bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome and Proteome of Acholeplasma laidlawii
Authors: Lazarev V. N. , Levitskii S. A. , Basovskii Y. I. , Chukin M. M. , Akopian T. A. , Vereshchagin V. V. , Kostrjukova E. S. , Kovaleva G. Y. , Kazanov M. D. , Malko D. B. , Vitreschak A. G. , Sernova N. V. , Gelfand M. S. , Demina I. A. , Serebryakova M. V. , Galyamina M. A. , Vtyurin N. N. , Rogov S. I. , Alexeev D. G. , Ladygina V. G. , Govorun V. M. 
Published: July 2011

ABSTRACT

We present the complete genome sequence and proteogenomic map for
Acholeplasma laidlawii
PG-8A (class
Mollicutes
, order
Acholeplasmatales
, family
Acholeplasmataceae
). The genome of
A. laidlawii
is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the
Mollicutes
with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress.
Acholeplasma laidlawii
and phytoplasmas are the only
Mollicutes
known to use the universal genetic code, in which UGA is a stop codon. Within the
Mollicutes
group, only the sterol-nonrequiring
Acholeplasma
has the capacity to synthesize saturated fatty acids
de novo
. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of
A. laidlawii
proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to
A. laidlawii
, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.
Provirus Induction in Hyperthermophilic Archaea: Characterization of Aeropyrum pernix Spindle-Shaped Virus 1 and Aeropyrum pernix Ovoid Virus 1
Authors: Mochizuki Tomohiro , Sako Yoshihiko , Prangishvili David 
Published: July 2011

ABSTRACT

By
in silico
analysis, we have identified two putative proviruses in the genome of the hyperthermophilic archaeon
Aeropyrum pernix
, and under special conditions of
A. pernix
growth, we were able to induce their replication. Both viruses were isolated and characterized. Negatively stained virions of one virus appeared as pleomorphic spindle-shaped particles, 180 to 210 nm by 40 to 55 nm, with tails of heterogeneous lengths in the range of 0 to 300 nm. This virus was named
Aeropyrum pernix
spindle-shaped virus 1 (APSV1). Negatively stained virions of the other virus appeared as slightly irregular oval particles with one pointed end, while in cryo-electron micrographs, the virions had a regular oval shape and uniform size (70 by 55 nm). The virus was named
Aeropyrum pernix
ovoid virus 1 (APOV1). Both viruses have circular, double-stranded DNA genomes of 38,049 bp for APSV1 and 13,769 bp for APOV1. Similarities to proteins of other archaeal viruses were limited to the integrase and Dna1-like protein. We propose to classify APOV1 into the family
Guttaviridae
.
Identification and Characterization of a
Re
-Citrate Synthase in Dehalococcoides Strain CBDB1
Authors: Marco-Urrea Ernest , Paul Steffanie , Khodaverdi Viola , Seifert Jana , von Bergen Martin , Kretzschmar Utta , Adrian Lorenz 
Published: July 2011

ABSTRACT

The genome annotations of all sequenced
Dehalococcoides
strains lack a citrate synthase, although physiological experiments have indicated that such an activity should be encoded. We here report that a
Re
face-specific citrate synthase is synthesized by
Dehalococcoides
strain CBDB1 and that this function is encoded by the gene cbdbA1708 (NCBI accession number
CAI83711
), previously annotated as encoding homocitrate synthase. Gene cbdbA1708 was heterologously expressed in
Escherichia coli
, and the recombinant enzyme was purified. The enzyme catalyzed the condensation of oxaloacetate and acetyl coenzyme A (acetyl-CoA) to citrate. The protein did not have homocitrate synthase activity and was inhibited by citrate, and Mn
2+
was needed for full activity. The stereospecificity of the heterologously expressed citrate synthase was determined by electrospray ionization liquid chromatography-mass spectrometry (ESI LC/MS). Citrate was synthesized from [2-
13
C]acetyl-CoA and oxaloacetate by the
Dehalococcoides
recombinant citrate synthase and then converted to acetate and malate by commercial citrate lyase plus malate dehydrogenase. The formation of unlabeled acetate and
13
C-labeled malate proved the
Re
face-specific activity of the enzyme. Shotgun proteome analyses of cell extracts of strain CBDB1 demonstrated that cbdbA1708 is expressed in strain CBDB1.
Quantifying Aggregation Dynamics during Myxococcus xanthus Development
Authors: Zhang Haiyang , Angus Stuart , Tran Michael , Xie Chunyan , Igoshin Oleg A. , Welch Roy D. 
Published: July 2011

