A new R tool is described that rapidly identifies, ranks, and clusters sequence patterns coordinated to metallocofactors. This tool, PdPDB, fills a void because unlike currently available tools, PdPDB searches through sequences with metal coordination as the primary determinant and can identify patterns consisting of amino acids, nucleotides, and small molecule ligands at once. PdPDB was tested by analyzing structures that coordinate Fe2+/3+, [2Fe-2S], [4Fe-4S], Zn2+, and Mg2+ cofactors. PdPDB confirmed previously identified sequence motifs and revealed which residues are enriched, e.g. glycine, and are underrepresented, e.g. glutamine, near ligands to metal centers. The data reveal the similarities and differences between different metal-binding sites. The patterns that coordinate metallocofactors vary depending upon whether the metal ions play a structural or catalytic role, with catalytic metal centers exhibiting partial coordination by small molecule ligands. PdPDB 2.0 is freely available as a CRAN package.
A gene-directed chemical communication pathway between synthetic protocell signaling transmitters (lipid vesicles) and receivers (proteinosomes) was designed, built and tested using a bottom-up modular approach comprising small molecule transcriptional control, cell-free gene expression, porin-directed efflux, substrate signaling, and enzyme cascade-mediated processing.
Recent work by Bonfio et al. suggests a plausible route toward protein catalysts by exploiting biologically relevant ligands for the formation of model prebiotic iron−sulfur clusters.
Iron-sulfur clusters are ancient cofactors that play a fundamental role in metabolism and may have impacted the prebiotic chemistry that led to life. However, it is unclear whether iron-sulfur clusters could have been synthesized on prebiotic Earth. Dissolved iron on early Earth was predominantly in the reduced ferrous state, but ferrous ions alone cannot form polynuclear iron-sulfur clusters. Similarly, free sulfide may not have been readily available. Here we show that UV light drives the synthesis of [2Fe-2S] and [4Fe-4S] clusters through the photooxidation of ferrous ions and the photolysis of organic thiols. Iron-sulfur clusters coordinate to and are stabilized by a wide range of cysteine containing peptides, and the assembly of iron-sulfur cluster-peptide complexes can take place within model protocells in a process that parallels extant pathways. Our experiments suggest that iron-sulfur clusters may have formed easily on early Earth, facilitating the emergence of an iron-sulfur cluster dependent metabolism.
Artificial cells capable of both sensing and sending chemical messages to bacteria have yet to be built. Here we show that artificial cells that are able to sense and synthesize quorum signaling molecules can chemically communicate with V. fischeri, V. harveyi, E. coli, and P. aeruginosa. Activity was assessed by fluorescence, luminescence, RT-qPCR, and RNA-seq. Two potential applications for this technology were demonstrated. First, the extent to which artificial cells could imitate natural cells was quantified by a type of cellular Turing test. Artificial cells capable of sensing and in response synthesizing and releasing N-3-(oxohexanoyl)homoserine lactone showed a high degree of likeness to natural V. fischeri under specific test conditions. Second, artificial cells that sensed V. fischeri and in response degraded a quorum signaling molecule of P. aeruginosa (N-20(3-oxododecanoyl)homoserine lactone) was constructed, laying the foundation for future technologies that control complex networks of natural cells.
Attempts to build lifelike synthetic protocells must consider extracellular influences in order to accurately reflect the behaviours and characteristics of real ecosystems. Now, this concept has been demonstrated by the synthesis of a community of protocells in which one cell type preys upon another.
Although RNA synthesis can be reliably controlled with different T7 transcriptional promoters during cell-free gene expression with the PURE system, protein synthesis remains largely unaffected. To better control protein levels, a series of ribosome binding sites (RBS) was investigated. While RBS strength did strongly affect protein synthesis, the RBS sequence could explain less than half of the variability of the data. Protein expression was found to depend on other factors besides the strength of the RBS, including GC content. The complexity of protein synthesis in comparison to RNA synthesis was observed by the higher degree of variability associated with protein expression. This variability was also observed in an E. coli cell extract-based system. However, the coefficient of variation was larger with E. coli RNA polymerase than with T7 RNA polymerase, consistent with the increased complexity of E. coli RNA polymerase.
Based on UV-Vis, NMR, and EPR spectroscopies and DFT and molecular dynamics calculations, a model prebiotic [2Fe-2S] tripeptide was shown to accept and donate electrons. Duplications of the tripeptide sequence led to a protoferredoxin with increased stability. Duplications of primitive peptides may have contributed to the formation of contemporary ferredoxins.
