Analysis of Fox genes in Schmidtea mediterranea reveals new families and a conserved role of Smed-foxO in controlling cell death

Abstract

The forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa clade, and specifically from planarians, which are a unique model for understanding development, due to the striking plasticity of the adult. The aim of this study was to identify and perform evolutionary and functional studies of the Fox genes of lophotrochozoan species and, specifically, of the planarian Schmidtea mediterranea. Generating a pipeline for identifying Forkhead domains and using phylogenetics allowed us the phylogenetic reconstruction of Fox genes. We corrected the annotation for misannotated genes and uncovered a new family, the QD, present in all metazoans. According to the new phylogeny, the 27 Fox genes found in Schmidtea mediterranea were classified into 12 families. In Platyhelminthes, family losses were accompanied by extensive gene diversification and the appearance of specific families, the A(P) and N(P). Among the newly identified planarian Fox genes, we found a single copy of foxO, which shows an evolutionary conserved role in controlling cell death.

Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping

“…Strikingly, a recent example of 3D-DS under physiological conditions has been observed in the FoxP subfamily of transcription factors. Fox proteins are present in yeast and metazoans, and several evolutionary analyses have strongly suggested that these proteins were present in the ancestor of all eukaryotes [ 19 , 20 ]. Their absence in plants suggests that their origin is linked to a clade of unicellular organisms that gave rise to both the fungal and animal lineages [ 21 ].…”

“…This increased diversity is reflected in the number of Fox proteins in different lineages from this branch, with mammalian genomes presenting at least 34 distinct Fox orthologs whereas only four genes are present in fungi [ 19 ]. In this regard, it has been suggested that the expansion of this protein family is the result of several duplications followed by loss and diversification events through multiple metazoan lineages during evolution [ 20 ]. This is the case for the emergence of the FoxS subfamily in the mammal and bird lineage divergence due to a duplication of a Fox gene from the original cluster present in basal Bilateria [ 24 ], which comprises the FoxC, FoxF, FoxL1, and FoxQ1 subfamilies [ 22 ].…”

FoxK1 is Required for Ectodermal Cell Differentiation During Planarian Regeneration

“…In a previous study, we identified 3 paralogs within the FoxK family in S. mediterranea ( foxK1-2-3 ) ( Pascual-Carreras et al, 2021 ). In this study, we have inhibited the three foxK genes by RNAi, showing that RNAi of foxk1 generates the strongest phenotype ( Figure 1A ) ( Supplementary Figure S1A ).…”

“…Forkhead box (Fox) genes belong to the “winged helix” superfamily of transcription factors, showing a Forkhead DNA-binding domain. Over 2,000 Fox proteins, phylogenetically classified into 25 families (A to S), have been identified in a number of species of fungi and metazoans ( Benayoun, Caburet, and Veitia 2011 ; Pascual-Carreras et al, 2021 ). Fox genes control essential processes such as cell death, cell cycle and cell differentiation during all stages of development and in adult tissues, although many members show a tissue/stage-specific expression and function ( Benayoun, Caburet, and Veitia 2011 ).…”

“…Previous studies of Fox genes function in planarians have demonstrated their evolutionary conserved role, and provided new data about their cellular function ( Scimone, Lapan, and Reddien 2014 ; Vogg et al, 2014 ; He et al, 2017 ; Scimone et al, 2018 ). For instance, foxA was found to be essential for the maintenance of the pharynx and endodermal tissues ( Koinuma et al, 2000 ; Adler et al, 2014 ) and foxO showed a conserved role in regulating metabolism during planarian regeneration and homeostasis ( Pascual-Carreras et al, 2021 ). In a recent study, we identified 3 foxK paralogs in the genome of the planarian species S. mediterranea ( Smed foxK-1-2-3 ).…”