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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
Nature. Author manuscript; available in PMC 2013 September 16.
Published in final edited form as:
PMCID: PMC3774833
NIHMSID: NIHMS511248

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

Recent advances in DNA synthesis technology have enabled the construction of novel genetic pathways and genomic elements, furthering our understanding of system-level phenomena1-7. The ability to synthesize large segments of DNA allows one to engineer pathways and genomes according to arbitrary sets of design principles. Here we describe a synthetic yeast genome project, Sc2.0, and the first partially synthetic eukaryotic chromosomes, Saccharomyces cerevisiae chromosome synIXR, and semi-synVIL. We defined design principles for a synthetic genome predicted to result in I) (near) wild-type phenotype and fitness II) a genome lacking destabilizing elements such as tRNA genes or transposons8, 9, and III) genetic flexibility to facilitate future studies (Box 1). The synthetic genome features multiple systemic modifications complying with the design principles, including an inducible evolution system, SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution). We show the utility of SCRaMbLE as a novel method of combinatorial mutagenesis, capable of generating complex genotypes and a broad variety of phenotypes. When complete, the fully synthetic yeast genome will allow massive restructuring of the yeast genome, and may open the door to a new type of combinatorial genetics based entirely on variations in gene content and copy number.

Box 1

Modifications in synthetic sequence

  • Elements removed: Retrotransposons (presumed nonessential)
  • Subtelomeric repeats (presumed nonessential)
  • Introns (none on IXR; presumed nonessential)
  • Elements relocated to extrachromosomal array: tRNA genes (genome-destabilizing7,8)
  • Element replaced: TAG Stop codons replaced by TAA (future code manipulation)
  • Individual synonymous codons (site engineering)
  • Strings of synonymous codons (PCRTags/markers)
  • Element introduced: LoxPSym sites (conditional genome instability; SCRaMbLE)
  • Not changed: Gene order
  • Noncoding regions (except as noted)

Design and synthesis

We designed the right arm of chromosome IX (IXR) according to the three principles outlined above and in Box 1. IXR is the smallest chromosome arm in the genome and features multiple genomic elements of interest (Fig. 1a), making this chromosome arm suitable for a pilot study. The designed sequence, synIXR, is based on a native IXR sequence extending from open reading frame (ORF) YIL002W through the centromere and the remainder of chromosome IXR, an 89,299 bp sequence (native IXR position 350585-43899310). In accordance with design principle II, a tRNA gene, a Ty1 LTR, and telomeric sequences were removed. The final synIXR sequence, 91010 bp, is slightly longer than the native sequence due to the inclusion of 43 loxPsym sites, replacing 20.3% of the native chromosome. A 30 kb telomeric segment of the left arm of chromosome VI (semi-synVIL) was similarly designed (Fig. 1b, Supplement “SynVIL design and incorporation”), and replaced 15.7% of the native chromosome. The two synthetic segments comprise 17% of original sequence lengths that were 1) changed by base substitution, 2) deleted, or 3) inserted (Table S1); sequences were submitted to GenBank (Supplement sequence files “SynIXR” and “Semi-synVIL”; synIXR: JN020955; semi-synVIL: JN020956).

Figure 1
Map of a) synIXR and b) semi-synVIL. Boxed text indicates elements deleted in the synthetic chromosomes. “Vector” in part a is circular. Vertical green bars inside ORFs indicate PCRTag amplicons; only sequences at the outside edges of ...

