Combining Genome Shuffling and Interspecific Hybridization Among Streptomyces Improved ε-Poly-l-Lysine Production

Enhancement of ε-poly-L-lysine production by Streptomyces albulus FQF-24 with feeding strategies using cassava starch as carbon source

ε-Poly-L-lysine (ε-PL) is a natural and wide-spectrum antimicrobial additive. In this study, the production of ε-PL by Streptomyces albulus FQF-24 using cassava starch (CS) as carbon source and the effects of different feeding methods were investigated in a fermenter. The initial shake flask experiments demonstrated the efficient production of ε-PL with CS, achieving the ε-PL production of 1.18 g/L. Subsequent investigations in the fermenter identified that the ideal pH was 3.8 during the ε-PL synthesis phase. Under this condition, the production of ε-PL reached 1.35 g/L. When the pH was maintained at 3.8, the investigation of improvement of feeding composition was carried out in a 5 L fermenter. The intermittent feeding containing CS, inorganic and organic nitrogen sources resulted in the maximum ε-PL production and dry cell weight (DCW) reaching 17.17 g/L and 42.73 g/L. Additionally, continuous feeding with the composition of CS, organic and inorganic nitrogen sources, and inorganic salts further increased ε-PL production and DCW to 27.56 g/L and 38.5 g/L. Summarily, the above results indicate that the fermentation using low-cost CS and continuous feeding strategy with whole medium composition can provide a beneficial reference for the efficient production of ε-PL.

Enhancement of poly‑γ‑L‑diaminobutanoic acid production in Bacillus pumilus by repeated pH shocks

This study investigated the effect of pH on poly-γ-L-diaminobutanoic acid (γ-PAB) production by Bacillus pumilus in batch fermentation. In the natural fermentation where pH was not controlled, pH decreased from initial 7.0 to 3.0 in 18 h and γ-PAB production was 428.6 mg/L. In the pH-controlled fermentation, B. pumilus tended to proliferation at higher pH, while γ-PAB synthesis was favorable at lower pH, in which the optimal pH for γ-PAB production was 4.2, and γ-PAB yield reached 2284.5 mg/L. Adopting a pH shock strategy which lasted 9 h in the pre-fermentation phase, biomass (OD600) and γ-PAB yield of B. pumilus were obtained as 61.3 and 2794.6 mg/L, respectively, which were 10.8% and 22.4% higher than those in batch fermentation without pH shock. Subsequent fermentation of repeated pH shocks showed that a further higher productivity could be achieved, in which the final OD600 reached 65.1, and γ-PAB production reached as high as 3482.3 mg/L, which were increased by 6.2% and 17.1% compared with those in single pH shock, respectively. This study demonstrated that B. pumilus can synthesize more γ-PAB at suboptimal pH and provided a novel approach to regulate γ-PAB synthesis.

Multiple Functions of Compatible Solute Ectoine and Strategies for Constructing Overproducers for Biobased Production

Ectoine and its derivative 5-hydroxyectoine are compatible solutes initially found in the hyperhalophilic bacterium Ectothiorhodospira halochloris, which inhabits the desert in Egypt. The habitat of ectoine producers implies the primary function of ectoine as a cytoprotectant against harsh conditions such as high salinity, drought, and high radiation. More extensive and in-depth studies have revealed the multiple functions of ectoine in its native producer bacterial cells and other types of cells and its biomolecular components (such as proteins and DNA) as a general protective agent. Its chemical properties as a bio-based amino acid derivative make it attractive for basic scientific research and related industries, such as the food/agricultural industry, cosmetic manufacturing, biologics, and therapeutic agent preparation. This article first discusses the functions and applications of ectoine and 5-hydroxyectoine. Subsequently, more emphasis was placed on advances in bio-based ectoine and/or 5-hydroxyectoine production. Strategies for developing more robust cell factories for highly efficient ectoine and/or 5-hydroxyectoine production are further discussed. We hope this review will provide a valuable reference for studies on the bio-based production of ectoine and 5-hydroxyectoine.

