The functional evolution of Hox1 proteins

December 3, 2020

Dr. Singh is currently a Postdoctoral Fellow in the lab of Prof. Robb Krumlauf at Stowers Institute for Medical Research, Kansas City, USA. He published a paper titled “A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins” as the first author in Genes & Development (2020).

Author Interview

How would you explain your paper’s key results to the non-scientific community?

Many gene duplications occurred during the evolution of complex animals like humans, but how these duplications contributed to the rise of vertebrates from simple invertebrates is not well understood. We studied HOX proteins, which determine body plans in animals. Using gene-editing technologies, we replaced a Hox gene called labial in fruit flies with three related mouse genes: HOXA1, HOXB1, and HOXD1.

Only HOXA1 restored the original function in fruit flies, suggesting it retained an ancestral function over 600 million years. A small six-amino-acid region in HOXA1 was found to be critical for this ancestral function, affecting interactions with other proteins.

HOXB1 and HOXD1 have evolved new functions—facial expression in mammals and hair follicle development, respectively. Our study shows how genes can preserve essential functions while also evolving new ones, shedding light on how gene duplication and divergence drive complexity.

“This study shows how genes conserve the essential function and diverge to generate novelties.”

What are the possible consequences of these findings for your research area?

Genome projects have shown that many genes are shared across animals, and in vitro studies suggest similar DNA-binding abilities among transcription factors. Yet, they perform different roles. This study used a functional approach: inserting mouse Hox1 genes into fruit flies using CRISPR/Cas9.

Only HOXA1 retained the ability to perform the ancestral function. Further investigation revealed that just six amino acids were crucial for interacting with the PBX1 cofactor. This demonstrates that small sequence differences outside the main DNA-binding region can significantly alter function—something protein sequence similarity alone can’t predict.

“[…] protein sequence similarity is not always a good predictor of function and small changes during evolution may have a profound impact.”

What was the exciting moment (eureka moment) during your research?

The most exciting moment was discovering that the mouse HOXA1 protein retained labial-like ancestral activity, even after 600 million years of evolution.

What do you hope to do next?

This study established a new method to functionally analyze related proteins. I aim to apply this approach to other transcription factor families to better understand how evolution shapes new body plan features in animals.

Where do you seek scientific inspiration?

Nature’s vast animal diversity is my biggest inspiration. I’ve also been fortunate to work with inspiring mentors who trained and motivated me throughout my research journey.

How do you intend to help Indian science improve?

I am currently seeking an Assistant Professor position to start my research program. I am open to positions in India where I hope to contribute to both teaching and research.

Reference

Singh NP, De Kumar B, Paulson A, Parrish ME, Zhang Y, Florens L, Conaway JW, Si K, Krumlauf R.
A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins.
Genes Dev. 2020. DOI: 10.1101/gad.342329.120

Author Research Interests

My long-term interest lies in understanding the functional evolution of transcription factors (TFs). These TF families emerged early in animal evolution and expanded during vertebrate evolution through gene duplication. I’m using CRISPR/Cas9 in fruit flies to study how conserved TFs retain or change their functions. This research will shed light on how evolutionary mechanisms give rise to novel features in animal body plans.