David Savage

David Savage

Associate Professor of Biochemistry, Biophysics, and Structural Biology
Dept of Molecular & Cell Biology
(510) 643-7847
Research Expertise and Interest
biochemistry, metabolism, photosynthetic systems, Systems and Synthetic Biology, protein engineering
Research Description

The goal of the Savage Lab is to understand how protein machinery – including both enzymes and structural scaffolds - facilitates the biochemistry of the cell. We are particularly interested in photosynthesis, a complex set of reactions that must occur in the right place and time to capture and convert light into stored chemical energy. Photosynthesis is also uniquely important for human society. It catalyzes the assimilation of inorganic carbon into the organic world and is the ultimate source of nearly all nutritional calories on Earth. Our specific model system is the cyanobacterium Synechococcus elongatus PCC7942, which uses the multi-scale cooperation of many different protein components to increase the fidelity and rate of the critical enzyme ribulose-1,5-bisphosphate carboxylase / oxygenase (RuBisCO) in a process known as the Carbon dioxide Concentrating Mechanism (CCM). We use the tools of biochemistry, molecular biology, and synthetic biology to identify and interrogate the key players and mechanistic principles underlying CCM function. Ultimately, we hope to develop a total cell biological understanding of how CCM function emerges from individual components and to use this understanding for the improvement of carbon dioxide assimilation in plants. We are therefore also interested in the development of novel genome editing technologies to facilitate these experiments. Our specific areas of research are as follows.

Towards a Total Cell Biological Understanding of the CCM

Cyanobacteria carry out photosynthetic carbon dioxide assimilation by controlling when and where these biochemical reactions occur. Perhaps most amazing is the use of a protein organelle, the carboxysome, to achieve improved activity of RuBisCO. RuBisCO is a notoriously bad enzyme, and it is thought the inside of the carboxysome provides a microenvironment within the cell of high carbon dioxide (and possibly low oxygen) as a means of improving rate and specificity. Despite numerous structural studies of carboxysome components, there are many open questions we are currently investigating related to how this massive complex self-assembles and functions in the context of the cellular milieu. For example, our systems model of the CCM (Mangan et al. 2016) suggests that pH, carbon transport, and carboxysome permeability are highly intertwined and we are interested in mechanisms that can control the permeability of the carboxysome shell. Second, work from our group has demonstrated the inherent genetic modularity of the CCM may all for it to be transferred to other organisms in order to improve their growth (Bonacci et al. 2012). We are therefore also developing tractable genetic systems to explore, in a synthetic biological context, how CCMs can be constructed de novo. Finally, we are interested in elucidating novel regulatory pathways (Hood et al. 2016) and isolating uncharacterized components that contribute to CCM function.

Understanding the Diversity and Functions of Protein Compartments

The carboxysome is a 250 MDa+ complex formed from thousands of proteins, yet it self-assembles in the bacterial cytosol into monodisperse particles. How does this amazing process occur? In previous work, we have used microscopy to demonstrate the importance of carboxysome partitioning during cell division and the surprising connection between this process and the bacterial cytoskeleton (Savage et al. 2010; Yokoo et al. 2015). More recently we have focused on assembly directly and have demonstrated the minimal set of proteins sufficient to produce the carboxysome in a heterologous host (Bonacci et al. 2012), and honed in on one of these proteins, CsoS2, as particularly critical to the process (Chaijarasphong et al. 2016). We are now currently building on these advances to understand how specific protein-protein interactions direct the assembly process and are attempting to elucidate the fundamental biophysical principles leading to high fidelity assembly. Finally, we now believe that the carboxysome is yet one example of myriad ways in which protein compartments can facilitate biochemical function (Nichols et al. 2017). We are thus also interested identifying novel compartments and, more broadly, understanding the functional principles of compartmentalization.   

Tools for Protein Engineering

Our group takes an integrative view of protein function. That is, we are interested not only in protein mechanism but also in trying to understand this mechanism in its native, cellular context. We therefore also develop genetic tools to interrogate proteins in the cell. Much of this effort has been focused on leveraging recent advances in DNA sequencing to interrogate protein function in higher throughput and also demonstrating that protein sequence topology is a critical, yet often unexplored, dimension of the sequence-function landscape (Higgins and Savage 2017). Highlights of our recent work including developing a novel systematic mutagenesis method (Higgins et al. 2017), a transposon-based method for rapidly constructing metabolite biosensors (Nadler et al. 2016), and development of an allosterically regulated Cas9 variant (Oakes et al. 2016).

Genome Editing Applications

An important application of our protein engineering work is to make more robust and controllable tools for genome editing. For example, the study of many model organisms, particularly plants, is constrained by our ability to quickly and easily manipulate gene sequence and gene expression. Although recent advances with CRISPR-Cas proteins, such as Cas9, have accelerated this progress, much remains to be done. We are therefore focused on constructing highly engineered versions of the Cas9 protein that are robust, yet tunable (Oakes et al. 2016), more optimal as a genetic fusion partner for interrogating the genome, and easier to deliver to many cell types. 

Representative Publications

Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF. 2012. Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci USA 109: 478–483.

Chaijarasphong T, Nichols RJ, Kortright KE, Nixon CF, Teng PK, Oltrogge LM, Savage DF. 2016. Programmed Ribosomal Frameshifting Mediates Expression of the α-Carboxysome. J Mol Biol 428: 153–164.

Higgins SA, Ouonkap SVY, Savage DF. 2017. Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering. ACS Synth Biol 6: 1825–1833.

Higgins SA, Savage DF. 2017. Protein Science by DNA Sequencing: How Advances in Molecular Biology Are Accelerating Biochemistry. Biochemistry.

Hood RD, Higgins SA, Flamholz A, Nichols RJ, Savage DF. 2016. The stringent response regulates adaptation to darkness in the cyanobacterium Synechococcus elongatus. Proc Natl Acad Sci USA 113: E4867–76.

Mangan NM, Flamholz A, Hood RD, Milo R, Savage DF. 2016. pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism. Proc Natl Acad Sci USA 113: E5354–62.

Nadler DC, Morgan S-A, Flamholz A, Kortright KE, Savage DF. 2016. Rapid construction of metabolite biosensors using domain-insertion profiling. Nature Communications 7: 12266.

Nichols RJ, Cassidy-Amstutz C, Chaijarasphong T, Savage DF. 2017. Encapsulins: molecular biology of the shell. Crit Rev Biochem Mol Biol 52: 583–594.

Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF. 2016. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nat Biotechnol 34: 646–651.

Savage DF, Afonso B, Chen AH, Silver PA. 2010. Spatially ordered dynamics of the bacterial carbon fixation machinery. Science 327: 1258–1261.

Yokoo R, Hood RD, Savage DF. 2015. Live-cell imaging of cyanobacteria. Photosynthesis Research 126: 33–46.

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