Life as we know it is completely dependent on metal ions. Gradients of metal ions drive metabolism, metal centers often form the active sites of enzymes, and metal-ion coordination is largely responsible for protein and RNA folding. This dependence on metal ions likely reflects the environment from which cellular life emerged. However, long chain biological polymers were not present on prebiotic Earth. Therefore, the chemical reactions leading to Earth’s first cells must have made use of alternative catalysts that were later superseded by RNA and protein. Here, we discuss the similarities between free metal ions, minerals, and biological enzyme catalysts, and how cellular life could have exploited prebiotic metallocomplexes.
Intercellular chemical communication is commonly exploited for the engineering of living cells but has been largely ignored by efforts to build artificial cells. Since communication is a fundamental feature of life, the construction of artificial cells capable of chemical communication will likely lead to a deeper understanding of biology and allow for the development of life-like technologies. Herein we highlight recent progress towards the construction of artificial systems that are capable of chemically communicating with natural living cells. Artificial systems that exploit both biological and abiological material for function are discussed.
Model prebiotic dipeptide sequences were identified by bioinformatics and DFT and molecular dynamics calculations. The peptides were then synthesized and evaluated for metal affinity and specificity. Cysteine containing dipeptides were not associated with metal affinities that followed the Irving–Williams series but did follow the concentration trends found in seawater.
The selection of RNA and DNA aptamers now has a long history. However, the ability to directly select for conformational changes upon ligand binding has remained elusive. These difficulties have stymied attempts at making small molecule responsive strand displacement circuitry as well as synthetic riboswitches. Herein we present a detailed strand displacement based selection protocol to directly select for RNA molecules with switching activity. The library was based on a previously selected thiamine pyrophosphate riboswitch. The fully in vitro methodology gave sequences that showed strong strand displacement activity in the presence of thiamine pyrophosphate. Further, the selected sequences possessed riboswitch activity similar to that of natural riboswitches. The presented methodology should aid in the design of more complex, environmentally responsive strand displacement circuitry and in the selection of riboswitches responsive to toxic ligands.
An in vitro selection method for ligand-responsive RNA sensors was developed that exploited strand displacement reactions. The RNA library was based on the thiamine pyrophosphate (TPP) riboswitch, and RNA sequences capable of hybridizing to a target duplex DNA in a TPP regulated manner were identified. After three rounds of selection, RNA molecules that mediated a strand exchange reaction upon TPP binding were enriched. The enriched sequences also showed riboswitch activity. Our results demonstrated that small-molecule-responsive nucleic acid sensors can be selected to control the activity of target nucleic acid circuitry.
Ethylene is a plant hormone widely used to ripen fruit. However, the synthesis, handling, and storage of ethylene are environmentally harmful and dangerous. We engineered E. coli to produce ethylene through the activity of the ethylene-forming enzyme (EFE) from Pseudomonas syringae. EFE converts a citric acid cycle intermediate, 2-oxoglutarate, to ethylene in a single step. The production of ethylene was placed under the control of arabinose and blue light responsive regulatory systems. The resulting bacteria were capable of accelerating the ripening of tomatoes, kiwifruit, and apples.
A laboratory exercise is described that helps students learn about lipid self-assembly by making vesicles under different solution conditions. Concepts covering the chemical properties of different lipids, the dynamics of lipids, and vesicle stability are explored. Further, the described protocol is easy and cheap to implement. One to two laboratory periods of 4 h each are sufficient to perform the experiments.
Previous efforts to control cellular behaviour have largely relied upon various forms of genetic engineering. Once the genetic content of a living cell is modified, the behaviour of that cell typically changes as well. However, other methods of cellular control are possible. All cells sense and respond to their environment. Therefore, artificial, non-living cellular mimics could be engineered to activate or repress already existing natural sensory pathways of living cells through chemical communication. Here we describe the construction of such a system. The artificial cells expand the senses of Escherichia coli by translating a chemical message that E. coli cannot sense on its own to a molecule that activates a natural cellular response. This methodology could open new opportunities in engineering cellular behaviour without exploiting genetically modified organisms.
The construction of genetically encoded cellular mimics in compartments containing organized synthetic cytosols is desirable for the development of artificial cells. Phase separated aqueous domains were placed within water-in-oil emulsion droplets in a manner compatible with transcription and translation machinery. Aqueous two-phase and three-phase systems (ATPS and A3PS) were assembled with dextran, poly(ethylene glycol), and Ficoll. Aqueous two-phase systems were capable of supporting the cell-free expression of protein within water droplets, whereas the aqueous three-phase-based system did not give rise to detectable protein synthesis. The expressed protein preferentially partitioned to the dextran-enriched phase. The system could serve as a foundation for building cellular mimics with liquid organelles.
