bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shifting the Fermentative/Oxidative Balance in
Saccharomyces cerevisiae
by Transcriptional Deregulation of Snf1 via Overexpression of the Upstream Activating Kinase Sak1p
Authors: Raab Andreas M. , Hlavacek Verena , Bolotina Natalia , Lang Christine 
Published: January 2011

ABSTRACT

With the aim to reduce fermentation by-products and to promote respiratory metabolism by shifting the fermentative/oxidative balance, we evaluated the constitutive overexpression of the
SAK1
and
HAP4
genes in
Saccharomyces cerevisiae
. Sak1p is one of three kinases responsible for the phosphorylation, and thereby the activation, of the Snf1p complex, while Hap4p is the activator subunit of the Hap2/3/4/5 transcriptional complex. We compared the physiology of a
SAK1
-overexpressing strain with that of a strain overexpressing the
HAP4
gene in wild-type and
sdh2
deletion (respiratory-deficient) backgrounds. Both
SAK1
and
HAP4
overexpressions led to the upregulation of glucose-repressed genes and to reduced by-product formation rates (ethanol and glycerol).
SAK1
overexpression had a greater impact on growth rates than did
HAP4
overexpression. Elevated transcript levels of
SAK1
, but not
HAP4
, resulted in increased biomass yields in batch cultures grown on glucose (aerobic and excess glucose) as well as on nonfermentable carbon sources.
SAK1
overexpression, but not the combined overexpression of
SAK1
and
HAP4
or the overexpression of
HAP4
alone, restored growth on ethanol in an
sdh2
deletion strain. In glucose-grown shake flask cultures, the
sdh2
deletion strain with
SAK1
and
HAP4
overexpression produced succinic acid at a titer of 8.5 g liter
−1
and a yield of 0.26 mol (mol glucose)
−
1
within 216 h. We here report for the first time that a constitutively high level of expression of
SAK1
alleviates glucose repression and shifts the fermentative/oxidative balance under both glucose-repressed and -derepressed conditions.
Single-Nucleotide-Polymorphism Genotyping ofCoxiella burnetiiduring a Q Fever Outbreak in The Netherlands
Authors: Huijsmans Cornelis J. J. , Schellekens Jeroen J. A. , Wever Peter C. , Toman Rudolf , Savelkoul Paul H. M. , Janse Ingmar , Hermans Mirjam H. A. 
Published: January 2011

ABSTRACTCoxiella burnetiiis the etiological agent of Q fever. Currently, the Netherlands is facing the largest Q fever epidemic ever, with almost 4,000 notified human cases. Although the presence of a hypervirulent strain is hypothesized, epidemiological evidence, such as the animal reservoir(s) and genotype of theC. burnetiistrain(s) involved, is still lacking. We developed a single-nucleotide-polymorphism (SNP) genotyping assay directly applicable to clinical samples. Ten discriminatory SNPs were carefully selected and detected by real-time PCR. SNP genotyping appeared to be highly suitable for discrimination ofC. burnetiistrains and easy to perform with clinical samples. With this new method, we show that the Dutch outbreak is caused by at least 5 differentC. burnetiigenotypes. SNP typing of 14 human samples from the outbreak revealed the presence of 3 dissimilar genotypes. Two genotypes were also present in livestock at 9 farms in the outbreak area. SNP analyses of bulk milk from 5 other farms, commercial cow milk, and cow colostrum revealed 2 additional genotypes that were not detected in humans. SNP genotyping data from clinical samples clearly demonstrate that at least 5 differentC. burnetiigenotypes are involved in the Dutch outbreak.
Prevalence and Genetic Diversity of Aichi Viruses in Wastewater and River Water in Japan
Authors: Kitajima Masaaki , Haramoto Eiji , Phanuwan Chanetta , Katayama Hiroyuki 
Published: January 2011

ABSTRACT
Aichi virus (AiV) genomes were detected in 12 (100%) influent and 11 (92%) effluent wastewater and 36 (60%) river water samples. Among 260 strains identified, 255 were genotype A and 5 were genotype B. This is the first report describing the molecular characterization of AiVs in aquatic environments in Japan.
Cupriavidus taiwanensis
Bacteroids in
Mimosa pudica
Indeterminate Nodules Are Not Terminally Differentiated
Authors: Marchetti Marta , Catrice Olivier , Batut Jacques , Masson-Boivin Catherine 
Published: January 2011

