Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses

Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing. 
	In contrast to a book which would be the appropriate space to outline in depth all communicative pathways inherent in bacterial life in this current article I want to give an overview for a broader readership over the great variety of bacterial bio-communication: In a first step I describe how they interpret and coordinate, what semiochemical vocabulary they share and which goals they try to reach. In a second stage I describe the main categories of sign-mediated interactions between bacterial and non-bacterial organisms, and between bacteria of the same or related species. In a third stage I will focus on the relationship between bacteria and their obligate settlers, i.e. viruses. We will see that bacteria are important hosts for multiviral colonisation and virally-determined order of nucleic acid sequences.

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Force for ancient and recent life: viral and stem-loop RNA consortia promote life.

Lytic viruses were thought to kill the most numerous host (i.e., kill the winner). But persisting viruses/defectives can also protect against viruses, especially in a ubiquitous virosphere. In 1991, Yarmolinsky et al. discovered the addiction modules of P1 phage, in which opposing toxic and protective functions stabilize persistence. Subsequently, I proposed that lytic and persisting cryptic virus also provide addiction modules that promote group identity. In eukaryotes (and the RNA world), a distinct RNA virus-host relationship exists. Retrovirurses/retroposons are major contributors to eukaryotic genomes. Eukaryotic complexity appears to be mostly mediated by regulatory complexity involving noncoding retroposon-derived RNA. RNA viruses evolve via quasispecies, which contain cooperating, minority, and even opposing RNA types. Quasispecies can also demonstrate group preclusion (e.g., hepatitis C). Stem-loop RNA domains are found in long terminal repeats (and viral RNA) and mediate viral regulation/identity. Thus, stem-loop RNAs may be ancestral regulators. I consider the RNA (ribozyme) world scenario from the perspective of addiction modules and cooperating quasispecies (i.e., subfunctional agents that establish group identity). Such an RNA collective resembles a "gang" but requires the simultaneous emergence of endonuclease, ligase, cooperative catalysis, group identity, and history markers (RNA). I call such a collective a gangen (pathway to gang) needed for life to emerge

Telomeres in Evolution and Development from Biosemiotic Perspective

Telomeres identify natural chromosome ends being different from broken DNA through differences in their "molecular syntax" (M.Eigen) which determines the functions of reverse transcriptase and its integrated RNA template, telomerase. Although telomeres play a crucial role in the linear chromosome organization of eukaryotic cells, their molecular syntax descended from an ancient retroviral competence. This is an indicator for the early retroviral colonization of large double stranded DNA viruses, which are putative ancestors of the eukaryotic nucleus.
This talk will demonstrate certain advantages of the biosemiotic approach towards our evolutionary understanding of telomeres: focus on the genetic/genomic structures as language-like text which follows combinatorial (syntactic), context-sensitive (pragmatic) and
content-specific (semantic) semiotic rules. Genetic/genomic organization from the biosemiotic perspective is not seen any longer as an object of randomly derived alterations (mutations) but as functional innovation coherent with the broad variety of natural genome editing competences of viruses.
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Biocommunication of Fungal Organisms

The development and growth of fungal organisms depend on successful communication processes (a) within the organism and between organisms, (b) with the same or related species and (c) with non-related organisms. In order to generate an appropriate response behaviour, fungal organisms must also be able to (d) correctly interpret meaningful information from the abiotic environment. However, these communication and interpretation processes can also fail. In such cases the overall results can induce disease-causing and even lethal consequences for the organism. 

