bluuebunny/crossref_metadata_2025 huggingface dataset:
Pollution Disrupts Endocrine Signaling
Authors: Gough Nancy R.
Published: July 2007

Dioxins are fat-soluble environmental pollutants that disrupt the endocrine system of humans (see Harper). The aryl hydrocarbon receptor (AhR) binds dioxins; interacts with the AhR nuclear-translocator protein (ARNT) and sex hormone steroid receptors, such as estrogen receptor α (ERα) and androgen receptor (AR); and promotes hormone-independent transcriptional activation. In addition, dioxins also inhibit sex steroid signaling, and Ohtake
et al
. show that one mechanism for this inhibition is by promoting the proteasome-mediated degradation of the steroid hormone receptors. Exposure of mammary tumor cells (MCF-7) or prostate cancer cells (LNCaP) to various dioxin chemicals decreased the abundance of ERα or AR, respectively. Ubiquitinated ERα was detectable in MCF-7 cells treated with dioxin and in which the proteasome was inhibited. Five dioxin-induced flag-tagged AhR-containing complexes were isolated from HeLa cells, and the "B" complex also contained ubiquitinated components. Complex B, which the authors name CUL4B
AhR
, contained the ubiquitin ligase components cullin 4B (CUL4B), damaged DNA binding protein (DDB1), and Rbx1; the proteasomal 19
S
regulatory particle; ARNT; transducin-β-like 3 (TBL3); and ligand-bound AhR. The complete complex was only formed in the presence of AhR dioxin ligand (in vivo detected by coimmunoprecipitation and in vitro by assembly of isolated constituents). The E3 ubiquitin ligase activity of CUL4B
AhR
for ERα required dioxin but did not require estrogen. When components of CUL4B
AhR
were knocked down, dioxin-induced ubiquitination and degradation of ERα were diminished. Injection of dioxin into mice reduced ERα (females) or AR (males) abundance regardless of whether sex steroids were present or absent. Dioxin had no effect in mice deficient for AhR. Thus, AhR appears to trigger the formation of a ligand-induced E3 ubiquitin ligase complex, with AhR serving as the substrate adaptor allowing this complex to target sex steroid receptors. This ligand-dependent E3 ubiquitin ligase is similar to that seen in plants for the auxin receptor, and it will be interesting to see whether there are endogenous ligands for AhR that trigger the formation of this CUL4B
AhR
E3 ubiquitin ligase.

F. Ohtake, A. Baba, I. Takada, M. Okada, K. Iwasaki, H. Miki, S. Takahashi, A. Kouzmenko, K. Nohara, T. Chiba, Y. Fujii-Kuriyama, S. Kato, Dioxin receptor is a ligand-dependent E3 ubiquitin ligase.
Nature
446
, 562-566 (2007).
[PubMed]

J. W. Harper, A degrading solution to pollution.
Nature
446
, 499-500 (2007).
[PubMed]
A Volatile Response to Injury
Authors: Adler Elizabeth M.
Published: July 2007

Plants defend themselves against herbivores by releasing volatile organic compounds (VOCs) that repel herbivores or attract herbivore predators. This response to herbivore-induced damage is mediated through jasmonic acid (JA). Herbivore-induced VOCs have also been reported to stimulate defenses in neighboring plants, thereby playing a role in plant-plant communication (see Gershenzon). Heil and Bueno found that regions of field-grown lima bean plants exposed to shoots that had been damaged by leaf beetles grew better, showed less herbivore damage, secreted more extrafloral nectar (EFN, which attracts herbivore predators), and attracted more ants than did regions that were unexposed to damaged shoots. When some leaves of field-grown lima bean plants were stimulated through damage and application of JA to produce VOCs, production of EFN was stimulated in nearby undamaged leaves from the same shoot or from a second shoot of the same plant. Enhanced production of EFN in undamaged leaves was inhibited, however, when the damaged leaves were covered with plastic bags. Exposure to VOCs also primed EFN secretion, so that the response to subsequent damage was greater in leaves previously exposed to VOCs. In experiments on potted plants, in which air from damaged leaves was blown toward undamaged leaves or directed away from them, only undamaged leaves exposed to air from damaged leaves responded with increased production of EFN. Thus, VOCs appear not only to function in plant-plant communication but also to act as an intraplant defense signal.

M. Heil, J. C. Silva Bueno, Within-plant signaling by volatiles leads to induction and priming of an indirect plant defense in nature.
Proc. Natl. Acad. Sci. U.S.A.
104
, 5467-5472 (2007).
[Abstract]
[Full Text]

J. Gershenzon, Plant volatiles carry both public and private messages.
Proc. Natl. Acad. Sci. U.S.A.
104
, 5257-5258 (2007).
[Full Text]
STAT3 Regulates the Generation of Th17 Cells
Authors: Foley John F.
Published: July 2007

CD4
+
helper T (Th) cells that produce interleukin-17 (IL-17) are a distinct lineage of Th cells (Th17 cells) and are important in autoimmune disorders. Exactly how cytokine signaling generates Th17 cells is only recently becoming clear. IL-6 stimulates Th17 differentiation in vitro, so Yang
et al
. analyzed splenocytes from immunized wild-type and
Il-6
knockout mice by flow cytometry and found that
Il-6
knockout mice had the fewest Th17 cells. Interferon-γ (IFN-γ) inhibits Th17 differentiation, so naïve T cells from IFN-γ-deficient mice were activated in vitro with anti-CD3 and anti-CD28 in the presence or absence of cytokines and/or cytokine-neutralizing antibodies. IL-6 simulated production of Th17 cells, whereas IL-23 resulted in few Th17 cells but synergized with IL-6. This effect might be due to the increased amounts of IL-23 receptor (IL-23R) mRNA observed in IL-6-treated naïve CD4
+
T cells, as measured by real-time polymerase chain reaction. Infection of naïve CD4
+
T cells from IFN-γ-deficient mice with a retrovirus encoding a hyperactive form of signal transducer and activator of transcription-3 (STAT3) resulted in more Th-17 cells and higher amounts of mRNAs for IL-17 and IL-22 than in control cells. Activation of naïve CD4
+
T cells from mice with a hematopoietic-specific deletion of
Stat3
produced fewer Th17 cells and lower amounts of IL-17 and IL-22 mRNAs than did equivalent treatment of wild-type cells. Activated CD4
+
T cells from
Stat3
knockout mice had lower amounts of mRNAs for IL-23R and RORγt (retinoic acid receptor-related orphan receptor γ-T), a Th17-specific transcription factor. This study nominates STAT3 as the essential regulator of Th17 cells, analogous to STAT4 and STAT1 in Th1 cells and STAT6 in Th2 cells.

