF. The authors discuss the case of a 5-year-old girl who developed CSF ascites and a pleural effusion after starting chemotherapy for a suprasellar pilocytic astrocytoma, 2 years post-VP shunt insertion, due to a secondary obstructive hydrocephalus. After the initial management of the presenting symptoms, the child's VP shunt was subsequently changed to a ventriculo-atrial shunt and the patient made an unremarkable recovery. We also review the literature pertaining to this rare complication, assessing identifiable risk factors and surgical management options.
The diagnostic dilemma of cerebellopontine angle lesions: re-evaluating your diagnosis
Authors: Walkden Andrew , Shekhar Himanshu , Fouyas Ioannis , Gibson Rod
Published: February 2013

An unusual presentation of a life-threatening cerebellopontine abscess shows the importance of re-evaluating existing diagnoses when the clinical picture changes. Despite being rare, brain abscess is a potentially fatal condition that requires early radiological and surgical intervention. It has a varied presentation, with many cases showing no localising typical features, making it hard to diagnose at presentation. A high index of suspicion should be applied to cases exhibiting rapidly changing neurology. This is the first reported case of cerebellopontine abscess with no primary infective foci.
Is socioeconomic status associated with dietary sodium intake in Australian children? A cross-sectional study
Authors: Grimes Carley A , Campbell Karen J , Riddell Lynn J , Nowson Caryl A
Published: February 2013

Objective

To assess the association between socioeconomic status (SES) and dietary sodium intake, and to identify if the major dietary sources of sodium differ by socioeconomic group in a nationally representative sample of Australian children.

Design

Cross-sectional survey.

Setting

2007 Australian National Children's Nutrition and Physical Activity Survey.

Participants

A total of 4487 children aged 2–16 years completed all components of the survey.

Primary and secondary outcome measures

Sodium intake was determined via one 24 h dietary recall. The population proportion formula was used to identify the major sources of dietary salt. SES was defined by the level of education attained by the primary carer. In addition, parental income was used as a secondary indicator of SES.

Results

Dietary sodium intake of children of low SES background was 2576 (SEM 42) mg/day (salt equivalent 6.6 (0.1) g/day), which was greater than that of children of high SES background 2370 (35) mg/day (salt 6.1 (0.1) g/day; p<0.001). After adjustment for age, gender, energy intake and body mass index, low SES children consumed 195 mg/day (salt 0.5 g/day) more sodium than high SES children (p<0.001). Low SES children had a greater intake of sodium from processed meat, gravies/sauces, pastries, breakfast cereals, potatoes and potato snacks (all p<0.05).

Conclusions

Australian children from a low SES background have on average a 9% greater intake of sodium from food sources compared with those from a high SES background. Understanding the socioeconomic patterning of salt intake during childhood should be considered in interventions to reduce cardiovascular disease.