A novel strategy for protein production using non-classical secretion pathway in Bacillus subtilis

Recombinant extracellular expression of β-glucosidase in Bacillus subtilis and its potential secretion mechanism

β-Glucosidase is an important specific β-1,4 glycosidic bond hydrolase. Here, β-glucosidase Bgl2A achieved extracellular secretory expression in Bacillus subtilis mediated by the signal peptide SPAmyQ, and its extracellular activity was increased 3.35-fold by signal peptide optimization. Interestingly, the recombinant extracellular activity of Bgl2A without signal peptide mediation was 5.05-fold higher than that with SPAmyQ mediation, and its stability was better at acidic conditions and low temperatures. Combining the results of classical secretory pathway knockout and cell integrity assays, Bgl2A without signal peptide can perform non-classical extracellular secretion in B. subtilis. Notably, the hydrophobic region I266-Q269 is a critical sequence affecting the non-classical secretion of Bgl2A. Mutants I267A and I267E increased the extracellular activity and secretion rate of Bgl2A by 1.42- and 1.58-fold, respectively. In addition, maintaining the hydrophobicity of the amino acids at positions 268 and 269 may be essential for the non-classical secretion of Bgl2A. To our knowledge, this study first reported that SPLipB was not detected at the N-terminus of the intracellular Bgl2A precursor from WBLBBgl-SPLipB mediated by the Sec-type signal peptide SPLipB. This offers a theoretical foundation for enhancing recombinant extracellular expression of β-glucosidase in B. subtilis and understanding the mechanism of non-classical secretion in this organism.

iNClassSec-ESM: Discovering potential non-classical secreted proteins through a novel protein language model

Non-classical secreted proteins (NCSPs) are a class of proteins lacking signal peptides, secreted by Gram-positive bacteria through non-classical secretion pathways. With the increasing demand for highly secreted proteins in recent years, non-classical secretion pathways have received more attention due to their advantages over classical secretion pathways (Sec/Tat). However, because the mechanisms of non-classical secretion pathways are not yet clear, identifying NCSPs through biological experiments is expensive and time-consuming, making it imperative to develop computational methods to address this issue. Existing NCSP prediction methods mainly use traditional handcrafted features to represent proteins from sequence information, which limits the models' ability to capture complex protein characteristics. In this study, we proposed a novel NCSP predictor, iNClassSec-ESM, which combined deep learning with traditional classifiers to enhance prediction performance. iNClassSec-ESM integrates an XGBoost model trained on comprehensive handcrafted features and a Deep Neural Network (DNN) trained on hidden layer embeddings from the protein language model (PLM) ESM3. The ESM3 is the recently proposed multimodal PLM and has not yet been fully explored in terms of protein representation. Therefore, we extracted hidden layer embeddings from ESM3 as inputs for multiple classifiers and deep learning networks, and compared them with existing PLMs. Benchmark experiments indicate that iNClassSec-ESM outperforms most of existing methods across multiple performance metrics and could serve as an effective tool for discovering potential NCSPs. Additionally, the ESM3 hidden layer embeddings, as an innovative protein representation method, show great potential for the application in broader protein-related classification tasks. The source code of iNClassSec-ESM and the ESM3 embeddings extraction script are publicly available at https://github.com/AmamiyaHoshie/iNClassSec-ESM/.

TasA Fibre Interactions Are Necessary for Bacillus subtilis Biofilm Structure

The extracellular matrix of biofilms provides crucial structural support to the community and protection from environmental perturbations. TasA, a key Bacillus subtilis biofilm matrix protein, forms both amyloid and non-amyloid fibrils. Non-amyloid TasA fibrils are formed via a strand-exchange mechanism, whereas the amyloid-like form involves non-specific self-assembly. We performed mutagenesis of the N-terminus to assess the role of non-amyloid fibrils in biofilm development. We find that the N-terminal tail is essential for the formation of structured biofilms, providing evidence that the strand-exchange fibrils are the active form in the biofilm matrix. Furthermore, we demonstrate that fibre formation alone is not sufficient to give structure to the biofilm. We build an interactome of TasA with other extracellular protein components, and identify important interaction sites. Our results provide insight into how protein-matrix interactions modulate biofilm development.

Unveiling antibiofilm potential: proteins from Priestia sp. targeting Staphylococcus aureus biofilm formation

Staphylococcus aureus is the etiologic agent of many nosocomial infections, and its biofilm is frequently isolated from medical devices. Moreover, the dissemination of multidrug-resistant (MDR) strains from this pathogen, such as methicillin-resistant S. aureus (MRSA) strains, is a worldwide public health issue. The inhibition of biofilm formation can be used as a strategy to weaken bacterial resistance. Taking that into account, we analysed the ability of marine sponge-associated bacteria to produce antibiofilm molecules, and we found that marine Priestia sp., isolated from marine sponge Scopalina sp. collected on the Brazilian coast, secretes proteins that impair biofilm development from S. aureus. Partially purified proteins (PPP) secreted after 24 hours of bacterial growth promoted a 92% biofilm mass reduction and 4.0 µg/dL was the minimum concentration to significantly inhibit biofilm formation. This reduction was visually confirmed by light microscopy and Scanning Electron Microscopy (SEM). Furthermore, biochemical assays showed that the antibiofilm activity of PPP was reduced by ethylenediaminetetraacetic acid (EDTA) and 1,10 phenanthroline (PHEN), while it was stimulated by zinc ions, suggesting an active metallopeptidase in PPP. This result agrees with mass spectrometry (MS) identification, which indicated the presence of a metallopeptidase from the M28 family. Additionally, whole-genome sequencing analysis of Priestia sp. shows that gene ywad, a metallopeptidase-encoding gene, was present. Therefore, the results presented herein indicate that PPP secreted by the marine Priestia sp. can be explored as a potential antibiofilm agent and help to treat chronic infections.

