In the Archaea Haloferax volcanii, Membrane Protein Biogenesis and Protein Synthesis Rates Are Affected by Decreased Ribosomal Binding to the Translocon

Sec-Dependent Secretion of Subtilase SptE in Haloarchaea Facilitates Its Proper Folding and Heterocatalytic Processing by Halolysin SptA Extracellularly

In response to high-salt conditions, haloarchaea export most secretory proteins through the Tat pathway in folded states; however, it is unclear why some haloarchaeal proteins are still routed to the Sec pathway. SptE is an extracellular subtilase of Natrinema sp. strain J7-2. Here, we found that SptE precursor comprises a Sec signal peptide, an N-terminal propeptide, a catalytic domain, and a long C-terminal extension (CTE) containing seven domains (C1 to C7). SptE is produced extracellularly as a mature form (M180) in strain J7-2 and a proform (ΔS) in the ΔsptA mutant strain, indicating that halolysin SptA mediates the conversion of the secreted proform into M180. The proper folding of ΔS is more efficient in the presence of NaCl than KCl. ΔS requires SptA for cleavage of the N-terminal propeptide and C-terminal C6 and C7 domains to generate M180, accompanied by the appearance of autoprocessing product M120 lacking C5. At lower salinities or elevated temperatures, M180 and M120 could be autoprocessed into M90, which comprises the catalytic and C1 domains and has a higher activity than M180. When produced in Haloferax volcanii, SptE could be secreted as a properly folded proform, but its variant (TSptE) with a Tat signal peptide does not fold properly and suffers from severe proteolysis extracellularly; meanwhile, TSptE is more inclined to aggregate intracellularly than SptE. Systematic domain deletion analysis reveals that the long CTE is an important determinant for secretion of SptE via the Sec rather than Tat pathway to prevent enzyme aggregation before secretion. IMPORTANCE While Tat-dependent haloarchaeal subtilases (halolysins) have been extensively studied, the information about Sec-dependent subtilases of haloarchaea is limited. Our results demonstrate that proper maturation of Sec-dependent subtilase SptE of Natrinema sp. strain J7-2 depends on the action of halolysin SptA from the same strain, yielding multiple hetero- and autocatalytic mature forms. Moreover, we found that the different extra- and intracellular salt types (NaCl versus KCl) of haloarchaea and the long CTE are extrinsic and intrinsic factors crucial for routing SptE to the Sec rather than Tat pathway. This study provides new clues about the secretion and adaptation mechanisms of Sec substrates in haloarchaea.

Proteomic analysis of the secretome of haloarchaeon Natrinema sp. J7-2

Although in silico predictions have revealed that haloarchaea can be distinguished from other organisms in that the Tat pathway is used more extensively than the Sec pathway for haloarchaeal protein secretion, only a few haloarchaeal-secreted proteins have been experimentally confirmed. Here, the culture supernatant and membrane fraction of the haloarchaeon Natrinema sp. J7-2 grown at 23% salt concentration were subjected to RPLC-ESI-MS/MS analysis. In total, 46 predicted Tat substrates, 14 predicted Sec substrates, and 3 class III signal peptide-bearing proteins were detected. Approximately 65% of the detected Tat substrates contain lipoboxes, emphasizing the role of the Tat pathway in haloarchaeal lipoprotein secretion. Most of the detected Tat substrates are extracellular substrate (solute)-binding proteins and redox proteins. Despite the small number of Sec substrates, two of them, a cell surface glycoprotein and a putative lipoprotein carrier protein, were identified to be high-abundance secreted proteins. While limited proteins were detected in the culture supernatant, most of the secreted proteins were found in the membrane fraction. The anchoring of secreted proteins to the cell surface via a lipobox or a PGF-CTERM seems to be an adaptation strategy of haloarchaea to handle the harsh extracellular environment. Additionally, ∼15% of the integral membrane proteins (IMPs) detected in the membrane fraction possess putative Sec signal peptides or signal anchors, implying that the Sec pathway is important for membrane insertion of IMPs. This is the first report to describe the experimental secretome of haloarchaea and provide new information for better understanding of haloarchaeal protein secretion patterns.

Is there a twist in the Escherichia coli signal recognition particle pathway?

