TIMELINE OF OUR RESEARCH
Our goal is to discover the general principles that govern cellular physiology. Our research asks how living cells allocate resources, coordinate biosynthesis, maintain organization, and ultimately reproduce. Rather than focusing on a particular organism, we combine quantitative experiments, theory, and technology development to identify principles that transcend individual species. This journey has taken us from bacterial chromosome organization and cell-size control to resource allocation and the broader physiology of growth across the three domains of life.
Between 2010 and 2020, much of our work helped establish single-cell physiology as a quantitative approach to bacterial growth and homeostasis. In 2010, we introduced the mother machine, which made it possible to follow individual cells over hundreds of generations under precisely controlled conditions. The resulting data led us to our report of the adder principle in 2014 and, subsequently, to its mechanistic origin in 2019. We now view this body of work within the broader framework of balanced growth and its consequences for homeostasis and precision control. These ideas remain an important intellectual pillar of our research.
During the pandemic, we began exploring several new directions and expanded our work beyond bacteria to archaea and eukaryotic cells. These efforts are now converging on a broader question: how living cells coordinate growth and biosynthesis across the three domains of life. By comparing systems in which balanced growth is maintained, challenged, or breaks down, we hope to uncover the general principles that govern cellular physiology across the tree of life.
CURRENT DIRECTIONS
While studying the origin and consequences of balanced biosynthesis in bacteria in the context of precision control, our current work also extends beyond bacteria to the organization, dynamics, and resource allocation of membrane-bound organelles in eukaryotic cells, to quantitative approaches to archaeal physiology, and to bringing fundamental concepts developed in economics to physiology and vice versa (econophysiology). Together, these efforts ask how balanced growth and resource allocation are maintained, challenged, or replaced across the three domains of life.
Conceptual breakthrough |
Tools development |
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Decoupling of global metabolic flux and proteome partitioning in bacteria (Science 2026)
R. Thiermann*, J. Yang*, A. Zodage*, F. She*, D. K. Fung, T. Rytlewski, F. Abdollah-Nia, F. Xiao, J. T. Sauls, S. Cox, Z. Ghulam-Jelani, V. Castillo, Q. A. Paulsen, D. M. Stevenson, D. Amador-Noguez, J. R. Williamson, J. D. Wang**, S. Jun**, Science 392, aeb6410 (2026)
Physiology is ultimately about flux. For twenty years, the field assumed the rule connecting flux to proteome composition, (p)ppGpp coupling amino acid supply to ribosome production in E. coli, was close to universal. In Bacillus subtilis, we found a different architecture entirely: not (p)ppGpp, but GTP itself, doing double duty as both a building block for protein synthesis and the signal that decides how much of it the cell can spend. So the relationship between proteome and flux isn't a fixed law. It's species-dependent.
That dual role also creates a choice we didn't expect. The cell can hold back growth to stay armored against stress, or let go and grow fast at the cost of surviving what comes next. We assume bacteria are wired to grow as fast as possible, but this one doesn't take that deal. When we removed the brake, growth sped up and survival collapsed. It looks like the cell is constantly gambling between the two, which may be part of why bacteria are so hard to kill.
It's time to go beyond E. coli.
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Robust and resource-optimal dynamic pattern formation of Min proteins in vivo (Nature Physics 2025)
Z. Ren*, H. Weyer*, M. Sandler*, L. Würthner*, H. Fu, C. B. Tangtartharakul, D. Li, C. Sou, D. Villarreal, J. E. Kim, E. Frey**, S. Jun**, Nature Physics 21, 1160–1170 (2025)
The Min system is a textbook problem: two proteins slosh from pole to pole inside the cell, and that oscillation is what tells the cell where the middle is, so division doesn't go wrong. Physicists have modeled the oscillation itself for twenty years. Almost nobody asked a physiologist's question: does the cell actually need to run this system the way it does, or could it get away with less? We built E. coli strains where we could dial MinD and MinE expression up and down across fast and slow growth, mapped out a full phase diagram of traveling waves, standing waves, and everything between, and found that the amount of Min protein the cell actually makes sits right at the resource-optimal point, robust to real physiological swings in concentration and growth rate. The wavelength of the pattern doesn't even move across most of that diagram.
The major lesson here is that by looking at classic biophysics problems through the eye of a physiologist, one opens a completely new and rich conceptual avenue.
