JCB biowrites

In Memoriam: Alan Hall

There's a new issue of JCB out today. We'll bring you a roundup of the issue's research highlights tomorrow, but, today, we'd like to focus on our tribute to JCB’s Editor-in-Chief Alan Hall. As many of you know, Alan passed away unexpectedly a few weeks ago. To commemorate his life and scientific legacy, this issue contains two memorials.  The first is an account from Alan’s close friend and early collaborator, Chris Marshall, of the start of Alan’s independent scientific career and the events that led to his seminal discoveries and to him becoming the great cell biologist we knew.  The second is a touching tribute from several of Alan’s friends and colleagues.  Their sentiments are echoed by the JCB staff; Alan was on the Editorial Board for 20 years and Editor-in-Chief for too short a period of time.  We can take some small measure of solace in knowing that Alan’s kind and generous spirit will live on through his remarkable scientific legacy.  As we all struggle to express how we feel about his sudden passing and what he meant to us and the community, I created a word cloud (on www.tagul.com) based on key words used to describe Alan in his tribute.  I think this visual summary says it all.  

New issue: February 16th 2015

In the latest issue of JCB, Mourier et al. reveal that the mitochondrial fusion protein Mitofusin 2 is required to maintain production of the respiratory chain cofactor coenzyme Q. As explained here, deleting Mitofusin 2 downregulates several components of the terpenoid biosynthetic pathway that synthesizes key precursors of coenzyme Q. Supplementing Mitofusin 2-deficient cells with the coenzyme partially restores mitochondrial function, suggesting that this approach could ameliorate the symptoms of patients with diseases, such as Charcot-Marie-Tooth type 2A, that are caused by mutations in the Mitofusin 2 gene.

Klebba and Galletta et al. reveal that the scaffold protein Asterless regulates centriole duplication by controlling turnover of the kinase Plk4. Asterless’ role in centriole duplication was thought to be limited to recruiting Plk4 to centrioles during mitosis. But Klebba and Galletta et al. now show that, in part through a newly identified Plk4-binding site, Asterless stabilizes the kinase during mitosis while promoting its turnover during interphase. More here.

Fennell et al. demonstrate that centromeres can stand in for telomeres to promote assembly of the fission yeast meiotic spindle. During meiotic prophase, the clustering of telomeres near the spindle pole body (the yeast equivalent of the centrosome) helps this structure insert into the nuclear envelope and assemble a bipolar spindle. As summarized in this article, Fennell et al. show that, in the absence of telomere clustering, centromeric chromatin can perform the same function as telomeres by contacting spindle pole bodies and promoting the recruitment of the inner nuclear membrane SUN protein Sad1.

Two papers by Comrie et al. (here and here) describe how actin functions on both sides of the immunological synapses that form between T cells and antigen-presenting cells. As summarized in this week’s In Focus, the researchers find that actin helps immobilize ICAM-1 on the surface of antigen-presenting dendritic cells. By binding to the T cell integrin LFA-1, immobilized ICAM-1 resists the forces exerted by the T cell’s actin cytoskeleton, generating tension that promotes LFA-1’s conversion to an active, high-affinity conformation that enhances T cell activation.

And Johnson et al. reveal that filopodial protrusions initiate and orient lamellipodia at the leading edge of migrating fibroblasts, helping the cells to navigate gradients of immobilized guidance cues. Senior author Jason Haugh describes his lab's results in more detail in this month’s biosights video podcast, available below or on iTunes.

And finally for today, I’d like to point you in the direction of our latest article celebrating JCB’s 60^th anniversary. I’ll let our reviews editor, Priya Prakash Budde, explain more:

JCB has a rich history of publishing groundbreaking cell biology, some of which we are highlighting to commemorate our 60th anniversary.  But we are not content to rest on our laurels; as part of our celebrations, we have asked cell biologists and scientists straddling other disciplines to provide their perspective on what is cell biology today and where it is going. These articles will cover some prominent topics such as the integration of the physical sciences with cell biology, as well as take a moment to reflect on some aspects that have been lost.  For example, today’s article from Graham Warren reminds us that many of cell biology’s breakthroughs were discovered in unusual model organisms, and our quest for molecular mechanism has come at the expense of exploring the remarkable cellular diversity in nature.  As other experts comment on a variety of topics from technology development to synthetic cell biology, we hope that their diverse opinions will further convince you of the relevance of cell biology and how it extends far beyond the cell.  Stay tuned this year as we take turns to look back and look forward. We hope you enjoy the ride!

