Silver: History and Philosophy

The Silver group has followed many different scientific paths over the years so I thought I would provide a little history and perspective here. Most of our success can be attributed to the numerous students and fellows who have travelled through the lab over the years.

The group began around my original discovery of one of the first nuclear localization signals – short peptides that target proteins to the nucleus. Following on this, the focus was on the organization of the nucleus and movement of molecules between the cytoplasm and the nucleus. In the course of this work, we developed and confirmed some of the models of nuclear transport, developed a systems-wide approach to the problem and people extended this work as they departed to establish their own groups. The lab was continuously funded by the NIH including with a MERIT award and was located for many years in the Dana Farber Cancer Institute and the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School. We even made a number of contributions to development of anti-cancer therapies – including a small molecule screen, which resulted in a novel cancer therapeutic now in successful clinical trials at Karyopharm Therapeutics as well as pioneering some of the first uses of GFP to track molecules within the nucleus.

Some years ago, I had the good fortune to meet a group of computer scientists and bio-engineers who formed the Synthetic Biology Working Group at MIT. My group became increasingly engaged in developing the fields of Systems and Synthetic Biology and we are now recognized as leaders in efforts to engineer biological systems to perform useful tasks. As a result of these efforts, I became one of the founding members of the Department of Systems Biology at Harvard Medical School. This was a good fit because Synthetic Biology seeks to provide a computational framework to make the engineering of biological systems faster and more predictable. I participated in formulating the first definitive report on Synthetic Biology for the US government, which helped set the international agenda for the field.

We have enjoyed a number of successes including the rational engineering of genetic circuits in both eukaryotes and prokaryotes, metabolic engineering to re-route carbon metabolism and the application of modularity in cell engineering and the design of organisms to report on states within animals. The development of the Bionic Leaf and natural gut bacteria that sense prior drug exposure to animals illustrate many of our approaches. Here are some key references.

Our group has a very informal atmosphere. We encourage people to work on interesting, unsolved problems that might have broad implications. We also encourage collaborations and forays into completely new areas. For example, we are working with Neri Oxman at MIT on photosynthetic wearables and Dan Nocera on the Bionic Leaf. I also believe in the empowerment of young researchers as they are the future of science. The engineering of biology is the technology of this century. To paraphrase a certain rock band of the last century - 'it's going to be a long strange trip.'

Here are some relevant references if you want to check them out.

• Kahana JA, Schnapp BJ, and Silver PA (1995).Kinetics of spindle pole body separation in budding yeast. Proc. Natl. Acad. Sci. 92:9707-9711. PMCID: PMC40871.
• Kau TR, Schroeder F, Wojciechowski C, Zhou JJ, Roberts T, Clardy J, Sellers W and Silver PA (2003). A chemical genetic screen for inhibitors of regulated export of a Forkhead transcription factor in tumor cells. Cancer Cell, 4:463-476. PMID: 14706338.
• Silver PA, Collins J and Weiss R (2013). A National Initiative for Mammalian Synthetic Biology. OSTP report.
• Way JC, Collins JJ, Keasling JD, Silver PA. (2014). Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell. 157(1):151-61. PMID: 24679533

Here I summarize some of our accomplishments over the years.

1. Nuclear organization and transport. During my postdoctoral work, I independently conceived of and discovered one of the first NLs and early work from my own lab therefore focused on factors required for nuclear protein and RNA transport. This led to identification of receptors for nuclear protein transport and the elucidation of the role of various nuclear pore proteins. We were among the first to move from a ‘single factor’ analysis to a more systems-based approach. We used novel imaging techniques to map interactions between transport factors and the nuclear pore. We were also among the first to investigate the interactions between the genome and nuclear transport. In doing so, we found that some activated genes moved to the nuclear pore upon activation in yeast. We extended these studies to mammalian cells including genome-wide mapping of binding of key transcription and transport factors. This work has laid the foundation for work in many labs and establishes our ability to image spatio-temporal events in living cells. It also led to the discovery of novel molecules that trap tumor suppressors in the nucleus and thereby reverse the tumorogenic phenotype. These molecules are now in successful clinical trials for a number of different types of cancer.

• Damelin, M. and Silver, P.A. Mapping interactions between nuclear transport factors in living cells reveals distinct pathways through the nuclear pore complex. 2000. Molecular Cell, 5:133-140.
• Casolari, J., Brown, CR, Komili, S., West, J., Hieronymus, H., and Silver, PA. Genome-wide localization of the nuclear transport machinery reveals coupling of transcriptional status and nuclear organization. 2004. Cell, 117:427-439
• Carrol JS, Liu XS, Brodsky AS, Meyer CA, Geistlinger TR, Fox EA, Silver PA and Brown M. Chromosome wide mapping of estrogen receptor binding reveals long-range combinatorial regulation requiring forkhead proteins. 2005. Cell, 122:33-43
• Brown CR, Kennedy CJ, Delmar VA, Forbes DJ and Silver PA. Global histone acetylation induces functional genomic reorganization at the mammalian nuclear pore complex. 2008. Genes & Dev. 22: 627-639.

