In pursuit of alien genes in bacteria

Posted on March 1, 2023   by Rajeev Azad

Rajeev Azad takes us behind the research and his recently published paper latest paper "Leveraging comparative genomics to uncover alien genes in bacterial genomes" in Microbial Genomics.

What is your name, job title and institution/company?

My name is Rajeev Azad, and I am currently an Associate Professor in the Department of Biological Sciences and Department of Mathematics at the University of North Texas.

Tell us a little bit about your research and why it is important.

Hard-wired into the genome of an organism is the information needed to make functional products including proteins, RNAs and metabolites. Decoding the information underlying genomes and transcriptomes is central to understanding different perspectives of life; particularly, the cell, the organism, relationships among organisms, and interactions between organisms and environments.

Research in my laboratory is focused on developing novel approaches to decipher structural and functional features in genomes, and elucidating their relationships in the context of evolution.  We are working on developing and applying mathematical and computational methods to understand how organisms, specifically microbes, innovate to adapt to changing environments. We are studying large omics datasets to determine how organisms respond to stress at the molecular and physiological level.

Understanding how microbes pick up novel traits through evolutionary processes is important for a myriad of purposes. It is important for deciphering the emergence and evolution of virulence and antibiotic resistance in pathogens for example. By performing systems-level analysis of organisms via interrogation of their genomes and/or transcriptomes, yet known molecular factors (e.g. genes or genetic networks) aiding in their adaptation to changing environmental conditions can be revealed. These studies have been pursued in my lab in many different contexts, for example:

• in understanding how microbes mobilise and exchange their genomic content to adapt to different environmental conditions or new niches,
• in understanding how plants utilise their genomic repertoire to acclimatise to changes in climatic conditions,
• in understanding how animals cope with stresses such as oxygen deprivation.

These could have wide ranging implications, e.g. in controlling bacterial infections, in making crops more resilient to deteriorating climatic conditions, etc.

Tell us about your most recent paper?

Bacteria have the ability to gain novel functions by acquiring genes from different sources through Horizontal Gene Transfer (HGT). They can acquire novel metabolic capabilities that can help them adapt to certain conditions or environments. Characterising and quantifying HGT is central to understanding bacterial evolution and its impacts on different life forms.

In our recently published paper in the Microbiology Society journal Microbial Genomics, we present a new method that infers horizontally acquired (“foreign”) genes in bacterial genomes by performing comparison of genes across different taxa. The success of this class of methods depends on breadth and depth of the sequence databases. Over 24,000 completely sequenced bacterial genomes are now available in the NCBI database alone thanks to the advances in high-throughput sequencing. The fast growing databases have made the comparative genomics methods even more relevant in addressing many different problems in biology or medicine.

In our work, we focused on uncovering foreign genes in bacterial genomes by leveraging information-rich genomic resources and developed a new protocol that is highly sensitive to foreign gene detection. Our protocol, Alienness by Phyletic Pattern (APP), leapfrogged current comparative genomics protocols in alien gene detection by ~7–68% in the overall accuracy when assessed on frequently used benchmarking datasets and on a collection of well-characterised genomes. Notably, APP’s taxonomy-aware framework renders the ability to predict both recent and ancient gene transfer events. As genome databases are continually growing and APP is a rapid, automated and relatively less resource intensive tool, it can be synced with database updates. This will generate the most up to date results. APP advances the state-of-the-art in alien gene detection further and can be used as a standalone tool or in combination with complementary algorithms for raising the bar in HGT detection.

Why did you decide to investigate this hypothesis/question?

Understanding bacterial evolution through HGT is one of my longstanding interests. My research group has developed a suite of complementary methods for identifying foreign genes in microbial genomes. Most of these methods are based on sequence composition (nucleotide or oligonucleotide distribution) and are suited for identifying recent gene acquisitions, as ancient foreign genes are likely to have their composition ameliorated to that of the recipient genome with the passage of time. Comparative genomics methods that rely on sequence alignment may, however, detect ancient acquisitions. These methods required rich sampling of closely related genomes (as well as of distant relatives), which has now been realised for many taxa due to rapid advances in genome sequencing. Unfortunately, despite these advances, very few such methods currently exist. We therefore revisited this problem and leveraged the large amount of genomic data and modern computational resources to delineate foreign genes in bacterial genomes. 

What do you hope the future implications of this research will be?

We hope that this study will spur further interest and research in bacterial genome evolution. Through this study, we have offered an efficient tool to the research community interested in HGT quantification. Application of APP to bacterial pathogens can unravel yet obscured genetic factors involved in pathogenicity, e.g. those conferring virulence or drug resistance, and their dissemination through HGT. By deciphering how bacteria modulate their metabolic repertoire, the fields of genetic engineering and biotechnology can be advanced further.    

Is there anything else you would like us to know about this published work?

This work stemmed from my graduate student and co-author, Soham Sengupta’s dissertation research. Our earlier goal was to construct a horizontal gene flow network using gene clustering based work. We decided to incorporate comparative genomics as well to place more confidence over the predictions. Initially conceived to be a small-scale exercise, it evolved into a large-scale project and culminated with the publication of the APP paper in Microbial Genomics.

Our other paper where APP was applied within an integrative framework for inferring horizontal flow of alien genes also got published recently. Soham has since graduated and moved to St. Jude Children's Research Hospital and no longer deconstructing the microbial world on a daily basis. He still reminisces about the best days of his graduate life in Texas and how tackling challenges in microbial research has prepared him to excel in other fields.

What do you enjoy most about your work?

Perhaps doing what I have always been passionate about. Solving mysteries of life hidden within genomes using mathematical and computational models. Teaching, advising, and mentoring the next generation of computational biologists. The pursuit of scientific discoveries and knowledge is all satisfying, I truly relish this.

You can read Rajeev Azad's latest paper "Leveraging comparative genomics to uncover alien genes in bacterial genomes" in Microbial Genomics.