Application of Strain Selection Technology in Alcoholic Beverages: A Review

The diversity of alcohol beverage microorganisms is of great significance for improving the brewing process and the quality of alcohol beverage products. During the process of making alcoholic beverages, a group of microorganisms, represented by yeast and lactic acid bacteria, conducts fermentation. These microorganisms have complex synergistic or competitive relationships, and the participation of different microorganisms has a major impact on the fermentation process and the flavor and aroma of the product. Strain selection is one of the key steps. Utilizing scientific breeding technology, the relationship between strains can be managed, the composition of the alcoholic beverage microbial community can be improved, and the quality and flavor of the alcoholic beverage products can be increased. Currently, research on the microbial diversity of alcohol beverages has received extensive attention. However, the selection technology for dominant bacteria in alcohol beverages has not yet been systematically summarized. To breed better-quality alcohol beverage strains and improve the quality and characteristics of wine, this paper introduces the microbial diversity characteristics of the world's three major brewing alcohols: beer, wine, and yellow wine, as well as the breeding technologies of related strains. The application of culture selection technology in the study of microbial diversity of brewed wine was reviewed and analyzed. The strain selection technology and alcohol beverage process should be combined to explore the potential application of a diverse array of alcohol beverage strains, thereby boosting the quality and flavor of the alcohol beverage and driving the sustainable development of the alcoholic beverage industry.

Enhanced ε‑poly‑L‑lysine production in Streptomyces species by combining interspecific hybridization with multiple antibiotic resistance

To improve the ε-PL production in wild-type strains of Streptomyces. albulus, Streptomyces. noursei, Streptomyces. rochei and Streptomyces. yunnanensis, the interspecific hybridization based on protoplast fusion was first performed. Two-species hybridizations failed to obtain hybrids with significant increase in ε-PL production, but four-species hybridizations succeed in acquiring many high-yield hybrids. 16S rDNA homology alignment and RAPD confirmed that the hybrid HX17 was restructured by integrating gene fragments from S. albulus and S. rochei with S. noursei as the carrier. S. noursei HX17 was subsequently suffered from mutagenesis and genome shuffling combining with multiple antibiotic resistance, and a mutant S. noursei GX6 was obtained with ε-PL yield of 2.23 g/L in shake-flask fermentation. In fed-batch fermentation, the ε-PL production of GX6 reached 47.2 g/L, which was increased by 95.6% to 136.8% over the wild parents. Ribosomal genes associated with antibiotics were sequenced and majority of mutant strains had mutations at different sites, indicating that the increase of antibiotic resistance was strongly associated with them. This research proved that combining interspecific hybridization with multiple antibiotic resistance was as an effective approach to rapidly improve the ε-PL production in Streptomyces species.

Design and optimization of ε-poly-l-lysine with specific functions for diverse applications

ε-Poly-l-lysine (ε-PL) is a natural homo-poly(amino acid) which can be produced by microorganisms. With the advantages in broad-spectrum antimicrobial activity, biodegradability, and biocompatibility, ε-PL has been widely used as a preservative in the food industry. Different molecular architectures endow ε-PL and ε-PL-based materials with versatile applications. However, the microbial synthesis of ε-PL is currently limited by low efficiencies in genetic engineering and molecular architecture modification. This review presents recent advances in ε-PL production and molecular architecture modification of microbial ε-PL, with a focus on the current challenges and solutions for the improvement of the productivity and diversity of ε-PL. In addition, we highlight recent examples where ε-PL has been applied to expand the versability of edible films and nanoparticles in various applications. Commercial production and the challenges and future research directions in ε-PL biosynthesis are also discussed. Currently, although the main use of ε-PL is as a food preservative, ε-PL and ε-PL-based polymers have shown excellent application potential in biomedical fields. With the development of synthetic biology, the design and synthesis of ε-PL with a customized molecular architecture are possible in the near future. ε-PL-based polymers with specific functions will be a new trend in biopolymer manufacturing.

