dictyNews

Electronic Edition

Volume 47, number 14

June 25, 2021



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Abstracts

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Transcriptional milestones in Dictyostelium development



Mariko Katoh-Kurasawa, Karin Hrovatin, Shigenori Hirose, 

Amanda Webb, Hsing-I Ho, Blaž Zupan and Gad Shaulsky



Department of Molecular and Human Genetics, Baylor College of 

Medicine, Houston, TX, 77030 USA

Faculty of Computer and Information Science, University of 

Ljubljana, SI-1000 Ljubljana, Slovenia





Genome Research, accepted 



The manuscript is available at 

https://www.biorxiv.org/content/10.1101/2021.05.27.445976v1 

and the data are available for exploration on dictyExpress.



Dictyostelium development begins with single-cell starvation 

and ends with multicellular fruiting bodies. Developmental 

morphogenesis is accompanied by sweeping transcriptional 

changes, encompassing nearly half of the 13,000 genes in the 

genome. We performed time-series RNA-sequencing analyses of 

the wild type and 20 mutants to explore the relationships between 

transcription and morphogenesis,. These strains exhibit 

developmental arrest at different stages, accelerated development, 

or atypical morphologies. Considering eight major morphological 

transitions, we identified 1,371 milestone genes whose expression 

changes sharply between consecutive transitions. We also identified 

1,099 genes as members of 21 regulons, which are groups of genes 

that remain coordinately regulated despite the genetic, temporal, 

and developmental perturbations. The gene annotations in these 

groups validate known transitions and reveal new developmental 

events. For example, DNA replication genes are tightly co-regulated 

with cell division genes, so they are expressed in mid-development 

even though chromosomal DNA is not replicated. Our dataset 

includes 486 transcriptional profiles that can help identify new 

relationships between transcription and development and improve 

gene annotations. We demonstrate its utility by showing that cycles 

of aggregation and disaggregation in allorecognition-defective 

mutants involve dedifferentiation. We also show sensitivity to 

genetic and developmental conditions in two commonly used actin 

genes, act6 and act15, and robustness of the coaA gene. Finally, 

we propose that gpdA is a better mRNA quantitation standard 

because it is less sensitive to external conditions than commonly 

used standards. The dataset is available for democratized 

exploration through the web application dictyExpress and the 

data mining environment Orange.





submitted by: Gad Shaulsky [[log in to unmask]]

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Macropinocytosis: biology and mechanisms



Robert R. Kay



MRC Laboratory of Molecular Biology Francis Crick Avenue

Cambridge CB2 0QH, UK





Cells & Development, in press



Macropinocytosis is a form of endocytosis performed by ruffles and 

cups of the plasma membrane. These close to entrap droplets of 

medium into micron-sized vesicles, which are trafficked through the 

endocytic system, their contents digested and useful products 

absorbed. Macropinocytosis is constitutive in certain immune cells 

and stimulated in many other cells by growth factors. It occurs 

across the animal kingdom and in amoebae, implying a deep 

evolutionary history. Its scientific history goes back 100 years, but 

increasingly work is focused on its medical importance in the immune 

system, cancer cell feeding, and as a backdoor into cells for viruses 

and drugs. Macropinocytosis is driven by the actin cytoskeleton whose 

dynamics can be appreciated with lattice light sheet microscopy: this 

revealsa surprising variety of routes for forming macropinosomes. In 

Dictyostelium amoebae, macropinocytic cups are organized around 

domains of PIP3 and active Ras and Rac in the plasma membrane. 

These attract activators of the Arp2/3 complex to their periphery, 

creating rings of actin polymerization that shape the cups. The size 

of PIP3 domains is by RasGAPs, such as NF1, and the lipid 

phosphatase, PTEN. It is likely that domain dynamics determine 

the shape, evolution and closing of macropinocytic structures.





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

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[End dictyNews, volume 47, number 14]