dictyNews

Electronic Edition

Volume 49, number 14

May 25, 2023



Please submit abstracts of your papers as soon as they have been

accepted for publication by sending them to [log in to unmask]

or by using the form at

http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit.



Back issues of dictyNews, the Dicty Reference database and other

useful information is available at dictyBase - http://dictybase.org.



Follow dictyBase on twitter:

http://twitter.com/dictybase





=========

Abstracts

=========





The Dictyostelium discoideum genome lacks significant DNA methylation 

and uncoverspalindromic sequences as a source of false positives

in bisulfite sequencing



Robert A. Drewell 1,*, Tayla C. Cormier1, Jacob L. Steenwyk 1,2, James 

St. Denis1,Javier F. Tabima1, Jacqueline M. Dresch1 and Denis A. Larochelle





NAR Genomics and Bioinformatics, Volume 5, Issue 2, June 2023, lqad035, 

https://doi.org/10.1093/nargab/lqad035



DNA methylation, the addition of a methyl (CH3)group to a cytosine residue, 

is an evolutionarily conserved epigenetic mark involved in a number of different 

biological functions in eukaryotes, including transcriptional regulation, chromatin 

structural organization, cellular differentiation and development. In the social 

amoeba Dictyostelium, previous studies have shown the existence of a DNA 

methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and 

function of 5-methylcytosine in the genome are unclear. Here, we present the 

whole genome DNA methylation profile of Dictyostelium discoideum using deep 

coverage replicate sequencing of bisulfite-converted gDNA extracted from 

poststarvation cells. We find an overall very low number of sites with any 

detectable level of DNA methylation, occurring at significant levels in only 

303–3432 cytosines out of the ~ 7.5 million total cytosines in the genome 

depending on the replicate. Furthermore, a knockout of the DNMA enzyme 

leads to no overall decrease in DNA methylation. Of the identified sites, 

significant methylation is only detected at 11 sites in all four of the methylomes 

analyzed. Targeted bisulfite PCR sequencing and computational analysis 

demonstrate that the methylation profile does not change during development 

and that these 11 cytosines are most likely false positives generated by protection 

from bisulfite conversion due to their location in hairpin-forming palindromic DNA 

sequences. Our data therefore provide evidence that there is no significant DNA 

methylation in Dictyostelium before fruiting body formation and identify a 

reproducible experimental artifact from bisulfite sequencing.





Submitted by Denis Larochelle [[log in to unmask]]

_________________________________________________________





The social amoeba Dictyostelium discoideum rescues Paraburkholderia hayleyella, 

but not P. agricolaris, from interspecific competition



James M. Medina, David C. Queller, Joan E. Strassmann, Justine R. Garcia





FEMS Microbiology Ecology, accepted



Bacterial endosymbionts can provide benefits for their eukaryotic hosts, but it is 

often unclear if endosymbionts benefit from these relationships. The social amoeba 

Dictyostelium discoideum associates with three species of Paraburkholderia 

endosymbionts, including P. agricolaris and P. hayleyella. These endosymbionts can 

be costly to host but are beneficial in certain contexts because they allow 

D. discoideum to carry prey bacteria through the dispersal stage. In experiments 

where no other species are present, P. hayleyella benefits from D. discoideum while 

P. agricolaris does not. However, the presence of other species may influence this 

symbiosis. We tested if P. agricolaris and P. hayleyella benefit from D. discoideum in 

the context of resource competition with Klebsiella pneumoniae, the typical laboratory 

prey of D. discoideum. Without D. discoideum, K. pneumoniae depressed the growth 

of both Paraburkholderia symbionts, consistent with competition. P. hayleyella was 

more harmed by interspecific competition than P. agricolaris. We found that 

P. hayleyella was rescued from competition by D. discoideum while P. agricolaris was 

not. This may be because P. hayleyella is more specialized as an endosymbiont; it 

has a highly reduced genome compared to P. agricolaris and may have lost genes 

relevant for resource competition outside of its host.





Submitted by Justine Garcia  [[log in to unmask]]

========================================================

[End dictyNews, volume 49, number 14]