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Abstract:

The species of the Mycobacterium tuberculosis Complex (MTBC)—M. tuberculosis, M. africanum, M. bovis, M. caprae, M. microti, and M. pinnipedii—are very closely related. In this webinar, we will discuss the techniques used to examine the MTBC in order to unravel this taxonomic mystery. Using phylogenomic techniques to compare the type strains of these species, we discovered that all of these “species” are, in fact, M. tuberculosis. We further examined all the strains deposited in GenBank under those species names and found all of them to be strains of M. tuberculosis. All known strains of three other putative MTBC members (“M. canettii”, “M. mungi”, and “M. orygis”) were similarly shown to be strain of M. tuberculosis. We have recently published a paper in the International Journal of Systematic and Evolutionary Microbiology officially unifying the previously separate MTBC species as M. tuberculosis.

Key Points:

  • Using whole-genome sequencing (WGS) and phylogenomic analysis of the MTBC species type strains, we discovered that all of these “species” are, in fact, Mycobacterium tuberculosis
  • By similarly analyzing all the MTBC non-type strain whole-genome sequences (>3,700) in GenBank, we determined that all of these strains similarly should be considered to be strains of Mycobacterium tuberculosis
  • We recommend the use of the infrasubspecific term ‘variant’ and infrasubspecific designations that generally retain the historical nomenclature associated with the groups or otherwise convey such characteristics (e.g., M. tuberculosis variant bovis). 
  • ATCC is currently in the process of updating the nomenclature used in our catalog to reflect this phylogenomically modernized taxonomy.

Abstract:

Cells utilize networks that span both temporal and spatial organizations, encompassing many individual steps of regulation. While the regulatory regimes to build networks in synthetic biology has grown from solely transcription to also include protein or RNA modalities, circuits comprised solely of protein-protein interactions have yet to be produced. Here, I'll describe several mechanisms relying on phosphorylation-activated localization and effector actuation for building OR and NOT gates from protein-protein phosphorylation events and their subsequent composition to form fast acting networks for ultrasensitive chemical sensing and phenotypic cellular control. Design and optimization of these networks were enabled by the use of a modular assembly method for rapid construction and testing of network variants. The final protein network spanned 15 individual member species to form a toggle switch that could sense chemical inputs as low as 1.0s in duration and maintain state over cellular division events. Motivated by these synthetic network designs, I will then describe one avenue in which synthetic biology network results can elucidate natural biological networks, i.e., synthetic biology-inspired discovery.

Key Points:

  • To create large (15-protein member) networks comprising solely protein-protein interactions, a toolkit for reliably assembling and fixed protein expression is necessary.
  • Formation of individual protein devices to implement the OR and NOT gates can be achieved by the creation of fusion proteins that are activated by phosphorylation, resulting in localization and effector domain actuation.
  • Protein-protein networks formed from synthetic interactions allows ease of implementation of complex cellular behavior that require fast information processing while also furthering our understanding of endogenous network composition and signal transduction.