The long-term goal of this project is to understand how metallo intramembrane-cleaving proteases (MIPs) function in bacteria. MIPs are membrane-embedded enzymes that cleave their substrates within a membrane or near the membrane surface. Bacterial MIPs are known to play important roles during sporulation, stress responses, mating, polar morphogenesis, cell division, and infection. Understanding how MIPs function in bacteria could lead to the development of new antibiotics. In eukaryotes, MIPs cleave transcription factors that regulate lipid metabolism and the response to unfolded proteins in the endoplasmic reticulum. These pathways are critical for human health. Knowledge about bacterial MIPs will facilitate studies of eukaryotic MIPs, which could lead to the development of novel therapeutics. Little is known about how MIPs recognize their substrates or how MIP activity can be modulated. To fill this knowledge gap, most of the project focuses on SpoIVFB, which cleaves Pro-?K during Bacillus subtilis sporulation. The cleavage reaction has been reconstituted in vitro and requires ATP. Both ATP and Pro-?K bind to the CBS domain of SpoIVFB. CBS domains have been proposed to sense cellular energy levels and regulate the activity of a variety of proteins. The CBS domain of SpoIVFB may sense the energy level in the mother cell compartment of the sporangium and regulate access of Pro-?K to the active site of the enzyme. To test this model and to better understand how SpoIVFB recognizes Pro-?K, a combination of biochemical, structural, and genetic approaches is proposed. Likewise, a combination of approaches is proposed to achieve a molecular understanding of the mechanism of SpoIVFB inhibition by its natural inhibitor, the protein BofA. Knowledge from studies of SpoIVFB inhibition, substrate recognition, and the role of ATP could guide efforts to develop MIP modulators that benefit human health. B. subtilis codes for three other MIPs in addition to SpoIVFB. The most-studied of these, RasP, is representative of a subfamily of MIPs that is even more broadly conserved than the SpoIVFB subfamily, yet no biochemical studies on RasP have been reported. RasP subfamily members contain a PDZ domain and do not contain a CBS domain. Like certain other PDZ-domain-containing MIPs that have been studied, RasP functions in stress response and appears to cleave an anti-? transmembrane segment after initial cleavage of the anti-? extracytoplasmic domain. However, evidence suggests that RasP cleaves a cell division protein without a prior cleavage. Genetic and biochemical approaches are proposed to test this potential new paradigm. Neither of the known substrates of RasP accounts for certain defects of a rasP mutant or for the effects of RasP depletion. An innovative approach is proposed to identify the unknown substrate(s) of RasP. In addition to expanding knowledge of RasP, the approach could be used to identify substrates of other MIPs, overcoming a critical barrier to progress in the field.

Public Health Relevance

Intramembrane-cleaving metalloproteases play important roles in bacteria when they infect humans, so these proteases are potential targets for the development of new antibiotics, and a closely related protease in humans functions in pathways critical for human health, making it a potential target for the development of novel therapeutics. The project aims to understand how intramembrane-cleaving metalloproteases function in bacteria, using the model organism Bacillus subtilis, which is closely related to several Bacillus species and Clostridia that cause disease, as well as to disease-causing bacteria such as Enterococcus faecalis, Staphylococcus aureus, and Streptococcus pneumoniae. Knowledge about how intramembrane-cleaving metalloproteases of Bacillus subtilis function is expected to facilitate studies of these proteases in other bacteria, as well as studies of the human protease.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Reddy, Michael K
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Michigan State University
Schools of Arts and Sciences
East Lansing
United States
Zip Code
Zhang, Yang; Halder, Sabyasachi; Kerr, Richard A et al. (2016) Complex Formed between Intramembrane Metalloprotease SpoIVFB and Its Substrate, Pro-σK. J Biol Chem 291:10347-62
Konovalova, Anna; Sogaard-Andersen, Lotte; Kroos, Lee (2014) Regulated proteolysis in bacterial development. FEMS Microbiol Rev 38:493-522
Chen, Bin; Himes, Paul; Liu, Yu et al. (2014) Structure of bacterial transcription factor SpoIIID and evidence for a novel mode of DNA binding. J Bacteriol 196:2131-42
Zhou, Ruanbao; Chen, Kangming; Xiang, Xianling et al. (2013) Features of Pro-σK important for cleavage by SpoIVFB, an intramembrane metalloprotease. J Bacteriol 195:2793-806
Kroos, Lee; Akiyama, Yoshinori (2013) Biochemical and structural insights into intramembrane metalloprotease mechanisms. Biochim Biophys Acta 1828:2873-85
Zhang, Yang; Luethy, Paul M; Zhou, Ruanbao et al. (2013) Residues in conserved loops of intramembrane metalloprotease SpoIVFB interact with residues near the cleavage site in pro-σK. J Bacteriol 195:4936-46
Imamura, Daisuke; Kuwana, Ritsuko; Kroos, Lee et al. (2011) Substrate specificity of SpoIIGA, a signal-transducing aspartic protease in Bacilli. J Biochem 149:665-71
Himes, Paul; McBryant, Steven J; Kroos, Lee (2010) Two regions of Bacillus subtilis transcription factor SpoIIID allow a monomer to bind DNA. J Bacteriol 192:1596-606
Imamura, Daisuke; Zhou, Ruanbao; Feig, Michael et al. (2008) Evidence that the Bacillus subtilis SpoIIGA protein is a novel type of signal-transducing aspartic protease. J Biol Chem 283:15287-99
Zhou, Ruanbao; Kroos, Lee (2005) Serine proteases from two cell types target different components of a complex that governs regulated intramembrane proteolysis of pro-sigmaK during Bacillus subtilis development. Mol Microbiol 58:835-46