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.

In 2009 we reported that depletion of Dicer-1, the enzyme that catalyzes the final step of miRNA biosynthesis, prevents metamorphosis in Blattella germanica. However, the precise regulatory roles of miRNAs in the process have remained elusive. In the present work, we have observed that Dicer-1 depletion results in an increase of mRNA levels of Krüppel homolog 1 (Kr-h1), a juvenile hormone-dependent transcription factor that represses metamorphosis, and that depletion of Kr-h1 expression in Dicer-1 knockdown individuals rescues metamorphosis. We have also found that the 3′UTR of Kr-h1 mRNA contains a functional binding site for miR-2 family miRNAs (for miR-2, miR-13a, and miR-13b). These data suggest that metamorphosis impairment caused by Dicer-1 and miRNA depletion is due to a deregulation of Kr-h1 expression and that this deregulation is derived from a deficiency of miR-2 miRNAs. We corroborated this by treating the last nymphal instar of B. germanica with an miR-2 inhibitor, which impaired metamorphosis, and by treating Dicer-1-depleted individuals with an miR-2 mimic to allow nymphal-to-adult metamorphosis to proceed. Taken together, the data indicate that miR-2 miRNAs scavenge Kr-h1 transcripts when the transition from nymph to adult should be taking place, thus crucially contributing to the correct culmination of metamorphosis.insect metamorphosis | microRNA | juvenile hormone | evolution of metamorphosis | insect hormones M icroRNAs (miRNAs) are endogenous, ca. 22-nt, singlestrand, noncoding RNAs that regulate gene expression by acting posttranscriptionally through basepairing between the socalled seed sequence of the miRNA (nucleotides 2-8 at its 5′ end) and the complementary seed match sequence in the target mRNA (1). Since miRNAs were first discovered in the nematode Caenorhabditis elegans in the 1990s (2) and subsequently detected in other species (3), a remarkable diversity of them has been reported in a variety of organisms, including insects, plants, viruses, and vertebrates (4). Information available indicates that miRNAs are key players in gene regulatory networks, driving cell differentiation, conferring robustness, and channeling the development of multicellular organisms (5-8). Furthermore, the escalation in complexity in early bilaterian evolution has been correlated with a strong increase in the number of miRNAs (9-11). In insects, miRNAs have been shown to be involved in fine-tuning a number of biological processes such as cell proliferation, apoptosis and growth, oogenesis, and development, as well as response to biological stress (12).In 2009 we first looked at whether miRNAs might have a relevant role in the regulation of insect metamorphosis. Only a few published studies had considered the contribution of miRNAs to this process, but these focused on specific aspects, such as wing formation and neuromuscular development (13-16). They also used the fly Drosophila melanogaster as a model, a species that follows the holometabolan mode of metamorphosis, in which the juvenile stages are extre...

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.

BackgroundMounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries.Presentation of the hypothesisWe hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls.Testing the hypothesisTesting this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics).Implications of the hypothesisOur hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success.ReviewersThis article was reviewed by This article was reviewed by Eugene V. Koonin, Tom Ellis (nominated by Purificación Lopez-Garcia) and Eörs Szathmary.