Integral membrane proteins (IMPs) are usually synthesized by membrane-bound ribosomes, and this process requires proper localization of ribosomes and IMP-encoding transcripts. However, the underlying molecular mechanism of the pathway has not yet been fully established in vivo. The prevailing hypothesis is that ribosomes and transcripts are delivered to the membrane together during IMP translation by the signal recognition particle (SRP) and its receptor. Here, I discuss an alternative hypothesis that posits that ribosomes and transcripts are targeted separately. Ribosome targeting to the membrane might be mediated by the SRP receptor, rather than by SRP, and IMP-encoding transcripts might be targeted to the membrane in a translation-independent manner. According to this scenario, the SRP executes its essential function on the membrane at a later stage of the targeting pathway.

Quantitative proteomic analysis of Sulfolobus solfataricus membrane proteins

A quantitative proteomic analysis of the membrane of the archaeon Sulfolobus solfataricus P2 using iTRAQ was successfully demonstrated in this technical note. The estimated number of membrane proteins of this organism is 883 (predicted based on Gravy score), corresponding to 30% of the total number of proteins. Using a modified iTRAQ protocol for membrane protein analysis, of the 284 proteins detected, 246 proteins were identified as membrane proteins, while using an original iTRAQ protocol, 147 proteins were detected with only 133 proteins being identified as membrane proteins. Furthermore, 97.2% of proteins identified in the modified protocol contained more than 2 distinct peptides compared to the original workflow. The successful application of this modified protocol offers a potential technique for quantitatively analyzing membrane-associated proteomes of organisms in the archaeal kingdom. The combination of 3 different iTRAQ experiments resulted in the detection of 395 proteins (>or=2 distinct peptides) of which 373 had predicted membrane properties. Approximately 20% of the quantified proteins were observed to exhibit >or=1.5-fold differential expression at temperatures well below the optimum for growth.

Crossing the membrane in Archaea, the third domain of life

Many of the recent advancements in the field of protein translocation, particularly from the structural perspective, have relied on Archaea. For instance, the solved structures of the translocon from the methanoarchaeon Methanocaldococcus jannaschii of the ribosomal large subunit from the haloarchaeon Haloarcula marismortui and of components of the SRP pathway from several archaeal species have provided novel insight into various aspects of the translocation event. Given the major contribution that Archaea have made to our understanding of how proteins enter and traverse membranes, it is surprising that relatively little is known of protein translocation in Archaea in comparison to the well-defined translocation pathways of Eukarya and Bacteria. What is known, however, points to archaeal translocation as comprising a mosaic of eukaryal and bacterial traits together with aspects of the process seemingly unique to this, the third domain of life. Here, current understanding of archaeal protein translocation is considered. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.

Outside the unusual cell wall of the hyperthermophilic archaeon Aeropyrum pernix K1

In contrast to the extensively studied eukaryal and bacterial protein secretion systems, comparatively less is known about how and which proteins cross the archaeal cell membrane. To identify secreted proteins of the hyperthermophilic archaeon Aeropyrum pernix K1 we used a proteomics approach to analyze the extracellular and cell surface protein fractions. The experimentally obtained data comprising 107 proteins were compared with the in silico predicted secretome. Because of the lack of signal peptide and cellular localization prediction tools specific for archaeal species, programs trained on eukaryotic and/or Gram-positive and Gram-negative bacterial signal peptide data sets were used. PSortB Gram-negative and Gram-positive analysis predicted 21 (1.2% of total ORFs) and 24 (1.4% of total ORFs) secreted proteins, respectively, from the entire A. pernix K1 proteome, 12 of which were experimentally identified in this work. Six additional proteins were predicted to follow non-classical secretion mechanisms using SecP algorithms. According to at least one of the two PSortB predictions, 48 proteins identified in the two fractions possess an unknown localization site. In addition, more than half of the proteins do not contain signal peptides recognized by current prediction programs. This suggests that known mechanisms only partly describe archaeal protein secretion. The most striking characteristic of the secretome was the high number of transport-related proteins identified from the ATP-binding cassette (ABC), tripartite ATP-independent periplasmic, ATPase, small conductance mechanosensitive ion channel (MscS), and dicarboxylate amino acid-cation symporter transporter families. In particular, identification of 21 solute-binding receptors of the ABC superfamily of the 24 predicted in silico confirms that ABC-mediated transport represents the most frequent strategy adopted by A. pernix for solute translocation across the cell membrane.