Constitutive and high gene expression in the diaminopimelate pathway accelerates ε-poly-L-lysine production in Streptomyces albulus

Streptomyces albulus NBRC14147 produces a homopoly(amino acid), ε-poly-L-lysine (ε-PL). Due to its antibiotic activity, thermostability, biodegradability, and non-toxicity to humans, ε-PL is used as a food preservative. In this study, homology searches of diaminopimelate (DAP) pathway genes (dapB and dapE), in an S. albulus genome database, were shown to encode predicted enzymes using dapB or dapE in Escherichia coli strain complementation assays. We observed that dapB and dapE transcriptional levels were weak during ε-PL production stages. Therefore, we strengthened this expression using an ermE constitutive promoter. Engineered strains generated faster growth and ε-PL production rates when compared with the control strain. Moreover, maximum ε-PL yields in S. albulus, where dapB was constitutively expressed, were approximately 14% higher when compared with the control strain. These findings showed that enhanced lysine biosynthetic gene expression generated faster and higher ε-PL production levels.

Integrative transcriptome and proteome revealed high-yielding mechanisms of epsilon-poly-L-lysine by Streptomyces albulus

Introduction

ε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by Streptomyces albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering.

Methods

Here, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18.

Results

Our results show that key genes in the glycolysis, pentose phosphate pathway, glyoxylate pathway, oxidative phosphorylation, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure and the biosynthesis of ε-PL. Overexpression of ppk gene and addition of polyP₆ further enhanced the ε-PL production.

Discussion

This study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing some genetic modification and fermentation strategies to further improve the ε-PL production.

Improved Production of ε-Poly-L-Lysine in Streptomyces albulus Using Genome Shuffling and Its High-Yield Mechanism Analysis

ε-Poly-L-lysine (ε-PL), a natural food preservative, has recently gained interest and mainly produced by Streptomyces albulus. Lacking of efficient breeding methods limit ε-PL production improving, knockout byproducts and increase of main product flux strategies as a logical solution to increase yield. However, removing byproduct formation and improving main product synthesis has seen limited success due to the genetic background of ε-PL producing organism is not clear. To overcome this limitation, random mutagenesis continues to be the best way towards improving strains for ε-PL production. Recent advances in Illumina sequencing opened new avenues to understand improved strains. In this work, we used genome shuffling on strains obtained by ribosome engineering to generate a better ε-PL producing strain. The mutant strain SG-86 produced 144.7% more ε-PL than the parent strain M-Z18. Except that SG-86 displayed obvious differences in morphology and ATP compared to parent strain M-Z18. Using Illumina sequencing, we mapped the genomic changes leading to the improved phenotype. Sequencing two strains showed that the genome of the mutant strain was about 2.1 M less than that of the parent strain, including a large number of metabolic pathways, secondary metabolic gene clusters, and gene deletions. In addition, there are many SNPs (single nucleotide polymorphisms) and InDels (insertions and deletions) in the mutant strain. Based on the results of data analysis, a mechanism of ε-PL overproduction in S. albulus SG-86 was preliminarily proposed. This study is of great significance for improving the fermentation performance and providing theoretical guidance for the metabolic engineering construction of ε-PL producing strains.

Recent advances in microbial ε-poly-L-lysine fermentation and its diverse applications

The naturally occurring homo-polyamide biopolymer, ε-poly-L-lysine (ε-PL) consists of 25-35 L-lysine residues with amide linkages between α-carboxyl groups and ε-amino groups. ɛ-PL exhibits several useful properties because of its unusual structure, such as biodegradability, water solubility, no human toxicity, and broad-spectrum antibacterial activities; it is widely applied in the fields of food, medicine, clinical chemistry and electronics. However, current industrial production of ε-PL is only performed in a few countries. Based on an analysis of the physiological characteristics of ε-PL fermentation, current advances that enhance ε-PL fermentation, from strain improvement to product isolation are systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulatory mechanism of ε-PL synthesis; (2) enhancing biosynthetic performance through mutagenesis, fermentation optimization and metabolic engineering; and (3) understanding and improving the biological activity and functional properties of ε-PL. Finally, perspectives on engineering and exploiting ε-PL as a source material for the production of various advanced materials are also discussed, providing scientific guidelines for researchers to further improve the ε-PL fermentation process.

