Toward a bacterial genome technology: integration of the Escherichia coli prophage lambda genome into the Bacillus subtilis 168 chromosome

Direct cloning strategies for large genomic fragments: A review

Mining large-scale functional regions of the genome helps to understand the essence of cellular life. The rapid accumulation of genomic information provides a wealth of material for genomic functional, evolutionary, and structural research. DNA cloning technology is an important tool for understanding, analyzing, and manipulating the genetic code of organisms. As synthetic biologists engineer greater and broader genetic pathways and expand their research into new organisms, efficient tools capable of manipulating large-scale DNA will offer momentum to the ability to design, modify, and construct engineering life. In this review, we discuss the recent advances in the field of direct cloning of large genomic fragments, particularly of 50-150 kb genomic fragments. We specifically introduce the technological advances in the targeted release and capture steps of these cloning strategies. Additionally, the applications of large fragment cloning in functional genomics and natural product mining are also summarized. Finally, we further discuss the challenges and prospects for these technologies in the future.

Advances on transfer and maintenance of large DNA in bacteria, fungi, and mammalian cells

Advances in synthetic biology allow the design and manipulation of DNA from the scale of genes to genomes, enabling the engineering of complex genetic information for application in biomanufacturing, biomedicine and other areas. The transfer and subsequent maintenance of large DNA are two core steps in large scale genome rewriting. Compared to small DNA, the high molecular weight and fragility of large DNA make its transfer and maintenance a challenging process. This review outlines the methods currently available for transferring and maintaining large DNA in bacteria, fungi, and mammalian cells. It highlights their mechanisms, capabilities and applications. The transfer methods are categorized into general methods (e.g., electroporation, conjugative transfer, induced cell fusion-mediated transfer, and chemical transformation) and specialized methods (e.g., natural transformation, mating-based transfer, virus-mediated transfection) based on their applicability to recipient cells. The maintenance methods are classified into genomic integration (e.g., CRISPR/Cas-assisted insertion) and episomal maintenance (e.g., artificial chromosomes). Additionally, this review identifies the major technological advantages and disadvantages of each method and discusses the development for large DNA transfer and maintenance technologies.

Cross-species microbial genome transfer: a Review

Synthetic biology combines the disciplines of biology, chemistry, information science, and engineering, and has multiple applications in biomedicine, bioenergy, environmental studies, and other fields. Synthetic genomics is an important area of synthetic biology, and mainly includes genome design, synthesis, assembly, and transfer. Genome transfer technology has played an enormous role in the development of synthetic genomics, allowing the transfer of natural or synthetic genomes into cellular environments where the genome can be easily modified. A more comprehensive understanding of genome transfer technology can help to extend its applications to other microorganisms. Here, we summarize the three host platforms for microbial genome transfer, review the recent advances that have been made in genome transfer technology, and discuss the obstacles and prospects for the development of genome transfer.

Stable mutants of restriction-deficient/modification-proficient Bacillus subtilis 168: hub strains for giant DNA engineering

Bacillus subtilis 168 has been explored as a platform for the synthesis and transmission of large DNA. Two inherent DNA incorporation systems, natural transformation and pLS20-based conjugation transfer, enable rapid handling of target DNA. Both systems are affected by the Bsu restriction-modification system that recognizes and cleaves unmethylated XhoI sites, limiting the choice of target DNA. We constructed B. subtilis 168 with stable mutation for restriction-deficient and modification-proficient (r-m+). It was demonstrated that the r-m+ strains can incorporate and transfer synthesized DNA with multiple XhoI sites. These should be of value as hub strains to integrate and disseminate giant DNA between B. subtilis 168 derivatives.

An anaerobic bacterium host system for heterologous expression of natural product biosynthetic gene clusters

Anaerobic bacteria represent an overlooked rich source of biological and chemical diversity. Due to the challenge of cultivation and genetic intractability, assessing the capability of their biosynthetic gene clusters (BGCs) for secondary metabolite production requires an efficient heterologous expression system. However, this kind of host system is still unavailable. Here, we use the facultative anaerobe Streptococcus mutans UA159 as a heterologous host for the expression of BGCs from anaerobic bacteria. A natural competence based large DNA fragment cloning (NabLC) technique was developed, which can move DNA fragments up to 40-kb directly and integrate a 73.7-kb BGC to the genome of S. mutans UA159 via three rounds of NabLC cloning. Using this system, we identify an anti-infiltration compound, mutanocyclin, from undefined BGCs from human oral bacteria. We anticipate this host system will be useful for heterologous expression of BGCs from anaerobic bacteria.

Anaerobic bacteria represent a rich source of biological and chemical diversity but are difficult to cultivate and there is a lack of heterologous expression systems. Here the authors develop an expression system based on S. mutans UA159 for biosynthetic gene clusters from anaerobic bacteria.

