Evolutionarily dynamic roles of a PUF RNA‐binding protein in the somatic development of Caenorhabditis briggsae

Abstract

Gene duplication and divergence has emerged as an important aspect of developmental evolution. The genomes of Caenorhabditis nematodes encode an ancient family of PUF RNA-binding proteins. Most have been implicated in germline development, and are often redundant with paralogs of the same sub-family. An exception is Cbr-puf-2 (one of three Caenorhabditis briggsae PUF-2 sub-family paralogs), which is required for development past the second larval stage. Here, we provide a detailed functional characterization of Cbr-puf-2. The larval arrest of Cbr-puf-2 mutant animals is caused by inefficient breakdown of bacterial food, which leads to starvation. Cbr-puf-2 is required for the normal grinding cycle of the muscular terminal bulb during early larval stages, and is transiently expressed in this tissue. In addition, rescue of larval arrest reveals that Cbr-puf-2 also promotes normal vulval development. It is expressed in the anchor cell (which induces vulval fate) and vulval muscles, but not in the vulva precursor cells (VPCs) themselves. This contrasts with the VPC-autonomous repression of vulval development described for the Caenorhabditis elegans homologs fbf-1/2. These different roles for PUF proteins occur even as the vulva and pharynx maintain highly conserved anatomies across Caenorhabditis, indicating pervasive developmental system drift (DSD). Because Cbr-PUF-2 shares RNA-binding specificity with its paralogs and with C. elegans FBF, we suggest that functional novelty of RNA-binding proteins evolves through changes in the site of their expression, perhaps in concert with cis-regulatory evolution in target mRNAs.

From “the Worm” to “the Worms” and Back Again: The Evolutionary Developmental Biology of Nematodes

“…Surprisingly, however, complete elimination of Cbr-puf-2 activity alone (via a deletion mutation) leads to a fully penetrant larval arrest. Subsequent studies revealed this was due to a defect in pharyngeal development, apparently related to the brief expression of Cbr-puf-2 in three pharyngeal muscle cells ( Liu and Haag 2014 ). This suggests that the PUF protein family may spin off paralogs as they acquire novel roles outside of the germ line, an example of the neofunctionalization process thought to favor retention of otherwise redundant gene copies ( Lynch et al 2001 ).…”

“…Gene duplication and divergence can also underlie DSD, as exemplified by C. briggsae puf-2 . Though Cbr-PUF-2 shares the same RNA-binding properties as its closest paralogs, it alone is required for pharyngeal development ( Liu and Haag 2014 ). This is true even as the pharynx itself has not changed in any obvious way.…”

Evolution and Developmental System Drift in the Endoderm Gene Regulatory Network of Caenorhabditis and Other Nematodes

“…Importantly, functional diversification of duplicate genes can also drive rapid changes in developmental programs and DSD (True and Haag, 2001;Haag et al, 2018). For example, the C. briggsae translational regulator PUF (PUmilio and FBF)-2 plays a non-redundant role in pharynx and vulva development, in addition to promoting gametogenesis, the sole known role of its paralog PUF-1.2 and its homologs in C. elegans (Liu et al, 2012;Liu and Haag, 2014). Although morphologically invariant, the molecular mechanisms underlying vulva development vary across nematodes (Sommer and Sternberg, 1994;Félix et al, 2000;Dichtel-Danjoy and Félix, 2004;Zheng et al, 2005;Félix, 2007), which may, at least partly, have been caused by DSD resulting from gene duplication.…”