An automated system for interrogating the evolution of microbial endosymbiosis

Can Huang; Fengguang Guo; Han Wang; Jasmine Olivares; James Dalton, III; Olga Belyanina; Alice R. Wattam; Clark A. Cucinell; Allan W. Dickerman; Qing-Ming Qin; Arum Han; Paul de Figueiredo

doi:10.1039/D2LC00602B

An automated system for interrogating the evolution of microbial endosymbiosis†

Can Huang,

‡^a Fengguang Guo,‡^b Han Wang,

^c Jasmine Olivares,^b James Dalton, III,^b Olga Belyanina,^b Alice R. Wattam,^d Clark A. Cucinell,^d Allan W. Dickerman,^d Qing-Ming Qin,^b Arum Han

*^aef and Paul de Figueiredo*^bg

Author affiliations

* Corresponding authors

^a Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA

^b Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA
E-mail: pjdefigueiredo@tamu.edu

^c Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China

^d Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA 22904, USA

^e Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA

^f Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA

^g Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA

Abstract

Inter-kingdom endosymbiotic interactions between bacteria and eukaryotic cells are critical to human health and disease. However, the molecular mechanisms that drive the emergence of endosymbiosis remain obscure. Here, we describe the development of a microfluidic system, named SEER ( [S with combining low line] ystem for the [E with combining low line] volution of ndosymbiotic [R with combining low line] elationships), that automates the evolutionary selection of bacteria with enhanced intracellular survival and persistence within host cells, hallmarks of endosymbiosis. Using this system, we show that a laboratory strain of Escherichia coli that initially possessed limited abilities to survive within host cells, when subjected to SEER selection, rapidly evolved to display a 55-fold enhancement in intracellular survival. Notably, molecular dissection of the evolved strains revealed that a single-point mutation in a flexible loop of CpxR, a gene regulator that controls bacterial stress responses, substantially contributed to this intracellular survival. Taken together, these results establish SEER as the first microfluidic system for investigating the evolution of endosymbiosis, show the importance of CpxR in endosymbiosis, and set the stage for evolving bespoke inter-kingdom endosymbiotic systems with novel or emergent properties.