bluuebunny/crossref_metadata_2025_split huggingface dataset:
Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli
Authors: Shen Claire R. , Lan Ethan I. , Dekishima Yasumasa , Baez Antonino , Cho Kwang Myung , Liao James C. 
Published: March 2011

ABSTRACT

1-Butanol, an important chemical feedstock and advanced biofuel, is produced by
Clostridium
species. Various efforts have been made to transfer the clostridial 1-butanol pathway into other microorganisms. However, in contrast to similar compounds, only limited titers of 1-butanol were attained. In this work, we constructed a modified clostridial 1-butanol pathway in
Escherichia coli
to provide an irreversible reaction catalyzed by
trans
-enoyl-coenzyme A (CoA) reductase (Ter) and created NADH and acetyl-CoA driving forces to direct the flux. We achieved high-titer (30 g/liter) and high-yield (70 to 88% of the theoretical) production of 1-butanol anaerobically, comparable to or exceeding the levels demonstrated by native producers. Without the NADH and acetyl-CoA driving forces, the Ter reaction alone only achieved about 1/10 the level of production. The engineered host platform also enables the selection of essential enzymes with better catalytic efficiency or expression by anaerobic growth rescue. These results demonstrate the importance of driving forces in the efficient production of nonnative products.
Novel Tandem Biotransformation Process for the Biosynthesis of a Novel Compound, 4-(2,3,5,6-Tetramethylpyrazine-1)-4′-Demethylepipodophyllotoxin
Authors: Tang Ya-Jie , Zhao Wei , Li Hong-Mei 
Published: March 2011

ABSTRACTAccording to the structure of podophyllotoxin and its structure-function relationship, a novel tandem biotransformation process was developed for the directional modification of the podophyllotoxin structure to directionally synthesize a novel compound, 4-(2,3,5,6-tetramethylpyrazine-1)-4′-demethylepipodophyllotoxin (4-TMP-DMEP). In this novel tandem biotransformation process, the starting substrate of podophyllotoxin was biotransformed into 4′-demethylepipodophyllotoxin (product 1) with the demethylation of the methoxyl group at the 4′ position byGibberella fujikuroiSH-f13, which was screened out from Shennongjia prime forest humus soil (Hubei, China). 4′-Demethylepipodophyllotoxin (product 1) was then biotransformed into 4′-demethylpodophyllotoxone (product 2) with the oxidation of the hydroxyl group at the 4 position byAlternaria alternataS-f6, which was screened out from the gatheredDysosma versipellisplants in the Wuhan Botanical Garden, Chinese Academy of Sciences. Finally, 4′-demethylpodophyllotoxone (product 2) and ligustrazine were linked with a transamination reaction to synthesize the target product 4-TMP-DMEP (product 3) byAlternaria alternataS-f6. Compared with podophyllotoxin (i.e., a 50% effective concentration [EC50] of 529 μM), the EC50of 4-TMP-DMEP against the tumor cell line BGC-823 (i.e., 0.11 μM) was significantly reduced by 5,199 times. Simultaneously, the EC50of 4-TMP-DMEP against the normal human proximal tubular epithelial cell line HK-2 (i.e., 0.40 μM) was 66 times higher than that of podophyllotoxin (i.e., 0.006 μM). Furthermore, compared with podophyllotoxin (i.e., logP= 0.34), the water solubility of 4-TMP-DMEP (i.e., logP= 0.66) was significantly enhanced by 94%. For the first time, the novel compound 4-TMP-DMEP with superior antitumor activity was directionally synthesized from podophyllotoxin by the novel tandem biotransformation process developed in this work.
Orthologues of the Anaphase-Promoting Complex/Cyclosome Coactivators Cdc20p and Cdh1p Are Important for Mitotic Progression and Morphogenesis in Candida albicans
Authors: Chou Hsini , Glory Amandeep , Bachewich Catherine 
Published: March 2011