We systematically introduced two systematic sets of changes in silico using the genome editing suite BioStudio (described elsewhere): introduction of TAG/TAA stop codon swaps and PCRTag sequences (see Supplement “Sequence design/editing algorithms”). In recognition of design principle III, the elimination of the TAG stop codon by recoding to TAA frees a codon for future genetic code expansion (e.g. by adding a 21st unnatural amino acid11, 12) and could serve as a future mechanism of reproductive isolation and control. PCRTags are short pairs of recoded sequences, unique to either the wild-type or synthetic genome, and serve as convenient, low cost and closely spaced genetic markers for verifying introduction of the synthetic sequence and removal of the native sequence. The inclusion of PCRTags allows design of PCR primers specific to either the native or synthetic sequence to rapidly evaluate the presence of synthetic and absence of native sequences, critical for evaluating incorporation of synthetic DNA (see below and Supplement, “SynVIL design and incorporation”). PCRTags, designed in silico, were tested in triplicate to verify specificity (Fig. S1, Tables S2 and S3).

LoxPsym sequences are nondirectional loxP sites capable of recombining in either orientation13, and theoretically produce inversions or deletions with equal probability. Under design principle III, these sites form the substrate for the inducible SCRaMbLE system and are intended to generate combinatorial diversity. We inserted loxPsym sites 3 bp after each nonessential gene's stop codon and at major landmarks, such as sites of LTR and tRNA deletions, flanking CEN9, and adjacent to telomeres (Fig. 1; Supplement “LoxPsym site insertion”). LoxPsym sites inserted at equivalent positions genome-wide will allow formation of many structurally distinct genomes.

Synthetic chromosome introduction and construction of “arm swap” strains

The synIXR chromosome, cloned in a circular BAC vector, includes all sequences needed for propagation in yeast and bacteria (Fig. 1a). We introduced synIXR into a diploid strain by transformation; typically, about 10-15% of the synIXR transformants obtained were positive for all PCRTag pairs tested (Fig. 2d). We choose one such transformant, strain A (Fig. 2a) and truncated one native IXR homolog(IXΔR) by transforming with a suitably designed linear DNA fragment14 introducing a selectable marker (URA3) and a telomere seed sequence, generating strain C (Fig. 2b). Chromosome truncation was confirmed by pulsed field gel electrophoresis analysis (Fig. 2c), and strain C was sporulated to generate haploids carrying synIXR and IXΔR. We observed more spore lethality than in control crosses, presumably due to segregation of synIXR away from IXΔR; cells bearing only synIXR or only IXΔR would lack many essential genes and not survive. PCRTag analysis of 14 synIXR candidate “arm swap” strains revealed 10 haploids with all synthetic PCRTags and no native PCRTags present (Fig. 2d, Fig. S2). The remaining four strains carried BACs with “patchworks” of synthetic and native sequences suggestive of meiotic gene conversion events (Fig. S2). Sanger sequencing and structural analyses (Table S4; Fig. S3; Supplement, “DNA sequence analysis”) of recovered synIXR BACs revealed no mutations had occurred in the synthetic chromosome. Thus the synthetic sequence is replicated faithfully.

Figure 2
Strain construction and verification. a) Generation of synIXR haploids. (I) synIXR BAC (L) was transformed into BY4743 to generate “A” (II). (III) One copy of native IXR in “A” was replaced with a URA3-telomere seed cassette ...

Whereas synIXR was incorporated in a circular form, we used an alternate strategy to integrate the semi-synVIL chromosome fragment into native chromosome VI (Fig. S4): a linear synthetic fragment marked with LEU2 was transformed into a YFL054C::kanMX strain. Approximately 13% (75/586) had the Leu+ G418S phenotype expected for the desired integrant. PCRTags analysis showed that 10 of 12 such strains contained only synthetic PCRTags, as expected for full replacement (Fig. S5).

Phenotypic and genetic analysis of synthetic haploids

Design principle I prioritizes a wild-type phenotype and high fitness level despite the incorporated modifications. SynIXR has a designed sequence alteration approximately every 500 bp, 2.64% of total sequence is altered, and it carries 43 loxPsym sites. To check for negative effects of these modifications on fitness, we 1) examined colony size and morphology under various conditions, and 2) performed transcript profiling. We examined colony size and morphology of synIXR swap strains under six distinct growth conditions. It was impossible to distinguish swap strains from the wild-type (BY4741) under these conditions, suggesting that any fitness defect attributable to synIXR is modest; fitness tests on semi-synVIL gave similar results (Fig. S6).

