Current Opinion in Systems Biology最新文献

The evolution of metabolic pathways in microbes is traditionally envisioned to take place within a single organism. The diverse repertoire of enzymes in the microbial community points to another exciting possibility: namely, that new metabolic pathways may evolve in a community setting, where pathway steps are distributed across several strains. The readiness with which microbes form stable relationships to collectively degrade manmade ‘xenobiotic’ pollutants, as evidenced from natural and laboratory-enriched consortia, provides valuable insights into the evolution of enzymes and pathways. Nonetheless, many open questions remain to be addressed. In this review, we consider the key determinants of pathway evolution in microbial communities, drawing from principles of social evolutionary theory in microbes, and also exploring the role of diffusion and horizontal gene transfer.

The development of bacterial chassis to increase productivity and reduce industrial costs in value-added biochemical production has gained significant attention. Current efforts have focused on model bacteria, thus limiting their suitability to produce specialized products. Therefore, there is a growing emphasis on developing specialized non-model bacterial chassis to expand the repertoire of bioproducts. However, the lack of genetic information and tools for non-model bacteria remains challenging. In this review, we categorize and introduce non-model chassis based on their characteristics in relation to the target products. We also provide an overview of the trends in the development of genome-reduced chassis to enhance productivity. Furthermore, we propose synthetic biology technologies that can be applied to a broad range of non-model bacteria.

The growth of microbial populations in nature is dynamic, as the cellular physiology and environment of these populations change. Population dynamics have wide-ranging consequences for ecology and evolution, determining how species interact and which mutations fix. Understanding these dynamics is also critical for clinical and environmental applications in which we need to promote or inhibit microbial growth. We first address the latest efforts and outstanding challenges in measuring microbial population dynamics in natural environments. We next summarize fundamental concepts and empirical data on how population dynamics both shape and are shaped by evolutionary processes. Finally, we discuss the role of tradeoffs in microbial population dynamics, which may reveal physiological constraints and help to maintain ecological diversity. We find that current evidence for tradeoffs in population dynamics is limited, but that consideration of the evolutionary context of these tradeoffs is necessary for designing future experiments that can better address this problem.

Present-day life is amazingly diverse and complex owing to Darwinian evolution. Despite the simplicity of the principle of Darwinian evolution, the process and its outcomes are largely unpredictable. Evolutionary simulation and experiments are useful methods for gaining insights into the process and outcomes of Darwinian evolution. In this short review, we discuss recent progress in theoretical and experimental approaches to understanding the possible evolutionary processes of prebiotic self-replicators. We especially focus on research addressing how a prebiotic self-replicator increases complexity through evolution, including our recent experiments, in which a complex replication network consisting of multiple self-replicating molecules spontaneously evolved from a single replicating RNA.

In cells, the microtubule network continually assembles and disassembles. The regulation of microtubule growth or shortening has almost exclusively been studied at their dynamic ends. However, microtubules are dynamic all along their entire shaft. A dynamic shaft increases the lifetime and length of a microtubule by reducing the shortening phases and promoting its regrowth. Here, we discuss how shaft dynamics can regulate microtubule network organization, intracellular transport, and polarization of the network.

Engineering new functions in the microbiome requires understanding how host genetic control and microbe–microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe–microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.

Collective cell behaviors are essential for the shape and function of tissues. The last decades have provided unequivocal experimental evidence that tissue mechanics are key drivers of morphogenesis. In particular, the spatiotemporal coordination of cellular contractility, adhesion and volume regulation can drive morphogenetic events in various epithelia. At the same time, the epithelial sheets themselves have remarkable mechanical properties, being able to distribute mechanical stress throughout the whole material to resist the physical deformations necessary for their function. In this review, we address recent findings on epithelia morphogenesis and mechanical resistance and highlight the importance of quantitative new approaches for achieving novel understanding.

Enhancers are genomic elements that regulate gene expression through a variety of mechanisms. In neuronal systems, enhancer-promoter interactions regulate cell- and tissue-specific transcriptional programs, during neuronal specification and upon terminal differentiation, and play major roles in the tight regulation of activity-dependent mechanisms, such as in memory formation. Enhancers are also hotspots for non-coding genetic variants associated with neurological disorders, such as schizophrenia and Parkinson's disease (PD). Understanding how enhancer grammar informs gene expression programs in neuronal systems in development and disease remains a major challenge, and is a growing avenue to discover the molecular mechanisms directly altered by non-coding genetic variants. In this review, we discuss the diverse mechanisms by which enhancers integrate internal and external stimuli to regulate the gene expression programs that guide neuronal specification and sustain neuronal-specific and activity-dependent processes.