ABSTRACT

The conserved anaphase-promoting complex/cyclosome (APC/C) system mediates protein degradation during mitotic progression. Conserved coactivators Cdc20p and Cdh1p regulate the APC/C during early to late mitosis and G
1
phase.
Candida albicans
is an important fungal pathogen of humans, and it forms highly polarized cells when mitosis is blocked through depletion of the polo-like kinase Cdc5p or other treatments. However, the mechanisms governing mitotic progression and associated polarized growth in the pathogen are poorly understood. In order to gain insights into these processes, we characterized
C. albicans
orthologues of Cdc20p and Cdh1p. Cdc20p-depleted cells were blocked in early or late mitosis with elevated levels of Cdc5p and the mitotic cyclin Clb2p, suggesting that Cdc20p is essential and has some conserved functions during mitosis. However, the yeast cells formed highly polarized buds in contrast to the large doublets of
S. cerevisiae
cdc20
mutants, implying a distinct role in morphogenesis. In comparison,
cdh1Δ/cdh1Δ
cells were viable but showed enrichment of Clb2p and Cdc5p, suggesting that Cdh1p may influence mitotic exit. The
cdh1Δ/cdh1Δ
phenotype was pleiotropic, consisting of normal or enlarged yeast, pseudohyphae, and some elongated buds, whereas
S. cerevisiae
cdh1Δ
yeast cells were reduced in size. Thus,
C. albicans
Cdh1p may have some distinct functions. Finally, absence of Cdh1p or Cdc20p had a minor or no effect on hyphal development, respectively. Overall, the results suggest that Cdc20p and Cdh1p may be APC/C activators that are important for mitosis but also morphogenesis in
C. albicans
. Their novel features imply additional variations in function and underscore rewiring in the emerging mitotic regulatory networks of the pathogen.
Staphylococcus epidermidis Uses Distinct Mechanisms of Biofilm Formation To Interfere with Phagocytosis and Activation of Mouse Macrophage-Like Cells 774A.1
Authors: Schommer Nina N. , Christner Martin , Hentschke Moritz , Ruckdeschel Klaus , Aepfelbacher Martin , Rohde Holger 
Published: March 2011

ABSTRACT

Assembly of adherent biofilms is the key mechanism involved in
Staphylococcus epidermidis
virulence during device-associated infections. Aside from polysaccharide intercellular adhesin (PIA), the accumulation-associated protein Aap and the extracellular matrix binding protein Embp act as intercellular adhesins, mediating
S. epidermidis
cell aggregation and biofilm accumulation. The aim of this study was to investigate structural features of PIA-, Aap-, and Embp-mediated
S. epidermidis
biofilms in more detail and to evaluate their specific contributions to biofilm-related
S. epidermidis
immune escape. PIA-, Embp-, and Aap-mediated biofilms exhibited substantial morphological differences. Basically, PIA synthesis induced formation of macroscopically visible, rough cell clusters, whereas Aap- and Embp-dependent biofilms preferentially displayed a smooth layer of aggregated bacteria. On the microscopic level, PIA was found to form a string-like organized extracellular matrix connecting the bacteria, while Embp produced small deposits of intercellular matrix and Aap was strictly localized to the bacterial surface. Despite marked differences,
S. epidermidis
strains using PIA, Aap, or Embp for biofilm formation were protected from uptake by J774A.1 macrophages, with similarly efficiencies. In addition, compared to biofilm-negative
S. epidermidis
strains, isogenic biofilm-forming
S. epidermidis
induced only a diminished inflammatory J774A.1 macrophage response, leading to significantly (88.2 to 88.7%) reduced NF-κB activation and 68.8 to 83% reduced interleukin-1β (IL-1β) production. Mechanical biofilm dispersal partially restored induction of NF-κB activation, although bacterial cell surfaces remained decorated with the respective intercellular adhesins. Our results demonstrate that distinct
S. epidermidis
biofilm morphotypes are similarly effective at protecting
S. epidermidis
from phagocytic uptake and at counteracting macrophage activation, providing novel insights into mechanisms that could contribute to the chronic and persistent course of biofilm-related
S. epidermidis
foreign material infections.
Genome Sequences of Two Staphylococcus aureus Ovine Strains That Induce Severe (Strain O11) and Mild (Strain O46) Mastitis
Authors: Le Maréchal Caroline , Hernandez David , Schrenzel Jacques , Even Sergine , Berkova Nadia , Thiéry Richard , Vautor Eric , Fitzgerald J. Ross , François Patrice , Le Loir Yves 
Published: March 2011

ABSTRACT

Staphylococcus aureus
is a major etiological agent of mastitis in ruminants. We report here the genome sequences of two ovine strains that were isolated from gangrenous (strain O11) and subclinical (strain O46) ewe mastitis. Both strains belong to the same clonal complex. Despite this close genotypic relationship, the two isolates were shown to reproducibly induce highly divergent types of infections, either severe (O11) or mild (O46) mastitis, in an experimental ewe model.
The
spoIIE
Homolog of Epulopiscium sp. Type B Is Expressed Early in Intracellular Offspring Development
Authors: Miller David A. , Choat John Howard , Clements Kendall D. , Angert Esther R. 
Published: March 2011

