bluuebunny/crossref_metadata_2025_split huggingface dataset:
TatABC Overexpression Improves
Corynebacterium glutamicum
Tat-Dependent Protein Secretion
Authors: Kikuchi Yoshimi , Itaya Hiroshi , Date Masayo , Matsui Kazuhiko , Wu Long-Fei 
Published: December 2008

ABSTRACT

The twin-arginine translocation (Tat) pathway in
Corynebacterium glutamicum
has been described previously. The minimal functional Tat system in
C. glutamicum
required TatA and TatC but did not require TatB, although this component was required for maximal efficiency of Tat-dependent secretion. We previously demonstrated that
Chryseobacterium proteolyticum
pro-protein glutaminase (pro-PG) and
Streptomyces mobaraensis
pro-transglutaminase (pro-TG) could be secreted via the Tat pathway in
C. glutamicum
. Here we report that the amounts of pro-PG secreted were more than threefold larger when TatC or TatAC was overexpressed, and there was a further threefold increase when TatABC was overexpressed. These results show that the amount of TatC protein is the first bottleneck and the amount of TatB protein is the second bottleneck in Tat-dependent protein secretion in
C. glutamicum
. In addition, the amount of pro-TG that accumulated via the Tat pathway when TatABC was overexpressed with the TorA signal peptide in
C. glutamicum
was larger than the amount that accumulated via the Sec pathway. We concluded that TatABC overexpression improves Tat-dependent pro-PG and pro-TG secretion in
C. glutamicum
.
Novel Evolutionary Engineering Approach for Accelerated Utilization of Glucose, Xylose, and Arabinose Mixtures by Engineered
Saccharomyces cerevisiae
Strains
Authors: Wisselink H. Wouter , Toirkens Maurice J. , Wu Qixiang , Pronk Jack T. , van Maris Antonius J. A. 
Published: December 2008

ABSTRACT

Lignocellulosic feedstocks are thought to have great economic and environmental significance for future biotechnological production processes. For cost-effective and efficient industrial processes, complete and fast conversion of all sugars derived from these feedstocks is required. Hence, simultaneous or fast sequential fermentation of sugars would greatly contribute to the efficiency of production processes. One of the main challenges emerging from the use of lignocellulosics for the production of ethanol by the yeast
Saccharomyces cerevisiae
is efficient fermentation of
d
-xylose and
l
-arabinose, as these sugars cannot be used by natural
S. cerevisiae
strains. In this study, we describe the first engineered
S. cerevisiae
strain (strain IMS0003) capable of fermenting mixtures of glucose, xylose, and arabinose with a high ethanol yield (0.43 g g
−1
of total sugar) without formation of the side products xylitol and arabinitol. The kinetics of anaerobic fermentation of glucose-xylose-arabinose mixtures were greatly improved by using a novel evolutionary engineering strategy. This strategy included a regimen consisting of repeated batch cultivation with repeated cycles of consecutive growth in three media with different compositions (glucose, xylose, and arabinose; xylose and arabinose; and only arabinose) and allowed rapid selection of an evolved strain (IMS0010) exhibiting improved specific rates of consumption of xylose and arabinose. This evolution strategy resulted in a 40% reduction in the time required to completely ferment a mixture containing 30 g liter
−1
glucose, 15 g liter
−1
xylose, and 15 g liter
−1
arabinose.
Genetic Diversity and Host Range of Rhizobia Nodulating
Lotus tenuis
in Typical Soils of the Salado River Basin (Argentina)
Authors: Estrella María Julia , Muñoz Socorro , Soto María José , Ruiz Oscar , Sanjuán Juan 
Published: December 2008

