The main pathway for the transport of proteins across the cytoplasmic membrane in bacteria is the Sec pathway. The research in my lab is currently focused on understanding how the Sec pathway recognizes newly synthesized protein substrates and targets them for transport across the cytoplasmic membrane. Research in my lab combines the relative strengths of biochemistry and bacterial genetics to investigate the mechanistic details of Sec-dependent protein transport in Escherichia coli.
The mechanism of cotranslational targeting by the “posttranslational” branch of the Sec pathway by SecA.
The central component of the Sec pathway is an integral membrane protein complex, SecYEG, which forms a channel in the cytoplasmic membrane through which substrate proteins are transported. There are two main branches of the Sec pathway by which substrate proteins are delivered to SecYEG: the posttranslational branch and the cotranslational branch. The posttranslational branch is responsible for the export of the majority of soluble periplasmic and outer membrane proteins in E. coli. However, until recently very little was known about how substrate proteins were recognized by the posttranslational branch. Export of substrates of the posttranslational branch typically begins either very late in the process of protein synthesis or after synthesis is complete, which has led to the widespread assumption that substrate recognition is independent of protein synthesis. (In contrast, substrates of the cotranslational branch are recognized very early in translation by the SRP, and the ribosome is directly coupled to SecYEG.) However, I recently discovered that a component of the posttranslational Sec machinery, the ATPase SecA, binds to the ribosome and appears to play a role in cotranslationally channeling proteins into the “posttranslational” translocation pathway. My lab is currently investigating the details of the molecular mechanism of substrate recognition by SecA.
The role of targeting in the folding of substrate proteins in the periplasm.
The mechanism of delivery to SecYEG can significantly affect the folding of substrate proteins. For example, several recent studies report that cotranslational export of outer membrane proteins can lead to misfolding and defective assembly into the outer membrane. However, the molecular basis for these differences in folding is still unclear. I am interested in understanding how the mechanism of delivery to SecYEG can affect folding of proteins on the periplasmic side of the cytoplasmic membrane.
Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B. (2011) Selective ribosome profiling reveals the cotranslational chaperone action of Trigger Factor in vivo. Cell. 147:1295-308.
Huber D, Rajagopalan N, Preissler S, Rocco MA, Merz F, Kramer G, and Bukau B. (2011) SecA interacts with ribosomes in order to facilitate posttranslational translocation in bacteria. Mol Cell. 41:343-53
Mogk A, Huber D, and Bukau B. (2011) Integrating Protein Homeostasis Strategies in Prokaryotes. Cold Spring Harb Perspect Biol. 3(4). pii: a004366. doi: 10.1101/cshperspect.a004366
Huber D, Chaffotte A, Eser M, Planson A, and Beckwith J. (2010) Amino acid residues important for folding of thioredoxin are revealed only by study of the physiologically relevant reduced form of the protein. Biochemistry. 49:8922-8
Huber D and Bukau B. (2008) DegP: A Protein Death Star. Structure. 16:989-90
Desvaux M, Scott-Tucker A, Turner SM, Cooper LM, Huber D, Nataro JP, Henderson IR. (2007) A conserved extended signal peptide region directs posttranslational protein translocation via a novel mechanism. Microbiology. 153:59-70
Huber D and Beckwith J. (2006) Phage Display extends its reach. Nat Biotechnol. 24:793-4
Huber D, Cha M, Debarbieux L, Planson AG, Cruz N, López G, Tasayco ML, Chaffotte A, and Beckwith J. (2005) A selection for mutants that interfere with folding of E. coli thioredoxin-1 in vivo. Proc Natl Acad Sci USA. 102:18872-7
Huber D, Boyd D, Xia Y, Olma MH, Gerstein M, Beckwith J. (2005) Use of thioredoxin as a reporter to identify a subset of Escherichia coli signal sequences that promote signal recognition particle-dependent translocation. J Bacteriol. 187:2983-91
Schierle CF, Berkmen M, Huber DR, Kumamoto C, Boyd D, Beckwith J. (2003) The DsbA signal sequence directs efficient, co-translational export of passenger proteins to the E. coli periplasm via the SRP pathway. J Bacteriol. 185:5706-13
Leeds JA, Boyd D, Huber DR, Sonoda GK, Luu HT, Engelman DM, Beckwith J. (2001) Genetic selection for and molecular dynamic modeling of a protein transmembrane domain multimerization motif from a random Escherichia coli genomic library. J Mol Biol. 313:181-95
Phillips GJ, Park SK, and Huber D. (2000) High copy number plasmids compatible with commonly used cloning vectors. Biotechniques. 28: 400-402, 404, 406