ABSTRACT

The beta-rhizobium
Cupriavidus taiwanensis
forms indeterminate nodules on
Mimosa pudica. C. taiwanensis
bacteroids resemble free-living bacteria in terms of genomic DNA content, cell size, membrane permeability, and viability, in contrast to bacteroids in indeterminate nodules of the galegoid clade. Bacteroid differentiation is thus unrelated to nodule ontogeny.
Ecophysiology of Uncultured Filamentous Anaerobes Belonging to the Phylum KSB3 That Cause Bulking in Methanogenic Granular Sludge
Authors: Yamada Takeshi , Kikuchi Kae , Yamauchi Toshihiro , Shiraishi Koji , Ito Tsukasa , Okabe Satoshi , Hiraishi Akira , Ohashi Akiyoshi , Harada Hideki , Kamagata Yoichi , Nakamura Kazunori , Sekiguchi Yuji 
Published: January 2011

ABSTRACTA filamentous bulking of a methanogenic granular sludge caused by uncultured filamentous bacteria of the candidate phylum KSB3 in an upflow anaerobic sludge blanket (UASB) system has been reported. To characterize the physiological traits of the filaments, a polyphasic approach consisting of rRNA-based activity monitoring of the KSB3 filaments using the RNase H method and substrate uptake profiling using microautoradiography combined with fluorescencein situhybridization (MAR-FISH) was conducted. On the basis of rRNA-based activity, the monitoring of a full-scale UASB reactor operated continuously revealed that KSB3 cells became active and predominant (up to 54% of the total 16S rRNA) in the sludge when the carbohydrate loading to the system increased. Batch experiments with a short incubation of the sludge with maltose, glucose, fructose, and maltotriose at relatively low concentrations (approximately 0.1 mM) in the presence of yeast extract also showed an increase in KSB3 rRNA levels under anaerobic conditions. MAR-FISH confirmed that the KSB3 cells took up radioisotopic carbons from [14C]maltose and [14C]glucose under the same incubation conditions in the batch experiments. These results suggest that one of the important ecophysiological characteristics of KSB3 cells in the sludge is carbohydrate degradation in wastewater and that high carbohydrate loadings may trigger an outbreak of KSB3 bacteria, causing sludge bulking in UASB systems.
Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples
Authors: van den Bogert Bartholomeus , de Vos Willem M. , Zoetendal Erwin G. , Kleerebezem Michiel 
Published: January 2011

ABSTRACT

Large-scale and in-depth characterization of the intestinal microbiota necessitates application of high-throughput 16S rRNA gene-based technologies, such as barcoded pyrosequencing and phylogenetic microarray analysis. In this study, the two techniques were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, different forward primers were used for amplification to assess their impact on microbial profiling results. An average of 7,944 pyrosequences, spanning the V1 and V2 region of 16S rRNA genes, was obtained per sample. Although primer choice in barcoded pyrosequencing did not affect species richness and diversity estimates, detection of
Actinobacteria
strongly depended on the selected primer. Microbial profiles obtained by pyrosequencing and phylogenetic microarray analysis (HITChip) correlated strongly for fecal and ileal lumen samples but were less concordant for ileostomy effluent. Quantitative PCR was employed to investigate the deviations in profiling between pyrosequencing and HITChip analysis. Since cloning and sequencing of random 16S rRNA genes from ileostomy effluent confirmed the presence of novel intestinal phylotypes detected by pyrosequencing, especially those belonging to the
Veillonella
group, the divergence between pyrosequencing and the HITChip is likely due to the relatively low number of available 16S rRNA gene sequences of small intestinal origin in the DNA databases that were used for HITChip probe design. Overall, this study demonstrated that equivalent biological conclusions are obtained by high-throughput profiling of microbial communities, independent of technology or primer choice.
Mutational Analysis of Residues in the Helical Region of the Class IIa Bacteriocin Pediocin PA-1
Authors: Haugen Helén Sophie , Fimland Gunnar , Nissen-Meyer Jon 
Published: January 2011