ABSTRACT

A total of 103 root nodule isolates were used to estimate the diversity of bacteria nodulating
Lotus tenuis
in typical soils of the Salado River Basin. A high level of genetic diversity was revealed by repetitive extragenic palindromic PCR, and 77 isolates with unique genomic fingerprints were further differentiated into two clusters, clusters A and B, after 16S rRNA restriction fragment length polymorphism analysis. Cluster A strains appeared to be related to the genus
Mesorhizobium
, whereas cluster B was related to the genus
Rhizobium
. 16S rRNA sequence and phylogenetic analysis further supported the distribution of most of the symbiotic isolates in either
Rhizobium
or
Mesorhizobium
: the only exception was isolate BA135, whose 16S rRNA gene was closely related to the 16S rRNA gene of the genus
Aminobacter.
Most
Mesorhizobium
-like isolates were closely related to
Mesorhizobium amorphae
,
Mesorhizobium mediterraneum
,
Mesorhizobium tianshanense
, or the broad-host-range strain NZP2037, but surprisingly few isolates grouped with
Mesorhizobium loti
type strain NZP2213.
Rhizobium
-like strains were related to
Rhizobium gallicum
,
Rhizobium etli
, or
Rhizobium tropici
, for which
Phaseolus vulgaris
is a common host. However, no
nodC
or
nifH
genes could be amplified from the
L. tenuis
isolates, suggesting that they have rather divergent symbiosis genes. In contrast,
nodC
genes from the
Mesorhizobium
and
Aminobacter
strains were closely related to
nodC
genes from narrow-host-range
M. loti
strains. Likewise,
nifH
gene sequences were very highly conserved among the Argentinian isolates and reference
Lotus
rhizobia. The high levels of conservation of the
nodC
and
nifH
genes suggest that there was a common origin of the symbiosis genes in narrow-host-range
Lotus
symbionts, supporting the hypothesis that both intrageneric horizontal gene transfer and intergeneric horizontal gene transfer are important mechanisms for the spread of symbiotic capacity in the Salado River Basin.
Complete Genome Sequence ofMacrococcus caseolyticusStrain JSCS5402, Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci
Authors: Baba Tadashi , Kuwahara-Arai Kyoko , Uchiyama Ikuo , Takeuchi Fumihiko , Ito Teruyo , Hiramatsu Keiichi 
Published: December 2008

ABSTRACTWe isolated the methicillin-resistantMacrococcus caseolyticusstrain JCSC5402 from animal meat in a supermarket and determined its whole-genome nucleotide sequence. This is the first report on the genome analysis of a macrococcal species that is evolutionarily closely related to the human pathogensStaphylococcus aureusandBacillus anthracis. The essential biological pathways ofM. caseolyticusare similar to those of staphylococci. However, the species has a small chromosome (2.1 MB) and lacks many sugar and amino acid metabolism pathways and a plethora of virulence genes that are present inS. aureus. On the other hand,M. caseolyticuspossesses a series of oxidative phosphorylation machineries that are closely related to those in the familyBacillaceae. We also discovered a probable primordial form of aMacrococcusmethicillin resistance gene complex,mecIRAm, on one of the eight plasmids harbored by theM. caseolyticusstrain. This is the first finding of a plasmid-encoding methicillin resistance gene.Macrococcusis considered to reflect the genome of ancestral bacteria before the speciation of staphylococcal species and may be closely associated with the origin of the methicillin resistance gene complex of the notorious human pathogen methicillin-resistantS. aureus.
The YjbH Protein ofBacillus subtilisEnhances ClpXP-Catalyzed Proteolysis of Spx
Authors: Garg Saurabh K. , Kommineni Sushma , Henslee Luke , Zhang Ying , Zuber Peter 
Published: December 2008

ABSTRACTThe global transcriptional regulator Spx ofBacillus subtilisis controlled at several levels of the gene expression process. It is maintained at low concentrations during unperturbed growth by the ATP-dependent protease ClpXP. Under disulfide stress, Spx concentration increases due in part to a reduction in ClpXP-catalyzed proteolysis. Recent studies of Larsson and coworkers (Mol. Microbiol. 66:669-684, 2007) implicated the product of theyjbHgene as being necessary for the proteolytic control of Spx. In the present study, yeast two-hybrid analysis and protein-protein cross-linking showed that Spx interacts with YjbH. YjbH protein was shown to enhance the proteolysis of Spx in reaction mixtures containing ClpXP protease but not ClpCP protease. An N-terminal truncated form of YjbH with a deletion of residues 1 to 24 (YjbHΔ1-24) showed no proteolysis enhancement activity. YjbH is specific for Spx as it did not accelerate proteolysis of the ClpXP substrate green fluorescent protein (GFP)-SsrA, a GFP derivative with a C-terminal SsrA tag that is recognized by ClpXP. Using inductively coupled plasma atomic emission spectroscopy and 4-(2-pyridylazo) resorcinol release experiments, YjbH was found to contain zinc atoms. Zinc analysis of YjbHΔ1-24revealed that the N-terminal histidine-rich region is indispensable for the coordination of at least one Zn atom. A Zn atom coordinated by the N-terminal region was rapidly released from the protein upon treatment with a strong oxidant. In conclusion, YjbH is proposed to be an adaptor for ClpXP-catalyzed Spx degradation, and a model of YjbH redox control involving Zn dissociation is presented.
The
Bacillus anthracis
Protein MprF Is Required for Synthesis of Lysylphosphatidylglycerols and for Resistance to Cationic Antimicrobial Peptides
Authors: Samant Shalaka , Hsu Fong-Fu , Neyfakh Alexander A. , Lee Hyunwoo 
Published: December 2008