ABSTRACT

Epulopiscium
sp. type B is an enormous intestinal symbiont of the surgeonfish
Naso tonganus
. Intracellular offspring production in
Epulopiscium
shares features with endospore formation. Here, we characterize the
spoIIE
homolog in
Epulopiscium
. The timing of
spoIIE
gene expression and presence of interacting partners suggest that the activation of σ
F
occurs early in
Epulopiscium
offspring development.
Cadaverine Covalently Linked to the Peptidoglycan Serves as the Correct Constituent for the Anchoring Mechanism between the Outer Membrane and Peptidoglycan in Selenomonas ruminantium
Authors: Kojima Seiji , Kaneko Jun , Abe Naoki , Takatsuka Yumiko , Kamio Yoshiyuki 
Published: March 2011

ABSTRACT

In
Selenomonas ruminantium
, a strictly anaerobic and Gram-negative bacterium, cadaverine covalently linked to the peptidoglycan is required for the interaction between the peptidoglycan and the S-layer homologous (SLH) domain of the major outer membrane protein Mep45. Here, using a series of diamines with a general structure of NH
3
+
(CH
2
)

n

NH
3
+
(
n
= 3 to 6), we found that cadaverine (
n
= 5) specifically serves as the most efficient constituent of the peptidoglycan in acquiring the high resistance of the cell to external damage agents and is required for effective interaction between the SLH domain of Mep45 and the peptidoglycan, facilitating the correct anchoring of the outer membrane to the peptidoglycan.
Multilocus Sequence-Based Analysis Delineates a Clonal Population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of Human Origin
Authors: Aujoulat Fabien , Jumas-Bilak Estelle , Masnou Agnès , Sallé Fanny , Faure Denis , Segonds Christine , Marchandin Hélène , Teyssier Corinne 
Published: March 2011

ABSTRACT

The genus
Agrobacterium
includes plant-associated bacteria and opportunistic human pathogens. Taxonomy and nomenclature within the genus remain controversial. In particular, isolates of human origin were all affiliated with the species
Agrobacterium
(
Rhizobium
)
radiobacter
, while phytopathogenic strains were designated under the synonym denomination
Agrobacterium tumefaciens
. In order to study the relative distribution of
Agrobacterium
strains according to their origins, we performed a multilocus sequence-based analysis (MLSA) on a large collection of 89 clinical and environmental strains from various origins. We proposed an MLSA scheme based on the partial sequence of 7 housekeeping genes (
atpD
,
zwf
,
trpE
,
groEL
,
dnaK
,
glnA
, and
rpoB
) present on the circular chromosome of
A. tumefaciens
C58. Multilocus phylogeny revealed that 88% of the clinical strains belong to genovar A7, which formed a homogeneous population with linkage disequilibrium, suggesting a low rate of recombination. Comparison of genomic fingerprints obtained by pulsed-field gel electrophoresis (PFGE) showed that the strains of genovar A7 were epidemiologically unrelated. We present genetic evidence that genovar A7 may constitute a human-associated population distinct from the environmental population. Also, phenotypic characteristics, such as culture at 42°C, agree with this statement. This human-associated population might represent a potential novel species in the genus
Agrobacterium
.
Germination of Individual Bacillus subtilis Spores with Alterations in the GerD and SpoVA Proteins, Which Are Important in Spore Germination
Authors: Wang Guiwen , Yi Xuan , Li Yong-qing , Setlow Peter 
Published: March 2011

ABSTRACT

Release of Ca
2+
with dipicolinic acid (CaDPA) was monitored by Raman spectroscopy and differential interference contrast microscopy during germination of individual spores of
Bacillus subtilis
strains with alterations in GerD and SpoVA proteins. Notable conclusions about germination after the addition of nutrient were as follows. (i) Following
l
-alanine addition, wild-type and
gerD
spores and spores with elevated SpoVA protein levels (↑SpoVA spores) slowly released ∼10% of their CaDPA during a variable (6- to 55-min) period ending at
T
lag
, the time when faster CaDPA release began. (ii)
T
lag
times were lower for ↑SpoVA spores than for wild-type spores and were higher for
gerD
spores. (iii) The long
T
lag
times of
gerD
spores were partially due to slow commitment to germinate. (iv) The intervals between the commitment to germinate and CaDPA release were similar for wild-type and ↑SpoVA spores but longer for
gerD
spores. (v) The times for rapid CaDPA release, Δ
T
release
=
T
release
−
T
lag
(with
T
release
being the time at which CaDPA release was complete), were similar for wild-type,
gerD
, and ↑SpoVA spores. (vi) Spores with either one of two point mutations in the s
poVA
operon (
spoVA
1
and
spoVA
2
spores) exhibited a more rapid rate of CaDPA release beginning immediately after
l
-alanine addition leading to ∼65% CaDPA release prior to
T
lag
. (vii)
T
lag
times for
spoVA
1
and
spoVA
2
spores were longer than for wild-type spores. (viii) The intervals between
spoVA
1
and
spoVA
2
spores' commitment and CaDPA release were similar to those for wild-type spores, but commitment occurred later. In contrast to germination after the addition of nutrient,
T
lag
and Δ
T
release
times were relatively similar during dodecylamine germination of spores of the five strains. These findings suggest the following. (i) GerD plays no role in CaDPA release during spore germination. (ii) SpoVA proteins are involved in CaDPA release during germination with nutrients, and probably with dodecylamine. (iii) Spores release significant CaDPA before commitment. (iv) CaDPA release during
T
lag
and Δ
T
release
may signal subsequent germination events.
Complete Genome Sequence of the Canine Pathogen Staphylococcus pseudintermedius
Authors: Zakour Nouri L. Ben , Bannoehr Jeanette , van den Broek Adri H. M. , Thoday Keith L. , Fitzgerald J. Ross 
Published: March 2011

