The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons

WRKY and GCM1 are metal chelating DNA-binding domains (DBD) which share a four stranded fold. Using sensitive sequence searches, we show that this WRKY–GCM1 fold is also shared by the FLYWCH Zn-finger domain and the DBDs of two classes of Mutator-like element (MULE) transposases. We present evidence that they share a stabilizing core, which suggests a possible origin from a BED finger-like intermediate that was in turn ultimately derived from a C2H2 Zn-finger domain. Through a systematic study of the phyletic pattern, we show that this WRKY–GCM1 superfamily is a widespread eukaryote-specific group of transcription factors (TFs). We identified several new members across diverse eukaryotic lineages, including potential TFs in animals, fungi and Entamoeba. By integrating sequence, structure, gene expression and transcriptional network data, we present evidence that at least two major global regulators belonging to this superfamily in Saccharomyces cerevisiae (Rcs1p and Aft2p) have evolved from transposons, and attained the status of transcription regulatory hubs in recent course of ascomycete yeast evolution. In plants, we show that the lineage-specific expansion of WRKY–GCM1 domain proteins acquired functional diversity mainly through expression divergence rather than by protein sequence divergence. We also use the WRKY–GCM1 superfamily as an example to illustrate the importance of transposons in the emergence of new TFs in different lineages

Amphioxus FGF signaling predicts the acquisition of vertebrate morphological traits

FGF signaling is one of the few cell–cell signaling pathways conserved among all metazoans. The diversity of FGF gene content among different phyla suggests that evolution of FGF signaling may have participated in generating the current variety of animal forms. Vertebrates possess the greatest number of FGF genes, the functional evolution of which may have been implicated in the acquisition of vertebrate-specific morphological traits. In this study, we have investigated the roles of the FGF signal during embryogenesis of the cephalochordate amphioxus, the best proxy for the chordate ancestor. We first isolate the full FGF gene complement and determine the evolutionary relationships between amphioxus and vertebrate FGFs via phylogenetic and synteny conservation analysis. Using pharmacological treatments, we inhibit the FGF signaling pathway in amphioxus embryos in different time windows. Our results show that the requirement for FGF signaling during gastrulation is a conserved character among chordates, whereas this signal is not necessary for neural induction in amphioxus, in contrast to what is known in vertebrates. We also show that FGF signal, acting through the MAPK pathway, is necessary for the formation of the most anterior somites in amphioxus, whereas more posterior somite formation is not FGF-dependent. This result leads us to propose that modification of the FGF signal function in the anterior paraxial mesoderm in an amphioxus-like vertebrate ancestor might have contributed to the loss of segmentation in the preotic paraxial mesoderm of the vertebrate head

Chronicling the Journey of the Society for the Advancement in Biology Education Research (SABER) in its Effort to Become Antiracist: From Acknowledgement to Action

The tragic murder of Mr. George Floyd brought to the head long-standing issues of racial justice and equity in the United States and beyond. This prompted many institutions of higher education, including professional organizations and societies, to engage in long-overdue conversations about the role of scientific institutions in perpetuating racism. Similar to many professional societies and organizations, the Society for the Advancement of Biology Education Research (SABER), a leading international professional organization for discipline-based biology education researchers, has long struggled with a lack of representation of People of Color (POC) at all levels within the organization. The events surrounding Mr. Floyd’s death prompted the members of SABER to engage in conversations to promote self-reflection and discussion on how the society could become more antiracist and inclusive. These, in turn, resulted in several initiatives that led to concrete actions to support POC, increase their representation, and amplify their voices within SABER. These initiatives included: a self-study of SABER to determine challenges and identify ways to address them, a year-long seminar series focused on issues of social justice and inclusion, a special interest group to provide networking opportunities for POC and to center their voices, and an increase in the diversity of keynote speakers and seminar topics at SABER conferences. In this article, we chronicle the journey of SABER in its efforts to become more inclusive and antiracist. We are interested in increasing POC representation within our community and seek to bring our resources and scholarship to reimagine professional societies as catalyst agents towards an equitable antiracist experience. Specifically, we describe the 12 concrete actions that SABER enacted over a period of a year and the results from these actions so far. In addition, we discuss remaining challenges and future steps to continue to build a more welcoming, inclusive, and equitable space for all biology education researchers, especially our POC members. Ultimately, we hope that the steps undertaken by SABER will enable many more professional societies to embark on their reflection journeys to further broaden scientific communities