	This review will not enrich the knowledge of specialists in fungal research, but will demonstrate to a broader readership the different levels of fungal communication and how versatile fungal communicative competences really are. Interestingly, certain rules of fungal communication are very similar to those of animals, while others resemble those of plants. The correspondence between all three eukaryotic kingdoms has two aspects: (1) the context determines the meaning of trans-, inter- and intra-organismic (inter- and intracellular) communication, while (2) differences in abiotic and biotic signal perception determine the content arrangement of response behaviour

Understanding the Regulation of Predatory and Anti-Prey Behaviours for an Artificial Organism

An organism’s behaviour can be categorised as being either predatory or anti-prey. Predatory behaviours are behaviours that try to improve the life of an organism. Anti-prey behaviours are those that attempt to prevent death. Regulation between these two opposing behaviours is necessary to ensure survivability—and gene regulatory networks and metabolic networks are the mechanisms that provide this regulation. We know that such regulatory behaviour is encoded in an organism’s genes. The question is, how is it encoded? The understanding of this encoding can help with the development of an artificial organism, for example an autonomous robotic system; whereby the robot will have the ability to autonomously regulate the switching between the opposing behaviours using this encoded mechanism, in order to ensure its sustainable and continuous system operations. This paper aims to look into the properties of an artificial bio-chemical network consisting of a genetic regulatory network and a metabolic network that can provide these capabilities

Symbiotic outcome modified by the diversification from 7 to over 700 nodule specific cysteine rich peptides

Legume-rhizobium symbiosis represents one of the most successfully co-evolved mutualisms. Within nodules, the bacterial cells undergo distinct metabolic and morphological changes and differentiate into nitrogen-fixing bacteroids. Legumes in the inverted repeat lacking clade (IRLC) employ an array of defensin-like small secreted peptides (SSPs), known as nodule-specific cysteine-rich (NCR) peptides, to regulate bacteroid differentiation and activity. While most NCRs exhibit bactericidal effects in vitro, studies confirm that inside nodules they target the bacterial cell cycle and other cellular pathways to control and extend rhizobial differentiation into an irreversible (or terminal) state where the host gains control over bacteroids. While NCRs are well established as positive regulators of effective symbiosis, more recent findings also suggest that NCRs affect partner compatibility. The extent of bacterial differentiation has been linked to species-specific size and complexity of the NCR gene family that varies even among closely related species, suggesting a more recent origin of NCRs followed by rapid expansion in certain species. NCRs have diversified functionally, as well as in their expression patterns and responsiveness, likely driving further functional specialisation. In this review, we evaluate the functions of NCR peptides and their role as a driving force underlying the outcome of rhizobial symbiosis, where the plant is able to determine the outcome of rhizobial interaction in a temporal and spatial manner

Investigating the properties of bio-chemical networks of artificial organisms with opposing behaviours

Organisms, be it singled-celled organisms or multi-cellular organisms, are constantly faced with opposing objectives requiring different sets of behaviours. These behaviours can be classified into two, predatory behaviours or anti-prey behaviours, with one set of behaviours causing an opposite effect to the other. A healthy organism aims to achieve its equilibrium state or to be in homeostasis. Homeostasis is achieved when a balance between the two opposing behaviours is created and maintained. This raises some questions: is there an innate mechanism that encodes for these categories of behaviours? Is there also an innate mechanism(s) that resolves conflicts and allows switching between these two opposing behaviours? If we consider artificial organisms as single-celled organisms, how do the organisms’ gene regulatory network, metabolic network and/or signalling network (their biochemical networks) maintain homeostasis of the organisms? This paper investigates the properties of the networks of best evolved artificial organisms, in order to help answer these questions, and guide the evolutionary development of controllers for artificial systems

Law of Genome Evolution Direction : Coding Information Quantity Grows

The problem of the directionality of genome evolution is studied. Based on the analysis of C-value paradox and the evolution of genome size we propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication, expansion of code, and gene transfer from outside. The function-coding information quantity of a genome consists of two parts, p-coding information quantity which encodes functional protein and n-coding information quantity which encodes other functional elements except amino acid sequence. The evidences on the evolutionary law about the function-coding information quantity are listed. The needs of function is the motive force for the expansion of coding information quantity and the information quantity expansion is the way to make functional innovation and extension for a species. So, the increase of coding information quantity of a genome is a measure of the acquired new function and it determines the directionality of genome evolution.Comment: 16 page

Evolutionary connectionism: algorithmic principles underlying the evolution of biological organisation in evo-devo, evo-eco and evolutionary transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions