Sec-independent Pathway Research Articles

In vivo associations of Escherichia coli NarJ with a peptide of the first 50 residues of nitrate reductase catalytic subunit NarG

The catalytic subunit of many Escherichia coli redox enzymes bares a twin-arginine translocation (Tat)-dependent signal peptide in its precursor, which directs the redox enzyme complex to this Sec-independent pathway. NarG of the E. coli nitrate reductase NarGHI complex possesses a vestige twin-arginine motif at its N terminus. During the cofactor insertion, and assembly and folding of the NarG-NarH complex, a chaperone protein, NarJ, is thought to interact with the N terminus and an unknown second site of NarG. Our previous in vitro study provided evidence that NarJ's role shows some Tat system dependence. In this work, we investigated the associations of NarJ with a peptide of the first 50 residues of NarG (NarG50) in living cells. Two approaches were used: the Förster resonance energy transfer (FRET) based on yellow fluorescent protein - cyan fluorescent protein (YFP-CFP) and the bimolecular fluorescence complementation (BiFC). Compared with the wild-type (WT) E. coli cotransformants expressing both NarJ-YFP and NarG50-CFP, tat gene mutants gave an apparent FRET efficiency (Eapp) that was on the order of 25%-40% lower. These experiments implied a Tat system dependency of the in vivo associations between NarJ and the NarG50 peptide. In the BiFC assay, a 4-fold lower specific fluorescence intensity was observed for the E. coli WT cotransformants expressing both NarJ-Yc and NarG50-Yn than for its tat mutants, again suggesting a Tat dependence of the interactions. Fluorescence microscopy showed a "dot" /unipolar distribution of the reassembled YFP-NarJ:NarG50 both in WT and tat mutants, demonstrating a distinct localization of the interaction. Thus, although the degree of the interaction shows Tat dependence, the cell localization is less so. Taken together, these data further support that NarJ's activity on NarG may be assisted by the Tat system.

Cysteine Residues in the Transmembrane Regions of M13 Procoat Protein Suggest that Oligomeric Coat Proteins Assemble onto Phage Progeny

The M13 phage assembles in the inner membrane of Escherichia coli. During maturation, about 2,700 copies of the major coat protein move from the membrane onto a single-stranded phage DNA molecule that extrudes out of the cell. The major coat protein is synthesized as a precursor, termed procoat protein, and inserts into the membrane via a Sec-independent pathway. It is processed by a leader peptidase from its leader (signal) peptide before it is assembled onto the phage DNA. The transmembrane regions of the procoat protein play an important role in all these processes. Using cysteine mutants with mutations in the transmembrane regions of the procoat and coat proteins, we investigated which of the residues are involved in multimer formation, interaction with the leader peptidase, and formation of M13 progeny particles. We found that most single cysteine residues do not interfere with the membrane insertion, processing, and assembly of the phage. Treatment of the cells with copper phenanthroline showed that the cysteine residues were readily engaged in dimer and multimer formation. This suggests that the coat proteins assemble into multimers before they proceed onto the nascent phage particles. In addition, we found that when a cysteine is located in the leader peptide at the -6 position, processing of the mutant procoat protein and of other exported proteins is affected. This inhibition of the leader peptidase results in death of the cell and shows that there are distinct amino acid residues in the M13 procoat protein involved at specific steps of the phage assembly process.

FlhB Regulates Ordered Export of Flagellar Components via Autocleavage Mechanism

The bacterial flagellum is a predominantly cell-external super-macromolecular construction whose structural components are exported by a flagellum-specific export apparatus. One of the export apparatus proteins, FlhB, regulates the substrate specificity of the entire apparatus; i.e. it has a role in the ordered export of the two main groups of flagellar structural proteins such that the cell-proximal components (rod-/hook-type proteins) are exported before the cell-distal components (filament-type proteins). The controlled switch between these two export states is believed to be mediated by conformational changes in the structure of the C-terminal cytoplasmic domain of FlhB (FlhB(C)), which is consistently and specifically cleaved into two subdomains (FlhB(CN) and FlhB(CC)) that remain tightly associated with each other. The cleavage event has been shown to be physiologically significant for the switch. In this study, the mechanism of FlhB cleavage has been more directly analyzed. We demonstrate that cleavage occurs in a heterologous host, Saccharomyces cerevisiae, deficient in vacuolar proteinases A and B. In addition, we find that cleavage of a slow-cleaving variant, FlhB(C)(P270A), is stimulated in vitro at alkaline pH. We also show by analytical gel-filtration chromatography and analytical ultracentrifugation experiments that both FlhB(C) and FlhB(C)(P270A) are monomeric in solution, and therefore self-proteolysis is unlikely. Finally, we provide evidence via peptide analysis and FlhB cleavage variants that the tertiary structure of FlhB plays a significant role in cleavage. Based on these results, we propose that FlhB cleavage is an autocatalytic process.