ABSTRACT

During inhalational anthrax,
Bacillus anthracis
survives and replicates in alveolar macrophages, followed by rapid invasion into the host's bloodstream, where it multiplies to cause heavy bacteremia.
B. anthracis
must therefore defend itself from host immune functions encountered during both the intracellular and the extracellular stages of anthrax infection. In both of these niches, cationic antimicrobial peptides are an essential component of the host's innate immune response that targets
B. anthracis
. However, the genetic determinants of
B. anthracis
contributing to resistance to these peptides are largely unknown. Here we generated Tn
917
transposon mutants in the ΔANR strain (pXO1
−
pXO2
−
) of
B. anthracis
and screened them for altered protamine susceptibility. A protamine-sensitive mutant identified carried the transposon inserted in the BA1486 gene encoding a putative membrane protein homologous to MprF known in several gram-positive pathogens. A mutant strain with the BAS1375 gene (the orthologue of BA1486) deleted in the Sterne 34F2 strain (pXO1
+
pXO2
−
) of
B. anthracis
exhibited hypersusceptibility not only to protamine but also to α-helical cathelicidin LL-37 and β-sheet defensin human neutrophil peptide 1 compared to the wild-type Sterne strain. Analysis of membrane lipids using isotopic labeling demonstrated that the BAS1375 deletion mutant is unable to synthesize lysinylated phosphatidylglycerols, and this defect is rescued by genetic complementation. Further, we determined the structures of these lysylphosphatidylglycerols by using various mass spectrometric analyses. These results demonstrate that in
B. anthracis
a functional MprF is required for the biosynthesis of lysylphosphatidylglycerols, which is critical for resistance to cationic antimicrobial peptides.
The Response Regulator RpaB Binds to the Upstream Element of Photosystem I Genes To Work for Positive Regulation under Low-Light Conditions in
Synechocystis
sp. Strain PCC 6803
Authors: Seino Yurie , Takahashi Tomoko , Hihara Yukako 
Published: December 2008

ABSTRACT

The coordinated high-light response of genes encoding subunits of photosystem I (PSI) is achieved by the AT-rich region located just upstream of the core promoter in
Synechocystis
sp. strain PCC 6803. The upstream element enhances the basal promoter activity under low-light conditions, whereas this positive regulation is lost immediately after the shift to high-light conditions. In this study, we focused on a high-light regulatory 1 (HLR1) sequence included in the upstream element of every PSI gene examined. A gel mobility shift assay revealed that a response regulator RpaB binds to the HLR1 sequence in PSI promoters. Base substitution in the HLR1 sequence or decrease in copy number of the
rpaB
gene resulted in decrease in the promoter activity of PSI genes under low-light conditions. These observations suggest that RpaB acts as a transcriptional activator for PSI genes. It is likely that RpaB binds to the HLR1 sequence under low-light conditions and works for positive regulation of PSI genes and for negative regulation of high-light-inducible genes depending on the location of the HLR1 sequence within target promoters.
Complete Genome Sequence of
Haemophilus parasuis
SH0165
Authors: Yue Min , Yang Fan , Yang Jian , Bei Weicheng , Cai Xuwang , Chen Lihong , Dong Jie , Zhou Rui , Jin Meilin , Jin Qi , Chen Huanchun 
Published: December 2008

ABSTRACT

Haemophilus parasuis
is the causative agent of Glässer's disease, which produces big losses in swine populations worldwide.
H. parasuis
SH0165, belonging to the dominant serovar 5 in China, is a clinically isolated strain with high-level virulence. Here, we report the first completed genome sequence of this species.
That warm fuzzy feeling: brain serotonergic neurons and the regulation of emotion
Authors: Lowry CA , Lightman SL , Nutt DJ 
Published: December 2008