 

Cover image of mitochondria (magenta) in a cardiomyocyte lacking Mitofusin 2 © 2015 Mourier et al.

 

New issue: November 11th 2013

Time for a quick roundup of today’s new issue of JCB.

Briguglio et al. investigate how different classes of cargo proteins are sorted into mucocysts, secretory granules found in the ciliate protozoan Tetrahymena thermophila.  The researchers find that sortilins, better known as receptors that transport hydrolase enzymes to lysosomes, also deliver soluble, non-aggregating cargo proteins to mucocysts. In contrast, self-aggregating cargo proteins are still sorted to mucocysts in the absence of sortilins, but, as described in this week’s In Focus, they aren’t processed to their mature, secretion-ready forms due to the mislocalization of cathepsin proteases.

Stephens et al. reveal that the chromatin-organizing proteins condensin and cohesin crosslink the pericentromeres of budding yeast chromosomes to coordinate their dynamics during mitosis. In metaphase, the pericentric chromatin surrounding each centromere forms a spring that resists the microtubule-based forces pulling chromosomes toward the spindle poles. By crosslinking the pericentromeres of different chromosomes, condensin and cohesin, along with the kinesin motor cin8, may help to distribute tension across multiple microtubule attachment sites. More here.

Hou et al. describe how neurons activate the protein phosphatase PP1 in response to synaptic stimulation. By reducing the function of active synapses, PP1 promotes a type of synaptic plasticity called long-term depression. Hou et al. show that the neuron-specific cyclin-dependent kinase Cdk5 phosphorylates and inhibits PP1. But synaptic stimulation triggers the degradation of the Cdk5 activator p35, so that PP1 can dephosphorylate and activate itself. As discussed here, the researchers also report a key role for the PP1 regulator Inhibitor-2.

Espenel et al. describe how a FRET-based biosensor can be used to track the activity of a kinesin motor protein in living cells. The researchers show that the active form of kinesin KIF17, which promotes epithelial cell polarization, accumulates on stable microtubules at the cell periphery through the combined actions of Protein Kinase C and the microtubule plus-end binding protein EB1. You can learn more here.

Zhang et al. demonstrate that the submembranous cytoskeleton formed by βII-spectrin acts as a barrier to organize axonal membranes. You can learn more in this commentary by Eshed-Eisenbach and Peles, and you can listen to the study’s senior author, Matthew Rasband, discuss his lab’s results in this month’s neurobiology-themed biobytes podcast, where you can also hear Nicolas Morel discuss his lab’s recent paper describing the function of V-ATPase in regulating neurotransmitter release.

And, sticking with the neurobiology theme, this issue sees the last in our series of “Cell biology in neuroscience” reviews. I’ll let our reviews editor, Priya Prakash Budde, wrap things up:

We finish our series on ‘cell biology in neuroscience’ (for an introduction to the series, see here) with two excellent reviews.  The first, from Dekkers, Nikoletopoulou and Barde, is on cell death in the brain, which focuses on how components of cell death pathways contribute to synaptic function, as well as to degeneration in response to injury.  We then end the series with a fascinating review from Megan Corty and Marc Freeman on the role that glia and cell-cell communication play in shaping the nervous system.  In addition to clearing neuronal debris in the brain, glia play instructive roles in brain development and, as the review discusses, control neuron number and connectivity. 

The entire collection of reviews is freely available here.  But if you are attending the annual ASCB meeting in New Orleans this December, please stop by the JCB booth and pick up our ‘Cell Biology in Neuroscience’ special issue, which has all seven reviews in the series plus highlights of some of the exciting research we have published this year, both in neuroscience and across the breadth of cell biology. 

Cover image of mucocysts (green) in a Tetrahymena cell © 2013 Briguglio et al.