Bacillus subtilis: current and future modification strategies as a protein secreting factory

Bacillus subtilis is regarded as a promising microbial expression system in bioengineering due to its high stress resistance, nontoxic, low codon preference and grow fast. The strain has a relatively efficient expression system, as it has at least three protein secretion pathways and abundant molecular chaperones, which guarantee its expression ability and compatibility. Currently, many proteins are expressed in Bacillus subtilis, and their application prospects are broad. Although Bacillus subtilis has great advantages compared with other prokaryotes related to protein expression and secretion, it still faces deficiencies, such as low wild-type expression, low product activity, and easy gene loss, which limit its large-scale application. Over the years, many researchers have achieved abundant results in the modification of Bacillus subtilis expression systems, especially the optimization of promoters, expression vectors, signal peptides, transport pathways and molecular chaperones. An optimal vector with a suitable promoter strength and other regulatory elements could increase protein synthesis and secretion, increasing industrial profits. This review highlights the research status of optimization strategies related to the expression system of Bacillus subtilis. Moreover, research progress on its application as a food-grade expression system is also presented, along with some future modification and application directions.

Let There Be Light: Genome Reduction Enables Bacillus subtilis to Produce Disulfide-Bonded Gaussia Luciferase

Bacillus subtilis is a major workhorse for enzyme production in industrially relevant quantities. Compared to mammalian-based expression systems, B. subtilis presents intrinsic advantages, such as high growth rates, high space-time yield, unique protein secretion capabilities, and low maintenance costs. However, B. subtilis shows clear limitations in the production of biopharmaceuticals, especially proteins from eukaryotic origin that contain multiple disulfide bonds. In the present study, we deployed genome minimization, signal peptide screening, and coexpression of recombinant thiol oxidases as strategies to improve the ability of B. subtilis to secrete proteins with multiple disulfide bonds. Different genome-reduced strains served as the chassis for expressing the model protein Gaussia Luciferase (GLuc), which contains five disulfide bonds. These chassis lack extracellular proteases, prophages, and key sporulation genes. Importantly, compared to the reference strain with a full-size genome, the best-performing genome-minimized strain achieved over 3000-fold increased secretion of active GLuc while growing to lower cell densities. Our results show that high-level GLuc secretion relates, at least in part, to the absence of major extracellular proteases. In addition, we show that the thiol-disulfide oxidoreductase requirements for disulfide bonding have changed upon genome reduction. Altogether, our results highlight genome-engineered Bacillus strains as promising expression platforms for proteins with multiple disulfide bonds.

Efficient secreted expression of natural intracellular β-galactosidase from Bacillus aryabhattai via non-classical protein secretion pathway in Bacillus subtilis

In this study, the natural intracellular β-galactosidase (lacZBa) from Bacillus aryabhattai was expressed extracellularly in Bacillus subtilis. Sec and Tat signal peptides from different secretion pathways were incorporated to facilitate extracellular secretion of lacZBa, resulting in a yield of only 0.54 U/mL. Interestingly, it was discovered that lacZBa could be efficiently expressed and secreted in B. subtilis via a non-classical secretory pathway without the need for a signal peptide. The extracellular activity and secretion ratio were 5.3 U/mL and 65 %, respectively. Compared to E. coli, the expression of lacZBa in B. subtilis resulted in increased acid resistance and higher pH stability and thermostability, with a 1.7-fold increase in half-life at 50 °C and pH 6.0. Additionally, we combined single-factor experiments and response surface methodology to enhance extracellular expression of β-galactosidase in shake-flasks. The resulting optimal medium contained 4.46 % glucose, 1.47 % corn steep liquor, 1.5 % beef extract, 0.82 % CaCl2, and 0.1 % MgSO4. Under optimal conditions, the yield of extracellularly secreted β-galactosidase at the shake flask level was 17.41 U/mL, representing a 32.2-fold increase in initial extracellular enzyme activity. This study represents the first successful report of natural intracellular β-galactosidase being expressed through the non-classical secretory pathway in B. subtilis.

Efficient Microfluidic Screening Method Using a Fluorescent Immunosensor for Recombinant Protein Secretions

Microbial secretory protein expression is widely used for biopharmaceutical protein production. However, establishing genetically modified industrial strains that secrete large amounts of a protein of interest is time-consuming. In this study, a simple and versatile high-throughput screening method for protein-secreting bacterial strains is developed. Different genotype variants induced by mutagens are encapsulated in microemulsions and cultured to secrete proteins inside the emulsions. The secreted protein of interest is detected as a fluorescence signal by the fluorescent immunosensor quenchbody (Q-body), and a cell sorter is used to select emulsions containing improved protein-secreting strains based on the fluorescence intensity. The concept of the screening method is demonstrated by culturing Corynebacterium glutamicum in emulsions and detecting the secreted proteins. Finally, productive strains of fibroblast growth factor 9 (FGF9) are screened, and the FGF9 secretion increased threefold compared to that of parent strain. This screening method can be applied to a wide range of proteins by fusing a small detection tag. This is a highly simple process that requires only the addition of a Q-body to the medium and does not require the addition of any substrates or chemical treatments. Furthermore, this method shortens the development period of industrial strains for biopharmaceutical protein production.

Improving the soluble expression of difficult-to-express proteins in prokaryotic expression system via protein engineering and synthetic biology strategies

Solubility and folding stability are key concerns for difficult-to-express proteins (DEPs) restricted by amino acid sequences and superarchitecture, resolved by the precise distribution of amino acids and molecular interactions as well as the assistance of the expression system. Therefore, an increasing number of tools are available to achieve efficient expression of DEPs, including directed evolution, solubilization partners, chaperones, and affluent expression hosts, among others. Furthermore, genome editing tools, such as transposons and CRISPR Cas9/dCas9, have been developed and expanded to construct engineered expression hosts capable of efficient expression ability of soluble proteins. Accounting for the accumulated knowledge of the pivotal factors in the solubility and folding stability of proteins, this review focuses on advanced technologies and tools of protein engineering, protein quality control systems, and the redesign of expression platforms in prokaryotic expression systems, as well as advances of the cell-free expression technologies for membrane proteins production.

Impact of c-di-GMP on the Extracellular Proteome of Rhizobium etli

Extracellular matrix components of bacterial biofilms include biopolymers such as polysaccharides, nucleic acids and proteins. Similar to polysaccharides, the secretion of adhesins and other matrix proteins can be regulated by the second messenger cyclic diguanylate (cdG). We have performed quantitative proteomics to determine the extracellular protein contents of a Rhizobium etli strain expressing high cdG intracellular levels. cdG promoted the exportation of proteins that likely participate in adhesion and biofilm formation: the rhizobial adhesion protein RapA and two previously undescribed likely adhesins, along with flagellins. Unexpectedly, cdG also promoted the selective exportation of cytoplasmic proteins. Nearly 50% of these cytoplasmic proteins have been previously described as moonlighting or candidate moonlighting proteins in other organisms, often found extracellularly. Western blot assays confirmed cdG-promoted export of two of these cytoplasmic proteins, the translation elongation factor (EF-Tu) and glyceraldehyde 3-phosphate dehydrogenase (Gap). Transmission Electron Microscopy immunolabeling located the Gap protein in the cytoplasm but was also associated with cell membranes and extracellularly, indicative of an active process of exportation that would be enhanced by cdG. We also obtained evidence that cdG increases the number of extracellular Gap proteoforms, suggesting a link between cdG, the post-translational modification and the export of cytoplasmic proteins.