The cell-free transcription–translation of multiple proteins typically exploits genes placed behind strong transcriptional promoters that reside on separate pieces of DNA so that protein levels can be easily controlled by changing DNA template concentration. However, such systems are not amenable to the construction of artificial cells with a synthetic genome. Herein, we evaluated the activity of a series of T7 transcriptional promoters by monitoring the fluorescence arising from a genetically encoded Spinach aptamer. Subsequently the influences of transcriptional promoter strength on fluorescent protein synthesis from one, two, and three gene operons were assessed. It was found that transcriptional promoter strength was more effective at controlling RNA synthesis than protein synthesis in vitro with the PURE system. Conversely, the gene position within the operon strongly influenced protein synthesis but not RNA synthesis.
We present a simple method to measure the real-time activity of riboswitches with purified components in vitro and inside of artificial cells. Typically, riboswitch activity is measured in vivo by exploiting β-galactosidase encoding constructs with a putative riboswitch sequence in the untranslated region. Additional in vitro characterization often makes use of in-line probing to explore conformational changes induced by ligand binding to the mRNA or analyses of transcript lengths in the presence and absence of ligand. However, riboswitches ultimately control protein levels and often times require accessory factors. Therefore, an in vitro system capable of monitoring protein production with fully defined components that can be supplemented with accessory factors would greatly aid riboswitch studies. Herein we present a system that is amenable to such analyses. Further, since the described system can be easily reconstituted within compartments to build artificial, cellular mimics with sensing capability, protocols are provided for building sense-response systems within water-in-oil emulsion compartments and lipid vesicles. Only standard laboratory equipment and commercially available material are exploited for the described assays, including DNA, purified transcription-translation machinery, i.e., the PURE system, and a spectrofluorometer.
As interest shifts from individual molecules to systems of molecules, an increasing number of laboratories have sought to build from the bottom up cellular mimics that better represent the complexity of cellular life. To date there are a number of paths that could be taken to build compartmentalized cellular mimics, including the exploitation of water-in-oil emulsions, microfluidic devices, and vesicles. Each of the available options has specific advantages and disadvantages. For example, water-in-oil emulsions give high encapsulation efficiency but do not mimic well the permeability barrier of living cells. The primary advantage of the methods described herein is that they are all easy and cheap to implement. Transcription-translation machinery is encapsulated inside of phospholipid vesicles through a process that exploits common instrumentation, such as a centrifugal evaporator and an extruder. Reactions are monitored by fluorescence spectroscopy The protocols can be adapted for recombinant protein expression, the construction of cellular mimics, the exploration of the minimum requirements for cellular life, or the assembly of genetic circuitry.
Several laboratories are pursuing the synthesis of cellular systems from different directions, including those that begin with simple chemicals to those that exploit existing cells. The methods that begin with nonliving components tend to focus on mimicking specific features of life, such as genomic replication, protein synthesis, sensory systems, and compartment formation, growth, and division. Conversely, the more prevalent synthetic biology approaches begin with something that is already alive and seek to impart new behavior on existing cells. Here we discuss advances in building cell-like systems that mimic key features of life with defined components.
To facilitate the construction of cell-free genetic devices, we evaluated the ability of 17 different fluorescent proteins to give easily detectable fluorescence signals in real-time from in vitro transcription-translation reactions with a minimal system consisting of T7 RNA polymerase and E. coli translation machinery, i.e., the PUREsystem. The data were used to construct a ratiometric fluorescence assay to quantify the effect of genetic organization on in vitro expression levels. Synthetic operons with varied spacing and sequence composition between two genes that coded for fluorescent proteins were then assembled. The resulting data indicated which restriction sites and where the restriction sites should be placed in order to build genetic devices in a manner that does not interfere with protein expression. Other simple design rules were identified, such as the spacing and sequence composition influences of regions upstream and downstream of ribosome binding sites and the ability of non-AUG start codons to function in vitro.
Synthetic biologists typically construct new pathways within existing cells. While useful, this approach in many ways ignores the undefined but necessary components of life. A growing number of laboratories have begun to try to remove some of the mysteries of cellular life by building life-like systems from non-living component parts. Some of these attempts rely on purely chemical and physical forces alone without the aid of biological molecules, while others try to build artificial cells from the parts of life, such as nucleic acids, proteins, and lipids. Both bottom-up strategies suffer from the complication of trying to build something that remains undefined. The result has been the development of research programs that try to build systems that mimic in some way recognized living systems. Since it is difficult to quantify the mimicry of life, success often times is evaluated with a degree of subjectivity. Herein we highlight recent advances in mimicking the organization and behavior of cellular life from the bottom-up.
