bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acetic Acid Bacteria, Newly Emerging Symbionts of Insects
Authors: Crotti Elena , Rizzi Aurora , Chouaia Bessem , Ricci Irene , Favia Guido , Alma Alberto , Sacchi Luciano , Bourtzis Kostas , Mandrioli Mauro , Cherif Ameur , Bandi Claudio , Daffonchio Daniele 
Published: September 2010

ABSTRACT

Recent research in microbe-insect symbiosis has shown that acetic acid bacteria (AAB) establish symbiotic relationships with several insects of the orders Diptera, Hymenoptera, Hemiptera, and Homoptera, all relying on sugar-based diets, such as nectars, fruit sugars, or phloem sap. To date, the fruit flies
Drosophila melanogaster
and
Bactrocera oleae
, mosquitoes of the genera
Anopheles
and
Aedes
, the honey bee
Apis mellifera
, the leafhopper
Scaphoideus titanus
, and the mealybug
Saccharicoccus sacchari
have been found to be associated with the bacterial genera
Acetobacter
,
Gluconacetobacter
,
Gluconobacter
,
Asaia
, and
Saccharibacter
and the novel genus
Commensalibacter
. AAB establish symbiotic associations with the insect midgut, a niche characterized by the availability of diet-derived carbohydrates and oxygen and by an acidic pH, selective factors that support AAB growth. AAB have been shown to actively colonize different insect tissues and organs, such as the epithelia of male and female reproductive organs, the Malpighian tubules, and the salivary glands. This complex topology of the symbiosis indicates that AAB possess the keys for passing through body barriers, allowing them to migrate to different organs of the host. Recently, AAB involvement in the regulation of innate immune system homeostasis of
Drosophila
has been shown, indicating a functional role in host survival. All of these lines of evidence indicate that AAB can play different roles in insect biology, not being restricted to the feeding habit of the host. The close association of AAB and their insect hosts has been confirmed by the demonstration of multiple modes of transmission between individuals and to their progeny that include vertical and horizontal transmission routes, comprising a venereal one. Taken together, the data indicate that AAB represent novel secondary symbionts of insects.
Maximizing Capture Efficiency and Specificity of Magnetic Separation for
Mycobacterium avium
subsp.
paratuberculosis
Cells
Authors: Foddai Antonio , Elliott Christopher T. , Grant Irene R. 
Published: September 2010

ABSTRACT

In order to introduce specificity for
Mycobacterium avium
subsp.
paratuberculosis
prior to a phage amplification assay, various magnetic-separation approaches, involving either antibodies or peptides, were evaluated in terms of the efficiency of capture (expressed as a percentage) of
M. avium
subsp.
paratuberculosis
cells and the percentage of nonspecific binding by other
Mycobacterium
spp. A 50:50 mixture of MyOne Tosylactivated Dynabeads coated with the chemically synthesized
M. avium
subsp.
paratuberculosis
-specific peptides biotinylated aMp3 and biotinylated aMptD (i.e., peptide-mediated magnetic separation [PMS]) proved to be the best magnetic-separation approach for achieving 85 to 100% capture of
M. avium
subsp.
paratuberculosis
and minimal (<1%) nonspecific recovery of other
Mycobacterium
spp. (particularly if beads were blocked with 1% skim milk before use) from broth samples containing 10
3
to 10
4
CFU/ml. When PMS was coupled with a recently optimized phage amplification assay and used to detect
M. avium
subsp.
paratuberculosis
in 50-ml volumes of spiked milk, the mean 50% limit of detection (LOD
50
) was 14.4 PFU/50 ml of milk (equivalent to 0.3 PFU/ml). This PMS-phage assay represents a novel, rapid method for the detection and enumeration of viable
M. avium
subsp.
paratuberculosis
organisms in milk, and potentially other sample matrices, with results available within 48 h.
Engineering of
Corynebacterium glutamicum
with an NADPH-Generating Glycolytic Pathway for
l
-Lysine Production
Authors: Takeno Seiki , Murata Ryosuke , Kobayashi Ryosuke , Mitsuhashi Satoshi , Ikeda Masato 
Published: September 2010