Secretome Analysis of the Plant Biostimulant Bacteria Strains Bacillus subtilis (EB2004S) and Lactobacillus helveticus (EL2006H) in Response to pH Changes

It is well-known that there is a high frequency of plant-growth-promoting strains in Bacillus subtilis and that these can be effective under both stressful and stress-free conditions. There are very few studies of this activity in the case of Lactobacillus helveticus. In this study, the effects of pH on the secretome (proteins) in the cell-free supernatants of two bacterial strains were evaluated. The bacteria were cultured at pH 5, 7 and 8, and their secretome profiles were analyzed, with pH 7 (optimal growth pH) considered as the "control". The results showed that acidity (lower pH 5) diminishes the detectable production of most of the secretome proteins, whereas alkalinity (higher pH 8) increases the detectable protein production. At pH 5, five (5) new proteins were produced by L. helveticus, including class A sortase, fucose-binding lectin II, MucBP-domain-containing protein, SLAP-domain-containing protein and hypothetical protein LHEJCM1006_11110, whereas for B. subtilis, four (4) types of proteins were uniquely produced (p ≤ 0.05), including helicase-exonuclease AddAB subunit AddB, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase, a cluster of ABC-F family ATP-binding-cassette-domain-containing proteins and a cluster of excinuclease ABC (subunit B). At pH 8, Bacillus subtilis produced 56 unique proteins. Many of the detected proteins were involved in metabolic processes, whereas the others had unknown functions. The unique and new proteins with known and unknown functions suggest potential the acclimatization of the microbes to pH stress.

ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning

Protein secretion has a pivotal role in many biological processes and is particularly important for intercellular communication, from the cytoplasm to the host or external environment. Gram-positive bacteria can secrete proteins through multiple secretion pathways. The non-classical secretion pathway has recently received increasing attention among these secretion pathways, but its exact mechanism remains unclear. Non-classical secreted proteins (NCSPs) are a class of secreted proteins lacking signal peptides and motifs. Several NCSP predictors have been proposed to identify NCSPs and most of them employed the whole amino acid sequence of NCSPs to construct the model. However, the sequence length of different proteins varies greatly. In addition, not all regions of the protein are equally important and some local regions are not relevant to the secretion. The functional regions of the protein, particularly in the N- and C-terminal regions, contain important determinants for secretion. In this study, we propose a new hybrid deep learning-based framework, referred to as ASPIRER, which improves the prediction of NCSPs from amino acid sequences. More specifically, it combines a whole sequence-based XGBoost model and an N-terminal sequence-based convolutional neural network model; 5-fold cross-validation and independent tests demonstrate that ASPIRER achieves superior performance than existing state-of-the-art approaches. The source code and curated datasets of ASPIRER are publicly available at https://github.com/yanwu20/ASPIRER/. ASPIRER is anticipated to be a useful tool for improved prediction of novel putative NCSPs from sequences information and prioritization of candidate proteins for follow-up experimental validation.

PncsHub: a platform for annotating and analyzing non-classically secreted proteins in Gram-positive bacteria

From industry to food to health, bacteria play an important role in all facets of life. Some of the most important bacteria have been purposely engineered to produce commercial quantities of antibiotics and therapeutics, and non-classical secretion systems are at the forefront of these technologies. Unlike the classical Sec or Tat pathways, non-classically secreted proteins share few common characteristics and use much more diverse secretion pathways for protein transport. Systematically categorizing and investigating the non-classically secreted proteins will enable a deeper understanding of their associated secretion mechanisms and provide a landscape of the Gram-positive secretion pathway distribution. We therefore developed PncsHub (https://pncshub.erc.monash.edu/), the first universal platform for comprehensively annotating and analyzing Gram-positive bacterial non-classically secreted proteins. PncsHub catalogs 4,914 non-classically secreted proteins, which are delicately categorized into 8 subtypes (including the 'unknown' subtype) and annotated with data compiled from up to 26 resources and visualisation tools. It incorporates state-of-the-art predictors to identify new and homologous non-classically secreted proteins and includes three analytical modules to visualise the relationships between known and putative non-classically secreted proteins. As such, PncsHub aims to provide integrated services for investigating, predicting and identifying non-classically secreted proteins to promote hypothesis-driven laboratory-based experiments.

Regulate the hydrophobic motif to enhance the non-classical secretory expression of Pullulanase PulA in Bacillus subtilis

Bacillus subtilis has been widely used as a prokaryotic host for the secretory expression of heterologous proteins. In this study, a pullulanase (PulA) from Anoxybacillus sp. LM18-11 was firstly identified to be expressed in Bacillus subtilis 1A751 through non-classical secretion pathway. Results showed that both the N- and C-terminal regions of PulA were essential for its soluble expression. To explore its specific structural basis of secretion in B. subtilis, we revealed a hydrophobic motif A501-H507 which is vital for the secretion of the whole protein of PulA. Through a series of site-specific mutagenesis, the triple-sites mutants R503E/I506E/H507E and R503E/I506Y/H507E showed the highest extracellular activity (160.07 U/mL) and total activity (243.37 U/mL) which was 1.71 times and 1.55 times higher than those of PulA. The highest secretion rate of mutant I506E/H507E was more than 50% which was 34.72% higher comparing with that of PulA. The glutamic acid substitution on these three key surface sites which decreased the surface hydrophobicity of that region was confirmed to be beneficial to improve the secretory expression of PulA. This novel discovery for the secretory expression of PulA in B. subtilis would make a new perspective on regulating a kind of non-classical secretion in B. subtilis.