Prebiotic soup experiments have shown that the molecular building blocks of life can be built under prebiotically plausible conditions. From this starting point, researchers have launched continued studies of polymerization and explorations of the breadth of RNA function. Recently, effort has intensified to examine experimentally another stage of the origins of life: the assembly of the molecular parts into model protocells intended to represent the first primitive, cell-like systems to emerge on Earth.
Although it may not be possible to recreate the precise sequence of events that led to cellular life, laboratory experiments have begun to show what was and was not possible. Prebiotically plausible lipid vesicles form easily and have many properties that are conducive to cellular function. In addition to protecting nascent replicating genetic systems from parasitic sequences, vesicles facilitate evolution. The data thus far suggest that prebiotically plausible vesicles could have grown, divided, and promoted competition between distinct chemical systems. Most protocellular studies to date have probed the role of self-replication, one feature of extant life in the emergence of the first cellular system. Undoubtedly replicating systems were crucial for protocellular evolution, but other features of life must have been important as well. For example, life does not exist in isolation. A living system must cope with and adapt to environmental fluctuations to survive. The protocell must have generated some of these fluctuations because cellular activity necessarily modifies its surroundings by selectively absorbing nutrients and releasing unwanted molecules. It seems likely that life would have faced this challenge early and either emerged in dynamic locales that continuously regenerated conditions conducive to life or exploited mechanisms to physically move to new areas not depleted in resources. Further studies that explore non-replication-based aspects of the origins of life could reveal a more complete picture of the transition from prebiotic chemistry to early life.
Synthetic riboswitches can be used to control protein expression under fully defined conditions in vitro, in water-in-oil emulsions, and in vesicles. The developed system could serve as a foundation for the construction of cellular mimics that respond to molecules of our choosing.
Schizosaccharomyces pombe (Sp) ferredoxin contains a C-terminal electron transfer protein ferredoxin domain (etpFd) that is homologous to adrenodoxin. The ferredoxin has been characterized by spectroelectrochemical methods, and Mössbauer, UV–Vis and circular dichroism spectroscopies. The Mössbauer spectrum is consistent with a standard diferric [2Fe–2S]2+ cluster. While showing sequence homology to vertebrate ferredoxins, the E°’ and the reduction thermodynamics for etpFd (− 0.392 V) are similar to plant-type ferredoxins. Relatively stable Cys to Ser derivatives were made for each of the four bound Cys residues and variations in the visible spectrum in the 380–450 nm range were observed that are characteristic of oxygen ligated clusters, including members of the [2Fe–2S] cluster IscU/ISU scaffold proteins. Circular dichroism spectra were similar and consistent with no significant structural change accompanying these mutations. All derivatives were active in an NADPH-Fd reductase cytochrome c assay. The binding affinity of Fd to the reductase was similar, however, Vmax reflecting rate limiting electron transfer was found to decrease ~ 13-fold. The data are consistent with relatively minor perturbations of both the electronic properties of the cluster following substitution of the Fe-bond S atom with O, and the electronic coupling of the cluster to the protein.
Bacterial and viral DNA replication was previously reconstituted in vitro from component parts [1-4]. Significant advances in building minimal cell-like structures also have been made recently [5-7]. Combining the two approaches would further attempts to build a minimal cell-like structure capable of undergoing evolution by combining membrane encapsulation and genome replication. Towards this end, we attempted to use purified genomic replication protein components from thermophilic bacterial sources to copy strands of DNA isothermally within lipid vesicles.
Bacterial replication components (such as helicases and DNA polymerases) are compatible with methods for the generation of lipid vesicles. Encapsulation inside phospholipid vesicles does not inhibit the activity of bacterial DNA genome replication machinery. Further the described system is efficient at isothermally amplifying short segments of DNA within phospholipid vesicles.
Herein we show that bacterial isothermal DNA replication machinery is functional inside of phospholipid vesicles, suggesting that replicating cellular mimics can be built from purified bacterial components.
Although model protocellular membranes consisting of monoacyl lipids are similar to membranes composed of contemporary diacyl lipids, they differ in at least one important aspect. Model protocellular membranes allow for the passage of polar solutes and thus can potentially support cell-to functions without the aid of transport machinery. The ability to transport polar molecules likely stems from increased lipid dynamics. Selectively permeable vesicle membranes composed of monoacyl lipids allow for many lifelike processes to emerge from a remarkably small set of molecules.
