bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metaproteomics Approach To Study the Functionality of the Microbiota in the Human Infant Gastrointestinal Tract
Authors: Klaassens Eline S. , de Vos Willem M. , Vaughan Elaine E. 
Published: December 2006

ABSTRACT
A metaproteomics approach comprising two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization-time of flight (mass spectrometry) was applied to the largely uncultured infant fecal microbiota for the first time. The fecal microbial metaproteome profiles changed over time, and one protein spot contained a peptide sequence that showed high similarity to those of bifidobacterial transaldolases.
Polyphosphate Accumulation by
Pseudomonas putida
CA-3 and Other Medium-Chain-Length Polyhydroxyalkanoate-Accumulating Bacteria under Aerobic Growth Conditions
Authors: Tobin Karen M. , McGrath John W. , Mullan Alan , Quinn John P. , O'Connor Kevin E. 
Published: December 2006

ABSTRACT

Pseudomonas putida
CA-3 accumulates polyphosphate (polyP) and medium-chain-length polyhydroxyalkanoate (mclPHA) concurrently under nitrogen limitation. Five other mclPHA-accumulating
Pseudomonas
strains are capable of simultaneous polyP and mclPHA biosynthesis. It appears that polyP is not the rate-limiting step for mclPHA accumulation in these
Pseudomonas
strains.
Expression of a Novel Small Antimicrobial Protein from the Seeds of Motherwort (
Leonurus japonicus
) Confers Disease Resistance in Tobacco
Authors: Yang Xingyong , Xiao Yuehua , Wang Xiaowen , Pei Yan 
Published: December 2006

ABSTRACT

Medicinal
plants are valuable resources of natural antimicrobial materials. A
novel small protein with antimicrobial activities, designated LJAMP1,
was purified from the seeds of a medicinal herb, motherwort
(
Leonurus japonicus
Houtt). LJAMP1 is a heat-stable protein
with a molecular mass of 7.8 kDa and a determined isoelectric point of
8.2. In vitro assays showed that LJAMP1 inhibits the growth of an array
of fungi and bacteria. The hyphal growth inhibition by LJAMP1 was more
evident against hyphomycete fungi, such as
Alternaria
alternata
,
Cercospora personata
, and
Aspergillus
niger
. The N-terminal amino acid sequence of LJAMP1 was
determined, and its coding gene was consequently cloned by the rapid
amplification of cDNA ends. The gene
LJAMP1
has no intron and
encodes a polypeptide of 95 amino acids, in which the first 27 residues
was deduced as a signal peptide. The mature LJAMP1 shows relatively low
identity to plant napin-like storage proteins. Northern blot assays
revealed that
LJAMP1
is expressed preferentially in seeds.
Bioassays in transgenic tobacco demonstrated that that overexpression
of
LJAMP1
significantly enhanced the resistance of tobacco
against not only the fungal pathogen
A. alternata
but also the
bacterial pathogen
Ralstonia solanacearum
, while no visible
alteration in plant growth and development was
observed.
Isolation and Characterization of Brewer's Yeast Variants with Improved Fermentation Performance under High-Gravity Conditions
Authors: Blieck Lies , Toye Geert , Dumortier Françoise , Verstrepen Kevin J. , Delvaux Freddy R. , Thevelein Johan M. , Van Dijck Patrick 
Published: December 2006

ABSTRACT

To save energy, space, and time, today's breweries make use of high-gravity brewing in which concentrated medium (wort) is fermented, resulting in a product with higher ethanol content. After fermentation, the product is diluted to obtain beer with the desired alcohol content. While economically desirable, the use of wort with an even higher sugar concentration is limited by the inability of brewer's yeast (
Saccharomyces pastorianus
) to efficiently ferment such concentrated medium. Here, we describe a successful strategy to obtain yeast variants with significantly improved fermentation capacity under high-gravity conditions. We isolated better-performing variants of the industrial lager strain CMBS33 by subjecting a pool of UV-induced variants to consecutive rounds of fermentation in very-high-gravity wort (>22° Plato). Two variants (GT336 and GT344) showing faster fermentation rates and/or more-complete attenuation as well as improved viability under high ethanol conditions were identified. The variants displayed the same advantages in a pilot-scale stirred fermenter under high-gravity conditions at 11°C. Microarray analysis identified several genes whose altered expression may be responsible for the superior performance of the variants. The role of some of these candidate genes was confirmed by genetic transformation. Our study shows that proper selection conditions allow the isolation of variants of commercial brewer's yeast with superior fermentation characteristics. Moreover, it is the first study to identify genes that affect fermentation performance under high-gravity conditions. The results are of interest to the beer and bioethanol industries, where the use of more-concentrated medium is economically advantageous.
Coral Disease Diagnostics: What's between a Plague and a Band?
Authors: Ainsworth T. D. , Kramasky-Winter E. , Loya Y. , Hoegh-Guldberg O. , Fine M. 
Published: December 2006