Engineering Escherichia coli for d-Allulose Production from d-Fructose by Fermentation

d-Allulose is considered an ideal alternative to sucrose and has shown tremendous application potential in many fields. Recently, most efforts on production of d-allulose have focused on in vitro enzyme-catalyzed epimerization of cheap hexoses. Here, we proposed an approach to efficiently produce d-allulose through fermentation using metabolically engineered Escherichia coli JM109 (DE3), in which a SecY (ΔP) channel and a d-allulose 3-epimerase (DPEase) were co-expressed, ensuring that d-fructose could be transported in its nonphosphorylated form and then converted into d-allulose by cells. Further deletion of fruA, manXYZ, mak, galE, and fruK and the use of Ni²⁺ in a medium limited the carbon flux flowing into the byproduct-generating pathways and the Embden-Meyerhof-Parnas (EMP) pathway, achieving a ≈ 0.95 g/g yield of d-allulose on d-fructose using E. coli (DPEase, SecY [ΔP], ΔFruA, ΔManXYZ, ΔMak, ΔGalE, ΔFruK) and 8 μM Ni²⁺. In fed-batch fermentation, the titer of d-allulose reached ≈23.3 g/L.

The multifunctionality of expression systems in Bacillus subtilis: Emerging devices for the production of recombinant proteins

Bacillus subtilis is a successful host for producing recombinant proteins. Its GRAS (generally recognized as safe) status and its remarkable innate ability to absorb and incorporate exogenous DNA into its genome make this organism an ideal platform for the heterologous expression of bioactive substances. The factors that corroborate its value can be attributed to the scientific knowledge obtained from decades of study regarding its biology that has fostered the development of several genetic engineering strategies, such as the use of different plasmids, engineering of constitutive or double promoters, chemical inducers, systems of self-inducing expression with or without a secretion system that uses a signal peptide, and so on. Tools that enrich the technological arsenal of this expression platform improve the efficiency and reduce the costs of production of proteins of biotechnological importance. Therefore, this review aims to highlight the major advances involving recombinant expression systems developed in B. subtilis, thus sustaining the generation of knowledge and its application in future research. It was verified that this bacterium is a model in constant demand and studies of the expression of recombinant proteins on a large scale are increasing in number. As such, it represents a powerful bacterial host for academic research and industrial purposes.

Recombinant protein secretion by Bacillus subtilis and Lactococcus lactis: pathways, applications, and innovation potential

Secreted recombinant proteins are of great significance for industry, healthcare and a sustainable bio-based economy. Consequently, there is an ever-increasing need for efficient production platforms to deliver such proteins in high amounts and high quality. Gram-positive bacteria, particularly bacilli such as Bacillus subtilis, are favored for the production of secreted industrial enzymes. Nevertheless, recombinant protein production in the B. subtilis cell factory can be very challenging due to bottlenecks in the general (Sec) secretion pathway as well as this bacterium’s intrinsic capability to secrete a cocktail of highly potent proteases. This has placed another Gram-positive bacterium, Lactococcus lactis, in the focus of attention as an alternative, non-proteolytic, cell factory for secreted proteins. Here we review our current understanding of the secretion pathways exploited in B. subtilis and L. lactis to deliver proteins from their site of synthesis, the cytoplasm, into the fermentation broth. An advantage of this cell factory comparison is that it identifies opportunities for protein secretion pathway engineering to remove or bypass current production bottlenecks. Noteworthy new developments in cell factory engineering are the mini-Bacillus concept, highlighting potential advantages of massive genome minimization, and the application of thus far untapped ‘non-classical’ protein secretion routes. Altogether, it is foreseen that engineered lactococci will find future applications in the production of high-quality proteins at the relatively small pilot scale, while engineered bacilli will remain a favored choice for protein production in bulk.

Consolidated bioprocessing for bioethanol production by metabolically engineered Bacillus subtilis strains

Bioethanol produced by fermentative microorganisms is regarded as an alternative to fossil fuel. Bioethanol to be used as a viable energy source must be produced cost-effectively by removing expense-intensive steps such as the enzymatic hydrolysis of substrate. Consolidated bioprocessing (CBP) is believed to be a practical solution combining saccharification and fermentation in a single step catalyzed by a microorganism. Bacillus subtills with innate ability to grow on a diversity of carbohydrates seems promising for affordable CBP bioethanol production using renewable plant biomass and wastes. In this study, the genes encoding alcohol dehydrogenase from Z. mobilis (adh_Z) and S. cerevisiae (adh_S) were each used with Z. mobilis pyruvate decarboxylase gene (pdc_Z) to create ethanologenic operons in a lactate-deficient (Δldh) B. subtilis resulting in NZ and NZS strains, respectively. The S. cerevisiae adh_S caused significantly more ethanol production by NZS and therefore was used to make two other operons including one with double copies of both pdc_Z and adh_S and the other with a single pdc_Z but double adh_S genes expressed in N(ZS)2 and NZS2 strains, respectively. In addition, two fusion genes were constructed with pdc_Z and adh_S in alternate orientations and used for ethanol production by the harboring strains namely NZ:S and NS:Z, respectively. While the increase of gene dosage was not associated with elevated carbon flow for ethanol production, the fusion gene adh_S:pdc_Z resulted in a more than two times increase of productivity by strain NS:Z as compared with NZS during 48 h fermentation. The CBP ethanol production by NZS and NS:Z using potatoes resulted in 16.3 g/L and 21.5 g/L ethanol during 96 h fermentation, respectively. For the first time in this study, B. subtilis was successfully used for CBP ethanol production with S. cerevisiae alcohol dehydrogenase. The results of the study provide insights on the potentials of B. subtilis for affordable bioethanol production from inexpensive plant biomass and wastes. However, the potentials need to be improved by metabolic and process engineering for higher yields of ethanol production and plant biomass utilization.

Construction of a Super-Folder Fluorescent Protein-Guided Secretory Expression System for the Production of Phospholipase D in Bacillus subtilis

Phospholipids (PLs) are one of the main ingredients in food and nutraceutical, cosmetics, agriculture, and pharmaceutical products. Phospholipase D (PLD) is a crucial enzyme for the biocatalytic synthesis or modification of PLs. Here, to prepare PLD more efficiently, we constructed a PLD expression and secretion system in Bacillus subtilis and developed an environmentally friendly reaction system. A nonclassical secretory pathway where a super-folder green fluorescent protein plays as an N-terminal guide protein was introduced. This expression system can not only achieve rapid screening of high-level expression strains but can also achieve the secretion of the target proteins. Under optimal fermentation conditions, the enzyme activity of the culture medium was 0.35 U/mL, which was 2.05-fold that of the Sec secretion pathway strains. Meanwhile, the effects of several organic solvents in the biphasic reaction media were compared. The results showed that when using cyclopentyl methyl ether as the organic phase, the final conversion rate reached 96.9%. It has shown good application potential in the synthesis of phosphatidylserine, laid the foundation for the synthesis and application of other rare and high-value PLs, and provided a reference for the production of other biocatalysts.