Mechanisms of Protein Export across the Bacterial Outer Membrane

Gram-negative bacteria secrete a wide range of proteins whose functions include biogenesis of organelles, such as pili and flagella; nutrient acquisition; virulence; and efflux of drugs and other toxins. Export of these proteins to the bacterial surface involves transport across the inner membrane (IM), periplasm, and outer membrane (OM) of the cell envelope. Several pathways have evolved to fulfill the task of secretion (Table ​(Table1).1). These pathways can be divided into two main groups: (i) Sec dependent and (ii) Sec independent (Fig. ​(Fig.1)1) (64). FIG. 1. Schematic presentation of Sec-dependent and Sec-independent secretion pathways in gram-negative bacteria. The type I pathway is exemplified by the hemolysin A (HlyA) secretion in pathogenic E. coli, the type II pathway by YopE secretion in Yersinia pestis ... TABLE 1. Representative members of the eight secretion systems Proteins secreted via the Sec-dependent pathways utilize a common machinery, the Sec translocase, for transport across the IM and are mainly differentiated based on their mechanisms of secretion across the OM (64). Sec-dependent pathways include the type II secretion (T2S); the autotransporter (AT), or type V secretion; the two-partner secretion (TPS); and the chaperone/usher (CU) secretion systems (34, 46, 58, 70, 73). The type IV secretion (T4S), or adapted-conjugation, pathway can be Sec dependent but is mostly considered Sec independent (21). Sec-independent pathways tend to allow direct export from the cytoplasm to the extracellular environment in one step and do not involve periplasmic intermediates. These pathways also include the type I secretion (T1S), or ABC (ATP-binding cassette), exporters (5) and the type III secretion (T3S) systems (31). An alternative Sec-independent pathway known as twin-arginine translocation (Tat) is employed for transport of already-folded proteins across the IM. Generally, Tat substrates are targeted to the periplasm of the cell (4) but can also be transported across the OM via the type II pathway, such as the phospholipases of Pseudomonas aeruginosa (77). The Sec and Tat machineries for transport across the IM will not be discussed further. In this review, we summarize the current knowledge of OM protein secretion in terms of the structure of the exporters and the mechanism of secretion and examine similarities and differences among the different export pathways (Table ​(Table2).2). Since many virulence factors are secreted proteins, a more complete understanding of the mechanisms underlying bacterial protein secretion is crucial to the development of new vaccines and treatments for a wide range of human pathogens. TABLE 2. Structural features of the OM components of protein secretion systems

Crystal Structures of the Precursor Form of Glucose-Fructose Oxidoreductase from Zymomonas mobilis and Its Complexes with Bound Ligands,

The NADP(H)-dependent enzyme glucose-fructose oxidoreductase (GFOR) is a classic example of a redox protein that is translocated across a membrane in fully folded form. GFOR is synthesized in the cytoplasm with a 52-residue signal peptide, giving a precursor form, preGFOR, that is fully active and has its cofactor tightly bound. A twin-arginine motif in the signal peptide directs it to a Sec-independent pathway by which it is translocated, in fully folded form, into the periplasm where it functions to produce sorbitol for osmoprotection. We have determined the crystal structures of four different forms of preGFOR, (i) oxidized preGFOR, with succinate bound in the active site, (ii) oxidized preGFOR with glycerol bound, (iii) reduced preGFOR in 0.3 M glucose, and (iv) reduced preGFOR in 1.5 M sorbitol, at resolutions of 2.2, 2.05, 2.5, and 2.6 A, respectively. In all four crystal structures, the signal peptide is disordered, implying a flexibility that may be important for its interaction with the translocation apparatus; a factor contributing to this disorder may be the high positive charge of the protein surface in the region where the signal peptide emerges. This may disfavor a stable association between the signal peptide and the rest of the protein. The crystal structures show that the mature enzyme portion of preGFOR is identical to native GFOR, in structure and cofactor binding, explaining the enzymatic activity of the precursor form. In the glycerol complex, preGFOR(gll), a bound glycerol molecule models the binding of the glucose substrate, with its O1 atom hydrogen bonded to the essential acid/base catalyst, Tyr269, and C1 only 3 A from C4 of the nicotinamide. In the glucose-soaked structure, preGFOR(glu), we identify a conformational change of the nearby Lys181 that probably results from the oxidation of glucose to gluconolactone, and functions to prevent rebinding of glucose prior to the binding of fructose. In this conformational change, the Lys181 side chain moves closer to the nicotinamide ring, stabilized by its increased negative charge.