EMBO 2013: Tales from the crypt

The Keynote lecture on Day 3 was from Hans Clevers, who is director of, and runs a lab at, the Hubrecht Institute in Utrecht and is also President of the Royal Netherlands Academy of Arts and Sciences.  Clevers gave an amazing presentation of his lab’s work on intestinal stem cells that was accompanied by movie-quality animations that really helped visualize the significance of his results.  The intestinal epithelium has very interesting morphology: we all know about villi and their importance in digestion but in between the villi are ‘crypts’, narrow tunnels at the bottom of which lie the intestine’s stem cells.   Each crypt makes 200 cells/day so this is a very active stem cell compartment. It has to be because the cells of this epithelium must be replaced every 4-5 days.  Defining the stem cell population in the crypt has been challenging and the subject of much controversy.  Clevers’ lab has made great strides in this area using sophisticated genetic engineering techniques that allow them to mark and manipulate single cells in the mouse intestine (for a great review on lineage tracing in epithelia, click here).  They identified a population of columnar epithelial cells at the bottom of the crypt, positive for the marker Lgr5 (see figure), that give rise to all the cell types of the intestine.  The surrounding Paneth cells serve as the niche for these stem cells. They isolated these Lgr5-positive cells, figured out the conditions to grow them in vitro and found, amazingly, that these single cells could grow into ‘miniguts’ with the right tissue morphology.  They then introduced these miniguts into mice and found that they attached only to damaged epithelia (which occurs for example with ulcers) and sealed the lesion, without any occurrence of adenomas.  These miniguts have great therapeutic potential;  Clevers showed that they can grow miniguts from intestinal stem cells isolated through patient biopsies and test the efficacy of drugs on this pseudotissue.  For example, they have used the miniguts to monitor CFTR channel function and test cystic fibrosis drugs.  I found this to be a very inspiring talk:  this lab came to this field through a long standing interest in Wnt signaling and now are actively exploring the therapeutic potential of their findings.  It really was a tour-de-force example of how basic cell biology can lead to more clinical applications.

Schematic of crypt © 2009 Van Keymeulen et al.

New issue: September 2nd 2013

In the latest issue of JCB, Hung et al. reveal how cells use different mechanisms to migrate through large or small spaces. The authors demonstrate that, in spacious surroundings, cell movement depends on the small GTPase Rac1, which inhibits myosin II and stimulates membrane protrusion. In confined spaces, however, Rac1 is inactive and cell migration is driven by myosin II activity. You can learn how the focal adhesion protein paxillin controls this switch in this week’s In Focus.

Huntwork-Rodriguez et al. describe a positive feedback loop involving the kinases JNK and DLK that promotes neuronal apoptosis in response to injury. JNK phosphorylation stabilizes DLK, which, in turn, enhances JNK activation, allowing the damage signal to spread and reach the neuronal cell body. More here.

And Worth et al. reveal how the cyclin-dependent kinase Cdk5 activates a protein called drebrin, which organizes actin filaments and links them to microtubules in neuronal growth cones. As explained here, the researchers show that Cdk5 phosphorylation triggers a conformational change in drebrin that uncovers the protein’s actin-bundling domains.

Meanwhile, Yi et al. describe how T cells move their centrosomes to the immunological synapse that connects them to antigen-presenting cells via a biphasic process involving the dynein-dependent capture and depolymerization of microtubules. Senior author John Hammer discusses his lab’s work in this month’s biosights video podcast. (You can watch below or subscribe in iTunes). And if you think you might like to present this paper in your next journal club, don’t forget you can download everything you need in our Journal Club Pack here.

And finally, a quick note from the JCB's reviews editor, Priya Prakash Budde, about our latest review series, which kicks off in today's new issue...

In this issue, we debut the first review of the series that we will package into a special issue for distribution at the annual ASCB meeting. This year, the series is on 'cell biology in neuroscience', which covers the cell biology underlying various topics in brain development, function and homeostasis. The first review from Jonathan Cooper is on cell migration in the developing nervous system.  One of the great feats in brain development is the long range migration that neurons undergo to get to their final destination.  Cooper does a wonderful job of describing the cellular basis of how neurons perform this migration.  Two key issues described in the review are that there are some unique aspects to the machinery used by neurons to migrate, and that neurons display a remarkable diversity in their modes of migration.  It is a really well-written, accessible review that brings out both unifying themes and important distinctions in how cell migration occurs in these cells.  