Production of proteins and commodity chemicals using engineered Bacillus subtilis platform strain

Currently, increasing demand of biochemicals produced from renewable resources has motivated researchers to seek microbial production strategies instead of traditional chemical methods. As a microbial platform, Bacillus subtilis possesses many advantages including the generally recognized safe status, clear metabolic networks, short growth cycle, mature genetic editing methods and efficient protein secretion systems. Engineered B. subtilis strains are being increasingly used in laboratory research and in industry for the production of valuable proteins and other chemicals. In this review, we first describe the recent advances of bioinformatics strategies during the research and applications of B. subtilis. Secondly, the applications of B. subtilis in enzymes and recombinant proteins production are summarized. Further, the recent progress in employing metabolic engineering and synthetic biology strategies in B. subtilis platform strain to produce commodity chemicals is systematically introduced and compared. Finally, the major limitations for the further development of B. subtilis platform strain and possible future directions for its research are also discussed.

Non-classical secretion of a type I L-asparaginase in Bacillus subtilis

L-asparaginase (EC 3.5.1.1) showed great commercial value owing to its effective treatment of acute lymphoblastic leukemia (ALL), lymphoid system malignancies and Hodgkin disease, and also to its use in the prevention of acrylamide formation in fried and baked foods. In this study, a type I L-asparaginase gene from Bacillus licheniformis Z-1 (BlAase) was cloned and expressed in Bacillus subtilis RIK 1285. Results showed that even without the mediation of any N-terminal signal peptides, BlAase can efficiently secrete into the medium. Further investigation indicated that the secretion of the BlAase was via neither Sec- nor Tat-dependent secretion pathway, and both the N- and C-terminal regions of the BlAase were essential for its expression and secretion, implying that BlAase might be secreted via a non-classical secretion pathway. To explore its secretion ability, BlAase was used as a signal peptide to direct the secretion of various heterologous proteins, where two of five proteins were successfully secreted with the mediation of BlAase. To the best of our knowledge, this is the first time to achieve extracellular expression of L-asparaginase via non-classical protein secretion pathway in B. subtilis, and provide a potential tool for secretion of recombinant proteins expressed in B. subtilis using BlAase as a signal peptide.

β-Galactosidase: From its source and applications to its recombinant form

Carbohydrate-active enzymes are a group of important enzymes playing a critical role in the degradation and synthesis of carbohydrates. Glycosidases can hydrolyze glycosides into oligosaccharides, polysaccharides, and glycoconjugates via a cost-effective approach. Lactase is an important member of β-glycosidases found in higher plants, animals, and microorganisms. β-Galactosidases can be used to degrade the milk lactose for making lactose-free milk, which is sweeter than regular milk and is suitable for lactose-intolerant people. β-Galactosidase is employed by many food industries to degrade lactose and improve the digestibility, sweetness, solubility, and flavor of dairy products. β-Galactosidase enzymes have various families and are applied in the food-processing industries such as hydrolyzed-milk products, whey, and galactooligosaccharides. Thus, this enzyme is a valuable protein which is now produced by recombinant technology. In this review, origins, structure, recombinant production, and critical modifications of β-galactosidase for improving the production process are discussed. Since β-galactosidase is a valuable enzyme in industry and health care, a study of its various aspects is important in industrial biotechnology and applied biochemistry.

A brief overview on the application and sources of α-amylase and expression hosts properties in order to production of recombinant α-amylase

By reducing the activation energy, enzymes accelerate the chemical reaction; therefore, they are good alternative for industrial catalysts. Amylase is a suitable enzyme as a catalyst for the chemical decomposition of starch. This enzyme is of great importance, and its production is highly profitable. α-Amylase is among the most important amylases produced naturally by animals, plants, and microorganisms. Still, the α-amylases produced by bacteria have a special place in industry and commerce. Moreover, a large volume of this enzyme can be produced by selecting an appropriate and optimized host to clone and express the α-amylase gene. The present study briefly reviews the structure, application, sources, and hosts used to produce recombinant α-amylase.

A wheat bran inducible expression system for the efficient production of α-L-arabinofuranosidase in Bacillus subtilis

α-l-arabinofuranosidases (EC 3.2.1.55; AFs) cause the release of arabinosyl residues from hemicellulose polymers such as xylans, and are receiving increased levels of research attention as they could be applied in a range of processes that involve the enzymatic degradation of xylans. The secretory production of bacterial AFs has not been attempted previously. In this study, we designed a unique induction system for the production of a recombinant AF in Bacillus subtilis in order to exploit its enzymic degradation of wheat bran. We found that non-starch phytochemicals were more efficient than d-xylose when inducing the expression of T7 RNA polymerase and driving the transcription of AF by the T7 promoter. The host cell, B. subtilis (ATCC 6051a-derived strain 164T7P) was engineered to incorporate a DNA cassette that expressed T7 RNA polymerase under the control of a d-xylose inducible promoter (P_xylA). The T7 promoter engineered into 164T7P was initially tested and compared with P43 in terms of GFP expression; we found that the expression level of GFP by the T7 promoter was ten-fold higher than that achieved by P43. When cultured in a flask with gentle shaking, and with d-xylose as an inducer, the recombinant strain successfully expressed arbf, a family 51 (GH 51) glycoside hydrolase from Bacillus licheniformis, and secreted 141.4 ± 4.8 U/mL of enzyme, with a Km of 1.4 ± 0.1 mM and a kcat of 139.4 s^-1. However, the protein was devoid of a secretary signal peptide. When cultures were supplemented with wheat bran, the maximal yield of the secreted AF reached 194.8 ± 4.1 U/mL. The results provide a foundation for the high level production of heterologous proteins using wheat bran as the inducer in B. subtilis.