Biotechnological production and application of epsilon-poly-L-lysine (ε-PL): biosynthesis and its metabolic regulation

Epsilon-poly-L-lysine (ε-PL) is an unusual biopolymer composed of L-lysine produced by several microorganisms, especially by the genus Streptomyces. Due to its excellent antimicrobial activity, good water solubility, high safety, and biodegradable nature, ε-PL with a GRAS status has been widely used in food and pharmaceutical industries. In the past years, studies have focused on the biotechnological production of ɛ-PL, the biosynthetic mechanism of microbial ɛ-PL, and its application. To provide new perspectives from recent advances, the review introduced the methods for the isolation of ɛ-PL producing strains and the biosynthetic mechanism of microbial ɛ-PL. We summarized the strategies for the improvement of ɛ-PL producing strains, including physical and chemical mutagenesis, ribosome engineering and gene engineering, and compared the different metabolic regulation strategies for improving ɛ-PL production, including medium optimization, nutrient supply, pH control, and dissolved oxygen control. Then, the downstream purification methods of ɛ-PL and its recent applications in food and medicine industries were introduced. Finally, we also proposed the potential challenges and the perspectives for the production of ε-PL.

AdpA, a developmental regulator, promotes ε-poly-l-lysine biosynthesis in Streptomyces albulus

Background

AdpA is a global regulator of morphological differentiation and secondary metabolism in Streptomyces, but the regulatory roles of the Streptomyces AdpA family on the biosynthesis of the natural product ε-poly-l-lysine (ε-PL) remain unidentified, and few studies have focused on increasing the production of ε-PL by manipulating transcription factors in Streptomyces.

Results

In this study, we revealed the regulatory roles of different AdpA homologs in ε-PL biosynthesis and morphological differentiation and effectively promoted ε-PL production and sporulation in Streptomycesalbulus NK660 by heterologously expressing adpA from S.neyagawaensis NRRLB-3092 (adpA_Sn). First, we identified a novel AdpA homolog named AdpA_Sa in S.albulus NK660 and characterized its function as an activator of ε-PL biosynthesis and morphological differentiation. Subsequently, four heterologous AdpA homologs were selected to investigate their phylogenetic relationships and regulatory roles in S.albulus, and AdpA_Sn was demonstrated to have the strongest ability to promote both ε-PL production and sporulation among these five AdpA proteins. The ε-PL yield of S.albulus heterologously expressing adpA_Sn was approximately 3.6-fold higher than that of the control strain. Finally, we clarified the mechanism of AdpA_Sn in enhancing ε-PL biosynthesis and its effect on ε-PL polymerization degree using real-time quantitative PCR, microscale thermophoresis and MALDI-TOF–MS. AdpA_Sn was purified, and its seven direct targets, zwf, tal, pyk2, pta, ack, pepc and a transketolase gene (DC74_2409), were identified, suggesting that AdpA_Sn may cause the redistribution of metabolic flux in central metabolism pathways, which subsequently provides more carbon skeletons and ATP for ε-PL biosynthesis in S.albulus.

Conclusions

Here, we characterized the positive regulatory roles of Streptomyces AdpA homologs in ε-PL biosynthesis and their effects on morphological differentiation and reported for the first time that AdpA_Sn promotes ε-PL biosynthesis by affecting the transcription of its target genes in central metabolism pathways. These findings supply valuable insights into the regulatory roles of the Streptomyces AdpA family on ε-PL biosynthesis and morphological differentiation and suggest that AdpA_Sn may be an effective global regulator for enhanced production of ε-PL and other valuable secondary metabolites in Streptomyces.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01785-6.

Epsilon-poly-L-lysine: Recent Advances in Biomanufacturing and Applications

ε-poly-L-lysine (ε-PL) is a naturally occurring poly(amino acid) of varying polymerization degree, which possesses excellent antimicrobial activity and has been widely used in food and pharmaceutical industries. To provide new perspectives from recent advances, this review compares several conventional and advanced strategies for the discovery of wild strains and development of high-producing strains, including isolation and culture-based traditional methods as well as genome mining and directed evolution. We also summarize process engineering approaches for improving production, including optimization of environmental conditions and utilization of industrial waste. Then, efficient downstream purification methods are described, including their drawbacks, followed by the brief introductions of proposed antimicrobial mechanisms of ε-PL and its recent applications. Finally, we discuss persistent challenges and future perspectives for the commercialization of ε-PL.

Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression of biosynthetic gene clusters

Streptomyces griseofuscus DSM 40191 is a fast growing Streptomyces strain that remains largely underexplored as a heterologous host. Here, we report the genome mining of S. griseofuscus, followed by the detailed exploration of its phenotype, including the production of native secondary metabolites and ability to utilise carbon, nitrogen, sulphur and phosphorus sources. Furthermore, several routes for genetic engineering of S. griseofuscus were explored, including use of GusA-based vectors, CRISPR-Cas9 and CRISPR-cBEST-mediated knockouts. Two out of the three native plasmids were cured using CRISPR-Cas9 technology, leading to the generation of strain S. griseofuscus DEL1. DEL1 was further modified by the full deletion of a pentamycin BGC and an unknown NRPS BGC, leading to the generation of strain DEL2, lacking approx. 500 kbp of the genome, which corresponds to a 5.19% genome reduction. DEL2 can be characterized by faster growth and inability to produce three main native metabolites: lankacidin, lankamycin, pentamycin and their derivatives. To test the ability of DEL2 to heterologously produce secondary metabolites, the actinorhodin BGC was used. We were able to observe a formation of a blue halo, indicating a potential production of actinorhodin by both DEL2 and a wild type.

Applications and research advance of genome shuffling for industrial microbial strains improvement

Genome shuffling, an efficient and practical strain improvement technology via recursive protoplasts fusion, can break through the limits of species even genus to accelerate the directed evolution of microbial strains, without requiring the comprehensively cognized genetic background and operable genetic system. Hence this technology has been widely used for many important strains to obtain the desirable industrial phenotypes. In this review, we introduce the procedure of genome shuffling, discuss the new aid strategies of genome shuffling, summarize the applications of genome shuffling for increasing metabolite yield, improving strain tolerance, enhancing substrate utilization, and put forward the outlook to the future development of this technology.

Enhancement of ε-poly-L-lysine production in Streptomyces griseofuscus by addition of exogenous astaxanthin

Addition of exogenous astaxanthin for improving ε-poly-L-lysine (ε-PL) production in Streptomyces griseofuscus was investigated in this study. By this unique strategy, the ε-PL production in shaker-flask fermentation was 2.48 g/L, which was 67.5% higher than the control at the addition dosage of 1.0 g/L, owing to the oxidation resistance of astaxanthin. In fed-batch fermentation, the ε-PL production reached 36.1 g/L, a 36.3% increase compared to the control. Intracellular response for oxidation in S. griseofuscus such as ROS generation and lipid peroxidation was reduced by astaxanthin addition. Illumina RNA deep sequencing (RNA-seq) technology further revealed that S. griseofuscus with astaxanthin addition showed down-regulated transcriptions of genes involved in oxidative stress. This research proved that the beneficial effect of astaxanthin addition was far better than glutathione (GSH) owing to the stronger antioxidant capacity, and provided a novel approach to regulate ε-PL synthesis.

Efficiently activated ε-poly-L-lysine production by multiple antibiotic-resistance mutations and acidic pH shock optimization in Streptomyces albulus

ε‐Poly‐L‐lysine (ε‐PL) is a food additive produced by Streptomyces and is widely used in many countries. Working with Streptomyces albulus FEEL‐1, we established a method to activate ε‐PL synthesis by successive introduction of multiple antibiotic‐resistance mutations. Sextuple mutant R6 was finally developed by screening for resistance to six antibiotics and produced 4.41 g/L of ε‐PL in a shake flask, which is 2.75‐fold higher than the level produced by the parent strain. In a previous study, we constructed a double‐resistance mutant, SG‐31, with high ε‐PL production of 3.83 g/L and 59.50 g/L in a shake flask and 5‐L bioreactor, respectively. However, we found that R6 did not show obvious advantages in fed‐batch fermentation when compared with SG‐31. For further activation of ε‐PL synthesis ability, we optimized the fermentation process by using an effective acidic pH shock strategy, by which R6 synthetized 70.3 g/L of ε‐PL, 2.79‐fold and 1.18‐fold greater than that synthetized by FEEL‐1 and SG‐31, respectively. To the best of our knowledge, this is the highest reported ε‐PL production to date. This ε‐PL overproduction may be due to the result of R99P and Q856H mutations in ribosomal protein S12 and RNA polymerase, respectively, which may be responsible for the increased transcription of the ε‐poly‐lysine synthetase gene (pls) and key enzyme activities in the Lys synthesis metabolic pathway. Consequently, ε‐PL synthetase activity, intracellular ATP, and Lys concentrations were improved and directly contributed to ε‐PL overproduction. This study combined ribosome engineering, high‐throughput screening, and targeted strategy optimization to accelerate ε‐PL production and probe the fermentation characteristics of hyperyield mutants. The information presented here may be useful for other natural products produced by Streptomyces.