In the issues leading up to the ASCB meeting, we will publish the other reviews in the series that will cover the cellular basis of axon growth, guidance, synapse formation, synaptic plasticity, cell death in the brain and on the role of glia in neuronal development.  In covering this range of topics, what struck me is that the reviews cover quintessential cell biological phenomena, such as cell migration, cell polarity, cytoskeletal dynamics, signaling in subcellular compartments, interactions between cells and the extracellular environment, cell death and cell-cell communication.  So there is something for every cell biologist in the series and we hope you enjoy it.  

Last, I want to thank former JCB editorial board member Josh Sanes, and JCB's Senior Editor Louis Reichardt for their invaluable help in crystallizing the topics and authors for this series.

That's all for today, but you can find plenty more interesting papers listed on our table of contents page here.

Cover image of dorsal root ganglion neurons lacking the ubiquitin ligase PHR1 stained for phosphorylated JNK © 2013 Huntwork-Rodriguez et al. 

New issue: March 19th

In today's new issue of JCB, Sarkar and Zohn reveal that the ubiquitin ligase Hectd1 restricts the migration of cranial mesenchyme cells by inhibiting secretion of the protein chaperone Hsp90. Excess extracellular Hsp90 enhances the motility of Hectd1-deficient cells, potentially explaining why Hectd1-mutant mouse embryos have an abnormally organized cranial mesenchyme and neural tube closure defects. You can read more in this week's In Focus.

Byrd et al. describe how a microRNA fine-tunes a cell's response to ER stress. The researchers identify a microRNA called miR-30C-2*, which is upregulated when ER function is compromised and which targets the mRNA encoding XBP1, a key transcription factor that boosts ER capacity and cell survival. Blocking miR-30C-2* leads to increased XBP1 levels and enhanced cell survival in response to ER stress. More here.

And Roux et al. report a new way to screen for protein-protein interactions. Proximity-dependent biotin identification, or BioID, involves tagging proteins of interest with a promiscuous bacterial biotin ligase. When the resulting fusion protein is expressed in mammalian cells, nearby proteins are biotinylated, allowing them to be purified and identified by mass spectrometry. Roux et al. tested their approach with the nuclear lamina protein Lamin-A and identified both known Lamin-A interacting proteins and a novel nuclear envelope protein called SLAP75. Senior author Kyle Roux explains some of the advantages of this new approach here.

Today also sees the release of our latest biosights video podcast, in which Johan de Rooij discusses his lab's recent paper (Huveneers et al.) describing how the remodeling of endothelial intercellular adhesions takes place at a specialized subset of adhesions called focal adherens junctions. These adhesions recruit the mechanosensory protein Vinculin to resist tension from the actomyosin cytoskeleton and avoid excessive disruption when the junctions transiently remodel in response to angiogenic growth factors and inflammatory cytokines. You can watch the video below, or subscribe in iTunes. (And remember, if you'd like to present this paper to your colleagues in a journal club, you can download everything you need - including a pdf of the paper and a PowerPoint file of all the figures - by clicking here to download our monthly Journal Club Pack).

And, finally for today, this issue's review by Richard Hynes on the evolution of the extracellular matrix is the last in our Evolution series (all articles are freely available here).  I'll let our reviews editor, Priya Prakash Budde, give you a quick series recap:

We have gotten a lot of great feedback on the series that started last summer with the evolution of membrane architecture (with a superbly funny title) from Field, Sali and Rout.  This was followed by the evolution of cadherins from Oda and Takeichi.  Masatoshi Takeichi discovered cadherins so it was a particular pleasure to have him write this article.  Next up Carvalho-Santos et al. traced the origins of centrioles, cilia, and flagella; this article was even mentioned in Carl Zimmer's blog The Loom.  We then moved on to the evolution of the cytoskeleton from Wickstead and Gull, and the nucleus from Wilson and Dawson.  The penultimate article in the series, from Rojas et al., was the evolution of the Ras superfamily-a heroic effort analyzing this huge family of proteins.  All of the articles use the amazing power of comparative genomics to provide a 'big picture' conceptual view of these topics.  One of the authors even said that writing the article made them think differently about their research.  I can't think of a better testimonial than that!  So, please check out the series and let us know what you think.

Lots of other interesting papers in today's new issue as well. You can find them all on our table of contents, by clicking here.

Cover image courtesy of Anjali Sarkar.