X. O. Yang, A. D. Panopoulos, R. Nurieva, S. H. Chang, D. Wang, S. S. Watowich, C. Dong, STAT3 regulates cytokine-mediated generation of inflammatory helper T cells.
J. Biol. Chem.
282
, 9358-9363 (2007).
[Abstract]
[Full Text]
Targeting Transmembrane Domains
Authors: Vinson Valda
Published: July 2007

Reagents such as antibodies that target specific proteins are useful in research and medicine. There are methods to engineer antibody-like molecules that target the soluble regions of proteins, but targeting transmembrane regions remains a challenge. Now Yin
et al
. describe a computational method to design peptides that target specific transmembrane helices. Peptides were designed that were specific for each of two closely related integrins involved in cell adhesion.

H. Yin, J. S. Slusky, B. W. Berger, R. S. Walters, G. Vilaire, R. I. Litvinov, J. D. Lear, G. A. Caputo, J. S. Bennett, W. F. DeGrado, Computational design of peptides that target transmembrane helices.
Science
315
, 1817-1822 (2007).
[Abstract]
[Full Text]
Sequestration and Segregation of Receptor Kinases in Epithelial Cells: Implications for ErbB2 Oncogenesis
Authors: Carraway Coralie A. Carothers , Carraway Kermit L.
Published: July 2007

Cell behaviors are regulated by signaling pathways triggered by the activation of cell surface receptors. A key aspect of receptor signaling is the location of these receptors relative to their ligands and to other receptors, particularly in epithelia, whose cells are polarized by tight junction barriers into apical and basolateral membrane regions. In polarized epithelia, the co-receptor ErbB2 is often localized to the apical surface by its intramembrane ligand Muc4, thus segregating it from its partner ErbB3, which is sequestered at the lateral surface, co-localized with cadherin junctions. The ErbB2-ErbB3 receptor heterodimer, when activated, is a potent stimulator of cell proliferation; thus, the segregation mechanism helps maintain these cells in a differentiated state. Similarly, epidermal growth factor, the ligand for ErbB1, which is present in the apical fluid of some epithelia, is segregated from its receptor by the tight junction barrier. Loss of cell polarity and the tight junction barrier facilitates the interaction of ErbB2 with the hemidesmosome integrin α
6
β
4
. This integrin acts as a docking site for signaling pathways to promote cell proliferation and further disruption of cell junctions. The ultimate dissolution of tight junctions may result from activation of transforming growth factor–β receptors, one subunit of which is directly associated with the junction. This activation triggers degradation of critical tight junction components. These sequestration and segregation phenomena provide a model by which overexpression of the ErbB2 receptor kinase may trigger oncogenesis by initiating junction breakdown. Equally important, these mechanisms may act as a sensor for epithelial damage that can activate repair mechanisms.
Understanding Inositol Pyrophosphates
Authors: Ray L. Bryan
Published: July 2007

Inositol pyrophosphates are relatively poorly understood, highly phosphorylated members of the inositol polyphosphate family. Two studies describe related advances in signaling involving inositol pyrophosphates. Mulugu
et al
. purified an inositol pyrophosphate synthase from yeast, called Vip1. Lee
et al
. purified a molecule that regulates the yeast Pho80-Pho85-Pho81 complex, a protein complex containing a cyclin, a cyclin-dependent kinase (CDK), and a CDK inhibitor. The active molecule turned out to be
myo
-D-inositol heptakisphosphate (IP7), which is synthesized through the kinase activity of Vip1.

S. Mulugu, W. Bai, P. C. Fridy, R. J. Bastidas, J. C. Otto, D. E. Dollins, T. A. Haystead, A. A. Ribeiro, J. D. York, A conserved family of enzymes that phosphorylate inositol hexakisphosphate.
Science
316
, 106-109 (2007).
[Abstract]
[Full Text]

Y.-S. Lee, S. Mulugu, J. D. York, E. K. O'Shea, Regulation of a cyclin-CDK-CDK inhibitor complex by inositol pyrophosphates.
Science
316
,109-112 (2007).
[Abstract]
[Full Text]
Sizing Up Man’s Best Friend
Authors: Kiberstis Paula A.
Published: July 2007

In contrast to most mammalian species,
Canis familiaris
(the domestic dog) shows extreme diversity in body size. Sutter
et al
. show that a single allele of the gene encoding insulin-like growth factor-1 (IGF-1) is shared by all small dog breeds but is nearly absent from giant dog breeds, implying that sequence variation in the IGF-1 gene plays a causal role in dog size. Discovery of the IGF-1 gene was facilitated by its localization within a genomic signature, or haplotype block, that probably arose as a result of centuries of dog breeding by humans.