Evidence against the double-arginine motif as the only determinant for protein translocation by a novel Sec-independent pathway in Escherichia coli

Proteins which are synthesized with a signal peptide containing a `double-arginine' motif may be translocated across the bacterial cytoplasmic membrane by a mechanism that is different from the known Sec and signal recognition particle pathways. The function of the double-arginine motif as a determinant for this novel pathway was studied by expressions of gene constructs coding for the high potential iron-sulfur protein (HiPIP) from Chromatium vinosum D in Escherichia coli. When the protein was produced with its original double-arginine motif-containing signal peptide, it was in part translocated into the periplasm and thereby processed, as shown by immunoblots after cell fractionation and N-terminal sequencing of purified HiPIP. Processing was not inhibited significantly by 3 mM sodium azide, indicating that translocation of HiPIP occurs by a SecA-independent pathway. Translocation of HiPIP could be altered to the SecA-dependent mode when its signal peptide was substituted by that of PelB from Erwinia carotovora. When the HiPIP double-arginine motif (S RR DAVK) was introduced into the corresponding position of the PelB signal peptide, the transport pathway remained SecA-dependent. This indicates that additional determinants are required for translocation by the Sec-independent pathway.

Evidence against the double-arginine motif as the only determinant for protein translocation by a novel Sec-independent pathway in Escherichia coli.

Proteins which are synthesized with a signal peptide containing a 'double-arginine' motif may be translocated across the bacterial cytoplasmic membrane by a mechanism that is different from the known Sec and signal recognition particle pathways. The function of the double-arginine motif as a determinant for this novel pathway was studied by expressions of gene constructs coding for the high potential iron-sulfur protein (HiPIP) from Chromatium vinosum D in Escherichia coli. When the protein was produced with its original double-arginine motif-containing signal peptide, it was in part translocated into the periplasm and thereby processed, as shown by immunoblots after cell fractionation and N-terminal sequencing of purified HiPIP. Processing was not inhibited significantly by 3 mM sodium azide, indicating that translocation of HiPIP occurs by a SecA-independent pathway. Translocation of HiPIP could be altered to the SecA-dependent mode when its signal peptide was substituted by that of PelB from Erwinia carotovora. When the HiPIP double-arginine motif (SRRDAVK) was introduced into the corresponding position of the PelB signal peptide, the transport pathway remained SecA-dependent. This indicates that additional determinants are required for translocation by the Sec-independent pathway.

Analysis of the C-terminal secretion signal of the Rhizobium leguminosarum nodulation protein NodO; a potential system for the secretion of heterologous proteins during nodule invasion.

We used deletions to analyze the domains required for secretion of the Rhizobium leguminosarum bv. viciae nodulation protein, NodO, by the sec-independent pathway. Deletion of the C-terminal 24 amino-acids (residues 261 to 284) reduced secretion by at least 95%. A monoclonal antibody that recognizes the C-terminal domain of NodO was used to identify four nested deletions that retained the C-terminal 24 residues of NodO but had lost up to 133 residues (amino acids 128 to 259); all four proteins were secreted into the growth medium with an efficiency between 50 and 90% of normal. A deleted derivative of NodO that retained residues 1 to 21 and 167 to 284 (and therefore lacked most of the N-terminal Ca(2+)-binding domain) was secreted at around 80% of normal efficiency. Taken together, these observations indicate that the C-terminal 24 amino acids are sufficient for NodO secretion although the region adjacent to this domain appears to affect secretion efficiency. A derivative of the Escherichia coli alkaline phosphatase (phoA) gene was cloned into two derivatives of nodO such that PhoA (lacking the N-terminal transit peptide) was in-frame at both ends, with the C terminus fused to either the last 24 or 50 amino acids of NodO. These fusion proteins were secreted at 40 and 80% of the wild-type level, respectively, and the larger of the two retained alkaline phosphatase activity. A hybrid protein, containing E. coli beta-glucuronidase (GUS) fused to the N terminus of NodO, was not secreted, and it reduced the levels of wild-type NodO secreted by R. leguminosarum bv. viciae. The nature of the NodO C-terminal secretion signal is discussed with regard to its use as a delivery system for heterologous proteins useful for investigating the Rhizobium-legume interaction.