ABSTRACT

Under starvation conditions, a swarm of
Myxococcus xanthus
cells will undergo development, a multicellular process culminating in the formation of many aggregates called fruiting bodies, each of which contains up to 100,000 spores. The mechanics of symmetry breaking and the self-organization of cells into fruiting bodies is an active area of research. Here we use microcinematography and automated image processing to quantify several transient features of developmental dynamics. An analysis of experimental data indicates that aggregation reaches its steady state in a highly nonmonotonic fashion. The number of aggregates rapidly peaks at a value 2- to 3-fold higher than the final value and then decreases before reaching a steady state. The time dependence of aggregate size is also nonmonotonic, but to a lesser extent: average aggregate size increases from the onset of aggregation to between 10 and 15 h and then gradually decreases thereafter. During this process, the distribution of aggregates transitions from a nearly random state early in development to a more ordered state later in development. A comparison of experimental results to a mathematical model based on the traffic jam hypothesis indicates that the model fails to reproduce these dynamic features of aggregation, even though it accurately describes its final outcome. The dynamic features of
M. xanthus
aggregation uncovered in this study impose severe constraints on its underlying mechanisms.
Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp
Authors: Bogdanove Adam J. , Koebnik Ralf , Lu Hong , Furutani Ayako , Angiuoli Samuel V. , Patil Prabhu B. , Van Sluys Marie-Anne , Ryan Robert P. , Meyer Damien F. , Han Sang-Wook , Aparna Gudlur , Rajaram Misha , Delcher Arthur L. , Phillippy Adam M. , Puiu Daniela , Schatz Michael C. , Shumway Martin , Sommer Daniel D. , Trapnell Cole , Benahmed Faiza , Dimitrov George , Madupu Ramana , Radune Diana , Sullivan Steven , Jha Gopaljee , Ishihara Hiromichi , Lee Sang-Won , Pandey Alok , Sharma Vikas , Sriariyanun Malinee , Szurek Boris , Vera-Cruz Casiana M. , Dorman Karin S. , Ronald Pamela C. , Verdier Valérie , Dow J. Maxwell , Sonti Ramesh V. , Tsuge Seiji , Brendel Volker P. , Rabinowicz Pablo D. , Leach Jan E. , White Frank F. , Salzberg Steven L. 
Published: July 2011

ABSTRACT

Xanthomonas
is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of
Xanthomonas campestris
pv. raphani strain 756C and
X. oryzae
pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology,
Arabidopsis thaliana
and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete
Xanthomonas
genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.
The RpiR-Like Repressor IolR Regulates Inositol Catabolism in Sinorhizobium meliloti
Authors: Kohler Petra R. A. , Choong Ee-Leng , Rossbach Silvia 
Published: July 2011

ABSTRACT

Sinorhizobium meliloti
, the nitrogen-fixing symbiont of alfalfa, has the ability to catabolize
myo
-,
scyllo
-, and
d
-
chiro
-inositol. Functional inositol catabolism (
iol
) genes are required for growth on these inositol isomers, and they play a role during plant-bacterium interactions. The inositol catabolism genes comprise the chromosomally encoded
iolA
(
mmsA
) and the
iolY
(
smc01163
)
RCDEB
genes, as well as the
idhA
gene located on the pSymB plasmid. Reverse transcriptase assays showed that the
iolYRCDEB
genes are transcribed as one operon. The
iol
genes were weakly expressed without induction, but their expression was strongly induced by
myo
-inositol. The putative transcriptional regulator of the
iol
genes, IolR, belongs to the RpiR-like repressor family. Electrophoretic mobility shift assays demonstrated that IolR recognized a conserved palindromic sequence (5′-GGAA-N
6
-TTCC-3′) in the upstream regions of the
idhA
,
iolY
,
iolR
, and
iolC
genes. Complementation assays found IolR to be required for the repression of its own gene and for the downregulation of the
idhA
-encoded
myo
-inositol dehydrogenase activity in the presence and absence of inositol. Further expression studies indicated that the late pathway intermediate 2-keto-5-deoxy-
d
-gluconic acid 6-phosphate (KDGP) functions as the true inducer of the
iol
genes. The
iolA
(
mmsA
) gene encoding methylmalonate semialdehyde dehydrogenase was not regulated by IolR. The
S. meliloti iolA
(
mmsA
) gene product seems to be involved in more than only the inositol catabolic pathway, since it was also found to be essential for valine catabolism, supporting its more recent annotation as
mmsA
.
Osmotically Controlled Synthesis of the Compatible Solute Proline Is Critical for Cellular Defense of Bacillus subtilis against High Osmolarity
Authors: Brill Jeanette , Hoffmann Tamara , Bleisteiner Monika , Bremer Erhard 
Published: July 2011