ABSTRACT

A sufficient supply of NADPH is a critical factor in
l
-lysine production by
Corynebacterium glutamicum
. Endogenous NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) of
C. glutamicum
was replaced with nonphosphorylating NADP-dependent glyceraldehyde 3-phosphate dehydrogenase (GapN) of
Streptococcus mutans
, which catalyzes the reaction of glyceraldehyde 3-phosphate to 3-phosphoglycerate with the reduction of NADP
+
to NADPH, resulting in the reconstruction of the functional glycolytic pathway. Although the growth of the engineered strain on glucose was significantly retarded, a suppressor mutant with an increased ability to utilize sugars was spontaneously isolated from the engineered strain. The suppressor mutant was characterized by the properties of GapN as well as the nucleotide sequence of the gene, confirming that no change occurred in either the activity or the basic properties of GapN. The suppressor mutant was engineered into an
l
-lysine-producing strain by plasmid-mediated expression of the desensitized
lysC
gene, and the performance of the mutant as an
l
-lysine producer was evaluated. The amounts of
l
-lysine produced by the suppressor mutant were larger than those produced by the reference strain (which was created by replacement of the preexisting
gapN
gene in the suppressor mutant with the original
gapA
gene) by ∼70% on glucose, ∼120% on fructose, and ∼100% on sucrose, indicating that the increased
l
-lysine production was attributed to GapN. These results demonstrate effective
l
-lysine production by
C. glutamicum
with an additional source of NADPH during glycolysis.
In Vivo
and
Ex Vivo
Evaluations of Bacteriophages e11/2 and e4/1c for Use in the Control of
Escherichia coli
O157:H7
Authors: Rivas Lucia , Coffey Brid , McAuliffe Olivia , McDonnell Mary J. , Burgess Catherine M. , Coffey Aidan , Ross R. Paul , Duffy Geraldine 
Published: September 2010

ABSTRACT

This study investigated the effect of bacteriophages (phages) e11/2 and e4/1c against
Escherichia
coli
O157:H7 in an
ex vivo
rumen model and in cattle
in vivo
. In the
ex vivo
rumen model, samples were inoculated with either 10
3
or 10
6
CFU/ml inoculum of
E. coli
O157:H7 and challenged separately with each bacteriophage. In the presence of phage e11/2, the numbers of
E. coli
O157:H7 bacteria were significantly (
P
< 0.05) reduced to below the limit of detection within 1 h. Phage e4/1c significantly (
P
< 0.05) reduced
E. coli
O157:H7 numbers within 2 h of incubation, but the number of surviving
E. coli
O157:H7 bacteria then remained unchanged over a further 22-h incubation period. The ability of a phage cocktail of e11/2 and e4/1c to reduce the fecal shedding of
E. coli
O157:H7 in experimentally inoculated cattle was then investigated in two cattle trials. Cattle (yearlings,
n
= 20 for trial one; adult fistulated cattle,
n
= 2 for trial two) were orally inoculated with 10
10
CFU of
E. coli
O157:H7. Animals (
n
= 10 for trial one;
n
= 1 for trial two) were dosed daily with a bacteriophage cocktail of 10
11
PFU for 3 days postinoculation.
E. coli
O157:H7 and phage numbers in fecal and/or rumen samples were determined over 7 days postinoculation.
E. coli
O157:H7 numbers rapidly declined in all animals within 24 to 48 h; however, there was no significant difference (
P
> 0.05) between the numbers of
E. coli
O157:H7 bacteria shed by the phage-treated or control animals. Phages were recovered from the rumen but not from the feces of the adult fistulated animal in trial two but were recovered from the feces of the yearling animals in trial one. While the results from the rumen model suggest that phages are effective in the rumen, further research is required to improve the antimicrobial effectiveness of phages for the elimination of
E. coli
O157:H7
in vivo
.
Nonlinear Biosynthetic Gene Cluster Dose Effect on Penicillin Production by
Penicillium chrysogenum
Authors: Nijland Jeroen G. , Ebbendorf Bjorg , Woszczynska Marta , Boer Rémon , Bovenberg Roel A. L. , Driessen Arnold J. M. 
Published: September 2010

