Genetic screen for signal peptides in Hydra reveals novel secreted proteins and evidence for non-classical protein secretion

We have screened a Hydra cDNA library for sequences encoding N-terminal signal peptides using the yeast invertase secretion vector pSUC [Jacobs et al., 1997. A genetic selection for isolating cDNAs encoding secreted proteins. Gene 198, 289–296]. We isolated and sequenced 907 positive clones; 88% encoded signal peptides; 12% lacked signal peptides. By searching the Hydra EST database we identified full-length sequences for the selected clones. These encoded 37 known proteins with signal peptides and 40 novel Hydra-specific proteins with signal peptides. Localization of two signal peptide-containing sequences, VEGF and ferritin, to the secretory pathway was confirmed with GFP fusion proteins. In addition, we isolated 105 clones which lacked signal peptides but which supported invertase secretion from yeast. Isolation of plasmids from these clones and retransformation in invertase-negative yeast cells confirmed the phenotype. A GFP fusion protein of one such clone encoding the foot morphogen pedibin was localized to the cytoplasm in transfected Hydra cells and did not enter the ER/Golgi secretory pathway. Secretion of pedibin and other proteins lacking signal peptides appears to occur by a non-classical protein secretion route.     

Comparison of different signal peptides for protein secretion in nonlytic insect cell system

Protein expression and secretion in insect cells have been widely studied in the baculovirus-infected insect cell system. In directly transfected insect cells only intracellular expression and purification of recombinant proteins have been studied in detail. To examine multiple recombinant protein variants, easy and fast expression and a purification screening system are required. The aim of this study was to establish an effective and rapid secretion system for human azurocidin using directly transfected insect cells. We also constructed and tested expression vectors possessing heterologous signal peptides derived from human azurocidin, yellow lupin diphosphonucleotide phosphatase/phosphodiesterase (PPD1), and papaya papain IV to secrete yellow lupin and red kidney bean purple acid phosphatases, PPD1, and papain IV. Our results demonstrate that the secretion vectors used here can direct recombinant proteins to the culture medium very effectively, allowing their simple purification on a small/medium scale. Based on secretion and activity analyses it seems that the azurocidin signal peptide is one of the most potent secretion signals.     

Secretion of xylanase A2 in Streptomyces lividans: dependence on signal peptides length, number and composition

The signal peptide (sp) in Streptomyces lividans xylanase A2 (XlnA2) was replaced by sps containing, in frame in their sequences, one, two, three or four initiation codons, each preceded by a Shine-Dalgarno (SD) sequence. Precursors of the corresponding proteins should thus have sps of, respectively, 27, 46, 82 and 91 amino acids (aa) long. By radiolabelling of S. lividans harboring the different constructs inserted in a multicopy plasmid and by immunoprecipitation with anti-xylanase antibodies followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation, precursors of the expected sizes were obtained in each clone. This indicates that ribosomes can synthesize different XlnA2 precursors from initiation codons inserted in the sp sequence, independently of their number. The amount of these synthesized precursors was also shown to be inversely proportional to their length when comparing the specific activity of labelling versus sp length. In clones producing more than one precursor, a smear appeared on the autoradiograms, suggesting some degree of precursor degradation. As determined by pulse-chase experiments, the rate of disappearance was almost the same for precursors of different lengths, but this might be the result of both true processing and proteolytic degradation. Furthermore, S. lividans rapidly degraded XlnA2 either when deprived of its sp or in the absence of the signal peptidase cleavage site.     

信号肽及化学通透剂对环糊精葡萄糖基转移酶胞外分泌的影响

【目的】研究不同的信号肽和化学通透剂对重组环糊精葡萄糖基转移酶(CGTase)胞外分泌的影响,提高CGTase的胞外分泌量。【方法】扩增地芽孢杆菌CHB1(Geobacillus sp.CHB1)的CGTase基因,构建带有地芽孢杆菌CHB1自身信号肽、Omp A、Pel B信号肽和不带信号肽的4种重组质粒;比较4种重组质粒对重组CGTase胞外分泌的影响,筛选最优的信号肽;考察甘氨酸、Triton X-100、SDS和Tween 80四种化学通透剂对重组CGTase胞外分泌的影响,确定最佳的化学通透剂及其浓度。【结果】Omp A信号肽介导的分泌效果最好,胞外酶活达到7.44 U/m L,分别是Pel B、CHB1信号肽的2.04倍和11.27倍,不带信号肽的重组质粒菌胞外检测不到酶活;携带Omp A信号肽的重组质粒菌发酵48 h,同时添加浓度为0.6%的甘氨酸和0.3%的Triton X-100,胞外酶活达最大到14.27 U/m L;SDS和Tween 80对该酶的胞外分泌具有明显的抑制作用。【结论】Omp A信号肽的介导效果最佳,同时添加浓度为0.6%和0.3%的甘氨酸和Triton X-100可以有效促进胞外分泌,为该重组酶的高效胞外分泌提供了一种有效的方法。     

