Metals like zinc are vital for all living organisms, including bacteria, but having too much or too little zinc in a cell can be harmful. To handle this, organisms have developed clever ways to keep metal levels balanced. One key system involves special proteins called transcription regulators, which act like sensors and switches, controlling how much zinc gets in or out of the cell. In our research, we found that in E. coli, two of these regulators—Zur and ZntR—don’t just monitor zinc levels independently. They can actually work together using DNA to fine-tune zinc management in the cell. Alongside these scientific discoveries, my postdoc experience has been a transformative chapter in my career. Here, I share both the research and the personal growth that marked this journey.

Putting pieces together

When I first joined the Chen group, I was tasked with taking over an ongoing project investigating Zur-DNA interactions using in vitro FRET measurements. This project had been started several years earlier and had passed through the hands of multiple postdocs and students. Each contributor had left behind a trail of data analysis steps scattered across different operating systems and software.

To streamline the workflow, I consolidated these fragmented processes by rewriting them in MATLAB. This unified approach made data analysis significantly faster and more efficient for the large volumes of image data we handled. Using this code, which are now available with the manuscript as Supplementary Software, I could analyze the original donor-aceptor dual-channel images to extract single-molecule FRET trajectories, distinguish multiple E_FRET states, and confirm that Zur interacts dynamically with DNA, specifically at its recognition site.

During my graduate research journey, I transitioned across fields—from nanoparticle synthesis to protein dynamics in mammalian cells, and now, as a postdoc, to bacterial cells. Working in interdisciplinary fields often made me feel my knowledge was scattered and lacked depth. However, I realized research can involve piecing together diverse elements rather than building on a single foundation. Now I believe this can be another meaningful way to move forward on the scientific journey.

New experience, new findings

While I was investigating Zur-DNA interactions in vitro, Udit, my co-first author, discovered something intriguing: the Zur recognition site shares partial sequence similarity with regions of DNA that ZntR recognizes. This hinted at the possibility that ZntR might bind near Zur, facilitating its unbinding from DNA. Udit explored this idea in live bacteria, and I extended my in vitro studies to examine Zur-DNA-ZntR interactions.

This required purifying ZntR protein on a very large scale, which was an entirely new challenge for me and made me hesitate to expand the work.

However, with Udit’s help, we purified ZntR protein and could discover that ZntR_apo enhances Zur’s facilitated unbinding from DNA by directly acting on the Zur-DNA complex, which is a first-of-its-kind ‘through-DNA’ mechanism for their cross-actions in regulating metal homeostasis. Also, Zur binding rate constant remained independent of ZntR concentration, suggesting that ZntR does not bind independently to DNA to block Zur binding but rather requires Zur to already be bound to DNA.

I think we all know that every challenge is an opportunity to grow—and that the “juicy fruits” of success come after the hardest efforts. It takes time, but persistence paid off.

Stitching a collaboration: As in vivo, so in vitro!

Facilitated unbinding of Zur from DNA by ZntR_apo was consistently observed in live bacteria, as demonstrated by Udit, my co-first author. By combining in vivo and in vitro studies, we not only validated our findings but also significantly strengthened and enriched them. We discovered that the Zur dimer bound at one specific dyad is preferentially disrupted by ZntR_apo—an insight only in vitro studies could reveal—consistent with the findings that the ZntR_apo recognition sequence near the specific dyad. Additionally, we uncovered the dynamics of Zur-ZntR-DNA interactions under zinc-depleted and zinc-excess cellular conditions, insights made possible only through in vivo studies.

It is quite difficult combining two parallel studies, requiring extensive collaborative teamwork. The key to this achievement was our collaboration: we inspired and supported each other through the tough moments. The resulting publication is a testament to the synergy between our respective contributions. Just as Zur and ZntR coordinate through DNA, our teamwork facilitated the “unbinding” from the Chen group, enabling both of us to transition to our next academic chapters.

Conclusion

This journey has deepened my appreciation for interdisciplinary work, highlighting how disparate pieces—be it techniques, knowledge, or perspectives—can come together to create a coherent and impactful story. From revamping fragmented workflows to tackling entirely new challenges, every hurdle has shaped my growth as a scientist. Much like the dynamics between Zur and ZntR, this chapter has been one of interaction and synergy—between colleagues, methods, and ideas. It has reaffirmed my belief that the most transformative discoveries emerge when we embrace challenges and nurture collaboration. This project wasn’t just about uncovering a novel molecular mechanism—it was also about learning how to navigate challenges, grow through collaboration, and prepare for what comes next.

Another blog post by co-author Udit Kumar Chakraborty is at (https://go.nature.com/4g3v1hl)