Uetz Lab Research
Welcome to the Uetz lab at VCU. We are working on proteins, protein function, protein-related bioinformatics and reptile taxonomy. Our main projects and selected publications are listed below. For a complete publication list go to Publications.
Our group has mapped the interactomes of 4 different microbial species, more than any other lab in the world. These interactomes continue to provide insights into the molecular organization of unicellular systems and the functions of their proteins:
• Wuchty, S et al. (2017)The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions. mSystems 2(3): e00019-17
• Häuser, R. et al. (2014) A Second-generation Protein-Protein Interaction Network of Helicobacter pylori. Mol Cell Proteomics 13(5):1318-29
Uetz, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627
Bioinformatics of protein networks
In addition to generating interactome data, we analyze the resulting networks with a variety of bioinformatics methods. We strive to understand complex networks but also individual proteins and protein domains (see Protein function ... below):
• Mariano R., Khuri S., Uetz P. & Wuchty S. (2016) Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages. mSystems 1 (2): e00030-15.
Uetz, P. et al. (2006) Herpesviral Protein Networks and Their Interaction with the Human Proteome. Science 311: 239-242
Schwikowski,B., Uetz, P. & Fields,S. (2000) A network of interacting proteins in yeast. Nature Biotechnology 18 (12): 1257-1261
Protein function, protein complexes, and protein domains
We are interested in protein function, especially the functions of uncharacterized and poorly understood proteins. We use both computational and experimental approaches to elucidate their function. Our group has solved the function of half a dozen uncharacterized proteins as well as several protein domains:
• Blasche, S. et al. (2013) The E. coli effector protein NleF is a caspase inhibitor. Plos One, 8(3): e58937.
• Caufield JH, Wimble C, Abreu M & Uetz P (2015) Protein complexes in bacteria. Plos. Comp. Biol., 27;11(2):e1004107.
• Goodacre, N.F., Gerloff, D.L. & Uetz, P. (2014) Protein domains of unknown function (DUFs) are essential in bacteria. mBio 5 (1): e00744-13.
Häuser, R. et al. (2012) RsfA (YbeB) proteins are conserved ribosomal silencing factors. Plos Genetics 8(7): e1002815.
Virus and phage interactomics
Viruses and phage are excellent models to study protein interaction networks and protein function because they are small and have loads of uncharacterized proteins. We have studied both human viruses and phage of various bacteria, including E. coli, Mycobacteria, and Streptococcus:
• Osterman A. et al. (2015) The Hepatitis E virus intraviral interactome. Scientific Reports 5: 13872.
• Blasche S. et al. (2013) The Protein Interaction Network of Bacteriophage Lambda with Its Host, Escherichia coli. J Virol. 2013 Dec;87(23):12745-55
Häuser, R., Sabri, M., Moineau, S. & Uetz, P. (2011) The proteome and interactome of Streptococcus pneumoniae phage Cp1. J. Bact. 193 (12): 3135–3138.
Fossum E. et al. (2009) Evolution and divergence of herpesviral protein interaction networks. PloS Pathogens 5 (9): 00570
Biodiversity: Reptile taxonomy and genomics
There are not only millions of proteins but also millions of species. Our contribution to biodiversity research is the Reptile Database and its integration with other data sources, including genomics and ecological data:
• Roll U et al. (2017) The global distribution of tetrapods reveals a need for targeted reptile conservation. Nature Ecol. Evol., DOI: 10.1038/s41559-017-0332-2
• Castoe, T. A. et al. (2013) The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. PNAS, Dec 2, 2013.
Uetz P et al. (2019) A global catalog of primary reptile type specimens. Zootaxa 4695 (5): 438–450
See also Lab Members