dictyNews

Electronic Edition

Volume 45, number 20

August 16, 2019



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Abstracts

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Living on soup: macropinocytic feeding in amoebae



Robert R. Kay, Thomas D. Williams, James D. Manton, David Traynor 

& Peggy Paschke



MRC Laboratory of Molecular Biology, Francis Crick Avenue, 

Cambridge CB2 0QH, UK





Int J Dev Biol, Special Edition 

edited by Ricardo Escalante & Elena Cardenal, in press



Macropinocytosis is used by a variety of amoebae for feeding on liquid 

medium. The amoebae project cups and ruffles from their plasma 

membrane, driven by actin polymerization, and eventually fuse these 

back to the membrane, entrapping droplets of medium into internal 

vesicles. These vesicles are of up to several microns in diameter and 

are processed through the lysosomal digestive system to extract 

nutrients. Recognizably the same process is used in metazoan cells for 

a number of medically important purposes, including the pathological 

growth of cancer cells. We describe the discovery of macropinocytosis 

in Dictyostelium amoebae, its genetic regulation by the NF1 RasGAP, 

and the tools available for its investigation. Work on Dictyostelium over 

the last 30 years has identified many genes that may be important for 

macropinocytosis, which are listed at dictyBase, and give a basis for 

mechanistic studies. We argue that the actin cytoskeleton is organized 

for macropinocytosis by a signalling patch of PIP3 and active Ras and 

Rac, together with their regulatory proteins and effectors, including the 

protein kinases Akt and SGK. The Scar/WAVE complex is recruited to 

the periphery of this patch, triggering the formation of a hollow ring of 

protrusive actin polymerization, and eventually a macropinocytic cup. 

Major problems to be addressed include: the dynamics sustaining 

macropinocytic patches and the mechanism of Scar/WAVE recruitment; 

the mechanisms of cup closure and of membrane fusion; the ecological 

situations where amoebae feed by macropinocytosis; and the evolutionary 

relationship between macropinocytosis and growth factor signalling.





submitted by:  Rob Kay [[log in to unmask]]

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dictyBase and the Dicty Stock Center Version 2 - a Progress Report



Petra Fey, Robert J. Dodson, Siddhartha Basu, Eric C. Hartline, 

Rex L. Chisholm



Northwestern University, Chicago, IL, USA.





Int J Dev Biol, Special Edition 

edited by Ricardo Escalante & Elena Cardenal, in press



After serving the Dictyostelium community for many years, the first 

version of dictyBase (Chisholm et al. 2006; Fey et al. 2006) was in 

need of a decisive update. The original dictyBase software was not 

adaptable to more current demands such as handling the import of 

large-scale data from recently sequenced genomes, keeping up with 

changes in the Gene Ontology (GO), or handling the automatic 

annotation of over 20,000 new strains. Therefore, we have embarked 

on a complete overhaul of dictyBase. The new infrastructure will allow 

the introduction of new data, such as more expressive GO annotations 

and Dictyostelium disease orthologs. A modern user interface aims to 

streamline usage of the database including orders from the Dicty Stock 

Center (DSC). New displays will allow novel views including the 

combination of data in two new tools. With the underlying software 

infrastructure now in place, dictyBase software engineers and curators 

are currently adding the user interfaces, new tools and content pages 

for the evolving Version 2 of dictyBase. This review highlights the 

emerging status of the new dictyBase, updated pages and annotations 

that will soon be available in the new environment, an overview of our

 annotation procedures, and plans to involve the community in curation 

 efforts. 





submitted by:  Petra Fey  [[log in to unmask]]

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[End dictyNews, volume 45, number 20]