ABSTRACT

Industrial penicillin production levels by the filamentous fungus
Penicillium chrysogenum
increased dramatically by classical strain improvement. High-yielding strains contain multiple copies of the penicillin biosynthetic gene cluster that encodes three key enzymes of the β-lactam biosynthetic pathway. We have analyzed the gene cluster dose effect on penicillin production using the high-yielding
P. chrysogenum
strain DS17690 that was cured from its native clusters. The amount of penicillin V produced increased with the penicillin biosynthetic gene cluster number but was saturated at high copy numbers. Likewise, transcript levels of the biosynthetic genes
pcbAB
[δ-(
l
-α-aminoadipyl)-
l
-cysteinyl-
d
-valine synthetase],
pcbC
(isopenicillin N synthase), and
penDE
(acyltransferase) correlated with the cluster copy number. Remarkably, the protein level of acyltransferase, which localizes to peroxisomes, was saturated already at low cluster copy numbers. At higher copy numbers, intracellular levels of isopenicillin N increased, suggesting that the acyltransferase reaction presents a limiting step at a high gene dose. Since the number and appearance of the peroxisomes did not change significantly with the gene cluster copy number, we conclude that the acyltransferase activity is limiting for penicillin biosynthesis at high biosynthetic gene cluster copy numbers. These results suggest that at a high penicillin production level, productivity is limited by the peroxisomal acyltransferase import activity and/or the availability of coenzyme A (CoA)-activated side chains.
Catalytic Biomineralization of Fluorescent Calcite by the Thermophilic Bacterium
Geobacillus thermoglucosidasius
Authors: Yoshida Naoto , Higashimura Eiji , Saeki Yuichi 
Published: September 2010

ABSTRACT

The thermophilic
Geobacillus
bacterium catalyzed the formation of 100-μm hexagonal crystals at 60°C in a hydrogel containing sodium acetate, calcium chloride, and magnesium sulfate. Under fluorescence microscopy, crystals fluoresced upon excitation at 365 ± 5, 480 ± 20, or 545 ± 15 nm. X-ray diffraction indicated that the crystals were magnesium-calcite in calcite-type calcium carbonate.
Development of an Environmental Functional Gene Microarray for Soil Microbial Communities
Authors: McGrath Ken C. , Mondav Rhiannon , Sintrajaya Regina , Slattery Bill , Schmidt Susanne , Schenk Peer M. 
Published: September 2010

ABSTRACT

Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA- and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N
2
O. A total of 109 genes displayed expression that differed significantly between soils with low and high N
2
O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities.
The Antiretroviral Lectin Cyanovirin-N Targets Well-Known and Novel Targets on the Surface of Entamoeba histolytica Trophozoites
Authors: Carpentieri Andrea , Ratner Daniel M. , Ghosh Sudip K. , Banerjee Sulagna , Bushkin G. Guy , Cui Jike , Lubrano Michael , Steffen Martin , Costello Catherine E. , O'Keefe Barry , Robbins Phillips W. , Samuelson John 
Published: September 2010

ABSTRACT

Entamoeba histolytica
, the protist that causes amebic dysentery and liver abscess, has a truncated Asn-linked glycan (
N
-glycan) precursor composed of seven sugars (Man
5
GlcNAc
2
). Here, we show that glycoproteins with unmodified
N
-glycans are aggregated and capped on the surface of
E. histolytica
trophozoites by the antiretroviral lectin cyanovirin-N and then replenished from large intracellular pools. Cyanovirin-N cocaps the Gal/GalNAc adherence lectin, as well as glycoproteins containing
O
-phosphodiester-linked glycans recognized by an anti-proteophosphoglycan monoclonal antibody. Cyanovirin-N inhibits phagocytosis by
E. histolytica
trophozoites of mucin-coated beads, a surrogate assay for amebic virulence. For technical reasons, we used the plant lectin concanavalin A rather than cyanovirin-N to enrich secreted and membrane proteins for mass spectrometric identification.
E. histolytica
glycoproteins with occupied
N
-glycan sites include Gal/GalNAc lectins, proteases, and 17 previously hypothetical proteins. The latter glycoproteins, as well as 50 previously hypothetical proteins enriched by concanavalin A, may be vaccine targets as they are abundant and unique. In summary, the antiretroviral lectin cyanovirin-N binds to well-known and novel targets on the surface of
E. histolytica
that are rapidly replenished from large intracellular pools.
Characterization of Glycoside Hydrolase Family 5 Proteins in Schizosaccharomyces pombe
Authors: Dueñas-Santero Encarnación , Martín-Cuadrado Ana Belén , Fontaine Thierry , Latgé Jean-Paul , del Rey Francisco , Vázquez de Aldana Carlos 
Published: September 2010