ABSTRACT

Bacillus subtilis
is known to accumulate large amounts of the compatible solute proline via
de novo
synthesis as a stress protectant when it faces high-salinity environments. We elucidated the genetic determinants required for the osmoadaptive proline production from the precursor glutamate. This proline biosynthesis route relies on the
proJ
-encoded γ-glutamyl kinase, the
proA
-encoded γ-glutamyl phosphate reductase, and the
proH
-encoded Δ
1
-pyrroline-5-caboxylate reductase. Disruption of the
proHJ
operon abolished osmoadaptive proline production and strongly impaired the ability of
B. subtilis
to cope with high-osmolarity growth conditions. Disruption of the
proA
gene also abolished osmoadaptive proline biosynthesis but caused, in contrast to the disruption of
proHJ
, proline auxotrophy. Northern blot analysis demonstrated that the transcription of the
proHJ
operon is osmotically inducible, whereas that of the
proBA
operon is not. Reporter gene fusion studies showed that
proHJ
expression is rapidly induced upon an osmotic upshift. Increased expression is maintained as long as the osmotic stimulus persists and is sensitively linked to the prevalent osmolarity of the growth medium. Primer extension analysis revealed the osmotically controlled
proHJ
promoter, a promoter that resembles typical SigA-type promoters of
B. subtilis
. Deletion analysis of the
proHJ
promoter region identified a 126-bp DNA segment carrying all sequences required in
cis
for osmoregulated transcription. Our data disclose the presence of ProA-interlinked anabolic and osmoadaptive proline biosynthetic routes in
B. subtilis
and demonstrate that the synthesis of the compatible solute proline is a central facet of the cellular defense to high-osmolarity surroundings for this soil bacterium.
Characterization of a Glucosamine/Glucosaminide
N
-Acetyltransferase of Clostridium acetobutylicum
Authors: Reith Jan , Mayer Christoph 
Published: July 2011

ABSTRACT

Many bacteria, in particular Gram-positive bacteria, contain high proportions of non-
N
-acetylated amino sugars, i.e., glucosamine (GlcN) and/or muramic acid, in the peptidoglycan of their cell wall, thereby acquiring resistance to lysozyme. However, muramidases with specificity for non-
N
-acetylated peptidoglycan have been characterized as part of autolytic systems such as of
Clostridium acetobutylicum
. We aim to elucidate the recovery pathway for non-
N
-acetylated peptidoglycan fragments and present here the identification and characterization of an acetyltransferase of novel specificity from
C. acetobutylicum
, named GlmA (for
gl
ucosa
m
ine/glucosaminide
N
-
a
cetyltransferase). The enzyme catalyzes the specific transfer of an acetyl group from acetyl coenzyme A to the primary amino group of GlcN, thereby generating
N
-acetylglucosamine. GlmA is also able to
N
-acetylate GlcN residues at the nonreducing end of glycosides such as (partially) non-
N-
acetylated peptidoglycan fragments and β-1,4-glycosidically linked chitosan oligomers.

K
m

values of 114, 64, and 39 μM were determined for GlcN, (GlcN)
2
, and (GlcN)
3
, respectively, and a 3- to 4-fold higher catalytic efficiency was determined for the di- and trisaccharides. GlmA is the first cloned and biochemically characterized glucosamine/glucosaminide
N
-acetyltransferase and a member of the large GCN5-related
N
-acetyltransferases (GNAT) superfamily of acetyltransferases. We suggest that GlmA is required for the recovery of non-
N
-acetylated muropeptides during cell wall rescue in
C. acetobutylicum
.
The Fimbrial Usher FimD Follows the SurA-BamB Pathway for Its Assembly in the Outer Membrane of Escherichia coli
Authors: Palomino Carmen , Marín Elvira , Fernández Luis Ángel 
Published: July 2011