Bacillus subtilis: a universal cell factory for industry, agriculture, biomaterials and medicine

Due to its clear inherited backgrounds as well as simple and diverse genetic manipulation systems, Bacillus subtilis is the key Gram-positive model bacterium for studies on physiology and metabolism. Furthermore, due to its highly efficient protein secretion system and adaptable metabolism, it has been widely used as a cell factory for microbial production of chemicals, enzymes, and antimicrobial materials for industry, agriculture, and medicine. In this mini-review, we first summarize the basic genetic manipulation tools and expression systems for this bacterium, including traditional methods and novel engineering systems. Secondly, we briefly introduce its applications in the production of chemicals and enzymes, and summarize its advantages, mainly focusing on some noteworthy products and recent progress in the engineering of B. subtilis. Finally, this review also covers applications such as microbial additives and antimicrobials, as well as biofilm systems and spore formation. We hope to provide an overview for novice researchers in this area, offering them a better understanding of B. subtilis and its applications.

Advances on systems metabolic engineering of Bacillus subtilis as a chassis cell

The Gram-positive model bacterium Bacillus subtilis, has been broadly applied in various fields because of its low pathogenicity and strong protein secretion ability, as well as its well-developed fermentation technology. B. subtilis is considered as an attractive host in the field of metabolic engineering, in particular for protein expression and secretion, so it has been well studied and applied in genetic engineering. In this review, we discussed why B. subtilis is a good chassis cell for metabolic engineering. We also summarized the latest research progress in systematic biology, synthetic biology and evolution-based engineering of B. subtilis, and showed systemic metabolic engineering expedite the harnessing B. subtilis for bioproduction.

CRISPR-dCas9 Mediated Cytosine Deaminase Base Editing in Bacillus subtilis

Base editing technology based on clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) is a recent addition to the family of CRISPR technologies. Compared with the traditional CRISPR/Cas9 technology, it does not rely on DNA double strand break and homologous recombination, and can realize gene inactivation and point mutation more quickly and simply. Herein, we first developed a base editing method for genome editing in Bacillus subtilis utilizing CRISPR/dCas9 (a fully nuclease-deficient mutant of Cas9 from S. pyogenes) and activation-induced cytidine deaminase (AID). This method achieved three and four loci simultaneous editing with editing efficiency up to 100% and 50%, respectively. Our base editing system in B. subtilis has a 5 nt editing window, which is similar to previously reported base editing in other microorganisms. We demonstrated that the plasmid curing rate is almost 100%, which is advantageous for multiple rounds of genome engineering in B. subtilis. Finally, we applied multiplex genome editing to generate a B. subtilis 168 mutant strain with eight inactive extracellular protease genes in just two rounds of base editing and plasmid curing, suggesting that it is a powerful tool for gene manipulation in B. subtilis and industrial applications in the future.

Heterologous expression of the novel α-helical hybrid peptide PR-FO in Bacillus subtilis

PR-FO is a novel α-helical hybrid antimicrobial peptide (AMP) with strong antimicrobial activities and high stability, and the potential to develop into a new generation of antimicrobial agents. In this study, the encoded gene sequence of SMT3-PR-FO was designed and transformed into B. subtilis WB800N. Fusion proteins with concentrations of 16 mg L^-1 (SP_amyQ) and 23 mg L^-1 (SP_sacB) were obtained after purification by a Ni-NTA resin column. A total of 3 mg (SP_amyQ) and 4 mg (SP_sacB) of PR-FO with a purity of 90% was obtained from 1 L fermentation cultures. Recombinant PR-FO exhibited high inhibition activities against both gram-negative bacteria and gram-positive bacteria, and low haemolytic activity against human red blood cells. These results indicated that the rSMT3-PR-FO could be expressed under the guidance of SP_amyQ and SP_sacB, and the maltose-induced expression strategy might be a safe and efficient method for the soluble peptides production in B. subtilis.

Progresses on bacterial secretomes enlighten research on Mycoplasma secretome

Bacterial secretome is a comprehensive catalog of bacterial proteins that are released or secreted outside the cells. They offer a number of factors that possess several significant roles in virulence as well as cell to cell communication and hence play a core role in bacterial pathogenesis. Sometimes these proteins are bounded with membranes giving them the shape of vesicles called extracellular vesicles (EVs) or outer membrane vesicles (OMVs). Bacteria secrete these proteins via Sec and Tat pathways into the periplasm. Secreted proteins have found to be important as diagnostic markers as well as antigenic factors for the development of an effective candidate vaccine. Recently, the research in the field of secretomics is growing up and getting more interesting due to their direct involvement in the pathogenesis of the microorganisms leading to the infection. Many pathogenic bacteria have been studied for their secretome and the results illustrated novel antigens. This review highlights the secretome studies of different pathogenic bacteria in humans and animals, general secretion mechanisms, different approaches and challenges in the secretome of Mycoplasma sp.

Expression of d-psicose-3-epimerase from Clostridium bolteae and Dorea sp. and whole-cell production of d-psicose in Bacillus subtilis

Purpose

d-psicose-3-epimerase (DPEase) catalyses the isomerisation of d-fructose to d-psicose, a rare sugar in nature with unique nutritional and biological functions. An effective industrial-scale method is needed for d-psicose production. Herein, the expression of a neutral and a slightly acidic pH DPEase in Bacillus subtilis was evaluated.

Methods

Two DPEase genes from Clostridium bolteae and Dorea sp. were separately expressed in B. subtilis via plasmid pSTOP1622, and an extra P43 promoter was employed to the expression cassette. The fermentation conditions of the engineered B. subtilis strains were also optimised, to facilitate both cell growth and enzyme production.

Result

The introduction of P43 promoter to the two DPEase genes increased enzyme production by about 20%. Optimisation of fermentation conditions increased DPEase production to 21.90 U/g at 55 °C and 24.01 U/g at 70 °C in B. subtilis expressing C. bolteae or Dorea sp. DPEase, equating to a 94.67% and 369.94% increase, respectively, relative to controls.

Conclusion

Enhanced DPEase production was achieved in B. subtilis expressing C. bolteae or Dorea sp. DPEase genes.

Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins

A large proportion of the recombinant proteins manufactured today rely on microbe-based expression systems owing to their relatively simple and cost-effective production schemes. However, several issues in microbial protein expression, including formation of insoluble aggregates, low protein yield, and cell death are still highly recursive and tricky to optimize. These obstacles are usually rooted in the metabolic capacity of the expression host, limitation of cellular translational machineries, or genetic instability. To this end, several microbial strains having precisely designed genomes have been suggested as a way around the recurrent problems in recombinant protein expression. Already, a growing number of prokaryotic chassis strains have been genome-streamlined to attain superior cellular fitness, recombinant protein yield, and stability of the exogenous expression pathways. In this review, we outline challenges associated with heterologous protein expression, some examples of microbial chassis engineered for the production of recombinant proteins, and emerging tools to optimize the expression of heterologous proteins. In particular, we discuss the synthetic biology approaches to design and build and test genome-reduced microbial chassis that carry desirable characteristics for heterologous protein expression.

Principle and potential applications of the non-classical protein secretory pathway in bacteria

In addition to the extracellular proteins secreted by known secretory pathways, a number of cytoplasmic proteins without predicable or known signal sequences or secretory motifs have been found in the extracellular milieu, and were consequently classified as non-classically secreted proteins. Non-classical protein secretion is considered to be a general, conserved cellular phenomenon in both eukaryotes and prokaryotes. There are several research hotspots on the non-classical protein secretory pathway, and the most important two of them are the recognition principle of substrate proteins and possible secretory mechanisms. To date, researchers have made some progress in understanding the characteristics of these proteins. For example, it was discovered that many non-classically secreted proteins exist and are secreted in multimeric form. Some of these proteins prefer to be clustered and exported at the poles and the septum of the cell. The majority of these proteins play different functions when they are in the intra- and extracellular environments, and several of their functions are related to survival and pathogenicity. Furthermore, non-classically secreted proteins can be used as leading proteins to guide a POI (protein of interest) out of the cells, which provides a novel strategy for protein secretion with potential applications in the industry. Summarizing these findings, this review emphasizes the hot spots related to non-classically secreted proteins in bacteria, lists the most important hypotheses on the selection and secretion mechanisms of non-classically secreted proteins, and put forward their potential applications.

Design of a high-efficiency synthetic system for l-asparaginase production in Bacillus subtilis

l-asparaginase has high application value in medicine and food industry, but the low yield limits its application. In this study, we designed a synthetic system in Bacillus subtilis to produce l-asparaginase by improving gene expression and optimizing the fermentation agitation speed. Gene expression was improved by respectively increasing transcription levels and translation speeds through screening promoters and RBS sequences. With the optimal promoter, P43, and the synthetic RBS sequence, the yield obtained in a shake flask was 371.87 U/mL, which was 2.09 times that with the original strain. To further enhance production in a 5-L fermenter, a multistage agitation speed control strategy was adopted, involving agitation at 600 rpm for the first 12 h, followed by a gradual increase in speed to 900 rpm, which resulted in the highest yield of l-asparaginase, 5321 U/mL, after 42 h of fermentation.

High-efficiency expression and secretion of human FGF21 in Bacillus subtilis by intercalation of a mini-cistron cassette and combinatorial optimization of cell regulatory components

Background

Recombinant human Fibroblast growth factor 21 (rhFGF21) is an endocrine hormone that has profound effects on treatment of metabolic diseases. However, rhFGF21 is prone to form inclusion body when expressed in bacteria, which results in, the downstream process of purification of bioactive rhFGF21 is time-consuming and labor intensive. The aim of this work is to explore a new method for improving the soluble expression and secretion level of rhFGF21 in B. subtilis.

Results

A codon optimized rhFGF21 gene was expressed under the control of a strong inducible promoter P_malA in B. subtilis. A mini-cistron cassette (from gsiB) was located upstream of rhFGF21 in expression vector (pMATEFc5), which could reduce the locally stabilized mRNA secondary structure of transcripts and enhance the efficiency of translation initiation. Then various chaperones were further overexpressed to improve the expression efficiency of rhFGF21. Results showed that overexpression of the chaperone DnaK contributed to the increase of solubility of rhFGF21. Moreover, an extracellular proteases deficient strain B. subtilis Kno6cf was used to accumulate the secreted rhFGF21 solidly. In addition, eleven signal peptides from B. subtilis were evaluated and the SP_dacB appeared the highest secretion yield of rhFGF21 in B. subtilis. Finally, the combinatorial optimized strain achieved an about ninefold increase of the soluble rhFGF21 production after 24 h of flask fermentation in comparison with the initial production strain.

Conclusion

This work provided a comprehensive strategy for secretory expressing the heterologous protein rhFGF21 in B. subtilis. To our knowledge, this is the first report of the highly efficient production of rhFGF21 in B. subtilis and this approach may provide some suggestions for heterologous proteins production in B. subtilis.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1066-4) contains supplementary material, which is available to authorized users.

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms

The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.

Tat-Independent Secretion of Polyethylene Terephthalate Hydrolase PETase in Bacillus subtilis 168 Mediated by Its Native Signal Peptide

Widespread utilization of polyethylene terephthalate (PET) has caused critical environmental pollution. The enzymatic degradation of PET is a promising solution to this problem. In this study, PETase, which exhibits much higher PET-hydrolytic activity than other enzymes, was successfully secreted into extracellular milieu from Bacillus subtilis 168 under the direction of its native signal peptide (named SP_PETase). SP_PETase is predicted to be a twin-arginine signal peptide. Intriguingly, inactivation of twin-arginine translocation (Tat) complexes improved the secretion amount by 3.8-fold, indicating that PETase was exported via Tat-independent pathway. To the best of our knowledge, this is the first report on the improvement of Tat-independent secretion by inactivating Tat components of B. subtilis 168 in LB medium. Furthermore, PET film degradation assay showed that the secreted PETase was fully active. This study paves the first step to construct an efficient engineered strain for PET degradation.

Extracellular overproduction of recombinant Iranian HPV-16 E6 oncoprotein in Lactococcus lactis using the NICE system

Aim: This study aimed to optimize production of HPV-16 E6 by recombinant Lactococcus lactis. Materials & methods: Optimization procedures were conducted on the factors of nisin amount, induction temperature, cell density at induction time, glucose and yeast extract concentrations. Results: Cell densities reached 5.2 and 1.74 g/l, and maximum rE6 production reached 45.25 and 15.91 μg/ml for optiE6 and E6, respectively, at 75 g/l initial glucose concentration in the batch study. During fed-batch fermentation, protein values were improved by feeding with yeast extract and GM17 medium, reaching the maximum of 80.92 and 15.95 μg/ml, and the maximum biomass reached 9.62 and 3.12 g/l, respectively. Conclusion: These encouraging outcomes represent L. lactis cells as an efficient cell factory for antigen production.

