Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean networks, which are intuitive, simple to describe, and can yield qualitative results even when data are sparse. We assembled the largest repository of expert-curated Boolean GRN models. A meta-analysis of this diverse set of models reveals several design principles. GRNs exhibit more canalization, redundancy, and stable dynamics than expected. Moreover, they are enriched for certain recurring network motifs. This raises the important question why evolution favors these design mechanisms.

This paper addresses two topics in systems biology, the hypothesis that biological systems are modular and the problem of relating structure and function of biological systems. The focus here is on gene regulatory networks, represented by Boolean network models, a commonly used tool. Most of the research on gene regulatory network modularity has focused on network structure, typically represented through either directed or undirected graphs. But since gene regulation is a highly dynamic process as it determines the function of cells over time, it is natural to consider functional modularity as well. One of the main results is that the structural decomposition of a network into modules induces an analogous decomposition of the dynamic structure, exhibiting a strong relationship between network structure and function. An extensive simulation study provides evidence for the hypothesis that modularity might have evolved to increase phenotypic complexity while maintaining maximal dynamic robustness to external perturbations.

A hallmark of HIV-1 infection is the continuously declining number of the virus’ predominant target cells, activated CD4⁺ T cells. With diminishing CD4⁺ T cell levels, the capacity to utilize alternate cell types and receptors, including cells that express low CD4 receptor levels such as macrophages, thus becomes crucial. To explore evolutionary paths that allow HIV-1 to acquire a wider host cell range by infecting cells with lower CD4 levels, we dissected the evolution of the envelope-CD4 interaction under in vitro culture conditions that mimicked the decline of CD4^high target cells, using a prototypic subtype B, R5-tropic strain. Adaptation to CD4^low targets proved to severely alter envelope functions including trimer opening as indicated by a higher affinity to CD4 and loss in shielding against neutralizing antibodies. We observed a strikingly decreased infectivity on CD4^high target cells, but sustained infectivity on CD4^low targets, including macrophages. Intriguingly, the adaptation to CD4^low targets altered the kinetic of the entry process, leading to rapid CD4 engagement and an extended transition time between CD4 and CCR5 binding during entry. This phenotype was also observed for certain central nervous system (CNS) derived macrophage-tropic viruses, highlighting that the functional perturbation we defined upon in vitro adaptation to CD4^low targets occurs in vivo. Collectively, our findings suggest that CD4^low adapted envelopes may exhibit severe deficiencies in entry fitness and shielding early in their evolution. Considering this, adaptation to CD4^low targets may preferentially occur in a sheltered and immune-privileged environment such as the CNS to allow fitness restoring compensatory mutations to occur. Untreated HIV-1 infection leads to a gradual depletion of CD4⁺ T cells forcing the virus to continuously adapt to an ever-decreasing number of suitable target cells. Our data based on experiments in a highly controlled in vitro setting describe one avenue of envelope adaptation that allows the virus to infect target cells expressing low amounts of CD4 such as macrophages. Analysis of the functional envelope phenotypes associated with adaptation of the virus to infect target cells expressing low levels of CD4 highlighted altered entry kinetics of the virus. These alterations resulted in extended exposure of CD4-induced neutralization sensitive epitopes in combination with an increased sensitivity to neutralizing antibodies targeting the CD4 binding site and the V3 loop. Interestingly, a similar phenotype was observed for macrophage-tropic HIV-1 isolates derived from the central nervous system (CNS) of infected individuals raising the possibility that the immune-privileged CNS may favor the development of macrophage-tropic / low CD4 level utilizing envelope variants.