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Tools and methods for high-throughput single-cell imaging with the mother machine (eLife 2024)
R. Thiermann et al., eLife (2024) 12, RP88463.
A decade ago we built our first mother machine analysis tool in C++, then rebuilt it in MATLAB, then Python, refining it in-house release after release while hundreds of other labs adopted the device itself but had no equivalent tool of their own. napari-MM3 is that decade of work, finally made public. Along the way we found something uncomfortable: two people using the same segmentation method, with slightly different settings, can end up measuring the same cells as 5–10% different in size. We call it WYPIWYG, what you put is what you get, and it's true whether you're using classical thresholding or a neural network. The good news is that the physiology survives it. Growth rate, added volume, the correlations that actually drive cell-size control, come out the same no matter which tool or which settings you use. This is the pipeline we use in our own lab, and now anyone can use it too.
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DNA replication initiation as precision control
H. Fu*, F. Xiao*, S. Jun**, PRX Life 1, 013011 (2023)
T. O. Boesen*, G. Charbon*, H. Fu*, C. Jensen, M. Sandler, S. Jun**, A. Løbner-Olesen**, PNAS 121, e2322772121 (2024)Bacterial physiology has a puzzle at its core: balanced growth. In balanced growth, the proteins that control the cell cycle sit at nearly constant concentration, so bacteria can't use concentration itself to control the cell cycle in a size-dependent way, a stark contrast to eukaryotes. Thirty years ago, a "titration" model proposed a way out: instead of sensing concentration, the cell counts available binding sites, and initiation fires once the initiator protein saturates them. It was elegant, but incomplete. We rebuilt it from the ground up and showed protein counting can explain the precision of replication initiation across growth conditions, not just its rough timing. The result was selected as a Viewpoint in Physics Magazine, one of the top 1% of articles published by the American Physical Society that year.
If titration is really doing the work, the cell shouldn't need much else beyond the master initiator protein, DnaA, to control initiation. But DnaA exists in two forms, DnaA-ATP and DnaA-ADP, and for decades the field assumed the cell needed a small army of regulators just to switch between them. Our collaborators (Løbner-Olesen) built a strain with all four known extrinsic regulators removed, something no one thought was possible, and found the cell cycle ran almost normally under slow growth. The surprise came at faster growth: once replication cycles began to overlap, the Δ4 strain's cell cycle became noticeably less robust, showing why the cell needs both forms of DnaA once multifork replication is in play.
Balanced growth turns out to reach much further than we expected, from the origin of the adder principle to precision control of replication initiation, and it's going to keep us busy for the next decade.
PRX Life 2023 PNAS 2024
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Mechanistic origin of cell-size control and homeostasis in bacteria (Current Biology 2019)
F. Si*, G. Le Treut*, J. T. Sauls, S. Vadia, P. A. Levin, S. Jun**, Current Biology 29, 1760–1770 (2019)
The adder principle had been sitting in plain sight since 2015: cells add a constant volume between birth and division, no matter their size at birth. Nobody knew why. Here we found the answer. Division fires when a fixed number of division proteins accumulates, and that accumulation tracks volume growth exactly. Two simple rules, threshold and balanced biosynthesis, are enough to produce the adder from scratch. It's not a coincidence of bookkeeping. It's what falls out when a cell counts proteins while growing steadily. The same two rules hold in both E. coli and B. subtilis, two organisms separated by a billion years of evolution. Once we understood the mechanism, we could reprogram cell size in both species, predictively, on demand.
This work concludes our 10-year journey: the invention of the mother machine (Curr. Biol. 2010), the discovery of the adder principle (Curr. Biol. 2014), the explanation of the growth law first observed by Schaechter et al. in the 1950s (Curr. Biol. 2017), and finally the mechanism of the adder principle itself (Curr. Biol. 2019).
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Video abstract explaining the mechanistic origin of adder. -
Fundamental principles in bacterial physiology: history, recent progress, and the future
S. Jun, F. Si, R. Pugatch, M. Scott, Reports on Progress in Physics 81, 056601 (2018)
The field discovered its deepest quantitative laws once, in the 1940s–70s — then spent thirty years forgetting them while molecular biology took over the conversation. This is the full story of that golden era, why it got lost, and how single-cell methods finally forced the field to rediscover what it already knew. 96 pages, 715 references — written to be the one place you go if you want to actually understand where the ideas in this field came from, rather than piece it together from scattered citations.
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The fundamental unit of cell size in bacteria (Current Biolology 2017)
F. Si et al., Current Biology 27, 1278–1287 (2017)
We explain the overarching quantitative principle of cell size control in bacteria. Briefly, we discovered the fundamental unit of cell size in bacteria, which remains invariant under extensive inhibition of biosynthesis. The cell size is therefore a sum of all invariant unit cells, and the resulting ‘general growth law’ predicts cell size under any growth condition. This is one of the most important results from our lab.