Quantitative Profiling of the Membrane Proteome in a Halophilic Archaeon

We present a large scale quantitation study of the membrane proteome from Halobacterium salinarum. To overcome problems generally encountered with membrane proteins, we established a membrane preparation protocol that allows the application of most proteomic techniques originally developed for soluble proteins. Proteins were quantified using two complementary approaches. For gel-based quantitation, DIGE labeling was combined with two-dimensional gel electrophoresis on an improved 16-benzyldimethyl-n-hexadecylammonium chloride/SDS system. MS-based quantitation was carried out by combining gel-free separation with the recently developed isotope-coded protein labeling technique. Good correlations between these two independent quantitation strategies were obtained. From computational analysis we conclude that labeling of free amino groups by isotope-coded protein labeling (Lys and free N termini) is better suited for membrane proteins than Cys-based labeling strategies but that quantitation of integral membrane proteins remains cumbersome compared with soluble proteins. Nevertheless we could quantify 155 membrane proteins; 101 of these had transmembrane domains. We compared two growth states that strongly affect the energy supply of the cells: aerobic versus anaerobic/phototrophic conditions. The photosynthetic protein bacteriorhodopsin is the most highly regulated protein. As expected, several other membrane proteins involved in aerobic or anaerobic energy metabolism were found to be regulated, but in total, however, the number of regulated proteins is rather small.

Protein N-glycosylation in Archaea: defining Haloferax volcanii genes involved in S-layer glycoprotein glycosylation

In this study, characterization of the N-glycosylation process in the haloarchaea Haloferax volcanii was undertaken. Initially, putative Hfx. volcanii homologues of genes involved in eukaryal or bacterial N-glycosylation were identified by bioinformatics. Reverse transcription polymerase chain reaction (RT-PCR) confirmed that the proposed N-glycosylation genes are transcribed, indicative of true proteins being encoded. Where families of related gene sequences were detected, differential transcription of family members under a variety of physiological and environmental conditions was shown. Gene deletions point to certain genes, like alg11, as being essential yet revealed that others, such as the two versions of alg5, are not. Deletion of alg5-A did, however, lead to slower growth and interfered with surface (S)-layer glycoprotein glycosylation, as detected by modified migration on SDS-PAGE and glycostaining approaches. As deletion of stt3, the only component of the oligosaccharide transferase complex detected in Archaea, did not affect cell viability, it appears that N-glycosylation is not essential in Hfx. volcanii. Deletion of stt3 did, nonetheless, hinder both cell growth and S-layer glycoprotein glycosylation. Thus, with genes putatively involved in Hfx. volcanii protein glycosylation identified and the ability to address the roles played by the encoded polypeptides in modifying a reporter glycoprotein, the steps of the archaeal N-glycosylation pathway can be defined.

Posttranslational protein modification in Archaea

One of the first hurdles to be negotiated in the postgenomic era involves the description of the entire protein content of the cell, the proteome. Such efforts are presently complicated by the various posttranslational modifications that proteins can experience, including glycosylation, lipid attachment, phosphorylation, methylation, disulfide bond formation, and proteolytic cleavage. Whereas these and other posttranslational protein modifications have been well characterized in Eucarya and Bacteria, posttranslational modification in Archaea has received far less attention. Although archaeal proteins can undergo posttranslational modifications reminiscent of what their eucaryal and bacterial counterparts experience, examination of archaeal posttranslational modification often reveals aspects not previously observed in the other two domains of life. In some cases, posttranslational modification allows a protein to survive the extreme conditions often encountered by Archaea. The various posttranslational modifications experienced by archaeal proteins, the molecular steps leading to these modifications, and the role played by posttranslational modification in Archaea form the focus of this review.

The Haloferax volcanii FtsY homolog is critical for haloarchaeal growth but does not require the A domain

The targeting of many Sec substrates to the membrane-associated translocation pore requires the cytoplasmic signal recognition particle (SRP). In Eukarya and Bacteria it has been shown that membrane docking of the SRP-substrate complex occurs via the universally conserved SRP receptor (Sralpha/beta and FtsY, respectively). While much has been learned about the archaeal SRP in recent years, few studies have examined archaeal Sralpha/FtsY homologs. In the present study the FtsY homolog of Haloferax volcanii was characterized in its native host. Disruption of the sole chromosomal copy of ftsY in H. volcanii was possible only under conditions where either the full-length haloarchaeal FtsY or an amino-terminally truncated version of this protein lacking the A domain, was expressed in trans. Subcellular fractionation analysis of H. volcanii ftsY deletion strains expressing either one of the complementing proteins revealed that in addition to a cytoplasmic pool, both proteins cofractionate with the haloarchaeal cytoplasmic membrane. Moreover, membrane localization of the universally conserved SRP subunit SRP54, the key binding partner of FtsY, was detected in both H. volcanii strains. These analyses suggest that the H. volcanii FtsY homolog plays a crucial role but does not require its A domain for haloarchaeal growth.