Reliable, scalable functional genetics in bloodstream-form Trypanosoma congolense in vitro and in vivo

Animal African trypanosomiasis (AAT) is a severe, wasting disease of domestic livestock and diverse wildlife species. The disease in cattle kills millions of animals each year and inflicts a major economic cost on agriculture in sub-Saharan Africa. Cattle AAT is caused predominantly by the protozoan parasites Trypanosoma congolense and T. vivax, but laboratory research on the pathogenic stages of these organisms is severely inhibited by difficulties in making even minor genetic modifications. As a result, many of the important basic questions about the biology of these parasites cannot be addressed. Here we demonstrate that an in vitro culture of the T. congolense genomic reference strain can be modified directly in the bloodstream form reliably and at high efficiency. We describe a parental single marker line that expresses T. congolense-optimized T7 RNA polymerase and Tet repressor and show that minichromosome loci can be used as sites for stable, regulatable transgene expression with low background in non-induced cells. Using these tools, we describe organism-specific constructs for inducible RNA-interference (RNAi) and demonstrate knockdown of multiple essential and non-essential genes. We also show that a minichromosomal site can be exploited to create a stable bloodstream-form line that robustly provides >40,000 independent stable clones per transfection–enabling the production of high-complexity libraries of genome-scale. Finally, we show that modified forms of T. congolense are still infectious, create stable high-bioluminescence lines that can be used in models of AAT, and follow the course of infections in mice by in vivo imaging. These experiments establish a base set of tools to change T. congolense from a technically challenging organism to a routine model for functional genetics and allow us to begin to address some of the fundamental questions about the biology of this important parasite.
Author summary The parasites Trypanosoma congolense and T. vivax are the most significant causative agents of Animal African trypanosomiasis (AAT). AAT kills an estimated 3 million cattle each year and represents a huge financial burden on food production in sub-Saharan Africa. A critical tool for understanding pathogen biology is the ability to make genetic modifications, especially creating specific mutants of target genes that can be used to investigate the locations of gene products, the effects of changes in expression, or consequence of complete gene removal. However, work on AAT is severely limited by difficulties in making even small genetic modifications and lack of tools for many functional genetics applications. Here, we design, test and validate a set of tools for T. congolense that brings for the first time: routine high-efficiency gene tagging and knockout, regulatable transgene expression from silent loci, a species-specific system for inducible gene knockdown, bioluminescent lines for in vivo disease models, and a means to generate highly complex libraries of mutants that will enable genome-scale work. These data and the tools around them will greatly aid research into AAT and T. congolense biology.