Abstract Whether lying on the beach in the midday sun on a Caribbean island, grabbing a few minutes in the sauna or spa after work, or sitting in a hot bath or Jacuzzi in the evening, we often associate feeling warm with a sense of relaxation and well-being. Even ‘working up a good sweat’, exercising or performing manual labour in the garden can have its rewards. Although we take these feelings for granted, convergent lines of evidence suggest that sensations of ‘warmth’ may alter neural circuits controlling cognitive function and mood, including serotonergic circuits, in addition to those directly involved in thermoregulatory cooling. One mechanism through which sensations of warmth may modulate neural circuits controlling cognitive function and mood is the activation of temperature-activated transient receptor potential (TRP) ion channels, including TRPv3 and TRPv4 which are active in the non-noxious thermal range, 27–42 °C, and subsequent activation of a subpopulation of brainstem serotonergic neurons. In this article, we explore the hypothesis that a subpopulation of serotonergic neurons are thermosensitive and form part of a thermoafferent pathway regulating physiology and behaviour. We also propose the novel hypothesis that dysregulation of this thermosensitive population of serotonergic neurons plays an important role in stress-related neuropsychiatric disorders, including anxiety and affective disorders.
Online Discussion
Authors: Skinner Barbara 
Published: December 2008

International students arriving at UK higher education institutions often find the first stage of the period of transition from home to British university difficult. Research has shown that the difficulties relate to finding themselves in a new culture. This University of Ulster project encouraged them to explore their feelings by participating in a series of online WebCT discussion tasks during their 6-week presessional programme with the aim of helping to mitigate any disabling effects of arriving in a new country. The article found that virtual contact did not help students to openly express their thoughts by producing comments at an emotional level; that supportive friendships can be built across cultures as well as in conational groups and that the provision of direct advice on practical and physical problems indirectly brought emotional benefits therefore helping students to manage this time of transition more effectively.
SHIP is required for a functional hematopoietic stem cell niche
Authors: Hazen Amy L. , Smith Michelle J. , Desponts Caroline , Winter Oliver , Moser Katrin , Kerr William G. 
Published: December 2008

Abstract
SH2-domain-containing inositol 5′-phosphatase-1 (SHIP) deficiency significantly increases the number of hematopoietic stem cells (HSCs) present in the bone marrow (BM). However, the reconstitution capacity of these HSCs is severely impaired, suggesting that SHIP expression might be an intrinsic requirement for HSC function. To further examine this question, we developed a model in which SHIP expression is ablated in HSCs while they are resident in a SHIP-competent milieu. In this setting, we find that long-term repopulation by SHIP-deficient HSCs is not compromised. Moreover, SHIP-deficient HSCs from this model repopulate at levels comparable with wild-type HSCs upon serial transfer. However, when HSCs from mice with systemic ablation of SHIP are transplanted, they are functionally compromised for repopulation. These findings demonstrate that SHIP is not an intrinsic requirement for HSC function, but rather that SHIP is required for the BM milieu to support functionally competent HSCs. Consistent with these findings, cells that comprise the BM niche express SHIP and SHIP deficiency profoundly alters their function.
Myeloid leukemic progenitor cells can be specifically targeted by minor histocompatibility antigen LRH-1–reactive cytotoxic T cells
Authors: Norde Wieger J. , Overes Ingrid M. , Maas Frans , Fredrix Hanny , Vos Johanna C. M. , Kester Michel G. D. , van der Voort Robbert , Jedema Inge , Falkenburg J. H. Frederik , Schattenberg Anton V. , de Witte Theo M. , Dolstra Harry 
Published: December 2008

Abstract
CD8+ T cells recognizing minor histocompatibility antigens (MiHAs) on leukemic stem and progenitor cells play a pivotal role in effective graft-versus-leukemia reactivity after allogeneic stem cell transplantation (SCT). Previously, we identified a hematopoiesis-restricted MiHA, designated LRH-1, which is presented by HLA-B7 and encoded by the P2X5 purinergic receptor gene. We found that P2X5 is significantly expressed in CD34+ leukemic subpopulations from chronic myeloid leukemia (CML) and acute myeloid leukemia (AML) patients. Here, we demonstrate that LRH-1–specific CD8+ T-cell responses are frequently induced in myeloid leukemia patients following donor lymphocyte infusions. Patients with high percentages of circulating LRH-1–specific CD8+ T cells had no or only mild graft-versus-host disease. Functional analysis showed that LRH-1–specific cytotoxic T lymphocytes (CTLs) isolated from 2 different patients efficiently target LRH-1–positive leukemic CD34+ progenitor cells from both CML and AML patients, whereas mature CML cells are only marginally lysed due to down-regulation of P2X5. Furthermore, we observed that relative resistance to LRH-1 CTL-mediated cell death due to elevated levels of antiapoptotic XIAP could be overcome by IFN-γ prestimulation and increased CTL-target ratios. These findings provide a rationale for use of LRH-1 as immunotherapeutic target antigen to treat residual or persisting myeloid malignancies after allogeneic SCT.
High-level expression of the T-cell chemokines CCL3 and CCL4 by chronic lymphocytic leukemia B cells in nurselike cell cocultures and after BCR stimulation
Authors: Burger Jan A. , Quiroga Maite P. , Hartmann Elena , Bürkle Andrea , Wierda William G. , Keating Michael J. , Rosenwald Andreas 
Published: December 2008

AbstractIn lymphatic tissues, chronic lymphocytic leukemia (CLL) cells are interspersed with CD68+ nurselike cells (NLCs), T cells, and other stromal cells that constitute the leukemia microenvironment. However, the mechanism regulating colocalization of CLL and these accessory cells are largely unknown. To dissect the molecular cross talk between CLL and NLCs, we profiled the gene expression of CD19-purified CLL cells before and after coculture with NLCs. NLC coculture induced high-level expression of B-cell maturation antigen and 2 chemoattractants (CCL3, CCL4) by CLL cells. CCL3/CCL4 induction in NLC cocultures correlated with ZAP-70 expression by CLL cells. High CCL3/CCL4 protein levels were found in CLL cocultures with NLCs, and CCL3/CCL4 induction was abrogated by R406, a Syk inhibitor, suggesting that NLCs induce these chemokines via B-cell receptor (BCR) activation. BCR triggering also caused robust CCL3/CCL4 protein secretion by CLL cells. High CCL3 and CCL4 plasma levels in CLL patients suggest that this pathway plays a role in vivo. These studies reveal a novel mechanism of cross talk between CLL cells and their microenvironment, namely, the secretion of 2 T-cell chemokines in response to NLC coculture and BCR stimulation. Through these chemokines, CLL cells can recruit accessory cells and thereby actively create a supportive microenvironment.
Regulation of TLR4-mediated signaling by IBP/Def6, a novel activator of Rho GTPases
Authors: Chen Qinzhong , Gupta Sanjay , Pernis Alessandra B 
Published: December 2008

AbstractTLRs play a fundamental role in innate immune responses. Although Rho GTPases have been implicated in TLR-mediated signaling pathways, the molecules that control their activation in response to TLR engagement are largely unknown. IFN regulatory factor-4-binding protein (IBP; which is encoded by the gene Def6) is a unique type of activator for Rac that plays a crucial role in TCR-mediated signaling and adaptive immune responses. Here, we demonstrate that IBP/Def6 also controls innate immune responses by modulating TLR-induced signaling events. Mice deficient in IBP/Def6 are protected from LPS-induced septic shock. This protection is associated with a decrease in the production of proinflammatory cytokines and is accompanied by diminished activation of MAPKs and NF-κB. Our results thus identify IBP/Def6 as a novel component of the TLR4-induced signaling cascade that controls the production of proinflammatory cytokines.
Expression and functional role of MDL-1 (CLEC5A) in mouse myeloid lineage cells
Authors: Aoki Naoko , Kimura Yuka , Kimura Shoji , Nagato Toshihiro , Azumi Makoto , Kobayashi Hiroya , Sato Keisuke , Tateno Masatoshi 
Published: December 2008

AbstractMyeloid DNAX activation protein 12 (DAP12)-associating lectin-1 (MDL-1), also known as C-type lectin domain family 5, member A, is a type II transmembrane protein belonging to the C-type lectin family and associates with DAP12 (also called KARAP or TYROBP). It has been reported that two isoforms of MDL-1—long form (MDL-1L) and short form (MDL-1S)—exist in mice. Previously, we observed the marked induction of MDL-1 mRNA expression during the pulmonary mycobacterial infection in mice. The data suggested that the MDL-1-expressing cells were involved in immune responses against mycobacterial infection; however, little is known about the function of MDL-1 as yet. In this study, we demonstrated the significant protein expression of MDL-1L and MDL-1S in mouse neutrophils and macrophages. MDL-1L was highly glycosylated by N-linked glycan and sialic acid. Interestingly, the expression pattern of MDL-1 was different between neutrophils and macrophages. MDL-1 expression was notably induced during the differentiation of the mouse myeloid cell line 32Dcl3 into neutrophils. Additionally, we observed that MDL-1 stimulation induced a significant amount of RANTES and macrophage-derived chemokine production in 32Dcl3 cells in cooperation with signaling through TLR. MDL-1 stimulation also up-regulated CD11b expression and maintained cell survival. Our findings indicate that MDL-1, therefore, plays an important role in immune defense as a result of an innate immunity, which involves neutrophils and macrophages.