Both a short hydrophobic domain and a carboxyl-terminal hydrophilic region are important for signal function in the Escherichia coli leader peptidase

Getting into mitochondria

The human mitochondrial glutamate dehydrogenase isoenzymes (hGDH1 and hGDH2) are abundant matrix-localized proteins encoded by nuclear genes. The proteins are synthesized in the cytoplasm, with an atypically long N-terminal mitochondrial targeting sequence (MTS). The results of secondary structure predictions suggest the presence of two α-helices within the N-terminal region of the MTS. Results from deletion analyses indicate that individual helices have limited ability to direct protein import and matrix localization, but that there is a synergistic interaction when both helices are present [Biochem. J. (2016) 473: , 2813-2829]. Mutagenesis of the MTS cleavage sites blocked post-import removal of the presequences, but did not impede import. The authors propose that the high matrix levels of hGDH can be attributed to the unusual length and secondary structure of the MTS.

A unifying mechanism for the biogenesis of membrane proteins co-operatively integrated by the Sec and Tat pathways

The majority of multi-spanning membrane proteins are co-translationally inserted into the bilayer by the Sec pathway. An important subset of membrane proteins have globular, cofactor-containing extracytoplasmic domains requiring the dual action of the co-translational Sec and post-translational Tat pathways for integration. Here, we identify further unexplored families of membrane proteins that are dual Sec-Tat-targeted. We establish that a predicted heme-molybdenum cofactor-containing protein, and a complex polyferredoxin, each require the concerted action of two translocases for their assembly. We determine that the mechanism of handover from Sec to Tat pathway requires the relatively low hydrophobicity of the Tat-dependent transmembrane domain. This, coupled with the presence of C-terminal positive charges, results in abortive insertion of this transmembrane domain by the Sec pathway and its subsequent release at the cytoplasmic side of the membrane. Together, our data points to a simple unifying mechanism governing the assembly of dual targeted membrane proteins.

Mechanism and hydrophobic forces driving membrane protein insertion of subunit II of cytochrome bo 3 oxidase

Subunit II (CyoA) of cytochrome bo(3) oxidase, which spans the inner membrane twice in bacteria, has several unusual features in membrane biogenesis. It is synthesized with an amino-terminal cleavable signal peptide. In addition, distinct pathways are used to insert the two ends of the protein. The amino-terminal domain is inserted by the YidC pathway whereas the large carboxyl-terminal domain is translocated by the SecYEG pathway. Insertion of the protein is also proton motive force (pmf)-independent. Here we examined the topogenic sequence requirements and mechanism of insertion of CyoA in bacteria. We find that both the signal peptide and the first membrane-spanning region are required for insertion of the amino-terminal periplasmic loop. The pmf-independence of insertion of the first periplasmic loop is due to the loop's neutral net charge. We observe also that the introduction of negatively charged residues into the periplasmic loop makes insertion pmf dependent, whereas the addition of positively charged residues prevents insertion unless the pmf is abolished. Insertion of the carboxyl-terminal domain in the full-length CyoA occurs by a sequential mechanism even when the CyoA amino and carboxyl-terminal domains are swapped with other domains. However, when a long spacer peptide is added to increase the distance between the amino-terminal and carboxyl-terminal domains, insertion no longer occurs by a sequential mechanism.

Mutational analysis of tetracycline resistance protein transmembrane segment insertion

The tetracycline resistance proteins (TetA) of gram-negative bacteria are secondary active transport proteins that contain buried charged amino acids that are important for tetracycline transport. Earlier studies have shown that insertion of TetA proteins into the cytoplasmic membrane is mediated by helical hairpin pairs of transmembrane (TM) segments. However, whether helical hairpins direct spontaneous insertion of TetA or are required instead for its interaction with the cellular secretion (Sec) machinery is unknown. To gain insight into how TetA proteins are inserted into the membrane, we have investigated how tolerant the class C TetA protein encoded by plasmid pBR322 is to placement of charged residues in TM segments. The results show that the great majority of charge substitutions do not interfere with insertion even when placed at locations that cannot be shielded internally within helical hairpins. The only mutations that frequently block insertion are proline substitutions, which may interfere with helical hairpin folding. The ability of TetA to broadly tolerate charge substitutions indicates that the Sec machinery assists in its insertion into the membrane. The results also demonstrate that it is feasible to engineer charged residues into the interior of TetA proteins for the purpose of structure-function analysis.

