The temporally regulated transcription factor sel-7 controls developmental timing in C. elegans

Unanticipated broad phylogeny of BEN DNA-binding domains revealed by structural homology searches

Organization of protein sequences into domain families is a foundation for cataloging and investigating protein functions. However, long-standing strategies based on primary amino acid sequences are blind to the possibility that proteins with dissimilar sequences could have comparable tertiary structures. Building on our recent findings that in silico structural predictions of BEN family DNA-binding domains closely resemble their experimentally determined crystal structures, we exploited the AlphaFold2 database for comprehensive identification of BEN domains. Indeed, we identified numerous novel BEN domains, including members of new subfamilies. For example, while no BEN domain factors had previously been annotated in C. elegans, this species actually encodes multiple BEN proteins. These include key developmental timing genes of orphan domain status, sel-7 and lin-14, the latter being the central target of the founding miRNA lin-4. We also reveal that the domain of unknown function 4806 (DUF4806), which is widely distributed across metazoans, is structurally similar to BEN and comprises a new subtype. Surprisingly, we find that BEN domains resemble both metazoan and non-metazoan homeodomains in 3D conformation and preserve characteristic residues, indicating that despite their inability to be aligned by conventional methods, these DNA-binding modules are probably evolutionarily related. Finally, we broaden the application of structural homology searches by revealing novel human members of DUF3504, which exists on diverse proteins with presumed or known nuclear functions. Overall, our work strongly expands this recently identified family of transcription factors and illustrates the value of 3D structural predictions to annotate protein domains and interpret their functions.

The heterochronic LIN-14 protein is a BEN domain transcription factor

Heterochrony is a foundational concept in animal development and evolution, first introduced by Ernst Haeckel in 1875 and later popularized by Stephen J. Gould1. A molecular understanding of heterochrony was first established by genetic mutant analysis in the nematode C. elegans, revealing a genetic pathway that controls the proper timing of cellular patterning events executed during distinct postembryonic juvenile and adult stages2. This genetic pathway is composed of a complex temporal cascade of multiple regulatory factors, including the first-ever discovered miRNA, lin-4, and its target gene, lin-14, which encodes a nuclear, DNA-binding protein2,3,4. While all core members of the pathway have homologs based on primary sequences in other organisms, homologs for LIN-14 have never been identified by sequence homology. We report that the AlphaFold-predicted structure of the LIN-14 DNA binding domain is homologous to the BEN domain, found in a family of DNA binding proteins previously thought to have no nematode homologs5. We confirmed this prediction through targeted mutations of predicted DNA-contacting residues, which disrupt in vitro DNA binding and in vivo function. Our findings shed new light on potential mechanisms of LIN-14 function and suggest that BEN domain-containing proteins may have a conserved role in developmental timing.

Steroid regulation of C. elegans diapause, developmental timing, and longevity

Hormones play a critical role in driving major stage transitions and developmental timing events in many species. In the nematode C. elegans the steroid hormone receptor, DAF-12, works at the confluence of pathways regulating developmental timing, stage specification, and longevity. DAF-12 couples environmental and physiologic signals to life history regulation, and it is embedded in a rich architecture governing diverse processes. Here, we highlight the molecular insights, extraordinary circuitry, and signaling pathways governing life stage transitions in the worm and how they have yielded fundamental insights into steroid regulation of biological time.

A proposal in relation to a genetic control of lifespan in mammals

This article proposes that behavioural advancement during mammalian evolution had been in part mediated through extension of total developmental time. Such time extensions would have resulted in increased numbers of neuronal precursor cells, hence larger brains and a disproportionate increase in the neocortex. Larger neocortical areas enabled new connections to be formed during development and hence expansion of existing behavioural circuits. To have been positively selected such behavioural advances would have required enough postdevelopmental time to enable the behaviour to be fully manifest. It is therefore proposed that the success of mammalian evolution depended on initiating a genetic control of total postdevelopmental time. This could have been mediated through the redeployment of gene regulatory networks controlling total developmental time to additionally control total postdevelopmental time. The result would be that any extension of developmental time, leading to a behavioural advancement, would be accompanied by a proportional extension to postdevelopmental time. In effect it is proposed that mammalian lifespan as a whole is genetically controlled.

miRNAs give worms the time of their lives: small RNAs and temporal control in Caenorhabditis elegans

Alteration in the timing of particular developmental events can lead to major morphological changes that have profound effects on the life history of an organism. Insights into developmental timing mechanisms have been revealed in the model organism Caenorhabditis elegans, in which a regulatory network of heterochronic genes times events during larval development, ensuring that stage-specific programs occur in the appropriate sequence and on schedule. Developmental timing studies in C. elegans led to the landmark discovery of miRNAs and continue to enhance our understanding of the regulation and activity of these small regulatory molecules. Current views of the heterochronic gene pathway are summarized here, with a focus on the ways in which miRNAs contribute to temporal control and how miRNAs themselves are regulated. Finally, the conservation of heterochronic genes and their functions in timing, as well as their related roles in stem cells and cancer, are highlighted.

Recent advances in understanding the molecular mechanisms regulating C. elegans transcription

We review recent studies that have advanced our understanding of the molecular mechanisms regulating transcription in the nematode C. elegans. Topics covered include: (i) general properties of C. elegans promoters; (ii) transcription factors and transcription factor combinations involved in cell fate specification and cell differentiation; (iii) new roles for general transcription factors; (iv) nucleosome positioning in C. elegans "chromatin"; and (v) some characteristics of histone variants and histone modifications and their possible roles in controlling C. elegans transcription.