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Chapter 17 : Protein Translocation into and across Archaeal Cytoplasmic Membranes
Category: Microbial Genetics and Molecular Biology; Environmental Microbiology
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Recent analyses of the archaeal Sec and Tat pathways have revealed novel and crucial information about archaeal protein translocation, as well as protein translocation in general. This chapter provides an overview on protein translocation into and across archaeal cytoplasmic membranes. The Sec pathway is the only known universally conserved protein translocation pathway. Protein translocation may be driven by one or several extracytoplasmic activities that provide directionality by preventing movement of the polypeptide chain back into the cytoplasm. In vitro studies suggest that the proton motive force (PMF), in concert with the action of SecA, facilitates bacterial secretion via the Sec pore. Furthermore, the PMF is apparently sufficient to drive translocation of proteins via the twin-arginine translocation (Tat) pore. Thus, it is possible that an ion gradient across the archaeal membrane is the sole source of energy for protein translocation. Many bacteria and archaea possess an additional general secretion pathway, described as the Tat pathway. The presence of the twin-arginine motif in the Tat signal sequence provided a means of identifying novel Tat substrates by computational pattern-matching techniques. Recent in vivo, in vitro, and in silico studies have led to a better understanding of archaeal protein translocation. Moreover, the elucidation of an archaeal Sec-pore X-ray crystal structure strikingly demonstrates how analysis of this pathway in archaea can significantly advance the field of protein translocation as a whole. In addition to standard molecular and biochemical approaches, it is now crucial to develop in vitro Sec and Tat protein translocation systems that will more clearly define the mechanisms of these pathways and reveal the energetics of these cellular processes in archaea.
Schematic representation of different classes of Sec and Tat signal sequences. Grey and hatched boxes represent N-ter-minally charged and hydrophobic (H region) domains, respectively. Arrows indicate the signal peptide cleavage sites. Cleavage of predicted class 2 signal peptides of Tat substrates by SPII has not yet been confirmed experimentally. Modified from FEMS Reviews (85) with permission of the publisher.
Mammalian SRP interaction with the ribosome. Upon cytoplasmic exposure of the initial TM or H region of many Sec substrates, the SRP interacts with the ribosome nascent chain (RNC) complex via several points of interaction. The SRP54 protein recognizes and binds the nascent polypeptide, while SRP9/14 bind and block the A site (see text). The bending of the SRP RNA molecule required for both of these interactions to occur simultaneously may be facilitated by SRP68/72. SRP proteins are represented by their corresponding numbers. Modified from Current Opinion in Structural Biology (25) with permission of the publisher.
Sec machinery in the three domains of life. Components of the Sec machinery in representatives of bacteria (E. coli), archaea (H. volcanii), and eucarya (S. cerevisiae). Sec substrates are translocated into or across hydrophobic membranes via the universally conserved heterotrimeric Sec61 (SecYEG in bacteria) pore. Translocation through this protein-conducting channel requires distinct sets of additional Sec components in bacteria, archaea, and eucarya. YidC and TRAM are only involved in the insertion of proteins into the bacterial cytoplasmic and the ER membrane, respectively. While ATP hydrolysis by SecA and Kar2p are involved in energizing Sec translocation in bacteria and eucarya, respectively, no archaeal translocation ATPases have been identified. Cyt, cytoplasm. Reprinted from Current Opinions in Microbiology (84) with permission of the publisher.
Models of putative archaeal protein translocation energetics. See text for details. (a) Cotranslational translocation. (b) Post-translational translocation with a cytoplasmic energy-coupling protein. (c) Posttranslational translocation with extracytoplasmic activity. (d) Posttranslational translocation harnessing a gradient (e.g., ΔpH) across the cytoplasmic membrane. Figure reprinted from FEMS Reviews (85) with permission of the publisher.
Tat components and model of Tat secretory mechanism. (A) Typcial structure of Tat machinery components in bacteria and archaea. The postamphipathic helical C terminus for TatA and TatB has been excluded for visual simplicity. (B) Model of Tat substrate translocation in E. coli. Tat substrates (oval) obtain tertiary structure in the cytoplasm and are targeted to the membrane TatBC complex in an unknown manner. Once bound to substrate, the TatBC complex interacts with a multimeric TatA ring in a ΔpH-dependent manner. The plugged inactive TatA ring likely alters to an active unplugged confirmation upon engaging substrate. There are insufficient data describing points of protein interactions, and the depicted points of interaction between proteins are not meant to be completely accurate.
Signal peptide classes in Archaea
The Tat pathway in Archaea deduced from complete genome sequences