The proton motive force, acting on acidic residues, promotes translocation of amino-terminal domains of membrane proteins when the hydrophobicity of the translocation signal is low

We have shown previously that the first transmembrane segment of leader peptidase can function to translocate the polar amino-terminal Pf3 domain across the membrane into the periplasm independently of the proton motive force (pmf) (Lee, J. I., Kuhn, A., and Dalbey, R. E. (1992) J. Biol. Chem. 267, 938-943). We now show that when the first transmembrane segment lacks a strong hydrophobic character, the pmf is required for translocation. In addition, we find that the amino-terminal acidic residue proximal to the transmembrane domain plays a critical role in pmf-dependent amino-terminal translocation. Moreover, the pmf is required to hold the amino-terminal domain in the periplasm to prevent it from slipping such that the amino terminus is no longer exposed to the periplasm. In all cases, translocation occurs under conditions in which the function of the Sec machinery is impaired. These studies show that the low hydrophobicity of the first apolar domain (the translocation signal) can be compensated for by a negative charge in the amino-terminal region, upon which the pmf acts.

Directionality in protein translocation across membranes: the N-tail phenomenon

Protein translocation normally starts from an N-terminal signal peptide and proceeds in an N-to-C-terminal direction. However, in certain integral membrane proteins an N-terminal tail is translocated even though it is not preceded by a signal peptide. In eukaryotic cells this process involves the normal Sec-machinery. In contrast, recent studies in Escherichia coli show that translocation of such N-terminal tails occurs by a mechanism that does not appear to involve the Sec proteins and is most efficient for short tails lacking positively charged residues. These novel observations suggest that the Sec-machinery has an inherent N-to-C-terminal directionality and cannot work 'in reverse'.

Characterization of a soluble, catalytically active form of Escherichia coli leader peptidase: requirement of detergent or phospholipid for optimal activity

Leader peptidase is a novel serine protease in Escherichia coli, which functions to cleave leader sequences from exported proteins. Its catalytic domain extends into the periplasmic space and is anchored to the membrane by two transmembrane segments located at the N-terminal end of the protein. At present, there is no information on the structure of the catalytic domain. Here, we report on the properties of a soluble form of leader peptidase (delta 2-75), and we compare its properties to those of the wild-type enzyme. We find that the truncated leader peptidase has a kcat of 3.0 S-1 and a Km of 32 microM with a pro-OmpA nuclease A substrate. In contrast to the wild-type enzyme (pI of 6.8), delta 2-75 is water-soluble and has an acidic isoelectric point of 5.6. We also show with delta 2-75 that the replacement of serine 90 and lysine 145 with alanine residues results in a 500-fold reduction in activity, providing further evidence that leader peptidase employs a catalytic serine/lysine dyad. Finally, we find that the catalysis of delta 2-75 is accelerated by the presence of the detergent Triton X-100, regardless if the substrate is pro-OmpA nuclease A or a peptide substrate. Triton X-100 is required for optimal activity of delta 2-75 at a level far below the critical micelle concentration. Moreover, we find that E. coli phospholipids stimulate the activity of delta 2-75, suggesting that phospholipids may play an important physiological role in the catalytic mechanism of leader peptidase.

Evidence for a loop-like insertion mechanism of pro-Omp A into the inner membrane of Escherichia coli

We have studied the insertion of pro-OmpA into the Escherichia coli membrane in vivo using various mutants that have either alterations in the amino-terminal parts of the signal peptide or in the mature region that flanks the signal peptide. A pro-OmpA mutant with an amino terminal extension of 142 residues derived from ribulokinase (AraB) was analysed for its membrane insertion. The AraB portion, which includes a cluster of seven charged residues close to the signal sequence, did not interfere with the Sec components and allowed efficient export of OmpA. During translocation the AraB portion remained in the cytoplasm. Further mutants of OmpA were constructed in the carboxy-terminal region flanking the signal sequence. Pro-OmpA does not translocate across the membrane when a charge cluster, comprised of Lys-Arg-Arg-Glu-Arg, is introduced after positions 5, 11 or 15 of the mature region, but is translocated when the cluster is introduced after position 22. This defines a region of about 20 residues in the mature part of pro-OmpA that is crucial for membrane insertion. These results suggest that in the case of the Sec-dependent pro-OmpA, as with the Sec-independent M13 procoat, the precursor assumes a loop-like structure involving the signal peptide and the early part of the mature region, leaving the amino terminus of the signal peptide at the cytoplasmic face.