ABSTRACT

We report the first whole-genome sequence for a clinical isolate of
Staphylococcus pseudintermedius
(ED99), the major pathogen responsible for canine bacterial pyoderma.
S. pseudintermedius
contains numerous mobile genetic elements and encodes an array of putative virulence factors, including superantigenic, cytolytic, and exfoliative toxins and cell wall-associated surface proteins.
Complete Genome Sequence of Lactobacillus helveticus H10
Authors: Zhao Wenjing , Chen Yongfu , Sun Zhihong , Wang Jicheng , Zhou Zhemin , Sun Tiansong , Wang Lei , Chen Wei , Zhang Heping 
Published: March 2011

ABSTRACT

Lactobacillus helveticus
strain H10 was isolated from traditional fermented milk in Tibet, China. We sequenced the whole genome of strain H10 and compared it to the published genome sequence of
Lactobacillus helveticus
DPC4571.
Complete Genome Sequence of the Commensal Enterococcus faecalis 62, Isolated from a Healthy Norwegian Infant
Authors: Brede Dag Anders , Snipen Lars Gustav , Ussery David Wayne , Nederbragt Alexander J. , Nes Ingolf F. 
Published: March 2011

ABSTRACT

The genome of
Enterococcus faecalis
62, a commensal isolate from a healthy Norwegian infant, revealed multiple adaptive traits to the gastrointestinal tract (GIT) environment and the milk-containing diet of breast-fed infants. Adaptation to a commensal existence was emphasized by lactose and other carbohydrate metabolism genes within genomic islands, accompanied by the absence of virulence traits.
Complete Genome Sequence of “Vulcanisaeta moutnovskia” Strain 768-28, a Novel Member of the Hyperthermophilic Crenarchaeal Genus Vulcanisaeta
Authors: Gumerov Vadim M. , Mardanov Andrey V. , Beletsky Alexey V. , Prokofeva Maria I. , Bonch-Osmolovskaya Elizaveta A. , Ravin Nikolai V. , Skryabin Konstantin G. 
Published: March 2011

ABSTRACT

Strain 768-28 was isolated from a hot spring in Kamchatka, Russia, and represents a novel member of the
Vulcanisaeta
genus. The complete genome sequence of this thermoacidophilic anaerobic crenarchaeon reveals genes for protein and carbohydrate-active enzymes, the Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid cycle, beta-oxidation of fatty acids, and sulfate reduction.
Genome Sequences of Three Acinetobacter baumannii Strains Assigned to the Multilocus Sequence Typing Genotypes ST2, ST25, and ST78
Authors: Zarrilli Raffaele , Giannouli Maria , Rocco Francesco , Loman Nicholas J. , Haines Anthony S. , Constantinidou Chrystala , Pallen Mark J. , Triassi Maria , Di Nocera Pier Paolo 
Published: March 2011

ABSTRACT

Acinetobacter baumannii
is an emerging opportunistic Gram-negative pathogen responsible for hospital-acquired infections.
A. baumannii
epidemics described in Europe and worldwide were caused by a limited number of genotypic clusters of multidrug-resistant strains. Here, we report the availability of draft genome sequences for three multidrug-resistant
A. baumannii
strains assigned to multilocus sequence typing genotypes ST2, ST25, and ST78 that were more frequently isolated during outbreaks occurred in Greece, Italy, Lebanon, and Turkey.
Complete Genome Sequence of Bacillus thuringiensis Serovar finitimus Strain YBT-020
Authors: Zhu Yiguang , Shang Hui , Zhu Qian , Ji Fang , Wang Pengxia , Fu Jingjing , Deng Yun , Xu Chengchen , Ye Weixing , Zheng Jinshui , Zhu Lei , Ruan Lifang , Peng Donghai , Sun Ming 
Published: March 2011

