Molecular Fitness Landscapes from High-Coverage Sequence Profiling

Abstract

The function of fitness (or molecular activity) in the space of all possible sequences is known as the fitness landscape. Evolution is a random walk on the fitness landscape, with a bias toward climbing hills. Mapping the topography of real fitness landscapes is fundamental to understanding evolution, but previous efforts were hampered by the difficulty of obtaining large, quantitative data sets. The accessibility of high-throughput sequencing (HTS) has transformed this study, enabling large-scale enumeration of fitness for many mutants and even complete sequence spaces in some cases. We review the progress of high-throughput studies in mapping molecular fitness landscapes, both in vitro and in vivo, as well as opportunities for future research. Such studies are rapidly growing in number. HTS is expected to have a profound effect on the understanding of real molecular fitness landscapes.

High throughput sequencing of in vitro selections of mRNA-displayed peptides: data analysis and applications

“…34,35 Another example is using mRNA display to mimic natural Darwinian protein evolution in the lab to examine protein fitness landscapes. [36][37][38][39] The high versatility of mRNA display methods adds value to its potential benefits for the in vitro selection of peptides and proteins.…”

“…Evolution over the fitness landscape can be conceptualized as a random walk with a bias toward climbing hills. 37,50 Knowledge of the fitness landscape is critical for understanding molecular evolution, as evolutionary outcomes could be predicted, in principle, given complete knowledge of the fitness landscape in a particular environment. However, prior to HTS, empirical data on fitness landscapes was quite limited.…”

“…52 Epistasis is therefore an important feature determining the viability of individual evolutionary pathways of protein sequences. 37 Calculations to measure epistasis in experimental fitness landscapes have been reviewed elsewhere. 53 To map fitness landscapes, individual sequences would be sampled and their fitness determined (such as by sequencing).…”

Substitutional landscape of a split fluorescent protein fragment using high-density peptide microarrays

“…High-density peptide microarrays provide a powerful technology for massively parallel screening of peptide-protein interactions. While DNA and RNA arrays have been extensively used in mappings of polynucleotide-protein interactions (10), peptide microarrays have mostly been reserved for antibody epitope mapping and screening receptor-ligand interactions (11). Peptide microarrays cannot, however, typically accommodate peptides longer than 15-20 residues and, in addition, the affinity of the peptide-protein interaction to be investigated needs to be less than µM (11).…”

Effective potential reveals evolutionary trajectories in complex fitness landscapes

“…In Wright's vivid words, the interaction of selection and variation enables populations to "continually find their way from lower to higher peaks" [4], thereby providing a universal mechanism for open-ended evolution [5]. Thanks to the explosive development of sequencing technologies, fitness landscapes have now been measured in a variety of real molecular [6], viral [7] or microbial [8] systems. As a result, the goal of predicting evolution no longer appears wholly out of reach [8][9][10][11][12].…”