ABSTRACT

Fimbrial ushers are the largest β-barrel outer membrane proteins (OMPs) known to date, which function in the polymerization of fimbriae and their translocation to the bacterial surface. Folding and assembly of these complex OMPs are not characterized. Here, we investigate the role of periplasmic chaperones (SurA, Skp, DegP, and FkpA) and individual components of the β-barrel assembly machinery (BAM) complex (BamA, BamB, BamC, and BamE) in the folding of the
Escherichia coli
FimD usher. The FimD level is dramatically reduced (∼30-fold) in a
surA
null mutant, but a strong cell envelope stress is constitutively activated with upregulation of DegP (∼10-fold). To demonstrate a direct role of SurA, FimD folding was analyzed in a conditional
surA
mutant in which SurA expression was controlled. In this strain, FimD is depleted from bacteria in parallel to SurA without significant upregulation of DegP. Interestingly, the dependency on SurA is higher for FimD than for other OMPs. We also demonstrate that a functional BAM complex is needed for folding of FimD. In addition, FimD levels were strongly reduced (∼5-fold) in a mutant lacking the accessory lipoprotein BamB. The critical role of BamB for FimD folding was confirmed by complementation and BamB depletion experiments. Similar to SurA dependency, FimD showed a stronger dependency on BamB than OMPs. On the other hand, folding of FimD was only marginally affected in
bamC
and
bamE
mutants. Collectively, our results indicate that FimD usher follows the SurA-BamB pathway for its assembly. The preferential use of this pathway for the folding of OMPs with large β-barrels is discussed.
Electrical modulation of the sympathetic nervous system in order to augment cerebral blood flow: a protocol for an experimental study
Authors: Ter Laan Mark , van Dijk J Marc C , Staal Michiel J , Elting Jan-Willem J 
Published: July 2011

IntroductionCerebral blood flow (CBF) is regulated by several mechanisms. Neurogenic control has been a matter of debate, even though several publications reported the effects of changes in sympathetic tone on CBF. Transcutaneous electrical nerve stimulation and spinal-cord stimulation have been shown to influence peripheral and cerebral blood flow through a sympathetic pathway. The authors hypothesise that certain pathological conditions result in a relative increase in the neurogenic regulation of CBF and that this regulation can be modulated electrically.Methods and analysisPatients with cerebral vasospasm after subarachnoid haemorrhage will be included. The experimental set-up measures several parameters that are involved in cerebral blood flow regulation in patients with cerebral vasospasm after subarachnoid haemorrhage. Measurements are taken at baseline and with stimulation in several frequencies. An ad hoc statistical analysis is used to evaluate different settings of the electrical stimulation. Autoregulation is evaluated with transfer function analysis and autoregulatory index calculations.Ethics and disseminationEthical registration was granted by Medical Review Ethics Committee Groningen (ID METc 2010.123). All participants provide written informed consent on participation. Upon finishing a pilot study to investigate feasibility and effect, either future prospective (randomised) studies will be designed, or other modalities of electrical stimulation will be explored using the same set-up.Trial RegistrationDutch Trial Registry: NTR2358.
Bcl-2 Family Genetic Profiling Reveals Microenvironment-Specific Determinants of Chemotherapeutic Response
Authors: Pritchard Justin R. , Gilbert Luke A. , Meacham Corbin E. , Ricks Jennifer L. , Jiang Hai , Lauffenburger Douglas A. , Hemann Michael T. 
Published: July 2011