Cloning and expression of the sucrose phosphorylase gene in Bacillus subtilis and synthesis of kojibiose using the recombinant enzyme

BACKGROUND

Kojibiose as a prebiotic and inhibitor of α-glucosidase exhibits potential for a wide range of applications in the food and medicine fields; however, large-scale separation and extraction of kojibiose from nature is difficult. Sucrose phosphorylase (SPase) can be used for the production of kojibiose, and currently, SPase is only heterologously expressed in E. coli, making it unsuitable for use in the food industry. However, Bacillus subtilis is generally considered to be a safe organism potentially useful for SPase expression.

RESULTS

Here, for the first time, we heterologously expressed Bifidobacterium adolescentis SPase in a food-grade B. subtilis strain. The results showed that SPase was efficiently secreted into the extracellular medium in the absence of a signal peptide. After culturing the recombinant strain in a 3-L bioreactor, crude SPase yield and activity reached 7.5 g/L and 5.3 U/mL, respectively, the highest levels reported to date. The optimal reaction conditions for kojibiose synthesis catalyzed by recombinant SPase were as follows: 0.5 M sucrose, 0.5 M glucose, 0.02 Uenzyme/mgall_substrates, pH 7.0, 50 °C, and 30 h. Furthermore, the substrate-conversion rate reached 40.01%, with kojibiose accounting for 104.45 g/L and selectivity for kojibiose production at 97%.

CONCLUSIONS

Here, we successfully expressed SPase in B. subtilis in the absence of a signal peptide and demonstrated its secretion into the extracellular medium. Our results indicated high levels of recombinant enzyme expression, with a substrate-conversion rate of 40.01%. These results provide a basis for large-scale preparation of kojibiose by the recombinant SPase.

Conformational determinants necessary for secretion of Paecilomyces thermophila β-1,4-xylosidase that lacks a signal peptide

In this study, we investigated the secretion mechanism of the hyper-secretion signal peptide-lacking β-xylosidase PtXyl43, a non-classically secreted protein, from the fungus Paecilomyces thermophila in Escherichia coli BL21(DE3). PtXyl43 secretion is a two-step process, and the second step is accompanied by cell periplasmic leakage, indicating that PtXyl43 secretion is the result of semi-specific secretion. Homology modeling of PtXyl43 suggested that PtXyl43 had a canonical GH43 family β-xylosidase structure containing five blades. Seventeen blade deletions or circular mutants were designed to identify the conformational motif(s) involved in secretion. These mutants were expressed as recombinant, codon-optimized proteins in E. coli. Notably, only mutants containing blades 2–4 were effectively secreted. Blades 2–4 are necessary for secretion, but it appears that blade 1 or 5 must be present to maintain the structure of blades 2–4. Simultaneous deletion of blades 1 and 5 dramatically reduces excretion. The covalent and sequential linking of blades of 2, 3 and 4 are important for the excretion of mutants, as separate blades of 2 and 3 or 3 and 4 abolishes excretion. Fusion with PtXyl43 promotes the excretion of GFP from the periplasm to the extracellular milieu, which suggested that PtXyl43 had the potential to carry proteins. This study provides new insights into secretory mechanism of secretable signal peptide-lacking proteins in E. coli. To our knowledge, this is the first to definitively identify the conformational determinants for secretion of a signal peptide-lacking GH43 family β-xylosidase. This finding also has application potential for the secretion of recombinant proteins.

A Feasibility Study to Evaluate Bacillus subtilis as a Host for Producing Recombinant Human Parathyroid Hormone

BACKGROUND

Biosynthetic teriparatide (1-34) (TPD) is a N-terminally truncated version of human parathyroid hormone (hPTH). The recombinant form of this polypeptide has been expressed in Escherichia coli (E. coli) and approved as the first anabolic treatment of osteoporosis in the EU and the USA. Feasibility of expression and secretion of a tag- fused form of TPD into Bacillus subtilis (B. subtilis) was examined due to several advantages of B. subtilis over E. coli in production of recombinant proteins with pharmacological activities.

METHODS

A codon optimized gene containing TPD open reading frame carrying enterokinase site in its upstream was fully synthesized. According to our cloning scheme, this synthetic polynucleotide was used as a template for PCR amplification using engineered primers in such a way that a polyhistidin tag was added in frame to the upstream of the amplicon as well as two restriction sites at its ends. The resulted amplicon, a cassette containing His-tag, enterokinase site and TPD, from 5' to 3', was cloned into pTZ57R/T vector and subjected to sequencing.The cassette was then subcloned into pHT43 shuttle vector and transformed into B. subtilis. Expression of target protein was analyzed by SDS-PAGE and western blotting upon induction by IPTG.

RESULTS

The accuracy of construction of pHT43-TPD was confirmed by sequencing and restriction map analyses. SDS-PAGE and western blotting results showed that the recombinant fusion form of hPTH was successfully expressed and secreted into cytoplasm and extracellular medium.

CONCLUSION

TPD may be successfully expressed and secreted in B. subtilis; however, optimization of expression conditions is required for enhancing target protein yield.

Protein Secretion in Gram-Positive Bacteria: From Multiple Pathways to Biotechnology

A number of Gram-positive bacteria are important players in industry as producers of a diverse array of economically interesting metabolites and proteins. As discussed in this overview, several Gram-positive bacteria are valuable hosts for the production of heterologous proteins. In contrast to Gram-negative bacteria, proteins secreted by Gram-positive bacteria are released into the culture medium where conditions for correct folding are more appropriate, thus facilitating the isolation and purification of active proteins. Although seven different protein secretion pathways have been identified in Gram-positive bacteria, the majority of heterologous proteins are produced via the general secretion or Sec pathway. Not all proteins are equally well secreted, because heterologous protein production often faces bottlenecks including hampered secretion, susceptibility to proteases, secretion stress, and metabolic burden. These bottlenecks are associated with reduced yields leading to non-marketable products. In this chapter, besides a general overview of the different protein secretion pathways, possible hurdles that may hinder efficient protein secretion are described and attempts to improve yield are discussed including modification of components of the Sec pathway. Attention is also paid to omics-based approaches that may offer a more rational approach to optimize production of heterologous proteins.

Bottleneck in secretion of α-amylase in Bacillus subtilis

Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.