Development of Microtiter Plate Culture Method for Rapid Screening of ε-Poly-L-Lysine-Producing Strains

ε-Poly-L-lysine (ε-PL) produced by Streptomyces albulus possesses a broad spectrum of antimicrobial activity and is widely used as a food preservative. To extensively screen ε-PL-overproducing strain, we developed an integrated high-throughput screening assay using ribosome engineering technology. The production protocol was scaled down to 24- and 48-deep-well microtiter plates (MTPs). The microplate reader assay was used to monitor ε-PL production. A good correlation was observed between the fermentation results obtained in both 24-(48)-deep-well MTPs and conventional Erlenmeyer flasks. Using this protocol, the production of ε-PL in an entire MTP was determined in <5 min without compromising on accuracy. The high-yielding strain selected through this protocol was also tested in Erlenmeyer flasks. The result showed that the ε-PL production of the high-yielding mutants was nearly 45% higher than that of the parent stain. Thus, development of this protocol is expected to accelerate the selection of ε-PL-overproducing strains.

Enhanced ε-poly-L-lysine production by inducing double antibiotic-resistant mutations in Streptomyces albulus

ε-Poly-L-lysine (ε-PL), as a food additive, has been widely used in many countries. However, its production still needs to be improved. We successfully enhanced ε-PL production of Streptomyces albulus FEEL-1 by introducing mutations related to antibiotics, such as streptomycin, gentamicin, and rifampin. Single- and double-resistant mutants (S-88 and SG-31) were finally screened with the improved ε-PL productions of 2.81 and 3.83 g/L, 1.75- to 2.39-fold compared with that of initial strain FEEL-1. Then, the performances of mutants S-88 and SG-31 were compared with the parent strain FEEL-1 in a 5-L bioreactor under the optimal condition for ε-PL production. After 174-h fed-batch fermentation, the ε-PL production and productivity of hyper-strain SG-31 reached the maximum of 59.50 g/L and 8.21 g/L/day, respectively, which was 138 and 105% higher than that of FEEL-1. Analysis of streptomycin-resistant mutants demonstrated that a point mutation occurred in rpsL gene (encoding the ribosomal protein S12). These single and double mutants displayed remarkable increases of the activities and transcriptional levels of key enzymes in ε-PL biosynthesis pathway, which may be responsible for the enhanced mycelia viability, respiratory activity, and ε-PL productions of SG-31. These results showed that the new breeding method, called ribosome engineering, could be a novel and effective breeding strategy for the evolution of ε-PL-producing strains.

Tools for metabolic engineering in Streptomyces

During the last few decades, Streptomycetes have shown to be a very important and adaptable group of bacteria for the production of various beneficial secondary metabolites. These secondary metabolites have been of great interest in academia and the pharmaceutical industries. To date, a vast variety of techniques and tools for metabolic engineering of relevant structural biosynthetic gene clusters have been developed. The main aim of this review is to summarize and discuss the published literature on tools for metabolic engineering of Streptomyces over the last decade. These strategies involve precursor engineering, structural and regulatory gene engineering, and the up or downregulation of genes, as well as genome shuffling and the use of genome scale metabolic models, which can reconstruct bacterial metabolic pathways to predict phenotypic changes and hence rationalize engineering strategies. These tools are continuously being developed to simplify the engineering strategies for this vital group of bacteria.

