Gene and genon concept: coding versus regulation. A conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology

Ligand-Responsive Artificial Protein-Protein Communication for Field-Deployable Cell-Free Biosensing

Natural protein-protein communications, such as those between transcription factors (TFs) and RNA polymerases/ribosomes, underpin cell-free biosensing systems operating on the transcription/translation (TXTL) paradigm. However, their deployment in field analysis is hampered by the delayed response (hour-level) and the complex composition of in vitro TXTL systems. For this purpose, we present a de novo-designed ligand-responsive artificial protein-protein communication (LIRAC) by redefining the connection between TFs and non-interacting CRISPR/Cas enzymes. By rationally designing a chimeric DNA adaptor and precisely regulating its binding affinities to both proteins, LIRAC immediately transduces target-induced TF allostery into rapid CRISPR/Cas enzyme activation within a homogeneous system. Consequently, LIRAC obviates the need for RNA/protein biosynthesis inherent to conventional TXTL-based cell-free systems, substantially reducing reaction complexity and time (from hours to 10 minutes) with improved sensitivity and tunable dynamic range. Moreover, LIRAC exhibits excellent versatility and programmability for rapidly and sensitively detecting diverse contaminants, including antibiotics, heavy metal ions, and preservatives. It also enables the creation of a multi-protein communication-based tristate logic for the intelligent detection of multiple contaminants. Integrated with portable devices, LIRAC has been proven effective in the field analysis of environmental samples and personal care products, showcasing its potential for environmental and health monitoring.

Is RNA the working genome in eukaryotes ? The 60 year evolution of a conceptual challenge

About 80 years ago, in 1943, after a century of biochemical and genetic research, DNA was established as the carrier of genetic information. At the onset of Molecular Biology around 1960, the genome of living organisms embodied 3 basic, still unknown paradigms: its composition, organisation and expression. Between 1980 and 1990, its replication was understood, and ideas about its 3D-organisation were suggested and finally confirmed by 2010. The basic mechanisms of gene expression in higher organisms, the synthesis of precursor RNAs and their processing into functional RNAs, were also discovered about 60 years ago in 1961/62. However, some aspects were then, and are still now debated, although the latest results in post-genomic research have confirmed the basic principles. When my history-essay was published in 2003, describing the discovery of RNA processing 40 years earlier, the main facts were not yet generally confirmed or acknowledged. The processing of pre-rRNA to 28 S and 18 S rRNA was clearly demonstrated, confirmed by others and generally accepted as a fact. However, the "giant" size of pre-mRNA 10-100 kb-long and pervasive DNA transcription were still to be confirmed by post-genomic methods. It was found, surprisingly, that up to 90% of DNA is transcribed in the life cycle of eukaryotic organisms thus showing that pervasive transcription was the general rule. In this essay, we shall take a journey through the 60-year history of evolving paradigms of gene expression which followed the emergence of Molecular Biology, and we will also evoke some of the "folklore" in research throughout this period. Most important was the growing recognition that although the genome is encoded in DNA, the Working Genome in eukaryotic organisms is RNA.

Biology, geometry and information

The main thesis developed in this article is that the key feature of biological life is the a biological process can control and regulate other processes, and it maintains that ability over time. This control can happen hierarchically and/or reciprocally, and it takes place in three-dimensional space. This implies that the information that a biological process has to utilize is only about the control, but not about the content of those processes. Those other processes can be vastly more complex that the controlling process itself, and in fact necessarily so. In particular, each biological process draws upon the complexity of its environment.

A reappraisal of the form: function problem-theory and phenomenology

This paper is aimed at demonstrating that some geometrical and topological transformations and operations serve not only as promoters of many specific genetic and cellular events in multicellular living organisms, but also as initiators of the organization and regulation of their functions. Thus, changes in the form and structure of macromolecular and cellular systems must be directly associated to their functions. There are specific classes of enzymes that manipulate the geometry and topology of complex DNA-protein structures, and thereby they perform many important cellular processes, including segregation of daughter chromosomes, gene regulation, and DNA repair. We argue that form has an organizing power, hence a causal action, in the sense that it enables to induce functional events during different biological processes, at the supramolecular, cellular, and organismal levels of organization. Clearly, topological forms must be matched with specific kinetic and dynamical parameters to have a functional effectiveness in living systems. This effectiveness is remarkably apparent, to give an example, in the regulation of the genome functions and in cell activity. In more general terms, we try to show that the conformational plasticity of biological systems depends on different kinds of topological manipulations performed by specific families of enzymes. In doing so, they catalyze all those spatial and dynamical changes of biological structures that are suitable for the functions to be acted by the organism.