Synonymous substitutions, loxPsym site introduction, or other changes might change gene expression. We performed transcript profiling experiments on swap strains synIXR-1D, synIXR-6B, and synIXR-22D (Supplement, “Transcriptional Profiling”); these studies revealed interesting but predictable trends (Fig. 3). As expected, genes present in two copies (YIL001W and YIL002C, present on both synIXR and IXΔR) were approximately doubled in transcript abundance. Most genes showed no significant expression change, although a few showed modest decreases; however, the subtelomeric genes YIR039C and YIR042C showed increased expression. We speculate that in the circular synthetic chromosome these are released from telomeric silencing, resulting in their overexpression. Overall synIXR genes show relatively normal expression, suggesting that loxPsym sites and PCRTags minimally effect expression. Similarly, no significant changes were observed by RNA blotting (Fig. S7a). To detect possible compensatory transcriptome changes, we profiled transcripts genome-wide. Except for trivial differences attributable to slightly different selectable marker configurations in the strains, there were no consistent statistically significant differences seen outside of IXR itself (Fig. S7b). Thus, modifications present in synIXR and semi-synVIL do not produce major fitness effects, nor compensatory transcriptomic alterations.

Figure 3
Transcript profiling of wild-type and synIXR strains. Transcript profiling of synIXR-1D, -6B, and -22D. Log2 ratio of RNA abundance relative to wild type (BY4741 or BY4742) is shown. ORFs labeled in blue exist in two copies. Essential genes are labeled ...

Conditional Genome Instability

The design principles dictate that SCRaMbLE be available for use on demand, yet lie dormant until intentional Cre recombinase induction, at which point generation of genetic diversity is desirable. To complete the SCRaMbLE toolkit, we incorporated an engineered Cre recombinase fused to the murine estrogen binding domain (EBD). This recently described Cre-EBD variant15 is estradiol inducible, has low basal activity, and is controlled by daughter cell-specific promoter SCW11 (Fig. S8). pSCW11-Cre-EBD should produce a pulse of recombinase activity once and only once in each cell's lifetime, and depend on estradiol exposure. The uninduced integrated construct is well tolerated even in swap strains, which, with 43 loxPsym sites, is expected to be Cre-hypersensitive. Upon estradiol addition, rearrangements are induced at the loxPsym sites and viability dropped by 100-fold in synIXR strains (Fig. 4a, Fig. S9). This loss of viability likely results from loss of synIXR essential genes. In contrast, viability in semi-synVIL, which lacks essential genes, is not affected by Cre induction (Fig. 1b, Fig. S9d).

Figure 4
SCRaMbLE rearranges genomes. a) Cre induction decreased fitness in synIXR strain (SYN) but not wild type (WT; BY4741). EST, estradiol; Hours, exposure time. b) PCR analysis of semi-synVIL SCRaMbLE. Map, primer positions. Amplicon 13 is spurious (wrong ...

Semi-synVIL contains just five loxPsym sites, including one immediately adjacent to the telomeric TG1-3 repeats (Fig. 1b). This simple configuration allows comprehensive PCR-based mapping of rearrangements of four of the loxPsym sites in SCRaMbLEd strains. A SCRaMbLEd semi-synVIL population was analyzed for most of the possible rearranged configurations by PCR, revealing a large variety of deletions and inversions (Fig. 4a); most predicted rearrangements were readily detected.

The symmetry of loxPsym sites allows alignment in two orientations, theoretically giving rise to deletions and inversions with equal frequency. SynIXR contains 43 loxPsym sites, allowing over 3600 potential pairwise interactions between synIXR loxPsym sites. We reasoned that SCRaMbLEd synIXR clones should display high phenotypic diversity. Indeed, SCRaMbLEd swap strains show more growth rate heterogeneity than wild-type controls (Fig. 4c, Fig. S10). These SCRaMbLE clones show many different phenotypes (Supplement, “SCRaMbLE Analysis”, Fig. S11). In summary, SCRaMbLE is sufficient to generate significant genetic heterogeneity and complex phenotypes.