ABSTRACT

In yeast, enzymes with β-glucanase activity are thought to be necessary in morphogenetic events that require controlled hydrolysis of the cell wall. Comparison of the sequence of the
Saccharomyces cerevisiae
exo-β(1,3)-glucanase Exg1 with the
Schizosaccharomyces pombe
genome allowed the identification of three genes that were named
exg1
+
(locus SPBC1105.05),
exg2
+
(SPAC12B10.11), and
exg3
+
(SPBC2D10.05). The three proteins have different localizations: Exg1 is secreted to the periplasmic space, Exg2 is a membrane protein, and Exg3 is a cytoplasmic protein. Characterization of the biochemical activity of the proteins indicated that Exg1 and Exg3 are active only against β(1,6)-glucans while no activity was detected for Exg2. Interestingly, Exg1 cleaves the glucans with an endohydrolytic mode of action.
exg1
+
showed periodic expression during the cell cycle, with a maximum coinciding with the septation process, and its expression was dependent on the transcription factor Sep1. The Exg1 protein localizes to the septum region in a pattern that was different from that of the endo-β(1,3)-glucanase Eng1. Overexpression of Exg2 resulted in an increase in cell wall material at the poles and in the septum, but the putative catalytic activity of the protein was not required for this effect.
Aspergillus fumigatus
flbB
Encodes Two Basic Leucine Zipper Domain (bZIP) Proteins Required for Proper Asexual Development and Gliotoxin Production
Authors: Xiao Peng , Shin Kwang-Soo , Wang Tianhong , Yu Jae-Hyuk 
Published: September 2010

ABSTRACT

The opportunistic human pathogen
Aspergillus fumigatus
reproduces asexually by forming a massive number of mitospores called conidia. In this study, we characterize the upstream developmental regulator
A. fumigatus
flbB
(
AfuflbB
). Northern blotting and cDNA analyses reveal that
AfuflbB
produces two transcripts predicted to encode two basic leucine zipper domain (bZIP) polypeptides,
Afu
FlbBβ (420 amino acids [aa]) and
Afu
FlbBα (390 aa). The deletion of
AfuflbB
results in delayed/reduced sporulation, precocious cell death, the lack of conidiophore development in liquid submerged culture, altered expression of
AfubrlA
and
AfuabaA
, and blocked production of gliotoxin. While introduction of the wild-type (WT)
AfuflbB
allele fully complemented these defects, disruption of the ATG start codon for either one of the
Afu
FlbB polypeptides leads to a partial complementation, indicating the need of both polypeptides for WT levels of asexual development and gliotoxin biogenesis. Consistent with this,
Aspergillus nidulans
flbB

+

encoding one polypeptide (426 aa) partially complements the
AfuflbB
null mutation. The presence of 0.6 M KCl in liquid submerged culture suppresses the defects caused by the lack of one, but not both, of the
Afu
FlbB polypeptides, suggesting a genetic prerequisite for
Afu
FlbB in
A. fumigatus
development. Finally, Northern blot analyses reveal that both
AfuflbB
and
AfuflbE
are necessary for expression of
AfuflbD
, suggesting that FlbD functions downstream of FlbB/FlbE in aspergilli.
Predicting Plasmid Promiscuity Based on Genomic Signature
Authors: Suzuki Haruo , Yano Hirokazu , Brown Celeste J. , Top Eva M. 
Published: September 2010