Far rapid synthesis of giant DNA in the Bacillus subtilis genome by a conjugation transfer system

Bacillus subtilis offers a platform for giant DNA synthesis, which is mediated by the connection of overlapping DNA segments called domino DNA, in the cloning locus of the host. The domino method was successfully used to produce DNA fragments as large as 3500 kbp. However, domino DNA is limited to <100 kbp because of size restrictions regarding the transformation (TF) of B. subtilis competent cells. A novel conjugal transfer (CT) method was designed to eliminate the TF size limit. The CT method enables rapid and efficient domino reactions in addition to the transfer of giant DNA molecules of up to 875 kbp to another B. subtilis genome within 4 hours. The combined use of the TF and CT should enable significantly rapid giant DNA production.

A simple method to provide a shuttling plasmid for delivery to other host ascertained by prolonged stability of extracellular plasmid DNA released from Escherichia coli K12 endA mutant, deficient in major endonuclease

Escherichia coli lyses by lambda phage propagation. Circular plasmid DNA was present during E. coli lysis as an extracellular plasmid DNA (excpDNA) that was stable enough to transform coexisting competent Bacillus subtilis cells. Detailed investigations unveiled that excpDNA is transient in both quality and quantity, with stability lasting no more than several hours. A survey using E. coli lambda lysogens with various genetic backgrounds demonstrated that the loss of Endonuclease I (ΔendA::kan) conferred extraordinary stability upon excpDNA for as long as 48 h. Studies on endA mutants suggested that excpDNA remained localized in cell debris, in contrast to E. coli genome DNA, which diffused into medium at an early point in lysis. Lambda lysogens constructed on endA recA mutants are presented for potential pipelines in delivery to other competent proficient microbes.

Conjugational transfer system to shuttle giant DNA cloned by Bacillus subtilis genome (BGM) vector

The Bacillus subtilis GenoMe (BGM) vector was designed as a versatile vector for the cloning of giant DNA segments. Cloned DNA in the BGM can be retrieved to a plasmid using our Bacillus recombinational transfer (BReT) method that takes advantage of competent cell transformation. However, delivery of the plasmid to a different B. subtilis strain by the normal transformation method is hampered by DNA size-related inefficiency. Therefore, we designed a novel method, conjugational plasmid-mediated DNA retrieval and transfer (CReT) from the BGM vector, and investigated conjugational transmission to traverse DNA between cells to circumvent the transformation-induced size limitation. pLS20, a 65-kb plasmid capable of conjugational transfer between B. subtilis strains, was modified to retrieve DNA cloned in the BGM vector by homologous recombination during normal culture. As the plasmid copy number was estimated to be 3, the retrieval plasmid was selected using increased numbers of marker genes derived from the retrieved DNA. We applied this method to retrieve Synechocystis genome segments up to 90 kb in length. We observed retrieved plasmid transfers between B. subtilis strains by conjugation in the absence of structural alterations in the DNA fragment. Our observations extend DNA transfer protocols over previously exploited size ranges.

Direct cloning of full-length mouse mitochondrial DNA using a Bacillus subtilis genome vector

The complete mouse mitochondrial genome (16.3 kb) was directly cloned into a Bacillus subtilis genome (BGM) vector. Two DNA segments of 2.06 and 2.14 kb that flank the internal 12 kb of the mitochondrial DNA (mtDNA) were subcloned into an Escherichia coli plasmid. Subsequent integration of the plasmid at the cloning locus of the BGM vector yielded a derivative specific for the targeted cloning of the internal 12-kb mtDNA region. The BGM vector took up mtDNA purified from mouse liver and integrated it by homologous recombination at the two preinstalled mtDNA-flanking sequences. The complete cloned mtDNA in the BGM vector was converted to a covalently closed circular (ccc) plasmid form via gene conversion in B. subtilis. The mtDNA carried on this plasmid was then isolated and transferred to E. coli. DNA sequence fidelity and stability through the BGM vector-mediated cloning process were confirmed.

Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome

Cloning the whole 3.5-megabase (Mb) genome of the photosynthetic bacterium Synechocystis PCC6803 into the 4.2-Mb genome of the mesophilic bacterium Bacillus subtilis 168 resulted in a 7.7-Mb composite genome. We succeeded in such unprecedented large-size cloning by progressively assembling and editing contiguous DNA regions that cover the entire Synechocystis genome. The strain containing the two sets of genome grew only in the B. subtilis culture medium where all of the cloning procedures were carried out. The high structural stability of the cloned Synechocystis genome was closely associated with the symmetry of the bacterial genome structure of the DNA replication origin (oriC) and its termination (terC) and the exclusivity of Synechocystis ribosomal RNA operon genes (rrnA and rrnB). Given the significant diversity in genome structure observed upon horizontal DNA transfer in nature, our stable laboratory-generated composite genome raised fundamental questions concerning two complete genomes in one cell. Our megasize DNA cloning method, designated megacloning, may be generally applicable to other genomes or genome loci of free-living organisms.