N. B. Sutter, C. D. Bustamante, K. Chase, M. M. Gray, K. Zhao, L. Zhu, B. Padhukasahasram, E. Karlins, S. Davis, P. G. Jones, P. Quignon, G. S. Johnson, H. G. Parker, N. Fretwell, D. S. Mosher, D. F. Lawler, E. Satyaraj, M. Nordborg, K. G. Lark, R. K. Wayne, E. A. Ostrander, A single
IGF1
allele is a major determinant of small size in dogs.
Science
316
, 112-115 (2007).
[Abstract]
[Full Text]
Regulation of PC12 Cell Differentiation by cAMP Signaling to ERK Independent of PKA: Do All the Connections Add Up?
Authors: Gerdin Matthew J. , Eiden Lee E.
Published: July 2007

Pituitary adenylate cyclase–activating polypeptide (PACAP) is a neuropeptide that elevates adenosine 3′,5′-monophosphate (cyclic AMP, also abbreviated cAMP) to elicit neuritogenesis in PC12 cells. This effect appears to be independent of cAMP-dependent protein kinase (PKA) yet dependent on cAMP, leading to the conclusion that another cAMP-binding protein and subsequent signaling pathway must exist to mediate this PKA-independent signaling mechanism. Such a protein was identified as exchange protein directly activated by cAMP (EPAC). Although EPAC may play an indirect role in PACAP-mediated neuritogenesis, it does not serve as the only PKA-independent link from cAMP that leads to neuritogenesis. Thus, the challenge remains to construct a signaling network that incorporates the known mediators, working independently of PKA, that are ultimately responsible for PACAP-mediated neuritogenesis.
Making Life or Death Choices with CBP
Authors: Adler Elizabeth M.
Published: July 2007

The transcriptional coactivator CBP (CREB-binding protein) can interact with p53, and thereby promote apoptosis, or with the functionally antagonistic transcription factor nuclear factor κB (NF-κB), and thereby promote cell proliferation. Huang
et al
. found that tumor necrosis factor-α (TNF-α) not only enhanced CBP association with the NF-κB p65 subunit (as previously shown) and CBP recruitment to NF-κB-responsive promoters but also decreased CBP binding to p53 and its association with p53-responsive promoters. These effects were reversed by inhibiting IKK (inhibitor of NF-κB kinase), which is involved in NF-κB activation. Similarly, in mouse embryonic fibroblasts lacking IKKα, TNF-α failed to stimulate CBP association with p65, despite translocation of p65 to the nucleus, but instead stimulated its association with p53. In vitro kinase assays combined with mutational analysis indicated that IKKα phosphorylated CBP on serine residues 1382 and 1386; moreover, TNF-α stimulated IKKα-dependent phosphorylation of CBP on Ser
1382
and Ser
1386
in HeLa cells. Furthermore, IKKα-dependent phosphorylation of CBP on Ser
1382
and Ser
1386
enhanced CBP binding to p65, thereby decreasing its association with p53, a shift that led to an increase in the transcription of NF-κB-responsive genes and a decrease in the transcription of p53 targets. A comparison of human lung cancer and adjacent nonmalignant tissue indicated that IKKα activation was associated with increased phosphorylation of CBP at Ser
1382
and Ser
1386
.

Stable transfection of wild-type or mutant CBP indicated that CBP phosphorylation on Ser
1382
and Ser
1386
mediated TNF-α-dependent stimulation of cell proliferation. Thus, the authors conclude that CBP phosphorylation by IKKα promotes CBP binding to NF-κB rather than p53, an effect that may be critical to the choice between proliferation and apoptosis.

W.-C. Huang, T.-K. Ju, M.-C. Hung, C.-C. Chen, Phosphorylation of CBP by IKKα promotes cell growth by switching the binding preference of CBP from p53 to NF-κB.
Mol. Cell
26
, 75-87 (2007).
[Online Journal]
Making LIGHT of Lipid Metabolism
Authors: Simpson Stephen
Published: July 2007

Atherosclerosis results from a combination of lipid dysregulation and inflammation-mediated pathology of the vasculature. Lo
et al
. show that increased expression of related members of the tumor necrosis factor family of inflammatory cytokines, LIGHT and lymphotoxin (LT), on T cells can elevate circulating blood cholesterol and triglycerides in mice. This effect appeared to be mediated via lymphotoxin β receptor (LTβR) signaling in hepatocytes, leading to a drop in the activity of hepatic lipase, an enzyme central to lipid metabolism. The normally high lipid levels found in mice that lack the low-density lipoprotein receptor gene were reduced when LTβR signaling was inhibited. These results raise questions about how the immune system detects and subsequently exacerbates dyslipidemia and whether this process makes any direct contribution to atherosclerosis in humans.

J. C. Lo, Y. Wang, A. V. Tumanov, M. Bamji, Z. Yao, C. A. Reardon, G. S. Getz, Y.-X. Fu, Lymphotoxin β receptor-dependent control of lipid homeostasis.
Science
316
, 285-288 (2007).
[Abstract]
[Full Text]

G. K. Hansson, LIGHT hits the liver.
Science
316
, 206-207 (2007).
[Summary]
[Full Text]
Adjusting Synaptic Plasticity
Authors: Ray L. Bryan
Published: July 2007

Researchers are beginning to dissect the complex signaling events that underlie sophisticated functions in the mammalian brain. One example occurs in the dorsal cochlear nucleus (DCN), where auditory sensations are combined with somatosensory input, which may allow orientation of the head with respect to sounds an animal is hearing. Nonauditory signals are transmitted from parallel fibers either directly to the principal neurons of the DCN, known as fusiform cells, or to so-called "cartwheel" interneurons, which then innervate and inhibit fusiform cells. At synapses where the parallel fibers talk to the fusiform cells, an increase in synaptic strength (long-term potentiation, LTP) occurs when an action potential in the postsynaptic cell follows that in the presynaptic neuron. Tzounopoulos
et al
. wanted to explain why just the opposite (long-term depression, LTD) occurred at the synapses between parallel fibers and the cartwheel interneurons. In electrophysiological studies of mouse brain slices in culture, the authors used a range of pharmacological manipulations along with histological analyses to show that distinct use of two signaling pathways in the different cells could account for the differences in effects on synaptic plasticity. Postsynaptic LTP in the fusiform cells required signaling through Ca
2+
/calmodulin-dependent protein kinase II, whereas LTD in the interneurons resulted from an additional presynaptically mediated effect of retrograde signaling by endocannabinoids. Distinct subcellular localization of presynaptic endocannabinoid receptors was largely responsible for the differences in cellular learning responses, and it appeared to be the balance of presynaptic and postsynaptic effects that determined the overall cellular response. Furthermore, the polarity of the plasticity (strengthening or weakening) in cartwheel cells depended on the frequency of neuronal stimulation. The authors explain how these mechanisms may allow cells to change the rules through which they and, in turn, the networks in which they participate respond to stimuli. Understanding these properties may eventually help explain how the brain manages, for example, to filter out predictable consequences of the animal’s movement in response to auditory signals or to suppress responses to self-generated sounds.