The reaction thermodynamics for the one-electron reduction of the [2Fe–2S] cluster of both human ferredoxin and various surface point mutants, in which each of the negatively charged residues Asp72, Glu73, Asp76, and Asp79 were converted to Ala, have been determined by variable temperature spectroelectrochemical measurements. The above are conserved residues that have been implicated in interactions between the vertebrate-type ferredoxins and their redox partners. In all cases, and similar to other 2Fe-ferredoxins, the reduction potentials are negative as a result of both an enthalpic and entropic stabilization of the oxidized state. Although all Hs Fd mutants, with the exception of Asp72Ala, show slightly higher E°′ values than that of wild type Hs Fd, according to expectations for a purely electrostatic model, they exhibit changes in the ∆H°′rc values that are electrostatically counter-intuitive. The observation of enthalpy–entropy compensation within the protein series indicates that the mutation-induced changes in ∆H°′rc and ∆S°′rc are dominated by reduction-induced solvent reorganization effects. Protein-based entropic effects are likely to be responsible for the low E°′ value of D72A
The complexity of modern biological life has long made it difficult to understand how life could emerge spontaneously from the chemistry of the early earth. The key to resolving this mystery lies in the simplicity of the earliest living cells, together with the ability of the appropriate molecular building blocks to spontaneously self-assemble into larger structures. In our view, the two key components of a primitive cell are not only self-assembling, but also self-replicating, structures: the nucleic acid genome and the cell membrane. Here, we summarize recent experimental progress toward the synthesis of efficient self-replicating nucleic acid and membrane vesicle systems and discuss some of the issues that arise during efforts to integrate these two subsystems into a coherent whole. We have shown that spontaneous nucleic-acid-copying chemistry can take place within membrane vesicles, using externally supplied activated nucleotides as substrates. Thus, membranes need not be a barrier to the uptake of environmentally supplied nutrients. We examine some of the remaining obstacles that must be overcome to enable the synthesis of a complete self-replicating protocell, and we discuss the implications of these experiments for our understanding of the emergence of Darwinian evolution and the origin and early evolution of cellular life.
Cellular and organellar membranes are dynamic materials that underlie many aspects of cell biology. Biological membranes have long been thought of as elastic materials with respect to bending deformations. A wealth of theory and experimentation on pure phospholipid membranes provides abundant support for this idea. However, biological membranes are not composed solely of phospholipids—they also incorporate a variety of amphiphilic molecules that undergo rapid transbilayer flip-flop. Here we describe several experimental systems that demonstrate deformation-induced molecular flip-flop. First we use a fluorescence assay to track osmotically controlled membrane deformation in single component fatty acid vesicles, and show that the relaxation of the induced bending stress is mediated by fatty acid flip-flop. We then look at two-component phospholipid/cholesterol composite vesicles. We use NMR to show that the steady-state rate of interleaflet diffusion of cholesterol is fast relative to biological membrane remodeling. We then use a Förster resonance energy transfer assay to detect the transbilayer movement of cholesterol upon deformation. We suggest that our results can be interpreted by modifying the area difference elasticity model to account for the time-dependent relaxation of bending energy. Our findings suggest that rapid interleaflet diffusion of cholesterol may play a role in membrane remodeling in vivo. We suggest that the molecular characteristics of sterols make them evolutionarily preferred mediators of stress relaxation, and that the universal presence of sterols in the membranes of eukaryotes, even at low concentrations, reflects the importance of membrane remodeling in eukaryotic cells
Significant progress has been made in the construction of laboratory models of protocells. Most frequently the developed vesicle systems utilize single-chain lipids rather than the double-chain lipids typically found in biological membranes. Although single-chain lipids yield less robust vesicles, their dynamic characteristics are highly exploitable for protocellular functions. Herein the advantages of using single-chain lipids in the construction of protocells are discussed.
The earliest cells may have consisted of a self-replicating genetic polymer encapsulated within a self-replicating membrane vesicle. Here, we show that vesicles composed of simple single-chain amphiphiles such as fatty acids, fatty alcohols, and fatty-acid glycerol esters are extremely thermostable and retain internal RNA and DNA oligonucleotides at temperatures ranging from 0°C to 100°C. The strands of encapsulated double-stranded DNA can be separated by denaturation at high temperature while being retained within vesicles, implying that strand separation in primitive protocells could have been mediated by thermal fluctuations without the loss of genetic material from the protocell. At elevated temperatures, complex charged molecules such as nucleotides cross fatty-acid-based membranes very rapidly, suggesting that high temperature excursions may have facilitated nutrient uptake before the evolution of advanced membrane transporters. The thermostability of these membranes is consistent with the spontaneous replication of encapsulated nucleic acids by the alternation of template-copying chemistry at low temperature with strand-separation and nutrient uptake at high temperature.
