The evolution of animals involved acquisition of an emergent gene repertoire
for gastrulation. Whether loss of genes also co-evolved with this developmental
reprogramming has not yet been addressed. Here, we identify twenty-four genetic
functions that are retained in fungi and choanoflagellates but undetectable in
animals. These lost genes encode: (i) sixteen distinct biosynthetic functions;
(ii) the two ancestral eukaryotic ClpB disaggregases, Hsp78 and Hsp104, which
function in the mitochondria and cytosol, respectively; and (iii) six other
assorted functions. We present computational and experimental data that are
consistent with a joint function for the differentially localized ClpB
disaggregases, and with the possibility of a shared client/chaperone
relationship between the mitochondrial Fe/S homoaconitase encoded by the lost
LYS4 gene and the two ClpBs. Our analyses lead to the hypothesis that the
evolution of gastrulation-based multicellularity in animals led to efficient
extraction of nutrients from dietary sources, loss of natural selection for
maintenance of energetically expensive biosynthetic pathways, and subsequent
loss of their attendant ClpB chaperones.Comment: This is a reformatted version from the recent official publication in
PLoS ONE (2015). This version differs substantially from first three arXiV
versions. This version uses a fixed-width font for DNA sequences as was done
in the earlier arXiv versions but which is missing in the official PLoS ONE
publication. The title has also been shortened slightly from the official
publicatio