T. Tzounopoulos, M. E. Rubio, J. E. Keen, L. O. Trussell, Coactivation of pre- and postsynaptic signaling mechanisms determines cell-specific spike-timing-dependent plasticity.
Neuron
54
, 291-301 (2007).
[Online Journal]
Turned On by a Low pH
Authors: Adler Elizabeth M.
Published: July 2007

Salmonellae
, facultative intracellular pathogens that cause gastroenteritis and typhoid fever, respond to the normally inhospitable environment inside macrophage phagosomes--in which pathogens are exposed to antimicrobial peptides, reactive oxygen species, and acidic pH--by activating the transcription of virulence genes. This process, which depends on phagosomal acidification, involves the activation of the membrane-bound sensor kinase PhoQ, which leads to its autophosphorylation and the subsequent phosphorylation of the transcriptional activator PhoP (the PhoPQ system). Using a bacterial strain that expressed a reporter that was transcriptionally activated by PhoP, Prost
et al
. showed that, in the presence of 1 mM Mg
2+
(the estimated phagosomal concentration), transcription increased when the pH was decreased from 7.5 to 5.5. When PhoQ was reconstituted in vesicles so that the periplasmic sensor domain faced inward and the cytoplasmic kinase domain faced outward, PhoP phosphorylation increased when lumenal pH was decreased from 7.5 to 5.5. Subinhibitory concentrations of antimicrobial peptides have previously been shown to activate PhoQ through a mechanism that may involve displacement of divalent cations, and the effects of antimicrobial peptides and pH on PhoP phosphorylation and PhoPQ-dependent transcription were additive. Nuclear magnetic resonance (NMR) spectroscopy revealed that the conformation of the PhoQ sensor domain was affected by changes in pH and that this conformational change did not depend on loss of divalent cation binding. Thus, the authors propose that PhoQ acts as a pH sensor and that antimicrobial peptides and low pH work together in macrophage phagosomes to activate the PhoPQ system.

L. R. Prost, M. E. Daley, V. Le Sage, M. W. Bader, H. Le Moual, R. E. Klevit, S. I. Miller, Activation of the bacterial sensor kinase PhoQ by acidic pH.
Mol. Cell
26
, 165-174 (2007).
[Online Journal]
Interacting at the ER
Authors: Gough Nancy R.
Published: July 2007

Toll-like receptors (TLRs) recognize microbial pathogens to trigger an immune response. TLR3, TLR7, and TLR9 recognize various microbial nucleic acids: TLR3, double-stranded RNA; TLR7, single-stranded RNA; and TLR9, unmethylated bacterial DNA. Previously, UNC93B, an endoplasmic reticulum protein predicted to have 12 transmembrane domains, was identified in a genetic screen as essential for signaling by TLR3, TLR7, and TLR9, as well as for antigen presentation by major histocompatibility complexes. Mice carrying the mutation H412R in UNC93B are highly susceptible to infections, and mutations in the encoding gene in humans are associated with susceptibility to viral infections. Brinkmann
et al
. found that wild-type UNC93B and the H412R mutant exhibited different mobilities upon electrophoresis, but both were produced in similar abundance and appeared to be associated with the endoplasmic reticulum based on their sensitivities to glycosidases. Large-scale isolation of tagged UNC93B or the H412R mutant from RAW macrophages, followed by mass spectrometry of proteins that specifically coprecipitated, revealed that the wild-type protein associated with TLR3, TLR7, TLR9, and TLR13. No TLR peptides were identified in the samples of the H412R mutant. Coexpression of tagged TLR3, TLR4, or TLR9, along with tagged UNC93B, showed that UNC93B selectively interacted with TLR3 and TLR9 but not with TLR4. Chimeras in which the transmembrane domains of TLR4 were exchanged with TLR3 or TLR9 showed that the interaction between UNC93B and TLR3 and TLR7 was mediated by the transmembrane domains. (The H412R mutation is in a predicted transmembrane domain of UNC93B.) To confirm that endogenous UNC93B and TLR7 interacted, the two proteins were coprecipitated from bone marrow-derived dendritic cells. Activation of the TLRs by addition of their respective ligands did not alter the interaction with UNC93B; however, the phenotypes associated with the H412R mutation suggest that these intracellular TLRs require the interaction of UNC93B to function properly. The mechanism by which this endoplasmic reticular protein contributes to TLR signaling remains to be determined.

M. M. Brinkmann, E. Spooner, K. Hoebe, B. Beutler, H. L. Ploegh, Y.-M. Kim, The interaction between the ER membrane protein UNC93B and TLR3, 7, and 9 is crucial for TLR signaling.
J. Cell Biol.
177
, 265-275 (2007).
[Abstract]
[Full Text]
Enlisting ERK5 and NF-κB in the G2 to M Transition
Authors: Gough Nancy R.
Published: July 2007