Contemporary phospholipid-based cell membranes are formidable barriers to the uptake of polar and charged molecules ranging from metal ions to complex nutrients. Modern cells therefore require sophisticated protein channels and pumps to mediate the exchange of molecules with their environment. The strong barrier function of membranes has made it difficult to understand the origin of cellular life and has been thought to preclude a heterotrophic lifestyle for primitive cells. Although nucleotides can cross dimyristoyl phosphatidylcholine membranes through defects formed at the gel-to-liquid transition temperature, phospholipid membranes lack the dynamic properties required for membrane growth. Fatty acids and their corresponding alcohols and glycerol monoesters are attractive candidates for the components of protocell membranes because they are simple amphiphiles that form bilayer membrane vesicles that retain encapsulated oligonucleotides and are capable of growth and division. Here we show that such membranes allow the passage of charged molecules such as nucleotides, so that activated nucleotides added to the outside of a model protocell spontaneously cross the membrane and take part in efficient template copying in the protocell interior. The permeability properties of prebiotically plausible membranes suggest that primitive protocells could have acquired complex nutrients from their environment in the absence of any macromolecular transport machinery; that is, they could have been obligate heterotrophs.
We present a structural and functional analysis of the evolutionary optimization of a non-biological protein derived from a library of random amino acid sequences. A series of previously described in vitro selection experiments transformed a low-affinity ancestral sequence into a stably folded, high affinity ATP binding protein structure. While the evolutionarily optimized protein differs from its ancestral sequence through the accumulation of 12 amino acid mutations, the means by which those mutations enhance the stability and functionality of the protein were not well understood. We used a combination of mutagenesis, biochemistry, and NMR spectroscopy to investigate the structural and functional significance of each mutation. We solved the three-dimensional structure of the folding optimized protein by solution NMR, which revealed a fourth strand of the β-sheet of the α/β-fold that was not observed in an earlier crystallographic analysis of a less stable version of the protein. The structural rigidity of the newly identified β-strand was confirmed by T1, T2, and heteronuclear nuclear Overhauser enhancement (NOE) measurements. Biochemical experiments were used to examine point mutations that revert the optimized protein back to the ancestral residue at each of the 12 sites. A combination of structural and functional data was then used to interpret the significance of each amino acid mutation. The enhanced ATP affinity was largely due to the emergence of a patch of positive charge density on the protein surface, while the increased solubility resulted from several mutations that increased the hydrophilicity of the protein surface, thereby decreasing protein aggregation. One mutation may stabilize the hydrophobic face of the β-sheet.
The transition from non-living to living matter may have resulted from the self-organizing properties of organic molecules and their interactions with a chemically rich inorganic environment. We have shown that a solution containing RNA, fatty acids and clay produces structures that contain a potentially catalytic surface (clay) and a potential informational biopolymer (RNA) encapsulated within a membrane. This highlights the ability of mineral surfaces to bring together and organize key components of primordial life. We have extended our analysis of mineral-mediated vesicle catalysis to include other natural minerals and synthetic surfaces of varying shape, size, and charge density. Our results show that while RNA polymerization on minerals may be restricted to the surface environment provided by montmorillonite, vesicle formation is enhanced in the presence of disparate types of surfaces. A model is presented in which new sheets of amphiphiles form just proximal to a surface. Similar interactions between amphiphiles and minerals on early Earth may have resulted in the encapsulation of a diverse array of mineral particulates with catalytic properties.
IscU functions as a scaffold for Fe-S cluster assembly and transfer, and is known to be a substrate protein for molecular chaperones. Kinetic studies of Fe-S cluster transfer from holo IscU to apo Fd in the presence of chaperone DnaK demonstrate an inhibitory effect on the rate of Fe-S cluster transfer from IscU. Binding of DnaK reduces the rate of formation of the IscU−Fd complex (greater than 8-fold), but has little influence on the intrinsic rate of iron−sulfur cluster transfer to apo Fd. Apparently the molecular chaperone DnaK does not facilitate the process of Fe-S cluster transfer from IscU. Rather, DnaK has a modest influence on the stability of the IscU-bound Fe-S cluster that may reflect a more important role in promoting cluster assembly. In accord with prior observations the cochaperone DnaJ stimulates the ATPase activity of DnaK, but has a minimal influence on IscU cluster transfer activity, either alone or in concert with DnaK.