2. RNA processing and transport. Our early studies of nuclear transport used a novel genetic screen in yeast. This led to the discovery of a number of key factors including RNA binding proteins that also control other aspects of mRNA processing indicating a close interplay between these processes. We determined the relative specificity for mRNAs for these factors using a genome-wide approach. We were also among the first to use GFP to show the kinetics of shuttling of these RNA transport factors between the nucleus and the cytoplasm. In subsequent studies, we translated this work to mammalian cells where mRNA splicing and transport is key to some genetic diseases.

• Hieronymus H and Silver PA. Genome-wide analysis of RNA-protein interactions reveals specificity of mRNA export machinery. 2003. Nature Genetics 2:155-61.
• Waks Z, Silver PA. Nuclear origins of cell-to-cell variability. Cold Spring Harb Symp Quant Biol. 2011 2010;75:87-94.
• Wang QQ, Moore MJ, Adelmant G, Marto JA and Silver PA. PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. 2013. Genes Dev, Mar 15;27(6):615-26

3. Gene Regulation. In the course of our studies of nuclear transport, we found an intimate connection between nuclear transport and gene regulation. One of our key discoveries was the identification of the first arginine methyltransferase, which not only plays a role in chromatin function but is also important in the movement of RNA binding proteins between the nucleus and the cytoplasm. In addition, we made a surprising discovery that not all ribosomes are created equal; there is a unique previously undescribed specificity for the matching between ribosomes and translation of mRNAs. This finding continues to have implications including in cancer cells as reported by others. We also used our knowledge of synthetic switching to build unique sensors for silent regions in mammalian cells.

• Yu MC, Lamming DW, Eskin JA, Sinclair DA and Silver PA. The role of arginine methylation in formation of silent chromatin. 2006. Genes and Dev. 20:3249-56.
• Komili S, Farny N, Roth F and Silver PA. Functional specificity among ribosome proteins regulates gene expression. 2007. Cell 131:557-71.
• Swinburne, I., Miguez, DG, Landgraf, D. and Silver, PA. Intron length increases oscillatory periods of gene expression in animal cells. 2008. Genes & Dev., 22:2342-6.
• Haynes KA, Ceroni F, Flicker D, Younger A. and Silver PA. A sensitive switch for visualizing natural gene silencing in single cells. 2012. ACS Synthetic Biology Mar 16;1(3):66-106

4. Photosynthesis and carbon fixation. Dave Savage, now a Professor at UC Berkeley brought the study of the photosynthetic cyanobacteria to the laboratory. Many people worked and continue to work on these fascinating organisms with great potential. We characterized the behavior of the major carbon-fixing unit, termed the carboxysome. We also engineered them to be commodity producing factories and showed how one might improve their photosynthetic efficiency. This has led to a general interest in intracellular compartments and their engineering.

• Savage DF*, Afonso B*, Chen A and Silver PA. Spatially ordered dynamics of the bacterial carbon fixation machinery. 2010. Science, 327:1258-61
• Niederholtmeyer, H, Wolfstadter, BT, Savage, DF, Silver PA, and Way JC. Engineering synthesis and export of hydrophilic products from cyanobacteria. 2010. App. & Env. Engineering, 76(11)3462-6.
• Ducat D, Sachdeva G and Silver PA. Rewiring Hydrogenase-dependent Redox Circuits in Cyanobacteria. 2011. Proc Natl Acad Sci, 108:3941-6.
• Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA and Savage DF. Modularity of a carbon-fixing organelle. 2011. Proc Natl Acad Sci.,.

5. Synthetic biology. For about the past ten years, much of my lab has focused on the building of predictable genetic circuits and new chromosomes with a goal of using the power of biology to enable real world applications. In brief, this includes the design of predictable circuits that can remember past events in both prokaryotes and eukaryotes, including the construction of mammalian cells that remember the amount of radiation to which they were exposed. This has implications medically and for space travel and was of interest to NASA. More recently, we engineered natural gut bacteria that can remember exposure to antibiotics in the context of whole animals (mice) and can ‘count’ the number of generations since exposure. These programmable sensors have potential as probiotics for treating inflammation and for diagnostics particularly in the livestock industry. They also tell us more about various cell population behaviors. We have devised new methods for constructing very large segments of human DNA that will be directly applicable to the construction of engineered organisms. And lastly, together with Dan Nocera we have developed the bionic leaf that is the first bioengineered system to beat photosynthesis.

• Delebecque CJ, Lindner AB, *Silver PA and Aldaye FA. Organization of intracellular reactions with rationally designed RNA assemblies. 2011. Science 333:470-4 (*corresponding author)
• Burrill DR, Inniss MC, Boyle PM and Silver PA. Synthetic memory circuits for tracking human cell fate. 2012 Genes Dev. Jul 1;26(13):1486-97
• Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA. Progammable bacteria detect and record environmental signals in the mammalian gut. 2014, PNAS Apr 1;111(13):4838-43.
• Torella JP, Gagliardi CJ, Chen JS, Bediako DK, Way JC, Silver PA, Nocera DG. Efficient solar to fuels production from a hybrid microbial water splitting catalyst system. 2015. Proc Natl Acad Sci Feb 9

Complete list of Published Work: http://www.ncbi.nlm.nih.gov/pubmed/?term=silver+pa