ABSTRACT
Recently, reports of coral disease have increased significantly across the world's tropical oceans. Despite increasing efforts to understand the changing incidence of coral disease, very few primary pathogens have been identified, and most studies remain dependent on the external appearance of corals for diagnosis. Given this situation, our current understanding of coral disease and the progression and underlying causes thereof is very limited. In the present study, we use structural and microbial studies to differentiate different forms of black band disease: atypical black band disease and typical black band disease. Atypical black band diseased corals were infected with the black band disease microbial consortium yet did not show any of the typical external signs of black band disease based on macroscopic observations. In previous studies, these examples, here referred to as atypical black band disease, would have not been correctly diagnosed. We also differentiate white syndrome from white diseases on the basis of tissue structure and the presence/absence of microbial associates. White diseases are those with dense bacterial communities associated with lesions of symbiont loss and/or extensive necrosis of tissues, while white syndromes are characteristically bacterium free, with evidence for extensive programmed cell death/apoptosis associated with the lesion and the adjacent tissues. The pathology of coral disease as a whole requires further investigation. This study emphasizes the importance of going beyond the external macroscopic signs of coral disease for accurate disease diagnosis.
Cyclohexane Carboxylate and Benzoate Formation from Crotonate in
Syntrophus aciditrophicus
Authors: Mouttaki Housna , Nanny Mark A. , McInerney Michael J. 
Published: December 2006

ABSTRACT

The anaerobic, syntrophic bacterium
Syntrophus aciditrophicus
grown in pure culture produced 1.4 ± 0.24 mol of acetate and 0.16 ± 0.02 mol of cyclohexane carboxylate per mole of crotonate metabolized. [U-
13
C]crotonate was metabolized to [1,2-
13
C]acetate and [1,2,3,4,5,7-
13
C]cyclohexane carboxylate. Cultures grown with unlabeled crotonate and [
13
C]sodium bicarbonate formed [6-
13
C]cyclohexane carboxylate. Trimethylsilyl (TMS) derivatives of cyclohexane carboxylate, cyclohex-1-ene carboxylate, benzoate, pimelate, glutarate, 3-hydroxybutyrate, and acetoacetate were detected as intermediates by comparison of retention times and mass spectral profiles to authentic standards. With [U-
13
C]crotonate, the
m/z
-15 ion of TMS-derivatized glutarate, 3-hydroxybutyrate, and acetoacetate each increased by +4 mass units, and the
m/z
-15 ion of TMS-derivatized pimelate, cyclohex-1-ene carboxylate, benzoate, and cyclohexane carboxylate each increased by +6 mass units. With [
13
C]sodium bicarbonate and unlabeled crotonate, the
m/z
-15 ion of TMS derivatives of glutarate, pimelate, cyclohex-1-ene carboxylate, benzoate, and cyclohexane carboxylate each increased by +1 mass unit, suggesting that carboxylation occurred after the synthesis of a four-carbon intermediate. With [1,2-
13
C]acetate and unlabeled crotonate, the
m/z
-15 ion of TMS-derivatized 3-hydroxybutyrate, acetoacetate, and glutarate each increased by +0, +2, and +4 mass units, respectively, and the
m/z
-15 ion of TMS-derivatized pimelate, cyclohex-1-ene carboxylate, benzoate, cyclohexane carboxylate, and 2-hydroxycyclohexane carboxylate each increased by +0, +2, +4, and +6 mass units. The data are consistent with a pathway for cyclohexane carboxylate formation involving the condensation of two-carbon units derived from crotonate degradation with CO
2
addition, rather than the use of the intact four-carbon skeleton of crotonate.
Benzoate Catabolite Repression of the Phthalate Degradation Pathway in
Rhodococcus
sp. Strain DK17
Authors: Choi Ki Young , Zylstra Gerben J. , Kim Eungbin 
Published: December 2006