ABSTRACT

Bacillus thuringiensis
is a Gram-positive, spore-forming bacterium that forms parasporal crystals at the onset of the sporulation phase of its growth. Here, we report the complete genome sequence of
B. thuringiensis
serovar finitimus strain YBT-020, whose parasporal crystals consist of Cry26Aa and Cry28Aa crystal proteins and are located between the exosporium and the spore coat and remain adhering to the spore after sporulation.
Genome Sequence of Victivallis vadensis ATCC BAA-548, an Anaerobic Bacterium from the Phylum Lentisphaerae, Isolated from the Human Gastrointestinal Tract
Authors: van Passel Mark W. J. , Kant Ravi , Palva Airi , Lucas Susan , Copeland Alex , Lapidus Alla , Glavina del Rio Tijana , Dalin Eileen , Tice Hope , Bruce David , Goodwin Lynne , Pitluck Sam , Davenport Karen Walston , Sims David , Brettin Thomas S. , Detter John C. , Han Shunsheng , Larimer Frank W. , Land Miriam L. , Hauser Loren , Kyrpides Nikolaos , Ovchinnikova Galina , Richardson P. Paul , de Vos Willem M. , Smidt Hauke , Zoetendal Erwin G. 
Published: March 2011

ABSTRACT

Victivallis vadensis
ATCC BAA-548 represents the first cultured representative from the novel phylum
Lentisphaerae
, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and
V. vadensis
therefore represents an important organism for evolutionary studies.
V. vadensis
is a strictly anaerobic sugar-fermenting isolate from the human gastrointestinal tract.
The Dimer Interface of Agrobacterium tumefaciens VirB8 Is Important for Type IV Secretion System Function, Stability, and Association of VirB2 with the Core Complex
Authors: Sivanesan Durga , Baron Christian 
Published: March 2011

ABSTRACT

Type IV secretion systems are virulence factors used by many Gram-negative bacteria to translocate macromolecules across the cell envelope. VirB8 is an essential inner membrane component of type IV secretion systems, and it is believed to form a homodimer. In the absence of VirB8, the levels of several other VirB proteins were reduced (VirB1, VirB3, VirB4, VirB5, VirB6, VirB7, and VirB11) in
Agrobacterium tumefaciens
, underlining its importance for complex stability. To assess the importance of dimerization, we changed residues at the predicted dimer interface (V97, A100, Q93, and E94) in order to strengthen or to abolish dimerization. We verified the impact of the changes on dimerization
in vitro
with purified V97 variants, followed by analysis of the
in vivo
consequences in a complemented
virB8
deletion strain. Dimer formation was observed
in vivo
after the introduction of a cysteine residue at the predicted interface (V97C), and this variant supported DNA transfer, but the formation of elongated T pili was not detected by the standard pilus isolation technique. Variants with changes at V97 and A100 that weaken dimerization did not support type IV secretion system functions. The T-pilus component VirB2 cofractionated with high-molecular-mass core protein complexes extracted from the membranes, and the presence of VirB8 as well as its dimer interface were important for this association. We conclude that the VirB8 dimer interface is required for T4SS function, for the stabilization of many VirB proteins, and for targeting of VirB2 to the T-pilus assembly site.
Triggered Mycobacterium tuberculosis Heparin-Binding Hemagglutinin Adhesin Folding and Dimerization
Authors: Lomino Joseph V. , Tripathy Ashutosh , Redinbo Matthew R. 
Published: March 2011

ABSTRACT

The heparin-binding hemagglutinin adhesin (HBHA) is a surface adhesin on the human pathogen
Mycobacterium tuberculosis
. Previously, it has been shown that HBHA exists as a dimer in solution. We investigated the detailed nature of this dimer using circular dichroism spectroscopy and analytical ultracentrifugation techniques. We demonstrate that the heparan sulfate (HS) binding region does not play a role in dimerization in solution, while the linker region between the predicted N-terminal coiled-coil and the C-terminal HS binding region does affect dimer stability. The majority of contacts responsible for dimerization, folding, and stability lie within the predicted coiled-coil region of HBHA, while the N-terminal helix preceding the coiled-coil appears to trigger the folding and dimerization of HBHA. Constructs lacking this initial helix or containing site-specific mutations produce nonhelical monomers in solution. Thus, we show that HBHA dimerization and folding are linked and that the N-terminal region of this cell surface adhesin triggers the formation of an HBHA coiled-coil dimer.