Positively charged amino acids placed next to a signal sequence block protein translocation more efficiently in Escherichia coli than in mammalian microsomes

Positively charged amino acids are known efficiently to block protein secretion in Escherichia coli, when placed within a short distance downstream of a signal sequence. It is not known whether the same applies to protein secretion in eukaryotic cells, though statistical studies of signal sequences of prokaryotic and eukaryotic secretory proteins have suggested that the situation may be different in this case. Here, we show that identical charge mutations in a model protein have different effects on membrane translocation in E. coli and in mammalian microsomes, and that the 'charge block' effect is much more pronounced in the prokaryotic system. This finding has implications not only for our understanding of the mechanisms of protein secretion, but also points to a potential problem in the expression of eukaryotic secretory proteins in bacteria.

Inter-molecular degradation of signal peptidase I in vitro

Highly purified preparations of signal peptidase I (36 kDa) were found to undergo an apparent inter-autocatalytic degradation at 4 degrees C and 37 degrees C. The disappearance of the 36 kDa protein coincided with the stable appearance of a 31 kDa and a 5 kDa species. Amino-terminal sequencing of the 31 kDa product indicated a site specific cleavage following Ala38-Gln-Ala of signal peptidase I. The 31 kDa fragment was purified and shown to have 100-fold less activity than the native enzyme, with pre-maltose binding protein as a substrate.

Leader peptidase

The Escherichia coli leader peptidase has been vital for unravelling problems in membrane assembly and protein export. The role of this essential peptidase is to remove amino-terminal leader peptides from exported proteins after they have crossed the plasma membrane. Strikingly, almost all periplasmic proteins, many outer membrane proteins, and a few inner membrane proteins are made with cleavable leader peptides that are removed by this peptidase. This enzyme of 323 amino acid residues spans the membrane twice, with its large carboxyl-terminal domain protruding into the periplasm. Recent discoveries show that its membrane orientation is controlled by positively charged residues that border (on the cytosolic side) the transmembrane segments. Cleavable pre-proteins must have small residues at -1 and a small or aliphatic residue at -3 (with respect to the cleavage site). Leader peptidase does not require a histidine or cysteine amino acid for catalysis. Interestingly, serine 90 and aspartic acid 153 are essential for catalysis and are also conserved in a mitochondrial leader peptidase, which is 30.7% homologous with the bacterial enzyme over a 101-residue stretch.

Fine-tuning the topology of a polytopic membrane protein: role of positively and negatively charged amino acids

The effects of positively and negatively charged residues on the membrane topology of a model E. coli protein with two transmembrane segments have been studied. We show that addition or removal of as little as a single positively charged lysine residue in one of two critical regions can be sufficient to reverse the transmembrane topology of the molecule from Nout-Cout to Nin-Cin. Negatively charged residues are much less potent and significantly affect the topology only if present in high numbers. Finally, we provide data to suggest that sec-independent and sec-dependent translocation mechanisms differ in their sensitivity to positively charged amino acids.

Molecular cloning of the Salmonella typhimurium lep gene in Escherichia coli

A system is described which enabled the selection of a heterologous lep gene, encoding signal peptidase I, in Escherichia coli. It is based on complementation of an E. coli mutant, in which the synthesis of signal peptidase I can be regulated. With this system the lep gene of Salmonella typhimurium was cloned and the nucleotide sequence was determined. The S. typhimurium lep gene encodes a protein of 324 amino acids. Expression of the gene in the E. coli mutant resulted in suppression of growth inhibition and in the restoration of processing activity under conditions where synthesis of E. coli signal peptidase I was repressed. The cloned S. typhimurium signal peptidase I had an apparent molecular weight of 36,000 daltons, which is in agreement with the calculated molecular weight of 35,782 daltons. The system described for selection of the S. typhimurium lep gene may permit the cloning and expression of other heterologous signal peptidase I genes.

Positively charged residues are important determinants of membrane protein topology

Membrane proteins are found in a variety of conformations, with each protein spanning the membrane a set number of times and adopting a particular orientation. Positively charged residues, often located near the boundaries of transmembrane segments, appear to be involved in specifying the topology of membrane proteins.