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1.
Nature ; 619(7970): 555-562, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37380776

ABSTRACT

Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.


Subject(s)
Chromosomes, Artificial, Bacterial , DNA , Escherichia coli , Genome, Bacterial , Synthetic Biology , Humans , DNA/genetics , DNA/metabolism , Escherichia coli/genetics , Genome, Bacterial/genetics , Plasmids/genetics , Repetitive Sequences, Nucleic Acid/genetics , Synthetic Biology/methods , Chromosomes, Artificial, Bacterial/genetics , Exons , Introns , G-Quadruplexes , Long Interspersed Nucleotide Elements/genetics , Short Interspersed Nucleotide Elements/genetics , Oligodeoxyribonucleotides/biosynthesis , Oligodeoxyribonucleotides/genetics , Oligodeoxyribonucleotides/metabolism , Time Factors
2.
Nat Microbiol ; 7(10): 1686-1701, 2022 10.
Article in English | MEDLINE | ID: mdl-36123441

ABSTRACT

During bacterial cell division, filaments of tubulin-like FtsZ form the Z-ring, which is the cytoplasmic scaffold for divisome assembly. In Escherichia coli, the actin homologue FtsA anchors the Z-ring to the membrane and recruits divisome components, including bitopic FtsN. FtsN regulates the periplasmic peptidoglycan synthase FtsWI. To characterize how FtsA regulates FtsN, we applied electron microscopy to show that E. coli FtsA forms antiparallel double filaments on lipid monolayers when bound to the cytoplasmic tail of FtsN. Using X-ray crystallography, we demonstrate that Vibrio maritimus FtsA crystallizes as an equivalent double filament. We identified an FtsA-FtsN interaction site in the IA-IC interdomain cleft of FtsA using X-ray crystallography and confirmed that FtsA forms double filaments in vivo by site-specific cysteine cross-linking. FtsA-FtsN double filaments reconstituted in or on liposomes prefer negative Gaussian curvature, like those of MreB, the actin-like protein of the elongasome. We propose that curved antiparallel FtsA double filaments together with treadmilling FtsZ filaments organize septal peptidoglycan synthesis in the division plane.


Subject(s)
Escherichia coli Proteins , Escherichia coli , Actins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cysteine/metabolism , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Lipids , Liposomes , Membrane Proteins/metabolism , Peptidoglycan/metabolism , Tubulin/metabolism
3.
Mol Cell ; 81(23): 4891-4906.e8, 2021 12 02.
Article in English | MEDLINE | ID: mdl-34739874

ABSTRACT

The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.


Subject(s)
Chromosomal Proteins, Non-Histone/chemistry , Chromosomes/ultrastructure , Cryoelectron Microscopy/methods , DNA/chemistry , Escherichia coli Proteins/chemistry , Repressor Proteins/chemistry , Adenosine Triphosphatases/chemistry , Cell Cycle Proteins/chemistry , Chromosomes, Bacterial , DNA/metabolism , DNA Repair , DNA-Binding Proteins/chemistry , Dimerization , Escherichia coli/metabolism , Genetic Techniques , Genome, Bacterial , Multiprotein Complexes/chemistry , Photorhabdus , Protein Binding , Protein Conformation , Protein Domains , Cohesins
4.
Science ; 372(6546): 1057-1062, 2021 06 04.
Article in English | MEDLINE | ID: mdl-34083482

ABSTRACT

It is widely hypothesized that removing cellular transfer RNAs (tRNAs)-making their cognate codons unreadable-might create a genetic firewall to viral infection and enable sense codon reassignment. However, it has been impossible to test these hypotheses. In this work, following synonymous codon compression and laboratory evolution in Escherichia coli, we deleted the tRNAs and release factor 1, which normally decode two sense codons and a stop codon; the resulting cells could not read the canonical genetic code and were completely resistant to a cocktail of viruses. We reassigned these codons to enable the efficient synthesis of proteins containing three distinct noncanonical amino acids. Notably, we demonstrate the facile reprogramming of our cells for the encoded translation of diverse noncanonical heteropolymers and macrocycles.


