ALBERT

Description: A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10(-3) or even about 10(-2), with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meer, Margarita V -- Kondrashov, Alexey S -- Artzy-Randrup, Yael -- Kondrashov, Fyodor A -- England -- Nature. 2010 Mar 11;464(7286):279-82. doi: 10.1038/nature08691. Epub 2010 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioinformatics and Genomics Programme, Centre for Genomic Regulation, C/Dr Aiguader 88, Barcelona Biomedical Research Park Building, 08003 Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20182427" target="_blank"〉PubMed〈/a〉

Description: Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarkisyan, Karen S -- Bolotin, Dmitry A -- Meer, Margarita V -- Usmanova, Dinara R -- Mishin, Alexander S -- Sharonov, George V -- Ivankov, Dmitry N -- Bozhanova, Nina G -- Baranov, Mikhail S -- Soylemez, Onuralp -- Bogatyreva, Natalya S -- Vlasov, Peter K -- Egorov, Evgeny S -- Logacheva, Maria D -- Kondrashov, Alexey S -- Chudakov, Dmitry M -- Putintseva, Ekaterina V -- Mamedov, Ilgar Z -- Tawfik, Dan S -- Lukyanov, Konstantin A -- Kondrashov, Fyodor A -- 55007424/Howard Hughes Medical Institute/ -- England -- Nature. 2016 May 11;533(7603):397-401. doi: 10.1038/nature17995.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia. ; Nizhny Novgorod State Medical Academy, Minin Sq. 10/1, 603005 Nizhny Novgorod, Russia. ; Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 88 Dr. Aiguader, 08003 Barcelona, Spain. ; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain. ; Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, g.Dolgoprudny 141700, Russia. ; Faculty of Medicine, Moscow State University, Lomonosov Avenue 31/5, Moscow 119192, Russia. ; Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, 4 Institutskaya Str., Pushchino, Moscow Region 142290, Russia. ; Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia. ; A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia. ; Department of Bioinformatics and Bioengineering, Moscow State University, Moscow 119234, Russia. ; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA. ; Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel. ; Institucio Catalana de Recerca i Estudis Avancats (ICREA), 23 Pg. Lluis Companys, 08010 Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27193686" target="_blank"〉PubMed〈/a〉