Are all genes regulatory genes?

Abstract

Although much has been learned about hereditary mechanisms since Gregor Mendel’s famous experiments, gene concepts have always remained vague, notwithstanding their central role in biology. During over hundred years of genetic research, gene concepts have often and dynamically changed to accommodate novel experimental findings, without ever providing a generally accepted definition of the ‘gene.’ Yet, the distinction between ‘regulatory genes’ and ‘structural genes’ has remained a common theme in modern gene concepts since the definition of the operon-model. This distinction is now challenged by recent findings which suggest that, at least in eukaryotes, structural genes may in many situations have a regulatory function that is independent of the function of the gene product (protein or non-coding RNA molecule). This brief paper discusses these new findings and some possible implications for the notion of the ‘regulatory gene.’

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Notes

  1. 1.

    This is clearly a too simplistic view. As for example Gatherer points out, no concept in molecular biology has proven to be able to capture everything that is implied by the term ‘gene’ in Mendelian genetics (Gatherer 2010).

  2. 2.

    Keller and Harel (2007), for example, argue for the greater flexibility of their concept of a genetic functor or genitor G = (ODB) that, for a given organism O, describes the relationship between a dene D, i.e. a predicate about the DNA (including epigenetic properties like DNA methylation states), and a bene B, i.e. a statement about an associated functionality or behavior (including complex modal and temporal characteristics). This notion, however, may turn out to be too flexible in order to be of practical use, because—as the authors themselves underscore—“anything goes” (Keller and Harel 2007, p. 6).

  3. 3.

    As Griffiths and Stotz (2007) point out, the conceptual space of the ‘Gene-D’ does also include what they call a ‘nominal’ gene (annotated sequences as used, for example, for databases and bioinformatics tools).

  4. 4.

    Jacob and Monod (1959) supposed that the lac repressor, i.e. the gene product of lacI, was not a protein but it was identified as such a few years later by Gilbert and Müller-Hill (1966).

  5. 5.

    Pseudogenes resemble copies of classical protein-coding genes, but are considered mostly biologically inactive due to mutations or premature stop codons that impair their translation into functional proteins. Yet, many pseudogenes appear to be under selective pressure and represent a significant portion of the ‘transcriptome’ (Harrison et al. 2005).

  6. 6.

    The region of an mRNA transcript that follows the stop codon and is thus not translated into amino acids during protein synthesis.

  7. 7.

    But then, most regulatory capabilities are indirect as they must generally rely on the existence of appropriate cellular processes, being these the synthesis of transcription factor proteins, the splicing of nascent transcripts, or the silencing mediated through microRNAs.

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Acknowledgments

I would like to thank the anonymous reviewers for their considerations and suggestions that have helped in significantly improving the manuscript.

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Correspondence to Rosario Michael Piro.

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Piro, R.M. Are all genes regulatory genes?. Biol Philos 26, 595–602 (2011). https://doi.org/10.1007/s10539-011-9251-9

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Keywords

  • Gene concepts
  • Regulatory genes
  • MicroRNAs
  • Pseudogenes
  • Transcript function