Cude
et al
. noted that when primary cultures of human foreskin cells and smooth muscle cells, as well as transformed HeLa cells, were arrested at M phase of the cell cycle there was an electrophoretic mobility shift (activation) of the kinase ERK5, a member of the mitogen-activated protein kinase family. Further analysis in synchronized HeLa cells showed that ERK5 activity--as well as that of MEK5, the kinase that activates ERK5--increased during G2 and remained high through M phase. Expression of a constitutively active form of MEK5 was sufficient to increase the number of mitotic cells of an asynchronous HeLa cell population, and expression of a dominant-negative ERK5 reduced the number of mitotic cells. Experiments in synchronized cells in which ERK5 activity was inhibited specifically from G2 onward (to avoid interfering with any roles ERK5 may have in the G1 and S phases) confirmed that ERK5 activity was required at the G2 and M stages. Studies in transfected HEK293 cells suggested that after nocodazole treatment to arrest the cells in G2, the transcription factor NF-κB was activated (as measured in reporter gene assays and DNA binding assays), and this was blocked by dominant-negative ERK5. ERK5 did not apparently directly phosphorylate the inhibitor of NF-κB (IκB), nor was the inhibitor of NF-κB kinase (IKK) complex active during G2 and M. Instead, ERK5 colocalized in the nucleus and coimmunoprecipitated with the ribosomal S6 kinase RSK2 in nocodazole-treated HeLa cells arrested in G2-M. RSK2 isolated from nocodazole-treated cells exhibited greater kinase activity toward IκB than that from nonarrested cells. Pharmacological inhibitors of NF-κB were used to show that NF-κB activity was required for progression through mitosis but not DNA replication (S phase). NF-κB stimulates the expression of several genes, the products of which are important for mitosis. Quantitative polymerase chain reaction experiments confirmed that transcripts for cyclin B1 and B2, polo-like kinase-1, and the protein phosphatase Cdc25B were increased at the time of G2 and that the increase in their transcription was blocked if NF-κB activation was inhibited. Thus, ERK5, acting through RSK2, appears to activate NF-κB to drive the expression of genes essential for the completion of mitosis.

K. Cude, Y. Wang, H.-J. Choi, S.-L. Hsuan, H. Zhang, C.-Y. Wang, Z. Xia, Regulation of the G2-M cell cycle progression by the ERK5-NFκB signaling pathway.
J. Cell Biol.
177
, 253-264 (2007).
[Abstract]
[Full Text]
An Antigenic Route Planner
Authors: Simpson Stephen
Published: July 2007

Antigenic peptides are presented to T cells from two sources: proteins generated inside the cell (as in the case of virally infected cells or tumor cells) or from an extracellular pool. In the latter situation, class II major histocompatibility complex (MHC) molecules on antigen-presenting cells (APCs) present peptide fragments to CD4
+
helper T cells, whereas MHC class I molecules display peptides to CD8
+
T cells in a process known as cross-presentation. Burgdorf
et al
. reveal that the two pathways for presenting peptides from the same extracellular antigen are determined by the mode of antigen uptake by the APCs. For class I restricted presentation, surface mannose receptors (MRs) routed antigen to the stable early endosome compartment where peptides could meet MHC class I molecules. In contrast, pinocytosis of the same antigen directed it to the lyosomal compartment for presentation by class II MHC. The findings will help resolve questions about how APCs activate and modulate different arms of the T cell response.

S. Burgdorf, A. Kautz, V. Böhnert, P. A. Knolle, C. Kurts, Distinct pathways of antigen uptake and intracellular routing in CD4 and CD8 T cell activation.
Science
316
, 612-616 (2007).
[Abstract]
[Full Text]
Cdc37 Regulation of the Kinome: When to Hold ‘Em and When to Fold ‘Em
Authors: Karnitz Larry M. , Felts Sara J.
Published: July 2007

Although massive genome sequencing efforts have identified the protein kinases encoded by several eukaryotic genomes and proteomic analyses have begun to determine the kinases expressed in a cell, there is still much to learn about the additional cellular events that shape eukaryotic kinomes. Large-scale analyses in
Saccharomyces cerevisiae
have indicated that a relatively small subset of kinases requires chaperoning by heat shock protein 90 (Hsp90). However, new evidence suggests that most kinases do require chaperoning and, furthermore, that Cdc37, a chaperone that has Hsp90-dependent and -independent functions, serves as the chaperone for a large portion of the yeast kinome.
Dscam Mediates Dendritic Self-Avoidance
Authors: Adler Elizabeth M.
Published: July 2007

Three groups, Soba
et al
., Hughes
et al
., and Matthews
et al
., have implicated
Dscam
in dendritic self-avoidance of dendritic arborization (da) neurons in
Drosophila
larvae. Typically, different branches of the often-elaborate dendritic arborization of a particular neuron avoid contacting each other, a phenomenon called self-avoidance. Similarly, the dendrites of certain classes of neurons avoid those of neurons of the same type (tiling), although they may coexist with dendrites of neurons from different classes (see Kidd and Condron). In insects, the gene
Dscam
(
Down’s syndrome cell adhesion molecule
) can encode 38,016 distinct isoforms, which exhibit isoform-specific homophilic interactions; the particular isoform repertoire expressed in a given neuron is distinct from that of its neighbors (see Zinn).
Dscam
was expressed in all four classes of da neurons; elimination of its activity in individual neurons abrogated dendritic self-avoidance so that sister branches crossed each other and ran in bundles. Expression of single Dscam isoforms rescued self-avoidance, an effect that required the intracellular domain. However, Pak (p21-activated protein kinase), which mediates some downstream effects of Dscam, did not appear to be involved. Overexpression of the same Dscam isoform in neurons that would not otherwise avoid each other elicited avoidance of neighboring dendrites. Indeed, overexpression of a common Dscam isoform across classes or in all da neurons or expression of a single isoform in all da neurons of
Dscam
mutant larvae led to interclass dendritic avoidance. In contrast to its effects on self-avoidance, loss of Dscam function in these neurons failed to affect tiling in class III and IV da neurons. Moreover, mutation of components of a signaling pathway implicated in tiling failed to affect self-avoidance in class I, II, and III da neurons or dendritic bundling in class IV da neurons. All three groups concluded that the mechanisms involved in
Drosophila
dendritic self-avoidance are distinct from those that mediate tiling, with Dscam playing a critical role in self-avoidance. Diversity of Dscam isoforms may enable individual neurons to distinguish their own dendrites from those of their neighbors and respond appropriately.

