Subcellular Organization of the Bacterial Cell

 

We are interested in uncovering the molecular intricacy at the poles and the physiological functions that are exerted from the poles

The complexity of bacterial cells has been underestimated for decades. Still, many bacterial proteins are known to specifically localize. Our current studies focus mainly on the cell poles, which emerge as special locals with a unique proteome. We discovered a novel protein, TmaR, which is the first E. coli pole-localizer. TmaR clusters at the poles and controls sugar metabolism by sequestering, EI, the major sugar regulator in most bacteria, and releasing it from the poles upon need. To generate a 3D TmaR-EI interaction model, we combined genetic screes, automated microscopy, protein-protein interaction modeling and biochemistry.

As opposed to proteins, the lack of a nucleus led to the accepted assumption that RNAs do not specifically localize in bacteria. Our surprising discovery that bacterial mRNAs localize to subcellular domains where their protein products are required in a translation-independent manner (Science, 2019) was recognized as one of the breakthroughs of the year. Our analysis of the spatiotemporal localization of the E. coli transcriptome uncovered that the polar transcriptome is unique, enriched with many stress-related sRNAs and mRNAs.

In addition to containing unique proteome and transcriptome, our results show that the poles contain a unique metabolome. The composition of the different polar omes suggests that the poles function as hubs for sensing and regulation. Therefore, we call them the microBrain.

 

Phase Separation at the bacterial cell poles

 

 

We use the simple bacterial cells as powerful models for uncovering the universal principles underlying organization without membranes in all cell types

Compartmentalization in all cell types might be achieved by the formation of phase-separated membraneless organelles, termed condensates. We have shown that the pole-localizer TmaR phase-separates at the poles. By doing so, TmaR regulates sugar metabolism by recruiting the major sugar regulator and releasing it upon need, cell motility by safeguarding flagella-related RNAs, thereby controlling flagella production, and small RNA-mediated regulation by recruiting the RNA chaperone Hfq during stress. Our studies highlight the relevance of phase separation for bacterial physiology and survival. 

We use multiomic analyses to uncover the content of the polar condensates, the physiological pathways that are compartmentalized within them, and the spatial and temporal changes in the poles’ composition and functionality in response to environmental cues.

A potential medically relevant finding is that TmaR condensates may transition to a solid state, forming aberrant condensates, similar to human proteins causing severe pathologies, such as Alzheimer.

 

Spatial organization of gene expression in bacteria

 

Our goal is to uncover the extant of coupling between transcription and translation and the subcellular localization of post-transcriptional processes in bacteria

The lack of a nuclear membrane that physically separates the bacterial chromosome from the cytosol in bacteria led to the well-accepted dogma in biology: the coupling between transcription and translation, termed CTT. Our finding that a significant fraction of bacterial transcripts localizes in a translation-independent manner challenged this dogma. The universality and extent of CTT in different bacterial species have been subsequently questioned by other groups. 

To determine the extent of CTT, we developed new protocols that are based on merging top-notch methodologies, such as Selective Ribosome Profiling (SeRP) and RNA-seq. Our results show that the transcription and translation in bacteria are not necessarily coupled. They also provide important insights into when CTT is applied at the gene and operon level and which families of genes undergo CTT and which do not.

We are now focusing of the poles, attempting to prove that localized translation occurs in bacteria, as in eukaryotes. We further ask if cotranslational assembly of protein complexes occurs in bacteria.

 

An anti-biofilm factor for prevention of urinary tract infections

 

 

Our goal is to identify small molecules that inhibit biofilm formation in order to develop novel anti-biofilm and anti-UTI treatments

In developed countries, urinary tract infection (UTI) is the second most common infectious cause for consultation and prescription of antibiotics among physicians, and uropathogenic E. coli (UPEC) is the most common for UTI. Formation of biofilms enables UPEC to evade the immune system and show resistance to antibiotics, thus explaining the high level of UTI recurrence and catheter-associated UTI.

We discovered that UPEC secretes a biofilm-inhibiting factor, which we termed BIF. We are attempting to uncover BIF components, its mechanism of action and its receptors.

 

Collaborators:

Jonathan Livny, Broad Institute

Roby Bhattacharyya, Broad Institute

Bernd Bukau & Guenter Kramer, Heidelberg Univ.

Ulrike Endesfelder, Bonn University

Emmanuel Levy, Weizmann Institute

Tami Geiger, Weizmann Institute

Maya Schuldiner, Weizmann Institute

Ora Schueler-Furman, Hebrew University

Sahar Melamed, Hebrew University