• Our laboratory is interested in understanding the fascinating biology of bacteria, bacteriophages and their interaction. We are an experimental biology lab and we use a range of approaches including fluorescence microscopy, classical genetics, CRISPR-Cas tools and biochemistry to address our questions. Some of the research areas we are currently focussing are given below.

Uncovering the molecular mechanisms of Bacterial Cell Organization

• If we open a bacterial cell and look inside, would we see any organized structures? For a long time, scientists thought that bacterial cells lack internal organization and are mere “bags of free-floating enzymes”. This view, which stemmed from the scarcity of membrane-bounded organelles, has completely changed in recent years. We now know that bacterial cells have an intricate intracellular organization with proteins, mRNAs, and lipids distributed in organized patterns. Thus, bacteria are the inventors of “organization without organelles”. The biological basis for the cellular organization in bacteria is only beginning to be understood. We have previously explored the organization of bacterial cell poles by studying the mechanism of polar targeting of the phosphotransferase system (PTS) in E. coli (Govindarajan S., et al. 2013, Govindarajan S., et al. 2018). We also uncovered the mechanism by which the SecA-dependent secretion system mediates membrane targeting of the bacterial actin homolog, MreB (Govindarajan S., et al. 2017). Currently, we are investigating novel filament-forming proteins in bacteria and uncovering their functions in cell organization.

Understanding the biology of ‘Jumbo-bacteriophages’

• Jumbophages are a class of bacterial viruses with exceptionally large (>200 kb) genomes. These phages exhibit a lifestyle that is very distinct from other phages. Two lines of evidence support this view: (a) Jumbophages encode a tubulin-like cytoskeletal protein (PhuZ) which is involved in centring of phage DNA and mediates cargo transport; (b) Jumbophages construct a proteinaceous shell structure, which we have recently shown to be necessary for protecting phage DNA from immune systems like the CRISPR-Cas (Mendoza SD., et al. 2020). Strangely, the jumbophage shell behaves like a eukaryotic nucleus i.e., replication and transcription of phage DNA occur within the shell; phage mRNAs are exported out of the shell for translation; phage proteins, translated by the cytoplasmic ribosomes, are then selectively imported into the shell. How these processes, which are typical of eukaryotes, evolved in a virus is a complete mystery. We are interested in solving some of the mysteries of jumbophages by strategically identifying and studying novel genes that are important for jumbophages life cycle. We foresee that understanding of the life cycle of jumbophages will shed light on how living cells are organized and will improve our ability to use these phages for biotechnological applications (phage therapy, gene delivery, synthetic biology).

Discovery of novel mechanisms of phage-mediated host take-over

• Bacteriophages proliferate strictly by exploiting the resources of the host bacterial cell. Several phages encode proteins that inhibit or reprogram host cellular processes in order to take-over. Examples of such processes include modulation or inhibition of host transcription and blockage of the CRISPR-Cas adaptive immune system. We have previously studied the mechanism by jumbo-bacteriophages take-over its host by protecting its genome within a proteinaceous nucleus-like compartment (Mendoza SD., et al. 2020) and the mechanism by which IsrK sRNA of Gifsy-1 prophage of Salmonella interferes with bacterial transcription termination (Hershko-Shalev T., et al. 2016). Currently, we do not know all the host processes that are controlled by phages during lytic or lysogeny infection. Towards this goal, we are interested in discovering new strategies that are employed by phages to take-over bacteria. To start with, we are focussing on E. coli and P. aeruginosa phages that alter the central processes of their respective hosts. Genes responsible for these processes are being identified and characterized. Knowledge gained from these studies will be used for development of novel antibacterial strategies.