M. E. Hughes, R. Bortnick, A. Tsubouchi, P. Bäumer, M. Kondo, T. Uemura, D. Schmucker, Homophilic Dscam interactions control complex dendrite morphogenesis.
Neuron
54
, 417-427 (2007).
[Online Journal]

P. Soba, S. Zhu, K. Emoto, S. Younger, S.-J. Yang, H.-H. Yu, T. Lee, L. Y. Jan, Y.-N. Jan,
Drosophila
sensory neurons require Dscam for dendritic self-avoidance and proper dendritic field organization.
Neuron
54
, 403-416 (2007).
[Online Journal]

B. J. Matthews, M. E. Kim, J. J. Flanagan, D. Hattori, J. C. Clemens, S. L. Zipursky, W. B. Grueber, Dendrite self-avoidance is controlled by
Dscam
.
Cell
129
, 593-604 (2007).
[Online Journal]

T. Kidd, B. Condron, Avoiding the SCAMs.
Neuron
54
, 350-352 (2007).
[Online Journal]

K. Zinn, Dscam and neuronal uniqueness.
Cell
129
, 455-456 (2007).
[Online Journal]
The Regulation of Nuclear Membrane Permeability by Ca
2+
Signaling: A Tightly Regulated Pore or a Floodgate?
Authors: Török Katalin
Published: July 2007

The nuclear pore complex functions both to separate and to connect the nucleus and the cytoplasm. Minute-to-minute changes in gene expression depend on rapid translocation of transcription factors and other regulatory proteins from the cytosol into the nucleus. However, a controversy exists as to whether cell signaling allows large molecules to enter the nucleus through tightly regulated facilitated transport or by the opening of a floodgate. A recent report suggesting that some hormones increase nuclear permeability through changes in intracellular Ca
2+
concentration has reignited this debate. Here, I consider both the basic permeability of the nuclear membrane under resting conditions and the effects of Ca
2+
on the permeability of the nuclear pore. I discuss facilitated transport through the nuclear pore complex, with particular attention to the nuclear transport of Ca
2+
-CaM signaling complexes. Finally, I weigh the arguments in favor of a generic increase in permeability versus stimulation of facilitated transport as possible mechanisms for mediating cell signaling to the nucleus.
Regaining the Lost Past
Authors: Adler Elizabeth M.
Published: July 2007

People with Alzheimer’s disease or related neurodegenerative disorders may progress from absentmindedness and difficulty learning new things to a heartbreaking state in which they forget their own past and no longer recognize the faces of people they love. Expression of p25 (a truncated form of the p35 regulatory subunit of cyclin-dependent kinase 5) is associated with various neurodegenerative disorders, and the CK-p25 Tg mouse, in which p25 expression--and thereby neuronal loss--can be conditionally regulated, is a model for these disorders. Fischer
et al
. found that exposing CK-p25 Tg mice to an enriched environment (after neuronal loss had occurred and learning was impaired) improved their associative and spatial learning. Moreover, environmental enrichment led to the recovery of long-term memories that had apparently been lost. Experiments in wild-type mice revealed that exposure to an enriched environment stimulated histone acetylation in the hippocampus and cortex. The histone deacetylase (HDAC) inhibitor sodium butyrate (SB) improved associative and spatial learning in wild-type and CK-p25 Tg mice (after p25 induction) and, like environmental enrichment, enhanced dendritic and synaptic growth in CK-p25 Tg mice without affecting brain atrophy or neuronal loss. Furthermore, SB enabled the recovery of lost memories. The authors conclude that their data raise the possibility that HDAC inhibitors may provide a means to enable people with neurodegenerative disorders associated with memory loss to recover lost memories. Sweatt provides thoughtful commentary, noting (as do the authors) that HDAC inhibitors may affect the acetylation status of proteins other than histones.

A. Fischer, F. Sananbenesi, X. Wang, M. Dobbin, L. H. Tsai, Recovery of learning and memory is associated with chromatin remodelling.
Nature
447
, 178-182 (2007).
[PubMed]

J. D. Sweatt, Down memory lane.
Nature
447
, 151-152 (2007).
[PubMed]
Regenerating Hair Follicles
Authors: Adler Elizabeth M.
Published: July 2007

Compared with newts and salamanders, adult humans (like other mammals) have a limited ability to regenerate tissues lost to injury, and the loss of adult hair follicles--complex structures comprising at least 10 cell types--has been considered permanent. Ito
et al.
observed structures that resembled early developing hair follicles in healing skin wounds in mice. Hair follicle neogenesis, which occurred in adult mice after injuries that resulted in healed wounds 0.25 cm
2
or larger, was associated with expression of the same genes and proteins found during embryonic follicle development. Lineage analysis indicated that, rather than arising from existing hair follicle stem cells, the newly generated follicles arose from extrafollicular epidermal cells or infundibular cells (cells from the upper portion of the follicle, outside of the follicle stem cell niche). The new follicles proliferated and produced unpigmented hair and appeared to reestablish a hair follicle stem cell population. Wnt signaling has been implicated in hair follicle development, and expression of the Wnt inhibitor Dkk1 prevented hair follicle neogenesis, but not re-epithelialization. Similarly, deletion of epidermal
Ctnnb1
(which encodes β-catenin) prior to injury blocked the formation of new hair follicles. In contrast, epidermal overexpression of Wnt7a enhanced wound-dependent hair follicle regeneration. Following injury, the processes of repair and regeneration often appear to compete (see Chuong); thus, the authors suggest that modulating Wnt signaling in wounds could provide a means of decreasing scarring and of treating alopecia.

M. Ito, Z. Yang, T. Andl, C. Cui, N. Kim, S.E. Millar, G. Cotsarelis, Wnt-dependent
de novo
hair follicle regeneration in adult mouse skin after wounding.
Nature
447
, 316-320 (2007).
[PubMed]

C. M. Chuong, New hair from healing wounds.
Nature
447
, 265-266 (2007).
[PubMed]
Seeing the Light
Authors: Vinson Valda
Published: July 2007

For organisms to adapt to environmental changes, external signals must affect protein function. Proteins in the PAS (Per-Arnt-Sim) superfamily are involved in transducing diverse external signals, but it has been a challenge to define the signaling pathways. Zoltowski
et al
. have determined crystal structures for the dark- and light-activated states of a fungal photoreceptor. Light-induced chemical changes at the active center propagate to large-scale conformational changes at the protein N terminus that are essential for cellular function.