Cyanobacterial leader peptides for protein secretion

The leader peptide of the major secreted protein PilA1 of the cyanobacterium Synechocystis sp. strain PCC 6803 and several artificial leader peptides have been used to study secretion of the reporter protein lichenase to the culture medium. The strains of Synechocystis carrying lichenase with the leader sequences of PilA and with the leader sequence of Slr2016 efficiently secreted the reporter protein. The artificial leader sequence that was characterized by the overall positive charge (as PilA1 and Slr2016 leaders) also allowed secretion. The artificial leader with negative charge, however, did not allow secretion of the reporter protein. Moreover, no secreted proteins have been isolated from this strain using conventional techniques for preparation of secreted proteins. These data suggest that the general secretion pathway in cyanobacteria, at least for pilins, recognizes the overall charge of the leader sequences, and operates in a sequence-non-specific manner.     

Proteome-based identification of fusion partner for high-level extracellular production of recombinant proteins in Escherichia coli

Extracellular production of recombinant proteins in Escherichia coli has several advantages over cytoplasmic or periplasmic production. However, nonpathogenic laboratory strains of E. coli generally excrete only trace amounts of proteins into the culture medium under normal growth conditions. Here we report a systematic proteome-based approach for developing a system for high-level extracellular production of recombinant proteins in E. coli. First, we analyzed the extracellular proteome of an E. coli B strain, BL21(DE3), to identify naturally excreted proteins, assuming that these proteins may serve as potential fusion partners for the production of recombinant proteins in the medium. Next, overexpression and excretion studies were performed for the 20 selected fusion partners with molecular weights below 40 kDa. Twelve of them were found to allow fused proteins to excrete into the medium at considerable levels. The most efficient excreting fusion partner, OsmY, was used as a carrier protein to excrete heterologous proteins into the medium. E. coli alkaline phosphatase, Bacillus subtilis alpha-amylase, and human leptin used as model proteins could all be excreted into the medium at concentrations ranging from 5 to 64 mg/L during the flask cultivation. When only the signal peptide or the mature part of OsmY was used as a fusion partner, no such excretion was observed; this confirmed that these proteins were truly excreted rather than released by outer membrane leakage. The recombinant protein of interest could be recovered by cleaving off the fusion partner by enterokinase as demonstrated for alkaline phosphatase as an example. High cell density cultivation allowed production of these proteins to the levels of 250-700 mg/L in the culture medium, suggesting the good potential of this approach for the excretory production of recombinant proteins.     

Heterologous protein secretion by Lactobacillus plantarum using homologous signal peptides

Aims: To test seven selected putative signal peptides from Lactobacillus plantarum WCFS1 in terms of their ability to drive secretion of two model proteins in Lact. plantarum, and to compare the functionality of these signal peptides with that of well‐known heterologous signal peptides (Usp45, M6). Methods and Results: Signal peptide functionality was assessed using a series of modular derivatives of the pSIP vectors for peptide pheromone‐controlled high‐level gene expression in lactobacilli. Several of the constructs with homologous signal peptides yielded similar or higher reporter protein activities than constructs with heterologous signal peptides. Two of the homologous signal peptides (Lp_0373 and Lp_0600) appeared as especially promising candidates for directing secretion, as they were among the best performing with both reporter proteins. Conclusions: We have identified homologous signal peptides for high‐level secretion of heterologous proteins in Lact. plantarum. With the model proteins, some of these performed better than commonly used heterologous signal peptides. Significance and Impact of the Study: The homologous signal peptides tested out, in this study, could be useful in food‐grade systems for secretion of interesting proteins in Lact. plantarum. The constructed modular secretion vectors are easily accessible for rapid signal peptide screening.     