To further characterize the utility of SCRaMbLE, we performed a mutagenesis study. SynIXR encodes both MET28 and LYS1, genes required for amino acid biosynthesis16, 17. Null mutants result in auxotrophy, and can be easily detected by replica-plating. We introduced episomal Cre-EBD (pSCW11-Cre-EBD-URA3MX cloned in a CEN plasmid) into strain C previously made LYS2+ (strain “D”, yJS587) and performed SCRaMbLE. We screened 20,242 colonies and 3% (604/20,242) were candidate lys1 and/or met28 auxotrophs. Of 360 candidates tested more rigorously, 295 (81.9%) were confirmed: we found 212 Lys auxotrophs (1.37%), 66 Met auxotrophs (0.43%), and interestingly, 17 LysMet double auxotrophs (0.11%). PCRTag profiles of 24 Met auxotrophs, 35 Lys auxotrophs, and 7 double auxotrophs (Fig. 4d) showed that all Met auxotrophs had deletions in the loxPsym-flanked segment containing MET28 and YAP5, whereas all Lys auxotrophs had deletions in the loxPsym-flanked segment containing LYS1. The deletion profiles of many SCRaMbLEd auxotrophs were highly variable, often with more than one segment missing.

To formally confirm the observed SCRaMbLE phenotypes resulted solely from deletions in synIXR, we recovered the synIXR chromosome from two Met auxotrophs into E. coli, then introduced them to a clean genetic background. In both cases the auxotrophic phenotype was associated with the presence of the SCRaMbLED chromosomes (Fig. S12; Supplement, “MET28 and LYS1 SCRaMbLE Mutagenesis”). Thus the SCRaMbLE system is a highly effective method of mutagenesis, giving rise to mutants with different genetic backgrounds, and generating a wide variety of double mutants.

Perspectives

We have shown there does not appear to be any significant theoretical impediment to extending the design strategy outlined here to the entire yeast genome, apart from the challenge of 12 Mb of DNA synthesis. Whether or not fitness defects will accumulate as design and synthesis are scaled up further remains to be seen; however, the overall high fitness of the swap strains described here validates the design strategy. Furthermore, the iterative bottom-up approach used will allow identification of potential “problem regions” in synthetic sequences as synthesis moves forward. If a given swap experiment results in only transformants with reduced fitness (or no transformants are obtainable), the underlying defect can be mapped by introducing sub-segments, facilitated by strategic placement of unique restriction sites throughout synthetic chromosome arms. Also, since a subset of transformants consist of patchworks of native and synthetic sequence (Fig. S2, S5), analysis of such strains can in principle be used to rapidly map phenotypic defects. The stability and sequence fidelity of large circular chromosomes observed here and elsewhere5-7 bode well for use of yeast as a host platform for synthetic biology.

SCRaMbLE may become a useful general strategy for analyzing genome structure, content, and function. One important feature of SCRaMbLE is its potential to be customized; expression of different Cre-EBD variants from various promoters at distinct inducer (estradiol) levels should produce distinct SCRaMbLE dynamics. Use of weaker promoters than pSCW11, promoters expressed at different cell cycle phases, performing SCRaMbLE in diploids, and lowering the inducer concentration should all contribute to decreased lethality of SCRaMbLE strains, an important consideration as additional segments of the genome are replaced with synthetic counterparts and the proportion of essential genes that can be lost by SCRaMbLEing increases. As shown here, SCRaMbLE mutagenesis is efficient and generates mutants with a wide variety of different genetic backgrounds. It is possible that different combinations of gene deletions will give rise to a variety of subtly different phenotypes that can be rapidly mapped by PCRTag analysis; more extensive analysis by deep sequencing will reveal changes in both genome structure and content. As the synthetic yeast genome grows, opportunities for genome rearrangement will increase exponentially. In principle, changes in chromosome number, ploidy, content, and structure are all possible, increasing the utility of the SCRaMbLE system. For example, there may be many different routes to a minimal genome, and exploring all of them by a hit or miss predictive approach is impractical and unlikely to yield comprehensive results. Using SCRaMbLE, many independent routes of genome minimization can be explored at one time, under manifold environmental conditions, for example by growing yeast cells long-term either in serially transferred batch cultures, or in a chemostat or turbidistat under conditions where Cre is minimally active. Such an approach may also lead to derivatives that are more fit than the parent, e.g. by gene duplication events facilitated by the Cre-EBD/loxPsym system employed here.

