Evaluation of ciliobrevins paper

I have evaluated the following paper for Faculty of 1000:

Small-molecule inhibitors of the AAA+ ATPase motor cytoplasmic dynein.
AJ Firestone, JS Weinger,…, TM Kapoor, JK Chen Nature 2012 Mar 18
PMID 22425997 DOI 10.1038/nature10936

The F1000 evaluation can be found here (£/€/$): http://f1000.com/14237961

This paper identifies and characterizes a series of small molecule inhibitors of the dynein motor. This work is significant as this represents only the second example of selective targeting of a member of the AAA+ ATPase family by a selective small molecule inhibitor, the first being inhibition of p97 by DBeQ {1}. These ‘ciliobrevins’ are benzoyl dihydroquinazolinone derivatives and are identified as inhibitors of dynein in an assay of Hedgehog (Hh) signalling, which occurs through primary cilia. The small molecules effectively block Hh signalling and localization of Arl13b to primary cilia (an assay for primary cilia formation). When cilia are formed, these ciliobrevins cause an accumulation of cargo (such as IFT88) at the distal tip, consistent with a defect in retrograde transport within the cilia. Dynein-2 is known to be the motor for retrograde transport along the ciliary axoneme. Together, these data indicate effective inhibition of dynein-2 function. These reagents have the potential to elucidate the role of dynein-2 in the very early stages of cilia formation. The authors also demonstrate that the ciliobrevins inhibit the more widely used motor dynein-1, effectively validating this in assays of mitotic spindle function, organelle motility, and in vitro assays. Further data are entirely consistent with the ciliobrevins competing for ATP binding and thereby inhibiting the ATPase activity of the motor. Specificity, it is shown by comparative analysis with a number of other AAA+ ATPases. Given that crystallography has achieved high resolution structures of p97 and the dynein motor, one might also expect some key atomic structures that could define why these compounds are selective in each case.

Please note that this is a distinct nomenclature to that of ‘ciliabrevin’, used previously for another inhibitor of cilia function {2}.

{1} Chou et al. Proc Natl Acad Sci U S A 2011, 108:4834-9 [PMID:21383145].
{2} Engel et al. Cytoskeleton 2011, 68:188-203 [PMID:21360831].


F1000 evaluation: ER Cargo Properties Specify a Requirement for COPII Coat Rigidity Mediated by Sec13p

I have just evaluated the following paper from Faculty of 1000:

ER Cargo Properties Specify a Requirement for COPII Coat Rigidity Mediated by Sec13p.

Alenka Čopič, Catherine F. Latham, Max A. Horlbeck, Jennifer G. D’Arcangelo, Elizabeth A. Miller
Science 2012
PMID 22300850
DOI 10.1126/science.1215909

This fascinating paper defines a link between structural features of an assembling vesicle coat complex with the cargo to be incorporated. Sec13 is an essential component of the COPII coat that drives export of secretory cargo from the endoplasmic reticulum (ER). The requirement for this gene can be bypassed by a series of suppressor mutations in mutants known as Bypass-Sec13 (Bst) (first identified by Chris Kaiser’s lab {1}). The authors took a genetic approach in yeast (using synthetic gene arrays) to identify all of the genes that alleviate the defects caused by loss of Sec13. As in the previous work from Kaiser et al., Miller and colleagues found that all identified genes relate to the synthesis and export of glycosylphosphatidylinositol (GPI)-anchored proteins from the ER. This provides a direct link between the presence of cargo in the inner leaflet (where GPI-anchored proteins reside) and the role of the coat complex on the cytosolic face of the membrane in the formation of vesicles. It was hypothesized that the absence of these cargo proteins from the sites of vesicle formation leads to more readily deformable membranes, eliminating the need for Sec13, the conclusion here being that Sec13 is required to enhance rigidity of the COPII coat to drive membrane deformation under normal conditions. Using a series of elegant mutations in Sec13 and its binding partner Sec31, the authors show quite convincingly that this model of structural rigidity holds true. The finding that Sec13 is required in this way also provides some insight into the apparent selective requirement for Sec13 in the secretion of procollagen (see ref {2}, on which I appear as an author). The structural rigidity of the procollagen triple helix might dictate the requirement for similar structural rigidity within the assembling COPII coat.


{1} Elrod-Erickson and Kaiser, Mol Biol Cell 1996, 7:1043-58 [PMID:8862519].

{2} Townley et al. J Cell Sci 2008, 121:3025-34 [PMID:18713835].


The original evaluation can be found here.

F1000 evaluation

I have evaluated the following article for Faculty of 1000.

Sec24p and Sec16p cooperate to regulate the GTP cycle of the COPII coat.
Kung LF, Pagant S, Futai E, D’Arcangelo JG, Buchanan R, Dittmar JC, Reid RJ, Rothstein R, Hamamoto S, Snapp EL, Schekman R, Miller EA.
EMBO Journal
DOI 10.1038/emboj.2011.444
PMID 22157747

This is a very nice set of data that show convincingly that Sec16 impacts on the Sar1-GTPase cycle during COPII coat assembly at the endoplasmic reticulum (ER) membrane. There are considerable nuances within the data set likely to be of major interest to COPII aficionados but, overall, this work gives some key insight into the control of vesicle formation by the COPII coat. The [http://f1000.com/13567956#eval14951056 Jon Audhya] evaluation describes this paper perfectly.

Additional comment: I don’t post the evaluation from Jon Audhya here. Jon highlights how this paper provides core mechanistic insight into COPII-dependent secretion through coupling the function of Sec16 to that of Sar1. This provides another piece of the puzzle in our understanding of Sec16 function. Bottom line: it is an interesting paper for those of us in this area. Read it!

Liz Miller also has a very intriguing Science paper recently published which I will comment on here once I have had time to read it properly.

F1000 evaluation: DCDC5 linking dynein and Rab8

I have evaluated the following paper for Faculty of 1000. The evaluation is also available on their site at: http://f1000.com/13459956

Linking cytoplasmic dynein and transport of Rab8 vesicles to the midbody during cytokinesis by the doublecortin domain-containing 5 protein.

A Kaplan, O Reiner

J Cell Sci 2011 Dec 1 124 Pt 23:3989-4000 PMID 22159412 DOI 10.1242/jcs.085407

This paper shows that the doublecortin domain-containing 5 protein (DCDC5) is expressed selectively during mitosis to link Rab8-positive vesicles to cytoplasmic dynein. This link is important for the completion of cytokinesis, presumably to drive post-Golgi trafficking to the midbody. The data show that DCDC5 interacts with both Rab8 and its exchange factor Rabin8 as well as dynein, potentially providing a link between dynein coupling and Rab8 activation. This work provides a simple and clearly defined role for this protein and highlights a cell-cycle specific mechanism used to link membranes to microtubules. In addition to the many ways that are used to link membranes to motors in interphase, this work provides a nice example of mitotic regulation of motor coupling through control of expression of the linker protein.

F1000 evaluations

Towards the end of last year I was reading some Casey Bergman about why they left Faculty of 1000. Casey’s post is here: http://caseybergman.wordpress.com/2011/12/16/goodbye-f1000-hello-faculty-of-a-million/. A primary driver here is the lack of open access and I do have some sympathy with this point of view. However, this also reminded me that as a F1000 contributor, I am free to post my evaluations on my site. This is now what I will do here going forwards. I have no other affiliation to F1000 and many of the caveats raised in Casey’s blog post apply to me. I do not evaluate all articles I find appealing – I just don’t have time. I do try to get out those which make me think in a different way or remind me of important concepts that others might also benefit from a reminder about. As with the rest of this blog – we’ll see how this works out.