Iron−sulfur clusters are among the most complex metal-containing prosthetic centers in biology. Most if not all of the proteins involved in the biosynthesis of “simple” Fe−S clusters have been identified. The structural and functional chemistry of these proteins has been the subject of intense research efforts, and many of the key details are now understood in structural and mechanistic detail. The fact that Fe−S cluster-binding proteins can be reconstituted in vitro with no accessory proteins provides an important indicator of the intracellular roles for many proteins on the Fe−S cluster assembly pathway. Indeed, such proteins are more correctly viewed as carrier proteins, rather than as catalysts for the reaction, that both avoid the toxicity associated with free iron and sulfide and allow delivery at lower intracellular concentrations of these species. The IscU (or ISU) family of proteins serves a key role as scaffolding proteins on which [2Fe−2S] building blocks are assembled prior to transfer to final apo target proteins. IscU in particular exhibits highly unusual conformational flexibility that appears critical to its function.
Important for the understanding of the functional properties of the iron-sulfur scaffold IscU is knowledge of the structure and dynamics of this protein class. Structural characterization of Thermotoga maritima IscU by CD (Mansy, S. S., Wu, G., Surerus, K. K., and Cowan, J. A. (2002) J. Biol. Chem. 277, 21397–21404) and high resolution NMR (Bertini, I., Cowan, J. A., Del Bianco, C., Luchinat, C., and Mansy, S. S. (2003) J. Mol. Biol. 331, 907–924) yielded data indicating a high degree of secondary structure. However, the latter also revealed IscU to exist in a dynamic equilibrium between two or more distinct conformations, possibly existing in a molten globule state. Herein, we further characterize the molten globule characteristics of T. maritima IscU by near-ultraviolet circular dichroism, 1-anilino-8-naphthalenesulfonic acid binding, free energy of unfolding, hydrodynamic radius measurements, and limited tryptic digestion. The data suggest unusual dynamic behavior that is not fully consistent with typical protein states such as fully folded, fully unfolded, or molten globule. For instance, the existence of a stable tertiary fold is supported by near-UV CD spectra and hydrodynamic radius measurements, whereas other data are less clearly interpretable and may be viewed as consistent with either a molten globule or fully folded state. However, all of the data are consistent with our previous hypothesis of a protein sampling multiple discrete tertiary conformations in which these structural transitions occur on a “slow” time scale. To describe such proteins, we introduce the term multiple discrete conformers.
The kinetics of electron transfer from reduced high-potential iron-sulfur protein (HiPIP) to the photooxidized tetraheme cytochrome c subunit (THC) bound to the photosynthetic reaction center (RC) from the purple sulfur bacterium Allochromatium vinosum were studied under controlled redox conditions by flash absorption spectroscopy. At ambient redox potential Eh = +200 mV, where only the high-potential (HP) hemes of the THC are reduced, the electron transfer from HiPIP to photooxidized HP heme(s) follows second-order kinetics with rate constant k = (4.2 +/- 0.2) 10(5) M(-1) s(-1) at low ionic strength. Upon increasing the ionic strength, k increases by a maximum factor of ca. 2 at 640 mM KCl. The role of Phe48, which lies on the external surface of HiPIP close to the [Fe4S4] cluster and presumably on the electron transfer pathway to cytochrome heme(s), was investigated by site-directed mutagenesis. Substitution of Phe48 with arginine, aspartate, and histidine completely prevents electron donation. Conversely, electron transfer is still observed upon substitution of Phe48 with tyrosine and tryptophan, although the rate is decreased by more than 1 order of magnitude. These results suggest that Phe48 is located on a key protein surface patch essential for efficient electron transfer, and that the presence of an aromatic hydrophobic residue on the putative electron-transfer pathway plays a critical role. This conclusion was supported by protein docking calculations, resulting in a structural model for the HiPIP-THC complex, which involves a docking site close to the LP heme farthest from the bacteriochlorophyll special pair.
Members of the IscU family of proteins are among the most conserved of all protein groups, extending across all three kingdoms of life. IscU serves as a scaffold for the assembly of intermediate iron–sulfur cluster centers and further mediates delivery to apo protein targets. Several proteins that mediate delivery of single metal ions to apo targets (termed metallochaperones) have recently been characterized structurally. Each displays a ferredoxin-like βαββαβ motif as a structural core. Assembly and delivery of a polynuclear iron–sulfur cluster is, however, a more complex pathway and presumably would demand a distinctive protein mediator. Here, we demonstrate Thermotoga maritima IscU (Tm IscU) to display unique structural and motional characteristics that distinguish it from other members of this class of proteins. In particular, IscU adopts a mobile, physiologically relevant, molten globule-like state that is vastly different from the previously identified ferredoxin-like fold that has thus far been characterized for other metallochaperones. The secondary structural content of Tm IscU is consistent with previous circular dichroism measurements on apo and holo protein, consisting of six α-helices and three β-strands, the latter forming an anti-parallel β-sheet. Extensive dynamics studies are consistent with a protein that has reasonably well defined secondary structural elements, but with a tertiary structure that is fluxional among widely different conformational arrangements. Analogous conformational flexibility does not exist in other structurally characterized metallochaperones; however, such a dynamic molecule may account for the lack of long-range NOEs, and allow both for the flexibility that is necessary for the multiple roles of Fe–S cluster assembly, and recognition and delivery of that cluster to a target protein. Additionally, the fluxionality of IscU is unique in that the protein appears to be more compact (based on 1H/2H exchange, R1, R2, and NOE data) but yet more fluid (lack of long-range NOEs) than typical molten globule proteins.
