Significance: MicroRNAs are short, single-stranded RNAs that bind to target mRNAs and block their translation. Five years ago we observed in the cockroachBlattella germanicathat general depletion of microRNAs prevents metamorphosis. This observation led to two key questions: Which microRNAs are involved in this action, and which target do they act on? The results reported herein show that the microRNAs involved are those of an miR-2 family (miR-2, miR-13a, and miR-13b), and the target is the transcription factor Krüppel homolog 1, a master repressor of insect metamorphosis. The data presented indicate that miR-2 microRNAs rapidly clear Krüppel homolog 1 transcripts in the last nymphal instar, a process that is crucial for proper metamorphosis. This reveals the elegant mechanism of an miRNA family leading metamorphosis to its correct conclusion.

Guiding synthetic organ exploration through acknowledging self-organisation and evolutionary constraints in the morphospace of the possible and the actual.

Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is not enough to predict the behavior of designed circuits and thus, a costly trial-error process is eventually required. In this work, we provide a new theoretical framework for the predictive treatment of the genetic load. We mathematically and experimentally demonstrate that dependences among genes follow a quantitatively predictable behavior. Our theory predicts the observed reduction of the expression of a given synthetic gene when an extra genetic load is introduced in the circuit. The theory also explains that such dependence qualitatively differs when the extra load is added either by transcriptional or translational modifications. We finally show that the limitation of the cellular resources for gene expression leads to a mathematical formulation that converges to an expression analogous to the Ohm's law for electric circuits. Similitudes and divergences with this law are outlined. Our work provides a suitable framework with predictive character for the design process of complex genetic devices in synthetic biology.

A major force contributing to the emergence of novelty in nature is the presence of cooperative interactions, where two or more components of a system act in synergy, sometimes leading to higher-order, emergent phenomena. Within molecular evolution, the so called hypercycle defines the simplest model of an autocatalytic cycle, providing major theoretical insights on the evolution of cooperation in the early biosphere. These closed cooperative loops have also inspired our understanding of how catalytic loops appear in ecological systems. In both cases, hypercycle and ecological cooperative loops, the role played by space seems to be crucial for their stability and resilience against parasites. However, it is difficult to test these ideas in natural ecosystems, where time and spatial scales introduce considerable limitations. Here, we use engineered bacteria as a model system to a variety of environmental scenarios identifying trends that transcend the specific model system, such an enhanced genetic diversity in environments requiring mutualistic interactions. Interestingly, we show that improved environments can slow down mutualistic range expansions as a result of genetic drift effects preceding local resource depletion. Moreover, we show that a parasitic strain is excluded from the population during range expansions (which acknowledges a classical prediction). Nevertheless, environmental deterioration can reshape population interactions, this same strain becoming part of a three-species mutualistic web in scenarios in which the two-strain mutualism becomes non functional. The evolutionary and ecological implications for the design of synthetic ecosystems are outlined. In order to achieve greater levels of complexity, complex systems often display cooperative interactions that enable the formation and stabilisation of mutualisms. Theoretical models have shown that closed chains of cooperative species or hypercycles might have been crucial in the evolution towards complexity in early molecular replicators. However, parasites can easily destroy the cooperative loop, unless the system is embedded in a spatial context where interactions are limited to nearest neighbours. A dynamically similar phenomenon occurs in ecological webs, where closed positive feedback loops contribute to global stability and ecophysiology. Here we explore this problem by engineering synthetic cooperative strains of microbes that grow and interact in a cell culture under the absence and presence of a synthetic parasitic strains. By analysing the impact of cooperation under different conditions, we find that cooperative replication is successful and overcomes competitive interactions in nutrient-poor environments. However, the same closed loop fails to establish in nutrient-rich media. Moreover, parasitic entities that jeopardise cooperation under well-mixed conditions can be overcome by hypercycles when growing in a two-dimensional space.