B. D. Zoltowski, C. Schwerdtfeger, J. Widom, J. J. Loros, A. M. Bilwes, J. C. Dunlap, B. R. Crane, Conformational switching in the fungal light sensor Vivid.
Science
316
, 1054-1057 (2007).
[Abstract]
[Full Text]
Parsing the Motion of Single Molecules: A Novel Algorithm for Deconvoluting the Dynamics of Individual Receptors at the Cell Surface
Authors: Ghosh Indraneel , Wirth Mary J.
Published: July 2007

To truly understand signal transduction, we will ultimately need to understand the dynamics and kinetics of individual proteins as they perform their functions in a single cell. Groundbreaking advances in single-molecule biophysics now allow us to follow the motion of many individual proteins on the cell surface with the use of fluorescent probes, such as quantum dots. However, discriminating the directed movement of single molecules from their natural Brownian motion remains a challenge. A recent paper provides a powerful statistical approach for distinguishing periods of directed motion of individual γ-aminobutyric acid (GABA) receptors from periods during which they undergo Brownian motion. This new methodology should help single-molecule researchers determine the dynamics of individual proteins participating in signaling cascades.
Nuclear Shut Off of NF-κB
Authors: Gough Nancy R.
Published: July 2007

Shutting off proinflammatory gene expression activated by the transcription factor nuclear factor κB (NF-κB) is an important part of resolving the inflammatory response. Although it is known that termination of NF-κB activity involves proteasomal degradation, Tanaka
et al
. report identification of the E3 ubiquitin ligase as the PDZ and LIM domain-containing protein PDLIM2 and that degradation occurs in the subnuclear structures called PML bodies. Activation of mouse embryo fibroblasts (MEFs) or a macrophage cell line with lipopolysaccharide (LPS) in the presence of a proteasome inhibitor lead to the accumulation of polyubiquitinated p65 subunit of NF-κB in an insoluble nuclear fraction. PDLIM2 coimmunoprecipitated with p65 when transfected into human embryonic kidney 293 cells and inhibited NF-κB-mediated reporter gene expression. Transfection of cells with both tagged p65 and PDLIM2 lacking the PDZ domain or lacking the LIM domain showed that the LIM domain was required for ubiquitination and degradation but not for trafficking of the p65 to the insoluble fraction. To prevent the rapid degradation of p65 that occurred in cells overexpressing PDLIM2, the authors assessed the subnuclear localization of p65 in cells expressing the LIM-deficient version PDLIM2. p65 accumulated in structures that were stained with antibodies that detected promyelocytic leukemia protein (so-called PML bodies) or components of the proteasome. The PDZ domain-lacking mutant did not alter p65 distribution, and despite efficient polyubiquitination, p65 was not degraded, which suggests that trafficking to the PML bodies was essential for degradation and required the PDZ domain of PDLIM2. In the reporter gene assay, the PDZ domain-lacking mutant partially inhibited NF-κB activity, and the mutant lacking the LIM domain retained full inhibitory activity, which suggests that sequestration of p65 in the PML even in the absence of ubiquitination is sufficient to inhibit NF-κB activity. Finally, compared with wild-type animals,
Pdlim2
knockout mice exhibited increased sensitivity to LPS-induced shock. T cells (CD11c
+
) from the knockout animals showed increased nuclear p65 and increased production of proinflammatory cytokines (IL-6 and IL-12p40).

T. Tanaka, M. J. Grusby, T. Kaisho, PDLIM2-mediated termination of transcription factor NF-κb activation by intranuclear sequestration and degradation of the p65 subunit.
Nat. Immunol.
8
, 584-591 (2007).
[PubMed]
R-spondins Signal Like Wnts, Sort Of
Authors: Ray L. Bryan
Published: July 2007

Wnt proteins are lipid-modified secreted molecules that initiate signaling by interacting with a receptor complex that includes the serpentine receptor Frizzled and low-density lipoprotein receptor—related protein 5 (LRP5) or LRP6. Wnt receptor activation leads to stabilization of β-catenin, which accumulates in the nucleus and activates transcription of Wnt target genes. Roof plate-specific spondins (R-spondins) are proteins unrelated in sequence to Wnts that, like Wnts, are implicated in regulation of development and that also activate signaling through β-catenin. Conflicting reports have been published as to whether R-spondins use the same receptors as Wnts and whether they bind to Frizzled or LRP6, both, or neither. Wei
et al
. present data showing that human R-spondin1 (hRspo1) binds to cultured human embryonic kidney (HEK293T) cells transfected with LRP6. Solid-phase binding assays showed that hRspo1 bound to the extracellular domain of LRP6 with high affinity (K
d
, 1.2 nM) but showed little if any binding to Frizzled. The hRspo1 protein also induced phosphorylation of LRP6 (as does Wnt). hRspo1 had synergistic effects with Wnt3A on phosphorylation of LRP6 in HEK293T cells and on phosphorylation of endogenous LRP6 in mouse embryo fibroblasts. R-spondins thus appear to work differently from Wnts in some ways (Wnts bind with high affinity to Frizzled, with weak or no binding to LRP6), but both ligands activate similar downstream signaling events. Furthermore, expression of R-spondins is stimulated by Wnts, leading the authors to propose that R-spondins may act in a positive feedback loop that reinforces Wnt signaling during development.