ABSTRACT
A 15-mer fragment that is derived from the helical region in the C-terminal half of pediocin PA-1 inhibited the activity of pediocin PA-1. Of 13 other pediocin-like (hybrid) bacteriocins, only the hybrid bacteriocin Sak/Ped was markedly inhibited by the 15-mer fragment. Sak/Ped was the only one of these bacteriocins that had a sequence (in the C-terminal helix-containing half) identical to that of the 15-mer fragment, indicating that the fragment inhibits pediocin-like bacteriocins in a sequence-dependent manner. By replacing (one at a time) all 15 residues in the fragment with Ala or Leu, five residues (K1, A2, T4, N8, and A15) were identified as being especially important for the inhibitory action of the fragment. The results suggest that the corresponding residues (K20, A21, T23, N27, and A34, respectively) in pediocin PA-1 might be involved in interactions between pediocin PA-1 and its receptor. To characterize the environment surrounding these five residues when pediocin PA-1 interacts with target cells, these residues were replaced (one at a time) with a hydrophobic large (Leu) residue, a hydrophilic charged (Asp or Arg) residue, and a small (Ala or Gly) residue. The results revealed that residues A21 and A34 are in a spatially constrained environment, since the replacement with a small (Gly) residue was the only substitution that did not markedly reduce the bacteriocin activity. The positive charge in K20 and the polar amide group in N27 appeared to interact with electronegative groups, since the replacement of these two residues with a positive (Arg) residue was well tolerated, while replacement with a negative (Asp) residue was detrimental to the bacteriocin activity. K20 was in a less constrained environment than N27, since the replacement of K20 with a large hydrophobic (Leu) residue was tolerated fairly well and to a greater extent than N27. T23 seemed to be in an environment that was not restricted with respect to size, polarity, and charge, since replacements with large (Leu) and small (Ala) hydrophobic residues and a hydrophilic negative (Asp) residue were tolerated fairly well (2- to 6-fold reduction in activity). Moreover, the replacement of T23 with a large positive (Arg) residue resulted in wild-type or better-than-wild-type activity.
Characterization of a T5-Like Coliphage, SPC35, and Differential Development of Resistance to SPC35 in
Salmonella enterica
Serovar Typhimurium and
Escherichia coli
Authors: Kim Minsik , Ryu Sangryeol 
Published: January 2011

ABSTRACT

The potential of bacteriophage as an alternative biocontrol agent has recently been revisited due to the widespread occurrence of antibiotic-resistant bacteria. We isolated a virulent bacteriophage, SPC35, that can infect both
Salmonella enterica
serovar Typhimurium and
Escherichia coli
. Morphological analysis by transmission electron microscopy and analysis of its 118,351-bp genome revealed that SPC35 is a T5 group phage belonging to the family
Siphoviridae
. BtuB, the outer membrane protein for vitamin B
12
uptake, was found to be a host receptor for SPC35. Interestingly, resistant mutants of both
E. coli
and
S.
Typhimurium developed faster than our expectation when the cultures were infected with SPC35. Investigation of the
btuB
gene revealed that it was disrupted by the IS
2
insertion sequence element in most of the resistant
E. coli
isolates. In contrast, we could not detect any
btuB
gene mutations in the resistant
S.
Typhimurium isolates; these isolates easily regained sensitivity to SPC35 in its absence, suggesting phase-variable phage resistance/sensitivity. These results indicate that a cocktail of phages that target different receptors on the pathogen should be more effective for successful biocontrol.
Integrative Expression System for Delivery of Antibody Fragments by Lactobacilli
Authors: Martín M. Cruz , Pant Neha , Ladero Victor , Günaydın Gökçe , Andersen Kasper Krogh , Álvarez Beatriz , Martínez Noelia , Alvarez Miguel A. , Hammarström Lennart , Marcotte Harold 
Published: January 2011

ABSTRACT

A series of expression cassettes which mediate secretion or surface display of antibody fragments was stably integrated in the chromosome of
Lactobacillus paracasei
.
L. paracasei
producing surface-anchored variable domain of llama heavy chain (VHH) (ARP1) directed against rotavirus showed efficient binding to rotavirus and protection in the mouse model of rotavirus infection.
Functional Study of Genes Essential for Autogamy and Nuclear Reorganization in Paramecium
Authors: Nowak Jacek K. , Gromadka Robert , Juszczuk Marek , Jerka-Dziadosz Maria , Maliszewska Kamila , Mucchielli Marie-Hélène , Gout Jean-François , Arnaiz Olivier , Agier Nicolas , Tang Thomas , Aggerbeck Lawrence P. , Cohen Jean , Delacroix Hervé , Sperling Linda , Herbert Christopher J. , Zagulski Marek , Bétermier Mireille 
Published: January 2011