ABSTRACT

Rhodococcus
sp. strain DK17 exhibits a catabolite repression-like response when provided simultaneously with benzoate and phthalate as carbon and energy sources. Benzoate in the medium is depleted to detection limits before the utilization of phthalate begins. The transcription of the genes encoding benzoate and phthalate dioxygenase paralleled the substrate utilization profile. Two mutant strains with defective benzoate dioxygenases were unable to utilize phthalate in the presence of benzoate, although they grew normally on phthalate in the absence of benzoate.
Chaperone Hsp31 Contributes to Acid Resistance in Stationary-PhaseEscherichia coli
Authors: Mujacic Mirna , Baneyx François 
Published: December 2006

ABSTRACTHsp31, the product of the σS- and σD-dependenthchAgene, is a heat-inducible chaperone implicated in the management of protein misfolding at high temperatures. We show here that Hsp31 plays an important role in the acid resistance of starvedEscherichia colibut that it has little influence on oxidative-stress survival.
Homologous Subunits of 1,3-Beta-Glucan Synthase Are Important for Spore Wall Assembly in
Saccharomyces cerevisiae
Authors: Ishihara Satoru , Hirata Aiko , Nogami Satoru , Beauvais Anne , Latge Jean-Paul , Ohya Yoshikazu 
Published: December 2006

ABSTRACT

During
sporulation in
Saccharomyces cerevisiae
, the four
haploid nuclei are encapsulated within multilayered spore walls.
Glucan, the major constituent of the spore wall, is synthesized by
1,3-β-glucan synthase, which is composed of a putative
catalytic subunit encoded by
FKS1
and
FKS2
. Although
another homolog, encoded by
FKS3
, was identified by homology
searching, its function is unknown. In this report, we show that
FKS2
and
FKS3
are required for spore wall assembly.
The ascospores of
fks2
and
fks3
mutants were
enveloped by an abnormal spore wall with reduced resistance to diethyl
ether, elevated temperatures, and ethanol. However, deletion of the
FKS1
gene did not result in a defective spore wall. The
construction of fusion genes that expressed Fks1p and Fks2p under the
control of the
FKS2
promoter revealed that asci transformed
with
FKS2p
-driven Fks1p and Fks2p were resistant to elevated
temperatures, which suggests that the expression of
FKS2
plays
an important role in spore wall assembly. The expression of
FKS1p
-driven Fks3p during vegetative growth did not affect
1,3-β-glucan synthase activity in vitro but effectively
suppressed the growth defect of the temperature-sensitive
fks1
mutant by stabilizing Rho1p, which is a regulatory subunit of glucan
synthase. Based on these results, we propose that
FKS2
encodes
the primary 1,3-β-glucan synthase in sporulation and that
FKS3
is required for normal spore wall formation because it
affects the upstream regulation of 1,3-β-glucan
synthase.
Small-Subunit rRNA Processome Proteins Are Translationally Regulated during Differentiation of
Trypanosoma cruzi
Authors: Nardelli Sheila Cristina , Ávila Andréa Rodrigues , Freund Aline , Motta Maria Cristina , Manhães Lauro , de Jesus Teresa Cristina Leandro , Schenkman Sergio , Fragoso Stenio Perdigão , Krieger Marco Aurélio , Goldenberg Samuel , Dallagiovanna Bruno 
Published: December 2006

ABSTRACT

We used differential display to select genes differentially expressed during differentiation of epimastigotes into metacyclic trypomastigotes in the protozoan parasite
Trypanosoma cruzi
. One of the selected clones had a sequence similar to that of the small-subunit (SSU) processome protein Sof1p, which is involved in rRNA processing. The corresponding
T. cruzi
protein, TcSof1, displayed a nuclear localization and is downregulated during metacyclogenesis. Heterologous RNA interference assays showed that depletion of this protein impaired growth but did not affect progression through the cell cycle, suggesting that ribosome synthesis regulation and the cell cycle are uncoupled in this parasite. Quantitative PCR (qPCR) assays of several SSU processome-specific genes in
T. cruzi
also showed that most of them were regulated posttranscriptionally. This process involves the accumulation of mRNA in the polysome fraction of metacyclic trypomastigotes, where TcSof1 cannot be detected. Metacyclic trypomastigote polysomes were purified and separated by sucrose gradient sedimentation. Northern blot analysis of the sucrose gradient fractions showed the association of TcSof1 mRNA with polysomes, confirming the qPCR data. The results suggest that the mechanism of regulation involves the blocking of translation elongation and/or termination.
Two-Component Response Regulators Ssk1p and Skn7p Additively Regulate High-Osmolarity Adaptation and Fungicide Sensitivity in
Cochliobolus heterostrophus
Authors: Izumitsu Kosuke , Yoshimi Akira , Tanaka Chihiro 
Published: December 2006