Methods Summary

DNA preparation

BAC DNA was prepared using the Qiagen Plasmid Midi kit or alkaline lysis18. The following protocol modifications were made: cells were diluted 1:100 from an overnight culture into 50 ml grown in LB plus 50 μg/ml carbenicillin, and grown at 30°C for 14-16 hours. Qiagen purified DNA was treated with 60 μg/ml proteinase K at 37°C overnight, then phenol/chloroform extracted. DNAs prepared without a column were phenol/chloroform extracted, and then RNAse treated immediately prior to use.

Yeast genomic DNA for use in PCRTag analysis was prepared by standard methods19. DNA preparation for recovery of the synIXR BAC into bacteria was as previously reported20.

PCR conditions

PCRTags were amplified using Taq polymerase (New England Biolabs). Template concentrations were 1 ng/μl for genomic DNA and 10 pg/μl for purified BAC DNA. The following program was used: 94°C 3 min; 30 cycles of 94°C 30 sec, 65°C 30 sec, 72°C 30 sec; 72°C 3 min.

RNA analysis

Total RNA was isolated by hot acid phenol extraction. Microarray hybridization and data analysis were performed at the Johns Hopkins Microarray Core Facility (www.microarray.jhmi.edu). Dubious ORFs and pseudogenes were omitted from synIXR transcript analysis.

Pulsed field gels

DNAs were prepared as described elsewhere21. Identity of the chromosomes was inferred from the known molecular karyotype of WT (BY4743) and from lambda ladders run on the same gel.

Methods

Yeast strains, transformation and tetrad analysis

Strains ABY7 and ABY8 were derived from strain BY47432222; ABY7 (MATa) and ABY7 (MATα) otherwise share the genotype:his3Δ1 leu2Δ0 ura3Δ0 lys2Δ0 met15Δ0 yil001::URA3 yir039::kanMX.

BY4743 spheroplasts were transformed with synIXR. The strain YFL054C::kanMX23 was transformed with synVIL restriction fragments by standard lithium acetate transformation.

Strains synIXR-1D and others were backcrossed to strains ABY7 and ABY8; resultant diploids were sporulated and genotyped to identify synIXR segregants.

Phenotypic screening

Single colonies were picked into 96-well plates and grown for 48 h in YPD at 30°C. (SCRaMbLE strains were grown 72 h in YPD at 30°C, diluted 1:10 and grown 4 h prior to plating.) Ten-fold dilutions were spotted on various agar medium types/selective conditions in OmniTrays (NUNC), as described24. Most cells were grown 72 hours (except YPGE plates, grown for 108 h), scored for growth, and photographed.

Yeast growth and media

Unless otherwise indicated, all experiments were performed at 30°C. YPGE was supplemented with 2% ethanol and 2% glycerol. Concentrations of drugs were as follows: hydroxyurea, 0.2M; methylmethane sulfonate, 0.05%; 6-azauracil, 100 μg/ml; benomyl, 15 μg/ml; hydrogen peroxide, 1 mM; cycloheximide, 10 μg/ml. Cycloheximide and hydrogen peroxide resistance were assayed by growing cells in treated medium for two hours, then plating on YPD. Other phenotypes were assayed by growing cells to mid-log phase in rich media then spotting ten-fold dilutions on selective media.