Subject(s)
Codon , Escherichia coli Proteins/genetics , Escherichia coli/genetics , Escherichia coli/virology , Macrocyclic Compounds/metabolism , Polymers/metabolism , Protein Biosynthesis , T-Phages/growth & development , Amino Acids/metabolism , Bacteriolysis , Codon Usage , Codon, Terminator , Directed Molecular Evolution , Escherichia coli/metabolism , Escherichia coli Proteins/biosynthesis , Gene Deletion , Genetic Code , Genome, Bacterial , Macrocyclic Compounds/chemistry , Mutagenesis , Peptide Termination Factors/genetics , Polymers/chemistry , RNA, Bacterial/genetics , RNA, Transfer/genetics , RNA, Transfer, Ser/genetics , Ubiquitin/biosynthesis , Ubiquitin/genetics
5.
Nat Protoc ; 16(5): 2345-2380, 2021 05.
Article in English | MEDLINE | ID: mdl-33903757

ABSTRACT

We previously developed REXER (Replicon EXcision Enhanced Recombination); this method enables the replacement of >100 kb of the Escherichia coli genome with synthetic DNA in a single step and allows the rapid identification of non-viable or otherwise problematic sequences with nucleotide resolution. Iterative repetition of REXER (GENESIS, GENomE Stepwise Interchange Synthesis) enables stepwise replacement of longer contiguous sections of genomic DNA with synthetic DNA, and even the replacement of the entire E. coli genome with synthetic DNA. Here we detail protocols for REXER and GENESIS. A standard REXER protocol typically takes 7-10 days to complete. Our description encompasses (i) synthetic DNA design, (ii) assembly of synthetic DNA constructs, (iii) utilization of CRISPR-Cas9 coupled to lambda-red recombination and positive/negative selection to enable the high-fidelity replacement of genomic DNA with synthetic DNA (or insertion of synthetic DNA), (iv) evaluation of the success of the integration and replacement and (v) identification of non-tolerated synthetic DNA sequences with nucleotide resolution. This protocol provides a set of precise genome engineering methods to create custom synthetic E. coli genomes.


Subject(s)
Escherichia coli/genetics , Genetic Engineering/methods , Genomics/methods , DNA, Bacterial/genetics , Genome, Bacterial/genetics , Recombination, Genetic
6.
Nat Biotechnol ; 38(8): 989-999, 2020 08.
Article in English | MEDLINE | ID: mdl-32284585

ABSTRACT

A central challenge in expanding the genetic code of cells to incorporate noncanonical amino acids into proteins is the scalable discovery of aminoacyl-tRNA synthetase (aaRS)-tRNA pairs that are orthogonal in their aminoacylation specificity. Here we computationally identify candidate orthogonal tRNAs from millions of sequences and develop a rapid, scalable approach-named tRNA Extension (tREX)-to determine the in vivo aminoacylation status of tRNAs. Using tREX, we test 243 candidate tRNAs in Escherichia coli and identify 71 orthogonal tRNAs, covering 16 isoacceptor classes, and 23 functional orthogonal tRNA-cognate aaRS pairs. We discover five orthogonal pairs, including three highly active amber suppressors, and evolve new amino acid substrate specificities for two pairs. Finally, we use tREX to characterize a matrix of 64 orthogonal synthetase-orthogonal tRNA specificities. This work expands the number of orthogonal pairs available for genetic code expansion and provides a pipeline for the discovery of additional orthogonal pairs and a foundation for encoding the cellular synthesis of noncanonical biopolymers.


Subject(s)
Amino Acyl-tRNA Synthetases/metabolism , RNA, Transfer/metabolism , Amino Acid Sequence , Amino Acyl-tRNA Synthetases/genetics , Computer Simulation , Escherichia coli , Gene Expression Regulation, Bacterial , Green Fluorescent Proteins , Protein Binding , Substrate Specificity
7.
Nature ; 569(7757): 514-518, 2019 05.
Article in English | MEDLINE | ID: mdl-31092918

ABSTRACT

Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon-out of up to 6 synonyms-to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme-with simple corrections at just seven positions-to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA.


Subject(s)
Cell Engineering/methods , Escherichia coli/genetics , Genetic Code/genetics , Genome, Bacterial/genetics , Synthetic Biology/methods , Amino Acids/genetics , Codon, Terminator/genetics , Escherichia coli/growth & development , Escherichia coli/metabolism , Genes, Essential/genetics , RNA, Transfer/genetics
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