ABSTRACT

Filamentous ascomycetous fungi possess many histidine kinases and two conserved response regulators, Ssk1p and Skn7p, in their two-component signaling systems. We previously reported that the fungus unique group III histidine kinase regulates high-osmolarity adaptation and iprodione/fludioxonil fungicide sensitivity by controlling the phosphorylation of Hog1-type mitogen-activated protein kinase (MAPK) in filamentous ascomycetes. Here, we have characterized the response regulator genes Ch
Ssk1
and Ch
Skn7
in the southern corn leaf blight fungus
Cochliobolus heterostrophus
. Both Ch
Ssk1
- and Ch
Skn7
-disrupted mutants showed little sensitivity to high-osmolarity stress and moderate resistance to the iprodione/fludioxonil fungicides. The phosphorylation of Hog1-type MAPK BmHog1p induced by high-osmolarity stress and fungicide treatments was only regulated by ChSsk1p, indicating that ChSkn7p has roles in high-osmolarity adaptation and fungicide sensitivity that are independent from the activation of BmHog1p. The Ch
ssk1
Ch
skn7
double mutants clearly showed higher sensitivity to osmolar stress and higher resistance to fungicides than the single mutants. The dose responses of the double mutants fit well with those of the group III histidine kinase-deficient strain. These results suggest that in filamentous ascomycetes, the Ssk1- and Skn7-type response regulators control high-osmolarity adaptation and fungicide sensitivity additively with differential mechanisms under the regulation of the group III histidine kinase. This study provides evidence that filamentous fungi have a unique two-component signaling system that is different from that of yeast and is responsible for high-osmolarity adaptation and fungicide sensitivity.
The Type IV Secretion System ofSinorhizobium melilotiStrain 1021 Is Required for Conjugation but Not for Intracellular Symbiosis
Authors: Jones Kathryn M. , Lloret Javier , Daniele Joseph R. , Walker Graham C. 
Published: December 2006

ABSTRACTThe type IV secretion system (T4SS) of the plant intracellular symbiontSinorhizobium meliloti1021 is required for conjugal transfer of DNA. However, it is not required for host invasion and persistence, unlike the T4SSs of closely related mammalian intracellular pathogens. A comparison of the requirement for a bacterial T4SS in plant versus animal host invasion suggests an important difference in the intracellular niches occupied by these bacteria.
Genomic Plasticity of therrn-nqrFIntergenic Segment in theChlamydiaceae
Authors: Liu Zhi , Rank Roger , Kaltenboeck Bernhard , Magnino Simone , Dean Deborah , Burall Laurel , Plaut Roger D. , Read Timothy D. , Myers Garry , Bavoil Patrik M. 
Published: December 2006

ABSTRACTInChlamydiaceae, the nucleotide sequence between the 5S rRNA gene and the gene for subunit F of the Na+-translocating NADH-quinone reductase (nqrFordmpP) has varied lengths and gene contents. We analyzed this site in 45Chlamydiaceaestrains having diverse geographical and pathological origins and including members of all nine species.
Signal Recognition Particle-Dependent Inner Membrane Targeting of the PulG Pseudopilin Component of a Type II Secretion System
Authors: Francetic Olivera , Buddelmeijer Nienke , Lewenza Shawn , Kumamoto Carol A. , Pugsley Anthony P. 
Published: December 2006

ABSTRACT

The pseudopilin PulG is an essential component of the pullulanase-specific type II secretion system from
Klebsiella oxytoca
. PulG is the major subunit of a short, thin-filament pseudopilus, which presumably elongates and retracts in the periplasm, acting as a dynamic piston to promote pullulanase secretion. It has a signal sequence-like N-terminal segment that, according to studies with green and red fluorescent protein chimeras, anchors unassembled PulG in the inner membrane. We analyzed the early steps of PulG inner membrane targeting and insertion in
Escherichia coli
derivatives defective in different protein targeting and export factors. The β-galactosidase activity in strains producing a PulG-LacZ hybrid protein increased substantially when the
dsbA
,
dsbB
, or all
sec
genes tested except
secB
were compromised by mutations. To facilitate analysis of native PulG membrane insertion, a leader peptidase cleavage site was engineered downstream from the N-terminal transmembrane segment (PrePulG*). Unprocessed PrePulG* was detected in strains carrying mutations in
secA
,
secY
,
secE
, and
secD
genes, including some novel alleles of
secY
and
secD
. Furthermore, depletion of the Ffh component of the signal recognition particle (SRP) completely abolished PrePulG* processing, without affecting the Sec-dependent export of periplasmic MalE and RbsB proteins. Thus, PulG is cotranslationally targeted to the inner membrane Sec translocase by SRP.
Hfq Modulates the σ
E
-Mediated Envelope Stress Response and the σ
32
-Mediated Cytoplasmic Stress Response in
Escherichia coli
Authors: Guisbert Eric , Rhodius Virgil A. , Ahuja Nidhi , Witkin Emily , Gross Carol A. 
Published: December 2006