Colony size measurements

Cells were plated at various dilutions so that similar numbers of colonies were observed on control and experimental (estradiol-treated) plates. Colony size was measured using ImageJ software25, and normalized against the total number of colonies on each plate. Sample sizes for data presented in Fig. 4c are as follows: WT, n = 488 colonies; WT+C+E, n = 486; 2.2.1D, n = 395; 2.2.1D +C, n = 251; 2.2.1D+E, n = 416; 2.2.1D +C+E, n = 394.

SynIXR BAC Sequence Analysis

The original synIXR BAC was sequenced by the manufacturer, Codon Devices26. SynIXR BACs were recovered into bacteria and sequenced by Agencourt (Beckman Coulter Genomics), using sequencing primers listed in Table S5. Repetitive sequences, including the highly internally repetitive MUC1 open reading frame, were PCR-amplified prior to sequencing where necessary.

Pulsed Field Gels

Samples were run on a 1.0% agarose gel in 0.5× TBE pH 8.0 for 20 hours at 14°C on a CHEF apparatus. The voltage was 3.5 V/cm, at an angle of 120° and 60-120 second switch time ramped over 20 hours.

NotI (Promega) digests were performed on whole chromosomes embedded in agarose plugs. Agarose plugs were removed from the 0.5 M EDTA storage buffer, washed with 0.05 M EDTA for one hour at room temperature, and then washed with 0.1× followed by 1× restriction enzyme buffer under the same conditions.

Northern and Southern Blots Probe Preparation

Probes were prepared using the Prime-It II kit (Stratagene), and hybridized using Ultrahyb hybridization solution (Ambion) according to the manufacturer's instructions.

SCRaMbLE

Cre activity was induced by exposure to 1 μM β-estradiol (Sigma-Aldrich) in rich media for either 48 hours (integrated Cre) or 4 hours (episomal Cre) except where indicated otherwise. PCRTag analysis of Met and Lys auxotrophs was performed with a non-redundant array using one primer pair per loxPsym-flanked segment.

Supplementary Material

Supplementary Materials

Acknowledgments

We thank George Church for suggesting the global substitution of TAG codons with TAA codons, Carla Connelly for sharing technical expertise and Victor Huang for generating a sequence visualizer. We are grateful to Brendan Cormack, Geraldine Seydoux and Jeremy Nathans for offering helpful advice, Patrick Cai and Jean Peccoud for suggesting methods to validate the sequence data, and Ed Louis for providing expert advice on telomeres. Supported by National Science Foundation grant MCB0718846 to J.D.B., J.S.B. and S.C., by a grant from Microsoft to J.S.B. and J.D.B., by Department of Energy Fellowship DE-FG02097ER25308 to S.M.R., National Institutes of Health grant AG023779 to D.E.G., and by a fellowship from Fondation pour la Recherche Médicale to H.M.

Footnotes

Supplementary Information is linked to the online version of the paper at www.nature.com/nature.

Author Contributions J.S.D., S.M.R., S.C., J.S.B., and J.D.B. designed experiments. J.S.D., S.M.R., C.E.C., T.B., H.M., N.A., J.W.S., J.D., and A.C.B. performed experiments. W.J.B built the synIXR chromosome. D.L.L. and D.E.G. generated the integrated CRE-EBD cassette. J.S.D., S.M.R., J.S.B., and J.D.B. analyzed data and wrote the manuscript.

Author information SynIXR and semi-synVIL sequences were deposited at GenBank (http://www.ncbi.nlm.nih.gov/genbank/; synIXR: JN020955; semi-synVIL: JN020956). Microarray data were submitted to GEO (http://www.ncbi.nlm.nih.gov/geo/).

Reprints and permissions information is available at www.nature.com/reprints.

The authors declare no competing financial interests.

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