Toward breeding new land-sea plant hybrid species irrigable with seawater for dry regions

A plant species growing in sea or coastal saltmarsh is greatly tolerant to high concentrations of salts, and a plant species growing in desert or dry regions is highly tolerant to drought. Breeding a new plant hybrid species from both species by means of cellular grafting, genome fusion or nuclear transfer would generate, at least in theory, a hybrid plant species that should be strongly tolerant to harsh aridity and salinity and would be potentially irrigable with seawater. Such prospective species can be used for example as a fodder, biofuel crop or stabilizer species to protect soil from wind erosion and sandy storms in dry regions. Breeding such species would change the surface of the world and help to solve major challenges of starvation, malnutrition and poverty. Here, I propose potential approaches that would be worthy of investigation toward this purpose.

Development of bio-based fine chemical production through synthetic bioengineering

Fine chemicals that are physiologically active, such as pharmaceuticals, cosmetics, nutritional supplements, flavoring agents as well as additives for foods, feed, and fertilizer are produced by enzymatically or through microbial fermentation. The identification of enzymes that catalyze the target reaction makes possible the enzymatic synthesis of the desired fine chemical. The genes encoding these enzymes are then introduced into suitable microbial hosts that are cultured with inexpensive, naturally abundant carbon sources, and other nutrients. Metabolic engineering create efficient microbial cell factories for producing chemicals at higher yields. Molecular genetic techniques are then used to optimize metabolic pathways of genetically and metabolically well-characterized hosts. Synthetic bioengineering represents a novel approach to employ a combination of computer simulation and metabolic analysis to design artificial metabolic pathways suitable for mass production of target chemicals in host strains. In the present review, we summarize recent studies on bio-based fine chemical production and assess the potential of synthetic bioengineering for further improving their productivity.

Evolutionary engineering by genome shuffling

An upsurge in the bioeconomy drives the need for engineering microorganisms with increasingly complex phenotypes. Gains in productivity of industrial microbes depend on the development of improved strains. Classical strain improvement programmes for the generation, screening and isolation of such mutant strains have existed for several decades. An alternative to traditional strain improvement methods, genome shuffling, allows the directed evolution of whole organisms via recursive recombination at the genome level. This review deals chiefly with the technical aspects of genome shuffling. It first presents the diversity of organisms and phenotypes typically evolved using this technology and then reviews available sources of genetic diversity and recombination methodologies. Analysis of the literature reveals that genome shuffling has so far been restricted to microorganisms, both prokaryotes and eukaryotes, with an overepresentation of antibiotics- and biofuel-producing microbes. Mutagenesis is the main source of genetic diversity, with few studies adopting alternative strategies. Recombination is usually done by protoplast fusion or sexual recombination, again with few exceptions. For both diversity and recombination, prospective methods that have not yet been used are also presented. Finally, the potential of genome shuffling for gaining insight into the genetic basis of complex phenotypes is also discussed.

An insight into the "-omics" based engineering of streptomycetes for secondary metabolite overproduction

Microorganisms produce a range of chemical substances representing a vast diversity of fascinating molecular architectures not available in any other system. Among them, Streptomyces are frequently used to produce useful enzymes and a wide variety of secondary metabolites with potential biological activities. Streptomyces are preferred over other microorganisms for producing more than half of the clinically useful naturally originating pharmaceuticals. However, these compounds are usually produced in very low amounts (or not at all) under typical laboratory conditions. Despite the superiority of Streptomyces, they still lack well documented genetic information and a large number of in-depth molecular biological tools for strain improvement. Previous attempts to produce high yielding strains required selection of the genetic material through classical mutagenesis for commercial production of secondary metabolites, optimizing culture conditions, and random selection. However, a profound effect on the strategy for strain development has occurred with the recent advancement of whole-genome sequencing, systems biology, and genetic engineering. In this review, we demonstrate a few of the major issues related to the potential of "-omics" technology (genomics, transcriptomics, proteomics, and metabolomics) for improving streptomycetes as an intelligent chemical factory for enhancing the production of useful bioactive compounds.