Biological information

In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology. Nevertheless, I argue that Shannon’s concept of information is useful in biology, although its application is not as straightforward as many people think. In fact, the recently developed theory of information decomposition can shed much light on the complementarity between coding and regulatory, or internal and environmental information. The key challenge that we formulate in this contribution is to understand how genetic information and external factors combine to create an organism, and conversely how the genome has learned in the course of evolution how to harness the environment, and analogously how coding, regulation and spatial organization interact in cellular processes.

Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review

The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.

LA ONTOGENIA Y LA EVOLUCIÓN DESDE LA PERSPECTIVA DE LA TEORÍA DE LOS SISTEMAS DE DESARROLLO (TSD)

La teoría de los sistemas de desarrollo (TSD) pretende realizar una síntesis conceptual que vincule el desarrollo ontogenético con la evolución. Sus antecedentes pueden ser encontrados básicamente en los trabajos de Waddington y de Bertalanffy quienes aportaron las bases de la canalización del desarrollo y la teoría de sistemas biológicos, respectivamente. El objetivo de este artículo es realizar un análisis conceptual preliminar de la TSD y reflexionar acerca de los aportes potenciales de la TSD como marco teórico para la biología del desarrollo en particular y la biología evolutiva en general. Para ello, se tendrán en cuenta algunos de los conceptos y propuestas que componen este marco y se trabajará sobre datos secundarios obtenidos de la bibliografía. Se concluye que la TSD: 1-logra argumentar en contra de la visión gen-centrista respecto de las explicaciones que pretenden justificar el desarrollo biológico y evolutivo; 2- argumenta de manera coherente a favor del rol de la epigenética en la ontogenia y la evolución; 3- en relación con lo anterior el rol de la selección natural se restringe a un segundo plano; 4- propone que la dicotomía naturaleza/cultura debe ser superada; y 5- constituye un posible programa de investigación metodológico compuesto de una diversidad de hipótesis y teorías no necesariamente relacionadas que pueden ser corroboradas de manera relativamente independientes del resto de la red teórica.   

Arbitrariness is not enough: towards a functional approach to the genetic code

Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about "code" in this case. Yet we suppose that there exist a code in the process of protein synthesis, but on a higher level than the nucleic bases chains. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). Even if the functional definition of meaning in the genetic code has been discussed in the field of biosemiotics, its further implications have not been considered. In fact, if the function of a protein represents the meaning of the genetic code (the sign's object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view.

The Evolving Definition of the Term "Gene"

This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge.

Why genes are like lemons

In the last few years, the lack of a unitary notion of gene across biological sciences has troubled the philosophy of biology community. However, the debate on this concept has remained largely historical or focused on particular cases presented by the scientific empirical advancements. Moreover, in the literature there are no explicit and reasonable arguments about why a philosophical clarification of the concept of gene is needed. In our paper, we claim that a philosophical clarification of the concept of gene does not contribute to biology. Unlike the question, for example, "What is a biological function?", we argue that the question "What is a gene?" could be answered by means of empirical research, in the sense that biologists' labour is enough to shed light on it.

Information theory, gene expression, and combinatorial regulation: a quantitative analysis

According to a functional definition of the term "gene", a protein-coding gene corresponds to a polypeptide and, hence, a coding sequence. It is therefore as such not yet present at the DNA level, but assembled from possibly heterogeneous pieces in the course of RNA processing. Assembly and regulation of genes require, thus, information about when and in which quantity specific polypeptides are to be produced. To assess this, we draw upon precise biochemical data. On the basis of our conceptual framework, we also develop formal models for the coordinated expression of specific sets of genes through the interaction of transcripts and mRNAs and with proteins via a precise putative regulatory code. Thus, the nucleotides in transcripts and mRNA are not only arranged into amino acid-coding triplets, but at the same time may participate in regulatory oligomotifs that provide binding sites for specific proteins. We can then quantify and compare product and regulatory information involved in gene expression and regulation.

A biological relativity view of the relationships between genomes and phenotypes

This article explores the relativistic principle that there is no privileged scale of causality in biology to clarify the relationships between genomes and phenotypes. The idea that genetic causes are primary views the genome as a program. Initially, that view was vindicated by the discovery of mutations and knockouts that have large and specific effects on the phenotype. But we now know that these form the minority of cases. Many changes at the genome level are buffered by robust networks of interactions in cells, tissues and organs. The 'differential' view of genetics therefore fails because it is too restrictive. An 'integral' view, using reverse engineering from systems biological models to quantify contributions to function, can solve this problem. The article concludes by showing that far from breaking the supervenience principle, downward causation requires that it should be obeyed.