ABSTRACT

Like all ciliates,
Paramecium tetraurelia
is a unicellular eukaryote that harbors two kinds of nuclei within its cytoplasm. At each sexual cycle, a new somatic macronucleus (MAC) develops from the germ line micronucleus (MIC) through a sequence of complex events, which includes meiosis, karyogamy, and assembly of the MAC genome from MIC sequences. The latter process involves developmentally programmed genome rearrangements controlled by noncoding RNAs and a specialized RNA interference machinery. We describe our first attempts to identify genes and biological processes that contribute to the progression of the sexual cycle. Given the high percentage of unknown genes annotated in the
P. tetraurelia
genome, we applied a global strategy to monitor gene expression profiles during autogamy, a self-fertilization process. We focused this pilot study on the genes carried by the largest somatic chromosome and designed dedicated DNA arrays covering 484 genes from this chromosome (1.2% of all genes annotated in the genome). Transcriptome analysis revealed four major patterns of gene expression, including two successive waves of gene induction. Functional analysis of 15 upregulated genes revealed four that are essential for vegetative growth, one of which is involved in the maintenance of MAC integrity and another in cell division or membrane trafficking. Two additional genes, encoding a MIC-specific protein and a putative RNA helicase localizing to the old and then to the new MAC, are specifically required during sexual processes. Our work provides a proof of principle that genes essential for meiosis and nuclear reorganization can be uncovered following genome-wide transcriptome analysis.
G
1
/S Transcription Factor Orthologues Swi4p and Swi6p Are Important but Not Essential for Cell Proliferation and Influence Hyphal Development in the Fungal Pathogen Candida albicans
Authors: Hussein Bahira , Huang Hao , Glory Amandeep , Osmani Amin , Kaminskyj Susan , Nantel Andre , Bachewich Catherine 
Published: January 2011

ABSTRACT

The G
1
/S transition is a critical control point for cell proliferation and involves essential transcription complexes termed SBF and MBF in
Saccharomyces cerevisiae
or MBF in
Schizosaccharomyces pombe
. In the fungal pathogen
Candida albicans
, G
1
/S regulation is not clear. To gain more insight into the G
1
/S circuitry, we characterized Swi6p, Swi4p and Mbp1p, the closest orthologues of SBF (Swi6p and Swi4p) and MBF (Swi6p and Mbp1p) components in
S. cerevisiae
. The
mbp1
Δ/Δ cells showed minor growth defects, whereas
swi4
Δ/Δ and
swi6
Δ/Δ yeast cells dramatically increased in size, suggesting a G
1
phase delay.
G
ene
s
et
e
nrichment
a
nalysis (GSEA) of transcription profiles revealed that genes associated with G
1
/S phase were significantly enriched in cells lacking Swi4p and Swi6p. These expression patterns suggested that Swi4p and Swi6p have repressing as well as activating activity. Intriguingly,
swi4
Δ
/
Δ
swi6
Δ/Δ and
swi4
Δ
/
Δ
mbp1
Δ/Δ strains were viable, in contrast to the situation in
S. cerevisiae
, and showed pleiotropic phenotypes that included multibudded yeast, pseudohyphae, and intriguingly, true hyphae. Consistently, GSEA identified strong enrichment of genes that are normally modulated during
C. albicans
-host cell interactions. Since Swi4p and Swi6p influence G
1
phase progression and SBF binding sites are lacking in the
C. albicans
genome, these factors may contribute to MBF activity. Overall, the data suggest that the putative G
1
/S regulatory machinery of
C. albican
s contains novel features and underscore the existence of a relationship between G
1
phase and morphogenetic switching, including hyphal development, in the pathogen.
A Second Mitochondrial DNA Primase Is Essential for Cell Growth and Kinetoplast Minicircle DNA Replication in Trypanosoma brucei
Authors: Hines Jane C. , Ray Dan S. 
Published: January 2011

ABSTRACT

The mitochondrial DNA of trypanosomes contains two types of circular DNAs, minicircles and maxicircles. Both minicircles and maxicircles replicate from specific replication origins by unidirectional theta-type intermediates. Initiation of the minicircle leading strand and also that of at least the first Okazaki fragment involve RNA priming. The
Trypanosoma brucei
genome encodes two mitochondrial DNA primases, PRI1 and PRI2, related to the primases of eukaryotic nucleocytoplasmic large DNA viruses. These primases are members of the archeoeukaryotic primase superfamily, and each of them contain an RNA recognition motif and a PriCT-2 motif. In
Leishmania
species, PRI2 proteins are approximately 61 to 66 kDa in size, whereas in
Trypanosoma
species, PRI2 proteins have additional long amino-terminal extensions. RNA interference (RNAi) of
T. brucei PRI2
resulted in the loss of kinetoplast DNA and accumulation of covalently closed free minicircles. Recombinant PRI2 lacking this extension (PRI2ΔNT) primes poly(dA) synthesis on a poly(dT) template in an ATP-dependent manner. Mutation of two conserved aspartate residues (PRI2ΔNTCS) resulted in loss of enzymatic activity but not loss of DNA binding. We propose that PRI2 is directly involved in initiating kinetoplast minicircle replication.
Genome Sequence of
Lactobacillus farciminis
KCTC 3681
Authors: Nam Seong-Hyeuk , Choi Sang-Haeng , Kang Aram , Kim Dong-Wook , Kim Ryong Nam , Kim Aeri , Kim Dae-Soo , Park Hong-Seog 
Published: January 2011

