Engineering longevity—design of a synthetic gene oscillator to slow cellular aging

Synthetic biology enables the design of gene networks to confer specific biological functions, yet it remains a challenge to rationally engineer a biological trait as complex as longevity. A naturally occurring toggle switch underlies fate decisions toward either nucleolar or mitochondrial decline during the aging of yeast cells. We rewired this endogenous toggle to engineer an autonomous genetic clock that generates sustained oscillations between the nucleolar and mitochondrial aging processes in individual cells. These oscillations increased cellular life span through the delay of the commitment to aging that resulted from either the loss of chromatin silencing or the depletion of heme. Our results establish a connection between gene network architecture and cellular longevity that could lead to rationally designed gene circuits that slow aging. Description Editor’s summary Yeast cells have a transcriptional toggle switch that leads them to die by one of two fates: One causes death by nucleolar decline, the other by mitochondrial decay. By rewiring this transcriptional switch into a negative-feedback loop, Zhou et al. were able to cause yeast cells to oscillate between the two states and increase their life span by 82% (see the Perspective by Salis). These results represent a step forward toward the use of engineering principles to design synthetic gene circuits that control complex biological traits. —L. Bryan Ray Preventing yeast cells from normal deterioration of aging through synthetic biology markedly extends life span.

[1]  M. Elowitz,et al.  Synthetic multistability in mammalian cells , 2021, bioRxiv.

[2]  L. Tsimring,et al.  A programmable fate decision landscape underlies single-cell aging in yeast , 2020, Science.

[3]  Miha Mraz,et al.  Computational analysis of viable parameter regions in models of synthetic biological systems , 2019, Journal of Biological Engineering.

[4]  L. Tsimring,et al.  Advances in quantitative biology methods for studying replicative aging in Saccharomyces cerevisiae , 2019, Translational medicine of aging.

[5]  David Baker,et al.  Modular and tunable biological feedback control using a de novo protein switch , 2019, Nature.

[6]  Jeff Hasty,et al.  Divergent Aging of Isogenic Yeast Cells Revealed through Single-Cell Phenotypic Dynamics. , 2019, Cell systems.

[7]  Aleksey V. Belikov.  Age-related diseases as vicious cycles , 2019, Ageing Research Reviews.

[8]  B. Kennedy,et al.  The yeast replicative aging model. , 2018, Biochimica et biophysica acta. Molecular basis of disease.

[9]  Sindy K. Y. Tang,et al.  Programming self-organizing multicellular structures with synthetic cell-cell signaling , 2018, Science.

[10]  James J Collins,et al.  Understanding Biological Regulation Through Synthetic Biology. , 2018, Annual review of biophysics.

[11]  H. Alper,et al.  Condition-specific promoter activities in Saccharomyces cerevisiae , 2018, Microbial Cell Factories.

[12]  Anastasia Baryshnikova,et al.  Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome. , 2018, Cell systems.

[13]  L. You,et al.  Quantitative and synthetic biology approaches to combat bacterial pathogens. , 2017, Current opinion in biomedical engineering.

[14]  Jeff Hasty,et al.  Multigenerational silencing dynamics control cell aging , 2017, Proceedings of the National Academy of Sciences.

[15]  Jeffrey S. Smith,et al.  The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae , 2016, Genetics.

[16]  Yaron E. Antebi,et al.  Dynamics of epigenetic regulation at the single-cell level , 2016, Science.

[17]  Lingchong You,et al.  Coupling spatial segregation with synthetic circuits to control bacterial survival , 2016, Molecular systems biology.

[18]  Christopher J. Murakami,et al.  A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging. , 2015, Cell metabolism.

[19]  Matt Kaeberlein,et al.  The SAGA histone deubiquitinase module controls yeast replicative lifespan via Sir2 interaction. , 2014, Cell reports.

[20]  James J. Collins,et al.  Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation , 2014, Cell.

[21]  M. Kaeberlein,et al.  Yeast replicative aging: a paradigm for defining conserved longevity interventions. , 2014, FEMS yeast research.

[22]  Austen R. D. Ganley,et al.  Cellular Senescence in Yeast Is Regulated by rDNA Noncoding Transcription , 2013, Current Biology.

[23]  Kami Kim,et al.  Bright and stable near infra-red fluorescent protein for in vivo imaging , 2011, Nature Biotechnology.

[24]  P. Fearnhead,et al.  Optimal detection of changepoints with a linear computational cost , 2011, 1101.1438.

[25]  M. Elowitz,et al.  Build life to understand it , 2010, Nature.

[26]  C. Bashor,et al.  Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. , 2010, Annual review of biophysics.

[27]  Linda Partridge,et al.  Extending Healthy Life Span—From Yeast to Humans , 2010, Science.

[28]  L. Tsimring,et al.  A synchronized quorum of genetic clocks , 2009, Nature.

[29]  G. Church,et al.  Synthetic Gene Networks That Count , 2009, Science.

[30]  A. Shilatifard,et al.  Histone H4 lysine-16 acetylation regulates cellular lifespan , 2009, Nature.

[31]  J. Stelling,et al.  A tunable synthetic mammalian oscillator , 2009, Nature.

[32]  M. Bennett,et al.  A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.

[33]  Y. Kuznetsov,et al.  New features of the software MatCont for bifurcation analysis of dynamical systems , 2008 .

[34]  B. Zwaan,et al.  Genes encoding longevity: from model organisms to humans , 2008, Aging cell.

[35]  Matt Kaeberlein,et al.  Quantitative evidence for conserved longevity pathways between divergent eukaryotic species. , 2008, Genome research.

[36]  M. Bryk,et al.  Sir2 represses endogenous polymerase II transcription units in the ribosomal DNA nontranscribed spacer. , 2006, Molecular biology of the cell.

[37]  Brian K. Kennedy,et al.  Sirtuins in Aging and Age-Related Disease , 2006, Cell.

[38]  Matt Kaeberlein,et al.  Regulation of Yeast Replicative Life Span by TOR and Sch9 in Response to Nutrients , 2005, Science.

[39]  Marc Lavielle,et al.  Using penalized contrasts for the change-point problem , 2005, Signal Process..

[40]  B. Kennedy,et al.  Large-scale identification in yeast of conserved ageing genes , 2005, Mechanisms of Ageing and Development.

[41]  Matt Kaeberlein,et al.  Sir2-Independent Life Span Extension by Calorie Restriction in Yeast , 2004, PLoS biology.

[42]  A. Fournier,et al.  The S. Cerevisiae HAP Complex, a Key Regulator of Mitochondrial Function, Coordinates Nuclear and Mitochondrial Gene Expression , 2003, Comparative and functional genomics.

[43]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[44]  L. Guarente,et al.  Genetic pathways that regulate ageing in model organisms , 2000, Nature.

[45]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[46]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[47]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[48]  M. McVey,et al.  The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. , 1999, Genes & development.

[49]  L. Guarente,et al.  Yeast HAP2 and HAP3: transcriptional activators in a heteromeric complex. , 1988, Science.

[50]  Steven Hahn,et al.  Yeast HAP2 and HAP3 activators both bind to the CYC1 upstream activation site, UAS2, in an interdependent manner , 1987, Cell.

[51]  L. Guarente,et al.  Heme regulates transcription of the CYC1 gene of S. cerevisiae via an upstream activation site , 1983, Cell.