Clarifying omics concepts, challenges, and opportunities for Prunus breeding in the postgenomic era

The recent sequencing of the complete genome of the peach, together with the availability of new high-throughput genome, transcriptome, proteome, and metabolome analysis technologies, offers new possibilities for Prunus breeders in what has been described as the postgenomic era. In this context, new biological challenges and opportunities for the application of these technologies in the development of efficient marker-assisted selection strategies in Prunus breeding include genome resequencing using DNA-Seq, the study of RNA regulation at transcriptional and posttranscriptional levels using tilling microarray and RNA-Seq, protein and metabolite identification and annotation, and standardization of phenotype evaluation. Additional biological opportunities include the high level of synteny among Prunus genomes. Finally, the existence of biases presents another important biological challenge in attaining knowledge from these new high-throughput omics disciplines. On the other hand, from the philosophical point of view, we are facing a revolution in the use of new high-throughput analysis techniques that may mean a scientific paradigm shift in Prunus genetics and genomics theories. The evaluation of scientific progress is another important question in this postgenomic context. Finally, the incommensurability of omics theories in the new high-throughput analysis context presents an additional philosophical challenge.

Regulation of gene expression and the transcription factor cycle hypothesis

Post-genomic data show unexpected extent of the transcribed genome and the size of individual primary transcripts. Hence, most cis-regulatory modules (CRMs) binding transcription factors (TFs) at promotor, enhancer and other sites are actually transcribed within full domain transcripts (FDTs). The ensemble of these CRMs placed way upstream of exon clusters, downstream and in intronic or intergenic positions represent a program of gene expression which has been formally analysed within the Gene and Genon concept [1,2]. This concept has emphasised the necessity to separate product information from regulative information to allow information-theoretic analysis of gene expression. Classically, TFs have been assumed to act at DNA level exclusively but evidence has accumulated indicating eventual post-transcriptional functions. The transcription factor cycle (TFC) hypothesis suggests the transfer of DNA-bound factors to nascent RNA. Exerting downstream functions in RNA processing and transport, these factors would be liberated by RNA processing and cycle back to the DNA maintaining active transcription. Sequestered on RNA in absence of processing they would constitute a negative feedback loop. The TFC concept may explain epigenetic regulation in mitosis and meiosis. In mitosis control factors may survive as single proteins but also attached to FDTs as organised complexes. This process might perpetuate in cell division conditioning of chromatin for transcription. As observed on lampbrush chromosomes formed in avian and amphibian oogenesis, in meiosis the genome is fully transcribed and oocytes conserve high Mr RNA of high sequence complexity. When new interphase chromosomes form in daughter cells and early embryogenesis, TFs and other factors attached to RNA might be reinserted onto the DNA.

The use and abuse of -omes

The diverse fields of Omics research share a common logical structure combining a cataloging effort for a particular class of molecules or interactions, the underlying -ome, and a quantitative aspect attempting to record spatiotemporal patterns of concentration, expression, or variation. Consequently, these fields also share a common set of difficulties and limitations. In spite of the great success stories of Omics projects over the last decade, much remains to be understood not only at the technological, but also at the conceptual level. Here, we focus on the dark corners of Omics research, where the problems, limitations, conceptual difficulties, and lack of knowledge are hidden.

What is a gene? - Revisited

The dialectic discourse of the 'gene' as the unit of heredity deduced from the phenotype, whether an intervening variable or a hypothetical construct, appeared to be settled with the presentation of the molecular model of DNA: the gene was reduced to a sequence of DNA that is transcribed into RNA that is translated into a polypeptide; the polypeptides may fold into proteins that are involved in cellular metabolism and structure, and hence function. This path turned out to be more bewildering the more the regulation of products and functions were uncovered in the contexts of integrated cellular systems. Philosophers struggling to define a unified concept of the gene as the basic entity of (molecular) genetics confronted those who suggested several different 'genes' according to the conceptual frameworks of the experimentalists. Researchers increasingly regarded genes de facto as generic terms for describing their empiric data, and with improved DNA-sequencing capacities these entities were as a rule bottom-up nucleotide sequences that determine functions. Only recently did empiricists return to discuss conceptual considerations, including top-down definitions of units of function that through cellular mechanisms select the DNA sequences which comprise 'genomic-footprints' of functional entities.