ABSTRACT
Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts’ signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements.
Cadaverine Covalently Linked to Peptidoglycan Is Required for Interaction between the Peptidoglycan and the Periplasm-Exposed S-Layer-Homologous Domain of Major Outer Membrane Protein Mep45 in
Selenomonas ruminantium
Authors: Kojima Seiji , Ko Kyong-Cheol , Takatsuka Yumiko , Abe Naoki , Kaneko Jun , Itoh Yoshifumi , Kamio Yoshiyuki 
Published: September 2010

ABSTRACT

The peptidoglycan of
Selenomonas ruminantium
is covalently bound to cadaverine (PG-cadaverine), which likely plays a significant role in maintaining the integrity of the cell surface structure. The outer membrane of this bacterium contains a 45-kDa major protein (Mep45) that is a putative peptidoglycan-associated protein. In this report, we determined the nucleotide sequence of the
mep45
gene and investigated the relationship between PG-cadaverine, Mep45, and the cell surface structure. Amino acid sequence analysis showed that Mep45 is comprised of an N-terminal S-layer-homologous (SLH) domain followed by α-helical coiled-coil region and a C-terminal β-strand-rich region. The N-terminal SLH domain was found to be protruding into the periplasmic space and was responsible for binding to peptidoglycan. It was determined that Mep45 binds to the peptidoglycan in a manner dependent on the presence of PG-cadaverine. Electron microscopy revealed that defective PG-cadaverine decreased the structural interactions between peptidoglycan and the outer membrane, consistent with the proposed role for PG-cadaverine. The C-terminal β-strand-rich region of Mep45 was predicted to be a membrane-bound unit of the 14-stranded β-barrel structure. Here we propose that PG-cadaverine possesses functional importance to facilitate the structural linkage between peptidoglycan and the outer membrane via specific interaction with the SLH domain of Mep45.
Crystallographic Insights into the Pore Structures and Mechanisms of the EutL and EutM Shell Proteins of the Ethanolamine-Utilizing Microcompartment ofEscherichia coli
Authors: Takenoya Mihoko , Nikolakakis Kiel , Sagermann Martin 
Published: September 2010

ABSTRACTThe ethanolamine-utilizing bacterial microcompartment (Eut-BMC) ofEscherichia coliis a polyhedral organelle that harbors specific enzymes for the catabolic degradation of ethanolamine. The compartment is composed of a proteinaceous shell structure that maintains a highly specialized environment for the biochemical reactions inside. Recent structural investigations have revealed hexagonal assemblies of shell proteins that form a tightly packed two-dimensional lattice that is likely to function as a selectively permeable protein membrane, wherein small channels are thought to permit controlled exchange of specific solutes. Here, we show with two nonisomorphous crystal structures that EutM also forms a two-dimensional protein membrane. As its architecture is highly similar to the membrane structure of EutL, it is likely that the structure represents a physiologically relevant form. Thus far, of allEutproteins, only EutM and EutL have been shown to form such proteinaceous membranes. Despite their similar architectures, however, both proteins exhibit dramatically different pore structures. In contrast to EutL, the pore of EutM appears to be positively charged, indicating specificity for different solutes. Furthermore, we also show that the central pore structure of the EutL shell protein can be triggered to open specifically upon exposure to zinc ions, suggesting a specific gating mechanism.
A TRAP Transporter for Pyruvate and Other Monocarboxylate 2-Oxoacids in the Cyanobacterium
Anabaena
sp. Strain PCC 7120
Authors: Pernil Rafael , Herrero Antonia , Flores Enrique 
Published: September 2010

ABSTRACT

In the cyanobacterium
Anabaena
sp. strain PCC 7120, open reading frames (ORFs)
alr3026
,
alr3027
, and
all3028
encode a tripartite ATP-independent periplasmic transporter (TRAP-T). Wild-type filaments showed significant uptake of [
14
C]pyruvate, which was impaired in the
alr3027
and
all3028
mutants and was inhibited by several monocarboxylate 2-oxoacids, identifying this TRAP-T system as a pyruvate/monocarboxylate 2-oxoacid transporter.