 

 

 

 

 

Cell Biology This Week

Just a brief post this week.  A recent paper (Miyamoto et al.) points to a requirement for nuclear actin polymerization during oocyte reprogramming by the transcription factor Oct4.  The authors had noticed an enrichment of nuclear actin-regulatory proteins in their analysis of proteins that enhance reprogramming in Xenopus oocytes.  To examine the role of actin further, they transplanted mouse nuclei into Xenopus oocytes and, using a probe to visualize filamentous actin, found that there was a large amount of actin polymerization in the nuclei.  Blocking actin polymerization by a variety of methods interfered with reprogramming stimulated by the pluripotency factor Oct4.  What regulates actin polymerization in the nucleus?  The authors focused on actin nucleators described to be present in the nucleus and found that Toca-1 overexpression enhanced Oct4’s activity.  Nuclear actin is known to be important in chromatin remodeling and this function might be how it affects Oct4-dependent reprogramming.

 

For details on this series of posts, click here.

Cell Biology This Week

A new study points to a function for a VEGF receptor in neurogenesis.  In the brain, neural stem cells, which are glial cells, exist in a vascularized niche in the subventricular zone (SVZ).  VEGFs have been shown to stimulate neurogenesis though their receptors and target cells have not been clarified.  Here, Calvo et al. examine the role of VEGF-C and its receptor VEGFR3 in neural stem cells in the SVZ.  First, they show that VEGFR3 is expressed by neural stem cells and the VEGF-C ligand is expressed in these and surrounding cells.  They then isolate VEGFR3+ cells and showed that they had properties of neural stem cells in vitro and that these properties were enhanced significantly in the presence of VEGF-C.  Specifically, VEGF-C stimulated the ability of these cells to divide.  The authors then went back to an in vivo setting and overexpressed VEGF-C in the adult mouse SVZ.  This promoted neurogenesis by increasing the survival of SVZ cells and cell cycle entry of neural stem cells.  These effects seem independent of angiogenesis and were dependent on the receptor VEGFR3.  Axon guidance molecules have been shown to be crucial for angiogenesis and this study shows that angiogenic molecules are important for neurogenesis.  It will be interesting to determine the events downstream of the receptor in neural stem cells to see if they are the same as those involved in vessel formation.

 

There is a lot of buzz about how obesity is linked to chronic inflammation and how both lead to insulin resistance and Type II diabetes.  Now, Wen et al. show that saturated fatty acids like palmitate that are part of a high-fat diet can activate the NLRP3 inflammasome.  The inflammasome is a multiprotein complex that causes activation of caspase-1 to promote the processing and release of inflammatory cytokines like IL-1beta.  IL-1beta interferes with normal insulin signaling thereby leading to insulin resistance.  Specific signaling events include the inactivation of the kinase AMPK by palmitate, which dysregulates autophagy and causes generation of mitochondrial reactive oxygen species to activate the inflammasome.  I found this paper interesting because it provides a somewhat direct route from the ingestion of a high-fat diet to inflammation and insulin resistance.

 

For details on this series of posts, click here.

Cell Biology This Week

Several papers in the last couple of weeks on neuronal cell biology have caught my eye.  In the first, Amato et al. show that the kinase AMPK contributes to neuronal polarization.  This paper shows that activation of AMPK blocks polarization and axon growth.  AMPK phosphorylates the kinesin Kif5, blocking its association with PI3K and thereby preventing PI3K accumulation at the axon tip, an event necessary for polarization.  The reason I thought this was interesting is because AMPK is a cellular energy sensor and the paper therefore connects the process of axon initiation with energy homeostasis.  Elucidating the upstream signaling events should shed light on this interesting connection.

Next, Uytterhoeven et al. uncover some interesting cell biology that could be occurring at the synapse by analyzing a fly mutant called Skywalker.  Skywalker encodes a GTPase activating protein (GAP) for Rab35 that seems to be involved in trafficking of synaptic vesicles to endosomes at the fly neuromuscular junction.  This route seems to be important for removing or recycling ubiquitinated synaptic proteins in the mutants.  It will be interesting to determine whether this pathway is important in a wildtype situation. 

Lastly, two papers point to a role for beta-adducin in synaptic plasticity in both flies and mice.  Adducins cap the barbed ends of actin filaments and link them to the spectrin cytoskeleton.  Pielage et al. show that at the fly neuromuscular junction, adducin promotes synapse stability and growth.   Using a combination of genetic and biochemical assays, the authors propose that by stabilizing the spectrin cytoskeleton, adducin promotes synapse stability and by capping actin filaments, it promotes synaptic growth.  In mice, Bednarek and Caroni show that beta-adducin is important for synapse remodeling by promoting both disassembly and subsequent re-assembly during conditions that stimulate learning and memory.