ABSTRACT

Hfq, a chaperone for small noncoding RNAs, regulates many processes in
Escherichia coli
, including the σ
S
-mediated general stress response. Here we used microarray analysis to identify the changes in gene expression resulting from lack of Hfq. We identify several potential new targets for Hfq regulation, including genes encoding outer membrane proteins, enzymes, factors, and transporters. Many of these genes are involved in amino acid uptake and biosynthesis, sugar uptake and metabolism, and cell energetics. In addition, we find altered regulation of the σ
E
- and σ
32
-mediated stress responses, which we analyze further. We show that cells lacking Hfq induce the σ
E
-mediated envelope stress response and are defective in σ
E
-mediated repression of outer membrane proteins. We also show that the σ
32
-mediated cytoplasmic stress response is repressed in cells lacking Hfq due to increased expression of DnaK. Furthermore, we show that cells lacking Hfq are defective in the “long-term adaptation” of σ
32
to chronic chaperone overexpression. Together, our results indicate that Hfq may play a general role in stress response regulation in
E. coli
.
Role of a Conserved Membrane Glycine Residue in a Dicarboxylate Transporter from
Sinorhizobium meliloti
Authors: Trainer Maria A. , Yurgel Svetlana N. , Kahn Michael L. 
Published: December 2006

ABSTRACT
Nitrogen-fixing rhizobial bacteroids import dicarboxylates by using the DctA transporter. G114 of DctA is highly conserved. A G114D mutant is inactive, but DctA with a small amino acid (G114A) or a helix disrupter (G114P) retains significant activity. G114 probably interacts with other membrane helices in stabilizing a substrate-binding pocket.
Whole-Genome Analysis of the Methyl
tert
-Butyl Ether-Degrading Beta-Proteobacterium
Methylibium petroleiphilum
PM1
Authors: Kane Staci R. , Chakicherla Anu Y. , Chain Patrick S. G. , Schmidt Radomir , Shin Maria W. , Legler Tina C. , Scow Kate M. , Larimer Frank W. , Lucas Susan M. , Richardson Paul M. , Hristova Krassimira R. 
Published: December 2006

ABSTRACT

Methylibium petroleiphilum
PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl
tert
-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C
5
to C
12
) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an ∼4-Mb circular chromosome and an ∼600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (∼99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in
M. petroleiphilum
and other MTBE-degrading beta-proteobacteria.
A Protein from a Parasitic Microorganism,
Rickettsia prowazekii
, Can Cleave the Signal Sequences of Proteins Targeting Mitochondria
Authors: Kitada Sakae , Uchiyama Tsuneo , Funatsu Tomoyuki , Kitada Yumiko , Ogishima Tadashi , Ito Akio 
Published: December 2006

ABSTRACT
The obligate intracellular parasitic bacteria rickettsiae are more closely related to mitochondria than any other microbes investigated to date. A rickettsial putative peptidase (RPP) was found to resemble the α and β subunits of mitochondrial processing peptidase (MPP), which cleaves the transport signal sequences of mitochondrial preproteins. RPP showed completely conserved zinc-binding and catalytic residues compared with β-MPP but barely contained any of the glycine-rich loop region characteristic of α-MPP. When the biochemical activity of RPP purified from a recombinant source was analyzed, RPP specifically hydrolyzed basic peptides and presequence peptides with frequent cleavage at their MPP-processing sites. Moreover, RPP appeared to activate yeast β-MPP so that it processed preproteins with shorter presequences. Thus, RPP behaves as a bifunctional protein that could act as a basic peptide peptidase and a somewhat regulatory protein for other protein activities in rickettsiae. These are the first biological and enzymological studies to report that a protein from a parasitic microorganism can cleave the signal sequences of proteins targeted to mitochondria.