ABSTRACT

Lactobacillus farciminis
is one of the most prevalent lactic acid bacterial species present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of the type strain
Lactobacillus farciminis
KCTC 3681 (2,498,309 bp, with a G+C content of 36.4%), which consists of 5 scaffolds.
Draft Genome Sequence of a Dominant, Multidrug-Resistant
Neisseria gonorrhoeae
Strain, TCDC-NG08107, from a Sexual Group at High Risk of Acquiring Human Immunodeficiency Virus Infection and Syphilis
Authors: Chen Chun-Chen , Hsia Ko-Chiang , Huang Chung-Ter , Wong Wing-Wai , Yen Muh-Yong , Li Lan-Hui , Lin Kun-Yen , Chen Kuo-Wei , Li Shu-Ying 
Published: January 2011

ABSTRACT

Neisseria gonorrhoeae
infection is the second major cause of sexually transmitted diseases worldwide. Development of resistance to multiple classes of antimicrobials in
N. gonorrhoeae
has compromised treatment and disease control. Herein, we report the availability of the draft genome sequence of a multidrug-resistant
N. gonorrhoeae
isolate, TCDC-NG08107, which spread in groups of men who have sex with men (MSM) in Taiwan.
Genome Sequence of
Paracoccus
sp. Strain TRP, a Chlorpyrifos Biodegrader
Authors: Li Kang , Wang Shenghui , Shi Yanhua , Qu Jie , Zhai Yi , Xu Lili , Xu Yongxue , Song Jinlong , Liu Lili , Rahman M. Anisur , Yan Yanchun 
Published: January 2011

ABSTRACT

Paracoccus
sp. strain TRP, isolated from activated sludge, could completely biodegrade chlorpyrifos and 3,5,6-trichloro-2-pyridinol. Here we report the draft genome sequence of
Paracoccus
sp. strain TRP, which could be used to predict genes for xenobiotic biodegradation and metabolism.
A Selenium-Dependent Xanthine Dehydrogenase Triggers Biofilm Proliferation inEnterococcus faecalisthrough Oxidant Production
Authors: Srivastava Milan , Mallard Chris , Barke Theresa , Hancock Lynn E. , Self William T. 
Published: January 2011

ABSTRACTSelenium has been shown to be present as a labile cofactor in a small class of molybdenum hydroxylase enzymes in several species of clostridia that specialize in the fermentation of purines and pyrimidines. This labile cofactor is poorly understood, yet recent bioinformatic studies have suggested thatEnterococcus faecaliscould serve as a model system to better understand the way in which this enzyme cofactor is built and the role of these metalloenzymes in the physiology of the organism. An mRNA that encodes a predicted selenium-dependent molybdenum hydroxylase (SDMH) has also been shown to be specifically increased during the transition from planktonic growth to biofilm growth. Based on these studies, we examined whether this organism produces an SDMH and probed whether selenoproteins may play a role in biofilm physiology. We observed a substantial increase in biofilm density upon the addition of uric acid to cells grown in a defined culture medium, but only when molybdate (Mo) and selenite (Se) were also added. We also observed a significant increase in biofilm density in cells cultured in tryptic soy broth with 1% glucose (TSBG) when selenite was added. In-frame deletion ofselD, which encodes selenophosphate synthetase, also blocked biofilm formation that occurred upon addition of selenium. Moreover, mutation in the gene encoding the molybdoenzyme (xdh) prevented the induction of biofilm proliferation upon supplementation with selenium. Tungstate or auranofin addition also blocked this enhanced biofilm density, likely through inhibition of molybdenum or selenium cofactor synthesis. A large protein complex labeled with75Se is present in higher concentrations in biofilms than in planktonic cells, and the same complex is formed in TSBG. Xanthine dehydrogenase activity correlates with the presence of this labile selenoprotein complex and is absent in aselDor anxdhmutant. Enhanced biofilm density correlates strongly with higher levels of extracellular peroxide, which is produced upon the addition of selenite to TSBG. Peroxide levels are not increased in either theselDor thexdhmutant upon addition of selenite. Extracellular superoxide production, a phenomenon well established to be linked to clinical isolates, is abolished in both mutant strains. Taken together, these data provide evidence that an SDMH is involved in biofilm formation inEnterococcus faecalis, contributing to oxidant production either directly or alternatively through its involvement in redox-dependent processes linked to oxidant production.