DNA Shuttling Between Plasmid Vectors and a Genome Vector: Systematic Conversion and Preservation of DNA Libraries Using the Bacillus subtilis Genome (BGM) Vector

The combined use of the contemporary vector systems, the bacterial artificial chromosome (BAC) vector and the Bacillus subtilis genome (BGM) vector, makes possible the handling of giant-length DNA (above 100 kb). Our newly constructed BGM vector efficiently integrated DNA prepared in the BAC vector. A BAC library comprised of 18 independent clones prepared from mitochondrial DNA (mtDNA) of Arabidopsis thaliana was converted to a parallel BGM library using the new BGM vector. The effectiveness of the combined use of the vector systems was confirmed by the stable recovery of all 18 DNAs as BAC clones from the respective BGM clones. We show that DNA in BGM was stably preserved at room temperature after spore formation of the host B.subtilis. Rapid and stable shuttling between Escherichiacoli and the B. subtilis host, combined with spore-mediated DNA storage, may facilitate the long-term and low-cost preservation and the transportation of DNA resources.

Targeted isolation of a designated region of the Bacillus subtilis genome by recombinational transfer

A method for positional cloning of the Bacillus subtilis genome was developed. The method requires a set of two small DNA fragments that flank the region to be copied. A 38-kb segment that carries genes ppsABCDE encoding five enzymes for antibiotic plipastatin synthesis and another genome locus as large as 100 kb including one essential gene were examined for positional cloning. The positional cloning vector for ppsABCDE was constructed using a B. subtilis low-copy-number plasmid that faithfully copied the precise length of the 38-kb DNA in vivo via the recombinational transfer system of this bacterium. Structure of the copied DNA was confirmed by restriction enzyme analyses. Furthermore, the unaltered structure of the 38-kb DNA was demonstrated by complementation of a ppsABCDE deletion mutant.

Conversion of sub-megasized DNA to desired structures using a novel Bacillus subtilis genome vector

A novel genome vector using the 4215 kb Bacillus subtilis genome provides for precise target cloning and processing of the cloned DNA to the desired structure. Each process highly dependent on homologous recombination in the host B.subtilis is distinguished from the other cloning systems. A 120 kb mouse jumonji (jmj) genomic gene was processed in the genome vector to give a series of truncated sub-megasized DNA. One of these truncated segments containing the first intron was copied in a plasmid by a recombinational transfer method developed for B.subtilis. DNA manipulation previously considered difficult is argued with respect to DNA size and accuracy.

Recombinational transfer of 100-kilobase genomic DNA to plasmid in Bacillus subtilis 168

Transformation of Bacillus subtilis by a plasmid requires a circular multimeric form. In contrast, linearized plasmids can be circularized only when homologous sequences are present in the host genome. A recombinational transfer system was constructed with this intrinsic B. subtilis recombinational repair pathway. The vector, pGETS103, a derivative of the theta-type replicating plasmid pTB19 of thermophilic Bacillus, had the full length of Escherichia coli plasmid pBR322. A multimeric form of pGETS103 yielded tetracycline-resistant transformants of B. subtilis. In contrast, linearized pGETS103 gave tetracycline-resistant transformants only when the recipient strain had the pBR322 sequence in the genome. The efficiency and fidelity of the recombinational transfer of DNAs of up to 90 kb are demonstrated.

Genetic transfer of large DNA inserts to designated loci of the Bacillus subtilis 168 genome

It was found that contiguous DNA segments of up to 50 kb can be transferred between Bacillus subtilis genomes when a sufficient length of the flanking genomic region is provided for homologous recombination, although the efficiency of transfer was reduced as the insert size increased. Inserts were translocated to different loci, where appropriate integration sites were created.

Physical map of the Bacillus subtilis 166 genome: evidence for the inversion of an approximately 1900 kb continuous DNA segment, the translocation of an approximately 100 kb segment and the duplication of a 5 kb segment

An I-CeuI-NotI-SfiI endonuclease map of the Bacillus subtilis 166 genome was constructed. It was almost identical to that of B. subtilis 168 except for the inversion of an approximately 1900 kb DNA segment, the translocation of an approximately 100 kb segment and the duplication of a 5 kb segment. Continuity of the inverted segment was investigated by direct measurement of the distances between the two genomic loci where I-SceI recognition sites were created in the 168 and the 166 genomes. Size difference of the I-SceI fragments between the two strains fully demonstrated the inversion of an approximately 1900 kb long 'continuous' DNA segment and the 'location' of the two inversion junctions in the genome. The 100 kb DNA segment including the lysogenic SP beta prophage was translocated close to one of the inversion junctions and was probably associated with the duplication of a 5 kb segment. These rearrangements are consistent with those indicated by genetic analyses.