REVIEWS BIOLOGICAL ROBUSTNESS Hiroaki Kitano Abstract | Robustness is a ubiquitously observed property of biological systems. It is considered to be a fundamental feature of complex evolvable systems. It is attained by several underlying principles that are universal to both biological organisms and sophisticated engineering systems. Robustness facilitates evolvability and robust traits are often selected by evolution. Such a mutually beneficial process is made possible by specific architectural features observed in robust systems. But there are trade-offs between robustness, fragility, performance and resource demands, which explain system behaviour, including the patterns of failure. Insights into inherent properties of robust systems will provide us with a better understanding of complex diseases and a guiding principle for therapy design. LYSIS The discovery of fundamental, systems-level principles property has been widely observed across many species, Part of a bacteriophage life that underlie complex biological systems is a prime sci- from the level of gene transcription to the level of sys- cycle in which its genome is entific goal in systems biology1,2.Robustness is a prop- temic homeostasis. For example, fate decision of λ phage expressed to cause dissolution erty that allows a system to maintain its functions despite — the result of which is the activation of either LYSIS or of the bacterial host cell, leading to manufacture of external and internal perturbations. It is one of the fun- LYSOGENY pathways — was once considered the result of more bacteriophage particles damental and ubiquitously observed systems-level phe- fine tuning of the binding affinity of promoters to corre- and subsequent infection of nomena that cannot be understood by looking at the sponding regulatory factors. However, it has been shown other cells. individual components. A system must be robust to that it is the structure of the network, which involves both function in unpredictable environments using unreliable positive and negative feedback, that is responsible for LYSOGENY Part of a bacteriophage life cycle, components. Understanding the origin and principles of making sustainable commitment, not the specific bind- during which its genetic material robustness in biological systems will help us to put vari- ing affinity — the fate-decision behaviour was shown to is integrated into the genome of ous biological phenomena into perspective; it will also be robust against point mutations in the promoter its bacterial host, where it catalyse the formation of principles at the systems level. region3.In addition, cooperative binding of repressors remains in a latent state. In this article, I argue that robustness is a fundamen- that forms implicit local positive feedback also con- 4–6 SEGMENTAL POLARITY tal feature of evolvable complex systems. Complex bio- tributes to the stability of the switch .Many examples of A pathway that regulates the logical systems must be robust against environmental robust properties can be observed in different biological anteroposterior identity of and genetic perturbations to be evolvable. Evolution systems. segments during insect often selects traits that might enhance robustness of the Escherichia coli is capable of chemotaxis over a development. organism. Robustness is, therefore, ubiquitous in living wide range of chemo-attractant concentrations organisms that have evolved. However, systems that are owing to integral intracellular feedback that ensures Sony Computer Science robust face fragility and performance setback as an perfect adaptation and that is independent of ligand Laboratories, Inc., 3-14-13 inherent trade-off. Identification of the basic architecture concentration7–9. Higashi-Gotanda, Shinagawa, Tokyo 141-0022, for a robust system and the associated trade-offs is essen- A biochemical network that is involved in the estab- Japan, and The Systems tial for understanding their faults and countermeasures lishment of SEGMENTAL POLARITY in Drosophila melanogaster Biology Institute, Suite 6A, — diseases and therapies, respectively. has been shown to be robust against changes in initial M31, 6-31-15 Jingumae, values and rate constants of molecular interactions, Shibuya, Tokyo 150-0001, Robustness as an organizational principle 10,11 Japan. enabling stable pattern formation .Similar obser- e-mail: [email protected] Robustness enables the system to maintain its functional- vations have also been made for MORPHOGEN-pattern doi:10.1038/nrg1471 ities against external and internal perturbations. This formations10,12,13. 826 | NOVEMBER 2004 | VOLUME 5 www.nature.com/reviews/genetics © 2004 Nature Publishing Group REVIEWS Robustness is often misunderstood to mean stay- Robust adaptation (return to a periodic attractor) ing unchanged regardless of stimuli or mutations, so that the structure and components of the system, and therefore the mode of operation, is unaffected. In fact, robustness is the maintenance of specific functionali- Transition to a ties of the system against perturbations, and it often new attractor requires the system to change its mode of operation in a flexible way. In other words, robustness allows changes in the structure and components of the sys- tem owing to perturbations, but specific functions are Stochastic process maintained. influences the In the following sections, I outline the mechanisms trajectory that ensure the robustness of a system: system control, alternative (or fail-safe) mechanisms, modularity and decoupling. System control. System control consists of negative and positive feedback to attain a robust dynamic response observed in a wide range of regulatory net- works, including the cell cycle, the circadian clock and chemotaxis7,17,18.Negative feedback is the princi- Robust adaptation pal mode of control that enables robust response (return to a point attractor) (or robust adaptation) to perturbations. Bacterial chemotaxis is one of the most studied examples Unstable of robust adaptation that uses negative feedback — Figure 1 | Robust reactions of the system: to stay or to change. The state of a system INTEGRAL FEEDBACK in particular — to attain the perfect can be shown as a point in the state space. In this case, the state space is simplified into two adaptation that allows chemotaxis to occur in response dimensions. Perturbations forcefully move the point representing the system’s state. The state of to a wide range of stimuli7–9.Integral feedback, a par- the system might return to its original attractor by adapting to perturbations, often using a negative feedback loop. Bacterial chemotaxis is an example. There are basins of attractions in the state ticular control strategy, is essential to maintain robust space within which the state of the system moves back to that attractor. If the boundary is adaptation in both E. coli and Bacillus subtilis,despite exceeded, the system might move into an unstable region or move to other attractors. Positive the fact that the network topologies are not the feedback can either move the system’s state away from the current attractor, or push the system same19. towards a new state. The cell cycle involves a combination of positive and negative feedbacks that Positive feedback contributes to robustness by facilitate transition between two attractors (G1 and S/G2/M) creating a bistable system. Often, amplifying the stimuli, often producing bistability, stochastic processes affect transition between attractors, as seen in λ-phage fate decision, but maintenance of a new state has to be robust against minor perturbations. so that the activation level of a downstream pathway can be clearly distinguished from non-stimulated states, and so that these states can be maintained. In D. melanogaster segment-polarity formation — Diseases such as cancer and diabetes are manifesta- repetitive stripes of differential gene expression — is tions of co-opted robustness, in which mechanisms that observed along the antero-posterior axis of the devel- normally protect our bodies are effectively taken-over to oping embryo. The first stripe has to express wingless sustain and promote the epidemic states14–16.As more (wg), the second stripe has to express engrained (en), studies are done, it is becoming important to provide an but the third stripe expresses neither. von Dassow and integrated perspective on the robustness of biological colleagues10 created a computational model of this systems. system, initially without positive autoregulatory feed- MORPHOGEN A diffusible signal that acts at a The robustness of a system can manifest itself in one back on wg and en,but the model failed to reproduce distance to regulate pattern of two ways: the system returns to its current ATTRACTOR experimentally observed patterns. However, with two formation in a dose-dependent or moves to a new attractor that maintains the system’s positive feedbacks on wg and en activations, robust manner. functions (FIG. 1).A return to the current attractor is pattern formation was reproduced10.Recently, Ingolia11 often called ‘robust adaptation’.The attractor can be analysed this model and showed that the bistability ATTRACTOR A point or an orbit in the phase either static (a point attractor; a fixed point in the PHASE caused by positive feedback loops is responsible for space where different states of SPACE that the trajectory of the system state approaches robust pattern formation11. the system asymptotically asymptotically) or oscillatory (a periodic attractor; a Positive feedback