Copy Link
Add to Bookmark
Report
dictyNews Volume 38 Number 31
dictyNews
Electronic Edition
Volume 38, number 31
December 7, 2012
Please submit abstracts of your papers as soon as they have been
accepted for publication by sending them to dicty@northwestern.edu
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
=========
A new social gene in Dictyostelium discoideum, chtB
Lorenzo A. Santorelli, Adam Kuspa, Gad Shaulsky,
David C. Queller & Joan E. Strassmann
BMC Evolutionary Biology, in press
Background
Competitive social interactions are ubiquitous in nature, but their
genetic basis is difficult to determine. Much can be learned from
single gene knockouts in a eukaryote microbe. The mutants can be
competed with the parent to discern the social impact of that specific
gene. Dictyostelium discoideum is a social amoeba that exhibits
cooperative behavior in the construction of a multicellular fruiting
body. It is a good model organism to study the genetic basis of
cooperation since it has a sequenced genome and it is amenable to
genetic manipulation. When two strains of D. discoideum are mixed,
a cheater strain can exploit its social partner by differentiating more
spore than its fair share relative to stalk cells. Cheater strains can be
generated in the lab or found in the wild and genetic analyses have
shown that cheating behavior can be achieved through many
pathways.
Results
We have characterized the knockout mutant chtB, which was isolated
from a screen for cheater mutants that were also able to form normal
fruiting bodies on their own. When mixed in equal proportions with
parental strain cells, chtB mutants contributed almost 60% of the total
number of spores. To do so, chtB cells inhibit wild type cells from
becoming spores, as indicated by counts and by the wild type cellsÕ
reduced expression of the prespore gene, cotB. We found no obvious
fitness costs (morphology, doubling time in liquid medium, spore
production, and germination efficiency) associated with the cheating
ability of the chtB knockout.
Conclusions
In this study we describe a new gene in D. discoideum, chtB, which
when knocked out inhibits the parental strain from producing spores.
Moreover, under lab conditions, we did not detect any fitness costs
associated with this behavior.
Submitted by Lorenzo Santorelli [lorenzo.santorelli@zoo.ox.ac.uk]
---------------------------------------------------------------------------
GenColors-based comparative genome databases for small
eukaryotic genomes.
Felder M, Romualdi A, Petzold A, Platzer M, Shnel J, Glckner G.
Nucleic Acids Research database issue
Many sequence data repositories can give a quick and easily
accessible overview on genomes and their annotations. Less
widespread is the possibility to compare related genomes with
each other in a common database environment. We have previously
described the GenColors database system
(http://gencolors.fli-leibniz.de) and its applications to a number of
bacterial genomes such as Borrelia, Legionella, Leptospira and
Treponema. This system has an emphasis on genome comparison.
It combines data from related genomes and provides the user with
an extensive set of visualization and analysis tools. Eukaryote
genomes are normally larger than prokaryote genomes and thus
pose additional challenges for such a system. We have, therefore,
adapted GenColors to also handle larger datasets of small eukaryotic
genomes and to display eukaryotic gene structures. Further recent
developments include whole genome views, genome list options and,
for bacterial genome browsers, the display of horizontal gene transfer
predictions. Two new GenColors-based databases for two fungal
species (http://fgb.fli-leibniz.de) and for four social amoebas
(http://sacgb.fli-leibniz.de) were set up. Both new resources open up
a single entry point for related genomes for the amoebozoa and fungal
research communities and other interested users. Comparative
genomics approaches are greatly facilitated by these resources.
Submitted by Gernot Gloeckner [gernot.gloeckner@uni-koeln.de]
---------------------------------------------------------------------------
dictyBase 2013: Integrating Multiple Dictyostelid species
Siddhartha Basu, Petra Fey, Yogesh Pandit, Robert Dodson,
Warren A. Kibbe, Rex L. Chisholm
Nucleic Acids Research database issue 2013
dictyBase (http://dictybase.org) is the model organism database for the
social amoeba Dictyostelium discoideum. This contribution provides
an update on dictyBase that has been previously presented. During the
past three years, dictyBase has taken significant strides toward
becoming a genome portal for the whole Amoebozoa clade. In its
latest release, dictyBase has scaled up to host multiple Dictyostelids,
including Dictyostelium purpureum (Sucgang et al. 2011, Genome
biology, 12, R20.), Dictyostelium fasciculatum, and Polysphondylium
pallidum (Heidel et al. 2011, Genome research 21(11) 1882-91).
The new release includes a new Genome Browser with RNA-Seq
expression, interspecies BLAST alignments and a unified BLAST
search for cross-species comparisons.
Submitted by Petra Fey [pfey@northwestern.edu]
==============================================================
[End dictyNews, volume 38, number 31]