Q. Wei, C. Yokota, M. V. Semenov, B. Doble, J. Woodgett, X. He, R-spondin1 is a high affinity ligand for LRP6 and induces LRP6 phosphorylation and β-catenin signaling.
J. Biol. Chem.
282
, 15903-15911 (2007).
[Abstract]
[Full Text]
High-Sensitivity Detection and Quantitative Analysis of Native Protein-Protein Interactions and Multiprotein Complexes by Flow Cytometry
Authors: Schrum Adam G. , Gil Diana , Dopfer Elaine P. , Wiest David L. , Turka Laurence A. , Schamel Wolfgang W. A. , Palmer Ed
Published: July 2007

Most mechanisms of cell development, physiology, and signal transduction are controlled by protein-protein interactions. Immunoprecipitation of multiprotein complexes detected by flow cytometry (IP-FCM) is a means to quantitatively measure these interactions. The high sensitivity of this method makes it useful even when very little biomaterial is available for analysis, as in the case of rare primary cell subsets or patient samples. Detection of the T cell antigen receptor associated with the CD3 multiprotein complex from as few as 300 primary murine T cells is presented as an example. The method is compatible with quantitative flow cytometry techniques, making it possible to estimate the number of coimmunoprecipitated molecules. Both constitutive and inducible protein-protein interactions can be analyzed, as illustrated in related methodology using glutathione
S
-transferase–fusion protein pull-down experiments. IP-FCM represents a robust, quantitative, biochemical technique to assess native protein-protein interactions, without requiring genetic engineering or large sample sizes.
Shore Up That Wall!
Authors: Gough Nancy R.
Published: July 2007

Single-celled and multicellular organisms must control metabolic flux in response to changing cellular and organismal needs. For example, will glucose be used to create ATP, to synthesize glycogen, to generate NADPH, or to glycosylate lipids and proteins? Disruption of these processes underlies diseases such as diabetes and obesity. Smith and Rutter found a pathway in
Saccharomyces cerevisiae
controlling glucose partitioning from cell wall synthesis to glycogen storage. The kinases Psk1 and Psk2 (Psk1/2) phosphorylate UDP-glucose pyrophosphorylase (Ugp1), which is a key enzyme in producing UDP-glucose for either glycogen (energy storage) or glucan (cell wall synthesis). Yeast deficient in both Psk1 and Psk2 activity or expressing a mutant version of Ugp1 in which the phosphorylated serine is replaced by alanine (Ugp1-S11A) exhibit defective growth on galactose, increased glycogen content per cell, and decreased sensitivity to a toxin that binds to β-(1,6)-glucan. Although phosphorylation did not alter the catalytic activity of Ugp1, lack of Psk1/2 activity or expression of the Ugp1-S11A mutant resulted in the loss of one population of Ugp1. In wild-type yeast, there are two populations of Ugp1, corresponding to the phosphorylated (isoform 1) and the nonphosphorylated (isoform 2) forms that were readily separated by anion exchange chromatography, and these two forms exhibit differences in conformation based on their differences in sensitivity to proteases and different proteolysis profiles. Yeast that did not produce isoform 2 showed altered sensitivity to various chemicals that cause cell wall stress. The authors propose that phosphorylation alters the cellular distribution of Ugp1 from the cytosol (for glycogen synthesis) to the cell membrane (for cell wall synthesis). Forced localization of Ugp1 to the plasma membrane rescued the Psk1/2-deficient cells from inability to grow on galactose and reduced glycogen content and restored β-(1,6)-glucan content per cell to levels similar to those in wild-type yeast.

T. L. Smith, J. Rutter, Regulation of glucose partitioning by PAS kinase and Ugp1 phosphorylation.
Mol. Cell
26
, 491-499 (2007).
[PubMed]
Not Like Peas in a Pod
Authors: Zahn Laura
Published: July 2007

Legumes, such as peas and beans, have residing within nodules in their roots symbiotic bacteria that fix atmospheric nitrogen. The rhizobial symbiont produces signaling molecules, the so-called Nod factors, that are recognized by the plant. Giraud
et al
. (see the Perspective by Downie) report the complete genomic sequences of two photosynthetic
Bradyrhizobium
strains that produce nodules in their host plant roots but lack the
nodABC
genes and Nod factors. Instead, during this atypical symbiosis, a purine derivative may act as a signal molecule to trigger root nodule organogenesis.

E. Giraud, L. Moulin, D. Vallenet, V. Barbe, E. Cytryn, J.-C. Avarre, M. Jaubert, D. Simon, F. Cartieaux, Y. Prin, G. Bena, L. Hannibal, J. Fardoux, M. Kojadinovic, L. Vuillet, A. Lajus, S. Cruveiller, Z. Rouy, S. Mangenot, B. Segurens, C. Dossat, W. L. Franck, W.-S. Chang, E. Saunders, D. Bruce, P. Richardson, P. Normand, B. Dreyfus, D. Pignol, G. Stacey, D. Emerich, A. Verméglio, C. Médigue, M. Sadowsky, Legumes symbioses: Absence of
Nod
genes in photosynthetic Bradyrhizobia.
Science
316
, 1307-1312 (2007).
[Abstract]
[Full Text]

J. A. Downie, Infectious heresy.
Science
316
, 1296-1297 (2007).
[Summary]
[Full Text]
Signaling Central
Authors: Purnell Beverly
Published: July 2007

Wnt growth factors activate a signaling cascade that plays a key role in animal development, stem cell biology, and human cancer. Although many of the cascade components have been identified, how they come together to transmit the signal from the plasma membrane inside the cell is not clear. Bilić
et al
. show that Wnt ligands induce formation of large, ribosome-sized complexes, termed the low-density lipoprotein receptor-related protein 6 (LRP6) signalosome at the plasma membrane. The large protein assemblies contain activated Wnt receptors and cytoplasmic adaptor proteins. The scaffold protein Dishevelled and the Wnt co-receptor LRP6 play a central role in LRP6-signalosome formation, triggering subsequent molecular interactions that regulate the level of nuclear β-catenin.

J. Bilić, Y.-L. Huang, G. Davidson, T. Zimmermann, C.-M. Cruciat, M. Bienz, C, Niehrs, Wnt induces LRP6 signalosomes and promotes Dishevelled-dependent LRP6 phosphorylation.
Science
316
, 1619-1622 (2007).
[Abstract]
[Full Text]