Optimization of a heterologous signal peptide by site-directed mutagenesis for improved secretion of recombinant proteins in Escherichia coli

A heterologous signal peptide (SP) from Bacillus sp. G1 was optimized for secretion of recombinant cyclodextrin glucanotransferase (CGTase) to the periplasmic and, eventually, extracellular space of Escherichia coli. Eight mutant SPs were constructed using site-directed mutagenesis to improve the secretion of recombinant CGTase. M5 is a mutated SP in which replacement of an isoleucine residue in the h-region to glycine created a helix-breaking or G-turn motif with decreased hydrophobicity. The mutant SP resulted in 110 and 94% increases in periplasmic and extracellular recombinant CGTase, respectively, compared to the wild-type SP at a similar level of cell lysis. The formation of intracellular inclusion bodies was also reduced, as determined by sodium dodecyl sulfate-polyacrylamyde gel electrophoresis, when this mutated SP was used. The addition of as low as 0.08% glycine at the beginning of cell growth improved cell viability of the E. coli host. Secretory production of other proteins, such as mannosidase, also showed similar improvement, as demonstrated by CGTase production, suggesting that the combination of an optimized SP and a suitable chemical additive leads to significant improvements of extracellular recombinant protein production and cell viability. These findings will be valuable for the extracellular production of recombinant proteins in E. coli.     

High level secretion of TaqI restriction endonuclease by recombinant Escherichia coli

The production and high level secretion of TaqI restriction endonuclease using bacterial secretion signal within the malE gene was achieved by cloning the PCR-amplified gene from Thermus aquaticus into E. coli. The maltose binding protein (MBP) part of the MBP-TaqI fusion protein expressed by this construct did not interfere with the biological activity of the TaqI restriction endonuclease. E. coli XL1 carrying pH185 produced 332 U ml^–1 TaqI endonuclease 81% of which was secreted into the medium without apparent cell lysis. Optimization of culture conditions and selection of the host strain were found to be important for the efficient extracellular production of this protein.     

Computational differentiation of N-terminal signal peptides and transmembrane helices

Signal peptides and transmembrane helices both contain a stretch of hydrophobic amino acids. This common feature makes it difficult for signal peptide and transmembrane helix predictors to correctly assign identity to stretches of hydrophobic residues near the N-terminal methionine of a protein sequence. The inability to reliably distinguish between N-terminal transmembrane helix and signal peptide is an error with serious consequences for the prediction of protein secretory status or transmembrane topology. In this study, we report a new method for differentiating protein N-terminal signal peptides and transmembrane helices. Based on the sequence features extracted from hydrophobic regions (amino acid frequency, hydrophobicity, and the start position), we set up discriminant functions and examined them on non-redundant datasets with jackknife tests. This method can incorporate other signal peptide prediction methods and achieve higher prediction accuracy. For Gram-negative bacterial proteins, 95.7% of N-terminal signal peptides and transmembrane helices can be correctly predicted (coefficient 0.90). Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 99% (coefficient 0.92). For eukaryotic proteins, 94.2% of N-terminal signal peptides and transmembrane helices can be correctly predicted with coefficient 0.83. Given a sensitivity of 90%, transmembrane helices can be identified from signal peptides with a precision of 87% (coefficient 0.85). The method can be used to complement current transmembrane protein prediction and signal peptide prediction methods to improve their prediction accuracies.     

Coupling between codon usage, translation and protein export in Escherichia coli

Proteins destined for export via the Sec-dependent pathway are synthesized with a short N-terminal signal peptide. A requirement for export is that the proteins are in a translocationally competent state. This is a loosely folded state that allows the protein to pass through the SecYEG apparatus and pass into the periplasm. In order to maintain pre-secretory proteins in an export-competent state, there are many factors that slow the folding of the pre-secretory protein in the cytoplasm. These include cytoplasmic chaperones, such as SecB, and the signal recognition particle, which bind the pre-secretory protein and direct it to the cytoplasmic membrane for export. Recently, evidence has been published that non-optimal codons in the signal sequence are important for a time-critical early event to allow the correct folding of pre-secretory proteins. This review details the recent developments in folding of the signal peptide and the pre-secretory protein.     

Protein secretion in streptomycetes

Some aspects of the current knowledge on protein secretion in streptomycetes are presented, including recent data on the identification of genes involved in the general secretory pathway, on the importance of the signal peptide structure and on the number of ribosome-binding sites inside signal peptides which can influence the production level of a gene product.     

Construction of an Escherichia coli export-affinity vector for expression and purification of foreign proteins by fusion to cyclomaltodextrin glucanotransferase.