For details on this series of posts, click here.

Cell Biology This Week

The first cut may be the deepest but the final cut seems to be the hardest to grasp.  At least in the case of cytokinesis.  Contraction of an actomyosin ring narrows the connection between the two dividing cells to form an intercellular bridge. How this bridge is resolved is still a matter of debate.  Many mechanisms have been proposed for this last step of cytokinesis.  For example, in some organisms, vesicle fusion at the site of constriction is thought to contribute the membrane that enables cell separation.  Now, Guizetti et al. propose a new mechanism: membrane scission by ESCRT-III helical filaments.  Using GFP-labeled alpha tubulin, the authors examined microtubules at the intercellular bridge in HeLa cells.  They noticed that microtubules partially disassembled on one side of the bridge, on the same side as the midbody (the remnant of the central spindle that asymmetrically localizes to the constriction site).  This partial disassembly occurred coincident with abscission.  Using correlative live-cell and transmission electron microscopy, the authors noticed electron dense membrane ripples adjacent to the midbody (first observed in a very old JCB paper!) in the zone where the microtubules had disassembled. 

Black lines indicate electron-dense ridges at the intercellular bridge prior to abscission.  From Mullins and Biesele (1977).

Guizetti et al. show that the microtubule severing enzyme spastin is important for microtubule disassembly at the constriction site.  Furthermore, ESCRT-III, which is known to localize to the intercellular bridge and is essential for abscission, was enriched at the constriction zone (whereas actin and vesicles were not).  The electron-dense ripples at the constriction zone were absent in cells depleted of an ESCRT-III subunit.  ESCRT-III is targeted to the intercellular bridge by CEP55, a centrosomal protein, and ALIX, an ESCRT-related protein, both of which localize to the midbody at the time of abscission.  Electron tomography of the constriction zone in HeLa cells revealed cortical filaments perpendicular to the microtubule bundles.  These filaments formed single or intertwined helices across the intercellular bridge and were absent in cells depleted of the ESCRT-III complex by RNAi.  The authors proposed that these helical filaments are composed of ESCRT-III and that this complex provides the contractile force to deform the membrane.  This is in line with ESCRT-III function in other contexts.  Whether ESCRT-III is the molecular component of these helices and whether this mechanism occurs in vivo still remains to be shown.   Despite these major unresolved issues, the cutting-edge microscopy and interesting results make this paper worth checking out.

 

In brief, two other papers caught my eye this week.  In the first, Puneet et al. show that you can take a pathogenic molecule that is used to subvert the host immune system and exploit it to the potential benefit of the host.  Sepsis, which is a major health threat, occurs when the human body undergoes a tremendous inflammatory reaction in response to an infection.  The parasitic nematode, Acanthocheilonema viteae, produces a molecule called ES-62 that dampens the host innate immune system.  ES-62 downregulates signaling by TLR4 and TLR2—pattern-recognition receptors that recognize pathogenic molecules (TLR4, for example, recognizes the bacterial outer membrane protein lipopolysaccharide).  The authors show that ES-62 dampens these pathways by targeting MyD88—an adaptor of both of these pattern-recognition receptors—for degradation via the autophagosome (for more about autophagy and the immune system see review by Saitoh and Akira).  Importantly, when administered to mice before or after induction of sepsis, the molecule protected the majority of mice from sepsis-induced death.  The potential therapeutic benefits of these results could be quite promising. 

 

The second paper is about how ERK/MAP kinase controls lamellipodial protrusion during cell migration.  It was known previously that ERK was important for adhesion disassembly by phosphorylating the focal adhesion components FAK, Paxillin and MLCK.  Now, Mendoza et al. show that ERK localizes to the leading edge and phosphorylates and activates the WAVE2 regulatory complex (WAVE2 and Abi) that activates the actin nucleation complex Arp2/3.  Thus, this kinase that can respond to extracellular signals coordinates both focal adhesion disassembly and lamellipodial protrusion, two key events in cell migration.

 

For details on this series of posts, click here.