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A tunable CRISPR interference system
X. Li et al., Scientific Reports (2016) 6, 39076.
We developed "tCRISPRi" for precise and continuous titration of gene expression with minimal leaky repression, especially suitable for physiological studies. Construction of tCRISPRi to target a new gene requires only one-step of oligo recombineering.
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Discovery of the adder principle of size homeostasis (Current Biology 2015)
S. Taheri-Araghi et al., Current Biology 25, 385–391 (2015).
S. Jun, S. Taheri-Araghi, Trends Microbiol. 23, 4–6 (2015).We discovered and introduced the notion of the “adder” principle of cell size control and homeostasis. There is interesting story what led to our discovery originally in 2012 and why we named the principle “adder.” Those curious should look at the extended version of the supplementary information.
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Growth as the origin of morphological plasticity (PNAS 2014)
A. Amir, F. Babaeipour, D. B. McIntosh, D. R. Nelson, S. Jun, PNAS 111, 5778–5783 (2014).
This was originally a summer project for three interns in our previous lab at Harvard in 2009. We noticed that cells growing in the mother machine always bend during growth by the growth media flow, and do not recover their shape immediately even if the flow stops. However, when we repeated the experiments in water, thus without growth, cells bend like an elastic rod and recovers the original straight shape completely and immediately. We concluded that it is growth that is the origin of morphological plasticity of E. coli.
The pioneering interns playing ping pong in 2009: Emily Hanna (front left) and Alyssa Kanagaki (front right) were summer undergrad research students from Barry University and Hamilton College, respectively, and Christina Nürnberg (ping pong master) was a 12th grade of the Erzbischöfliche Gymnasium in Germany.
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Chromosome organization during overlapping cell cycles
AB. Youngren, H. Nielsen, S. Jun, S. Austin, Genes & Development 28, 71–84 (2014).
This work by Stuart Austin’s group is the first to crack the organization of the E. coli chromosome including replisome positions during multifork replication. The results are consistent with the entropic spring view of the E. coli chromosome.
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Bacterial chromosome as a “soft” entropic spring (PNAS 2012)
J. Pelletier et al., PNAS 109, E2649–56 (2012)
We originally developed the “mother machine” to do the experiments presented in this paper. Our idea was to build an artificial cell-like environment, confine ex vivo bacterial chromosomes, and physically and biochemically manipulate them. Eventually, our dream was to replicate the ex vivo chromosomes. This work presents novel, extensive experimental and theoretical results that show bacterial chromosomes behave as soft entropic springs. This work took 7 years from its conception to publication.
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Invention of the Micro-piston (PNAS 2012)
J. Pelletier et al., PNAS 109, E2649–56 (2012)
In the “mother machine”, we compressed and un-compressed individual ex vivo E. coli chromosomes. We used micro beads as a “piston” by manipulating it using optical tweezers. See movie below.
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E. coli growth is robust and does not show aging (Current Biology 2010)
P. Wang et al., Current Biology 20, 1099–1103 (2010).
Using the mother machine, we analyzed the growth and division patterns of hundreds of thousands E. coli cells from the beginning to their death. The growth rate remained remarkably constant, whereas the death rate increased exponentially (albeit very slowly). This is the first work that shows growth is robust and completely decoupled from death in E. coli. Researchers later discovered similar constant growth without aging in other organisms such as B. subtilis and fission yeast S. pombe.
Read moreInvention of the mother machine (Current Biology 2010)
P. Wang et al., Current Biology 20, 1099–1103 (2010).
The mother machine is a simple microfluidic device that is extremely versatile and robust. We originally developed it in 2007 to the “piston” experiment (see above micro-piston 2012). We soon realized that we can use the same device to grow and track thousands of individual mother cells for hundreds of consecutive divisions. The mother machine has been adopted by hundreds of labs from microbiology to systems biology across the world.
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Entropy-driven segregation of the bacterial chromosome (PNAS 2006)
S. Jun, B. Mulder, PNAS 103, 12388–12393 (2006).
Read moreThis is the theoretical work that proposed bacterial chromosomes segregate mainly driven by entropic forces. In physics, this work contributed to the resurgence of interests in polymers in confined space. In biology, this remains one of the major models in bacterial chromosome segregation with supports from both experiments (in vitro and in vivo) as well as modeling.
Icons made by Vignesh Oviyan and Freepik from Flaticon.