Differential and integral views of genetics in computational systems biology

This article uses an integrative systems biological view of the relationship between genotypes and phenotypes to clarify some conceptual problems in biological debates about causality. The differential (gene-centric) view is incomplete in a sense analogous to using differentiation without integration in mathematics. Differences in genotype are frequently not reflected in significant differences in phenotype as they are buffered by networks of molecular interactions capable of substituting an alternative pathway to achieve a given phenotype characteristic when one pathway is removed. Those networks integrate the influences of many genes on each phenotype so that the effect of a modification in DNA depends on the context in which it occurs. Mathematical modelling of these interactions can help to understand the mechanisms of buffering and the contextual-dependence of phenotypic outcome, and so to represent correctly and quantitatively the relations between genomes and phenotypes. By incorporating all the causal factors in generating a phenotype, this approach also highlights the role of non-DNA forms of inheritance, and of the interactions at multiple levels.

A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks

In this paper we present and discuss a model-based approach to link miRNA translational control with cell signalling networks. MicroRNAs are small regulatory RNAs that are able to regulate the activity and the stability of specific messenger RNA and have been implicated in tumour progression due to their ability to translationally regulate critical oncogenes and tumour suppressors. In our approach, data on protein-protein interactions and miRNA regulation, obtained from bioinformatics databases, are integrated with quantitative experimental data using mathematical modelling. Predictive computational simulations and qualitative (bifurcation) analyses of those mathematical models are employed to further support the investigation of such multifactorial networks in the context of cancer progression. We illustrate our approach with the C-Myc/E2F signalling network, involved in the progression of several tumour subtypes, including colorectal cancer.

Biophysics and systems biology

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

The origins of larval forms: what the data indicate, and what they don't

What is a larva, if it is not what survives of an ancestor's adult, compressed into a transient pre-reproductive phase, as suggested by Haeckel's largely disreputed model of evolution by recapitulation? A recently published article hypothesizes that larva and adult of holometabolous insects are developmental expressions of two different genomes coexisting in the same animal as a result of an ancient hybridization event between an onychophoran and a primitive insect with eventless post-embryonic development. More likely, however, larvae originated from late embryonic or early post-embryonic stages of ancestors with direct development. Evolutionary novelties would thus be intercalary rather than terminal, with respect to the ancestor's ontogenetic schedule. This scenario, supported by current research on holometabolous insects and marine invertebrates with complex life cycles, offers a serious alternative to the traditional scenario ('what is early in ontogeny is also early in phylogeny') underlying the current perception of the evolution of genetic regulatory networks.

Defining genes: a computational framework

The precise elucidation of the gene concept has become the subject of intense discussion in light of results from several, large high-throughput surveys of transcriptomes and proteomes. In previous work, we proposed an approach for constructing gene concepts that combines genomic heritability with elements of function. Here, we introduce a definition of the gene within a computational framework of cellular interactions. The definition seeks to satisfy the practical requirements imposed by annotation, capture logical aspects of regulation, and encompass the evolutionary property of homology.

Genes and causation

Relating genotypes to phenotypes is problematic not only owing to the extreme complexity of the interactions between genes, proteins and high-level physiological functions but also because the paradigms for genetic causality in biological systems are seriously confused. This paper examines some of the misconceptions, starting with the changing definitions of a gene, from the cause of phenotype characters to the stretches of DNA. I then assess whether the 'digital' nature of DNA sequences guarantees primacy in causation compared to non-DNA inheritance, whether it is meaningful or useful to refer to genetic programs, and the role of high-level (downward) causation. The metaphors that served us well during the molecular biological phase of recent decades have limited or even misleading impacts in the multilevel world of systems biology. New paradigms are needed if we are to succeed in unravelling multifactorial genetic causation at higher levels of physiological function and so to explain the phenomena that genetics was originally about. Because it can solve the 'genetic differential effect problem', modelling of biological function has an essential role to play in unravelling genetic causation.

"Genes"

In order to describe a cell at molecular level, a notion of a “gene” is neither necessary nor helpful. It is sufficient to consider the molecules (i.e., chromosomes, transcripts, proteins) and their interactions to describe cellular processes. The downside of the resulting high resolution is that it becomes very tedious to address features on the organismal and phenotypic levels with a language based on molecular terms. Looking for the missing link between biological disciplines dealing with different levels of biological organization, we suggest to return to the original intent behind the term “gene”. To this end, we propose to investigate whether a useful notion of “gene” can be constructed based on an underlying notion of function, and whether this can serve as the necessary link and embed the various distinct gene concepts of biological (sub)disciplines in a coherent theoretical framework. In reply to the Genon Theory recently put forward by Klaus Scherrer and Jürgen Jost in this journal, we shall discuss a general approach to assess a gene definition that should then be tested for its expressiveness and potential cross-disciplinary relevance.