About the Lab
Dr. Adam Kuspa's research involves the use of Dictyostelium to study problems of development and host-pathogen interactions, with an emphasis on cellular communication, cell differentiation and innate immunity. Dr. Kuspa initiated genomic studies in Dictyostelium as a postdoctoral fellow – a project that led to a collaboration with Dr. Richard Gibbs and the Human Genome Sequencing Center at Baylor College of Medicine and culminated in the completion of the first amoebal genome sequence in 2005. With Dr. Gad Shaulsky at Baylor, Dr. Kuspa also pioneered the functional analysis of the genome by developing methods for gene function discovery. Dr. Kuspa's laboratory has also discovered novel determinants of Legionella pathogenesis involving the cleavage of Dictyostelium’s mitochondrial ribosomal rRNA and conserved proteins involved in vesicular trafficking. Recently, Dr. Kuspa's laboratory discovered an innate immune system in Dictyostelium mediated by TIR domain signaling pathways. Intriguingly, mutants in this pathway are defective in immune function during development and are compromised in their bacterial feeding behavior during vegetative growth. The apparent requirement of innate immune functions for growth on bacteria suggests that innate immunity evolved from bacterial foraging mechanisms in the progenitor of the crown group eukaryotes.
Development in a Simple System
A long-term goal of Dr. Kuspa's is to define the cellular regulatory mechanisms that govern cell differentiation in eukaryotes using Dictyostelium as a model. This system can be used to provide a complete picture of the regulation of a significant biological problem: the integration of individual cells into distinct tissues with the proper form and function. Dictyostelium cells normally live as solitary amoebae in the soil, consuming other microbes by phagocytosis. Upon starvation, ~50,000 cells aggregate into a mound and become an integrated multicellular organism with distinct tissue types. Each organism consists of about 70 percent prespore cells and 30 percent prestalk cells. When conditions are favorable, they form a fruiting body, the terminal developmental structure that is made up of a sorus of dormant spores held aloft on a cellular stalk. The similarity between Dictyostelium and human genes provides a system where the function of protein ensembles can be tested in a simple system and the results applied to understanding the function of those proteins in other systems.
The Dictyostelium sequencing effort resulted in a highly accurate sequence of 34 million base pairs encoding 12,500 protein-coding genes. Amoebozoa such as Dictyostelium are noteworthy as representatives of one of the surviving branches of the crown group of eukaryotes. Comparisons between representatives of these branches (plants, amoebae, fungi and animals) promises to shed light not only on the nature and content of the ancestral eukaryotic genome, but on the diversity of ways in which its components have been adapted to meet the needs of complex organisms. The genome of Dictyostelium, as the first amoebozoa to be fully sequenced, should be particularly informative for these analyses. Accordingly, Dictyostelium has been designated by the NIH as one of the "model organisms."
Functional genomics holds the promise that we can define the functions of cells and organisms by using genome-scale techniques to obtain a global view of biological systems. The Kuspa laboratory has begun large-scale functional analyses of the Dictyostelium genome, in collaboration with Gad Shaulsky and Richard Sucgang here at Baylor College of Medicine, and Blaz Zupan at the University of Ljubljana in Slovenia. We are developing the technology that will allow us to generate and characterize mutants at a genomic scale. We have initiated a large-scale mutagenesis and "parallel phenotyping" project utilizing molecular barcodes. Recently, we have defined normal development from the viewpoint of the transcriptional profile of populations of cells using RNAseq, providing a robust "transcriptional fingerprint" of development that describes the major transitions in Dictyostelium development and defines the main cell types. This work has put us in a position to analyze mutants by comparison of their transcriptional profiles. The advantages of transcriptional profiling are now obvious since the method can be applied in a uniform way, it provides a universal phenotype and no prior knowledge of the mutated gene is required.