A novel export-affinity fusion vector employing the gene encoding cyclomaltodextrin glucanotransferase (CGTase; cgt) from Bacillus circulans var. alkalophilus (ATCC 21783) is described. CGTase binds to various sugar polymers, which makes it simple to purify it to near homogeneity in a single step. The CGTase fusion protein vector was constructed by deleting the translational stop codons from the gene encoding CGTase (cgt) by in vitro mutagenesis. As models, genes encoding Escherichia coli alkaline phosphatase (APase; phoA) and Bacillus stearothermophilus (ATCC 12980) alpha-amylase (BStA; amy) were fused to cgt. Overexpression of wild type CGTase and the hybrid proteins under the control of the lac promoter caused a 'leaky phenotype' in E. coli, the outer membrane became permeable, which enabled the adsorption of the fusion proteins directly from the culture medium onto alpha-cyclodextrin (alpha-CD) coupled agarose. The hybrid proteins were eluted from the column with alpha-CD solution under mild conditions at pH 7.5. The CGTase-APase' fusion had a good in vivo stability, whereas the CGTase-BStA' was less stable. In the latter case, according to protein sequencing, the proteolytically sensitive site was on the BStA' side of the fusion. The C-terminus of CGTase was stable against proteolysis as shown by narrow pH range isoelectric focusing. The fused enzymes retained their biological activities.     

Novel synthetic signal peptides for the periplasmic secretion of green fluorescent protein in Escherichia coli

New secretion vectors containing synthetic signal peptides were constructed to study the periplasmic translocation of green fluorescent protein (GFP) in Escherichia coli. These constructs encode synthetic signal peptides spA and spD fused to the amino terminal end of GFP, and expressed from T7/lac promoter in the BL21DE3 strain by induction with IPTG. The recombinant protein was detected in both the cytoplasmic and periplasmic fractions. Fluorescence analysis revealed that recombinant proteins with signal peptides were not fluorescent, indicating translocation to periplasmic space. In contrast, recombinant proteins without signal peptide were fluorescent. These results indicate that the expressed recombinant proteins were translocated into the periplasm. Therefore, the synthetic signal peptides derived from signal peptides of Bacillus sp. could efficiently secrete the heterologous proteins to the periplasmic space of E. coli.     

Artificial signal peptide prediction by a hidden markov model to improve protein secretion via Lactococcus lactis bacteria

A hidden Markov model (HMM) has been utilized to predict and generate artificial secretory signal peptide sequences. The strength of signal peptides of proteins from different subcellular locations via Lactococcus lactis bacteria correlated with their HMM bit scores in the model. The results show that the HMM bit score +12 are determined as the threshold for discriminating secreteory signal sequences from the others. The model is used to generate artificial signal peptides with different bit scores for secretory proteins. The signal peptide with the maximum bit score strongly directs proteins secretion.     

Secretion expression of recombinant glucagon in Escherichia coli

A novel approach for the preparation of recombinant human glucagon was described. An expression vector pAGluT, containing phoA promoter, phoA signal peptide and glucagon gene, was constructed by means of genetic engineering. Escherichia coli strain YK537 was transformed with pAGluT. High-level secretory expression of recombinant human glucagon was achieved. The expression yield of recombinant human glucagon was found to be 80 mg/L, approximately 30% of the total proteins in supernatant. The biological activities and the physicochemical properties of the purified recombinant human glucagon were found to be the same as that of native glucagon. In addition, our results suggested that phoA expression system may be suitable for the expression of other small peptides.     

Consequences of depletion of the signal recognition particle in Escherichia coli

Thus far, the role of the Escherichia coli signal recognition particle (SRP) has only been studied using targeted approaches. It has been shown for a handful of cytoplasmic membrane proteins that their insertion into the cytoplasmic membrane is at least partially SRP-dependent. Furthermore, it has been proposed that the SRP plays a role in preventing toxic accumulation of mistargeted cytoplasmic membrane proteins in the cytoplasm. To complement the targeted studies on SRP, we have studied the consequences of the depletion of the SRP component Fifty-four homologue (Ffh) in E. coli using a global approach. The steady-state proteomes and the proteome dynamics were evaluated using one- and two-dimensional gel analysis, followed by mass spectrometry-based protein identification and immunoblotting. Our analysis showed that depletion of Ffh led to the following: (i) impaired kinetics of the biogenesis of the cytoplasmic membrane proteome; (ii) lowered steady-state levels of the respiratory complexes NADH dehydrogenase, succinate dehydrogenase, and cytochrome bo(3) oxidase and lowered oxygen consumption rates; (iii) increased levels of the chaperones DnaK and GroEL at the cytoplasmic membrane; (iv) a σ(32) stress response and protein aggregation in the cytoplasm; and (v) impaired protein synthesis. Our study shows that in E. coli SRP-mediated protein targeting is directly linked to maintaining protein homeostasis and the general fitness of the cell.