In Vitro Protein Synthesis in Semipermeable Artificial Cells

Improved spectral resolution of [13C,1H]-HSQC spectra of aromatic amino acid residues in proteins produced by cell-free synthesis from inexpensive 13C-labelled precursors

Cell-free protein synthesis using eCells allows production of amino acids from inexpensive 13C-labelled precursors. We show that the metabolic pathway converting pyruvate, glucose and erythrose into aromatic amino acids is maintained in eCells. Judicious choice of 13C-labelled starting material leads to proteins, where the sidechains of aromatic amino acids display [13C,1H]-HSQC cross-peaks free of one-bond 13C-13C couplings. Selective 13C-labelling of tyrosine and phenylalanine residues is achieved simply by using different compositions of the reaction buffers.

Cell-free synthesis of proteins with selectively 13C-labelled methyl groups from inexpensive precursors

The novel eCell system maintains the activity of the entire repertoire of metabolic Escherichia coli enzymes in cell-free protein synthesis. We show that this can be harnessed to produce proteins with selectively 13 C-labelled amino acids from inexpensive 13 C-labelled precursors. The system is demonstrated with selective 13 C labelling of methyl groups in the proteins ubiquitin and peptidyl-prolyl cis-trans isomerase B. Starting from 3-13 C-pyruvate, 13 C-HSQC cross-peaks are obtained devoid of one-bond 13 C-13 C scalar couplings. Starting from 2-13 C-methyl-acetolactate, single methyl groups of valine and leucine are labelled. Labelling efficiencies are 70 % or higher, and the method allows us to produce perdeuterated proteins with protonated methyl groups in a residue-selective manner. The system uses the isotope-labelled precursors sparingly and is readily scalable.

Biological evolution requires an emergent, self-organizing principle

In this perspective review, we assess fundamental flaws in Darwinian evolution, including its modern versions. Fixed mutations 'explain' microevolution but not macroevolution including speciation events and the origination of all the major body plans of the Cambrian explosion. Complex, multifactorial change is required for speciation events and inevitably requires self-organization beyond what is accomplished by known mechanisms. The assembly of ribosomes and ATP synthase are specific examples. We propose their origin is a model for what is unexplained in biological evolution. Probability of evolution is modeled in Section 9 and values are absurdly improbable. Speciation and higher taxonomic changes become exponentially less probable as the number of required, genetically-based events increase. Also, the power required of the proposed selection mechanism (survival of the fittest) is nil for any biological advance requiring multiple changes, because they regularly occur in multiple generations (different genomes) and would not be selectively conserved by the concept survival of the fittest (a concept ultimately centered on the individual). Thus, survival of the fittest cannot 'explain' the origin of the millions of current and extinct species. We also focus on the inadequacies of laboratory chemistry to explain the complex, required biological self-organization seen in cells. We propose that a 'bioelectromagnetic' field/principle emerges in living cells. Synthesis by self-organization of massive molecular complexes involves biochemical responses to this emergent field/principle. There are ramifications for philosophy, science, and religion. Physics and mathematics must be more strongly integrated with biology and integration should receive dedicated funding with special emphasis for medical applications; treatment of cancer and genetic diseases are examples.

Update of the Pyrrolysyl-tRNA Synthetase/tRNAPyl Pair and Derivatives for Genetic Code Expansion

The cotranslational incorporation of pyrrolysine (Pyl), the 22nd proteinogenic amino acid, into proteins in response to the UAG stop codon represents an outstanding example of natural genetic code expansion. Genetic encoding of Pyl is conducted by the pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA, tRNA^Pyl. Owing to the high tolerance of PylRS toward diverse amino acid substrates and great orthogonality in various model organisms, the PylRS/tRNA^Pyl-derived pairs are ideal for genetic code expansion to insert noncanonical amino acids (ncAAs) into proteins of interest. Since the discovery of cellular components involved in the biosynthesis and genetic encoding of Pyl, synthetic biologists have been enthusiastic about engineering PylRS/tRNA^Pyl-derived pairs to rewrite the genetic code of living cells. Recently, considerable progress has been made in understanding the molecular phylogeny, biochemical properties, and structural features of the PylRS/tRNA^Pyl pair, guiding its further engineering and optimization. In this review, we cover the basic and updated knowledge of the PylRS/tRNA^Pyl pair's unique characteristics that make it an outstanding tool for reprogramming the genetic code. In addition, we summarize the recent efforts to create efficient and (mutually) orthogonal PylRS/tRNA^Pyl-derived pairs for incorporation of diverse ncAAs by genome mining, rational design, and advanced directed evolution methods.

Investigation of Genome Biology by Synthetic Genome Engineering

Synthetic genomes were designed based on an understanding of natural genomic information, offering an opportunity to engineer and investigate biological systems on a genome-wide scale. Currently, the designer version of the M. mycoides genome and the E. coli genome, as well as most of the S. cerevisiae genome, have been synthesized, and through the cycles of design-build-test and the following engineering of synthetic genomes, many fundamental questions of genome biology have been investigated. In this review, we summarize the use of synthetic genome engineering to explore the structure and function of genomes, and highlight the unique values of synthetic genomics.

Artificial cell design: reconstructing biology for life science applications

Artificial cells are developed to redesign novel biological functions in a programmable and tunable manner. Although it aims to reconstitute living cell features and address 'origin of life' related questions, rapid development over the years has transformed artificial cells into an engineering tool with huge potential in applied biotechnology. Although the application of artificial cells was introduced decades ago as drug carriers, applications in other sectors are relatively new and could become possible with the technological advancement that can modulate its designing principles. Artificial cells are non-living system that includes no prerequisite designing modules for their formation and therefore allow freedom of assembling desired biological machinery within a physical boundary devoid of complex contemporary living-cell counterparts. As stimuli-responsive biomimetic tools, artificial cells are programmed to sense the surrounding, recognise their target, activate its function and perform the defined task. With the advantage of their customised design, artificial cells are being studied in biosensing, drug delivery, anti-cancer therapeutics or artificial photosynthesis type fields. This mini-review highlights those advanced fields where artificial cells with a minimalistic setup are developed as user-defined custom-made microreactors, targeting to reshape our future 'life'.