Abstract
The Bcl-2 family encompasses a diverse set of apoptotic regulators that are dynamically activated in response to various cell-intrinsic and -extrinsic stimuli. An extensive variety of cell culture experiments have identified effects of growth factors, cytokines, and drugs on Bcl-2 family functions, but in vivo studies have tended to focus on the role of one or two particular members in development and organ homeostasis. Thus, the ability of physiologically relevant contexts to modulate canonical dependencies that are likely to be more complex has yet to be investigated systematically. In this study, we report findings derived from a pool-based shRNA assay that systematically and comprehensively interrogated the functional dependence of leukemia and lymphoma cells upon various Bcl-2 family members across many diverse in vitro and in vivo settings. This approach permitted us to report the first in vivo loss of function screen for modifiers of the response to a front-line chemotherapeutic agent. Notably, our results reveal an unexpected role for the extrinsic death pathway as a tissue-specific modifier of therapeutic response. In particular, our findings show that particular tissue sites of tumor dissemination play critical roles in demarcating the nature and extent of cancer cell vulnerabilities and mechanisms of chemoresistance. Cancer Res; 71(17); 5850–8. ©2011 AACR.
BIM Expression in Treatment-Naïve Cancers Predicts Responsiveness to Kinase Inhibitors
Authors: Faber Anthony C. , Corcoran Ryan B. , Ebi Hiromichi , Sequist Lecia V. , Waltman Belinda A. , Chung Euiheon , Incio Joao , Digumarthy Subba R. , Pollack Sarah F. , Song Youngchul , Muzikansky Alona , Lifshits Eugene , Roberge Sylvie , Coffman Erik J. , Benes Cyril H. , Gómez Henry L. , Baselga José , Arteaga Carlos L. , Rivera Miguel N. , Dias-Santagata Dora , Jain Rakesh K. , Engelman Jeffrey A. 
Published: July 2011

AbstractCancers with specific genetic mutations are susceptible to selective kinase inhibitors. However, there is a wide spectrum of benefit among cancers harboring the same sensitizing genetic mutations. Herein, we measured apoptotic rates among cell lines sharing the same driver oncogene following treatment with the corresponding kinase inhibitor. There was a wide range of kinase inhibitor-induced apoptosis despite comparable inhibition of the target and associated downstream signaling pathways. Surprisingly, pretreatment RNA levels of the BH3-only pro-apoptotic BIM strongly predicted the capacity of EGFR, HER2, and PI3K inhibitors to induce apoptosis in EGFR-mutant, HER2-amplified, and PIK3CA-mutant cancers, respectively, but BIM levels did not predict responsiveness to standard chemotherapies. Furthermore, BIM RNA levels in EGFR-mutant lung cancer specimens predicted response and duration of clinical benefit from EGFR inhibitors. These findings suggest assessment of BIM levels in treatment-naïve tumor biopsies may indicate the degree of benefit from single-agent kinase inhibitors in multiple oncogene-addiction paradigms.Significance: In several oncogene-addiction paradigms, assessment of BIM RNA levels identifies those cancers that fail to have substantial apoptotic responses to kinase inhibitors. BIM RNA levels may be assessed in diagnostic cancer specimens to predict which patients will receive less benefit from single-agent kinase inhibitors. Cancer Discovery: 1(4); 352–65. ©2011 AACR.Read the Commentary on this article by Yoshida and Haura, p. 289This article is highlighted in the In This Issue feature, p. 275
Drug-induced changes in cortical inhibition in medication overuse headache
Authors: Currà Antonio , Coppola Gianluca , Gorini Manuela , Porretta Elisa , Bracaglia Martina , Di Lorenzo Cherubino , Schoenen Jean , Pierelli Francesco 
Published: July 2011

Background: We investigated whether chronic headache related to medication overuse (MOH) is associated with changes in brain mechanisms regulating inhibitory cortical responses compared with healthy volunteers and episodic migraineurs recorded between attacks, and whether these changes differ according to the drug overused. Subjects and Methods: We studied 40 MOH patients whose symptoms were related to triptans alone, non-steroidal anti-inflammatory drugs (NSAIDs) or both medications combined, 12 migraineurs and 13 healthy volunteers. We used high-intensity transcranial magnetic stimulation over the primary motor cortex to assess the silent period from contracted perioral muscles. Results: In MOH patients the cortical silent period differed according to the type of headache medication overused: in patients overusing triptans alone it was shorter than in healthy volunteers (44.7 ± 14.2 vs. 108.1 ± 30.1 ms), but similar to that reported in migraineurs (59.9 ± 30.4 ms), whereas in patients overusing NSAIDs alone or triptans and NSAIDs combined duration of silent period was within normal limits (80.6 ± 46.4 and 103.8 ± 47.2 ms). Conclusions: Compared with episodic migraineurs, MOH patients overusing triptans have no significant change in cortical inhibition, whereas those overusing NSAIDs have an increase in cortical inhibitory mechanisms. We attribute these changes to medication-induced neural adaptation promoted by changes in central serotonin neurotransmission.