Genetic evidence has indicated that Isc proteins play an important role in iron-sulfur cluster biogenesis. In particular, IscU is believed to serve as a scaffold for the assembly of a nascent iron-sulfur cluster that is subsequently delivered to target iron-sulfur apoproteins. We report the characterization of an IscU fromThermatoga maritima, an evolutionarily ancient hyperthermophilic bacterium. The stabilizing influence of a D40A substitution allowed characterization of the holoprotein. Mössbauer (δ = 0.29 ± 0.03 mm/s, ΔEQ = 0.58 ± 0.03 mm/s), UV-visible absorption, and circular dichroism studies of the D40A protein show that T. maritima IscU coordinates a [2Fe-2S]2+ cluster. Thermal denaturation experiments demonstrate that T. maritima IscU is a thermally stable protein with a thermally unstable cluster. This is also the first IscU type domain that is demonstrated to possess a high degree of secondary and tertiary structure. CD spectra indicate 36.7% α-helix, 13.1% antiparallel β-sheet, 11.3% parallel β-sheet, 20.2% β-turn, and 19.1% other at 20 °C, with negligible spectral change observed at 70 °C. Cluster coordination also has no effect on the secondary structure of the protein. The dispersion of signals in1H-15N heteronuclear single quantum correlation NMR spectra of wild type and D40A IscU supports the presence of significant tertiary structure for the apoprotein, consistent with a scaffolding role, and is in marked contrast to other low molecular weight Fe-S proteins where cofactor coordination is found to be necessary for proper protein folding. Consistent with the observed sequence homology and proposed conservation of function for IscU-type proteins, we demonstrate T. maritimaIscU-mediated reconstitution of human apoferredoxin.
Eukaryotic Isa1 is one of several mitochondrial proteins that have been implicated in Fe-S cluster assembly paths in vivo. We report the first biochemical characterization of an eukaryotic member of this family and discuss this in the context of results from in vivo studies and studies of bacterial homologues. Schizosaccharomyces pombe Isa1 is a multimeric protein carrying [2Fe-2S]2+ clusters that have been characterized by Mössbauer and optical spectroscopic studies. Complex formation with a redox-active ferredoxin has been identified through crosslinking experiments and the coordination chemistry and stability of the native clusters has been investigated through site-directed mutagenesis and spectroscopic analysis. Electronic supplementary material to this paper, containing Mössbauer and UV-visible spectra for mutant Isa1 proteins, can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0330-2.
Genetic studies of bacteria and eukaryotes have led to identification of several gene products that are involved in the biosynthesis of protein-bound iron−sulfur clusters. One of these proteins, ISU, is homologous to the N-terminus of bacterial NifU. The mature forms of His-tagged wild-type and D37A Schizosaccharomyces pombe ISU1 were cloned and overexpressed as inclusion bodies in Escherichia coli. The recombinant D37A protein was purified under denaturing conditions and subsequently reconstituted in vitro. By use of a 5-fold excess of iron and sulfide the reconstituted product was found to be red-brown in color, forming a homodimer of 17 kDa per subunit with approximately two iron atoms per monomer determined by protein and iron quantitation. UV−vis absorption and Mössbauer spectroscopies (δ = 0.29 ± 0.05 mm/s; ΔEQ = 0.59 ± 0.05 mm/s) were used to characterize D37A ISU1 and show the presence of [2Fe-2S]2+ clusters in each subunit. Formation of the holo form of wild-type ISU1 was significantly less efficient using the same reconstitution conditions and is consistent with prior observations that the D37A substitution can stabilize protein-bound clusters. Relative to the human homologue, the yeast ISU is significantly less soluble at ambient temperatures. In both cases the native ISU1 is more sensitive to proton-mediated degradation relative to the D37A derivative. The lability of this family of proteins relative to [2Fe-2S] bearing ferredoxins most likely is of functional relevance for cluster transfer chemistry. Mössbauer parameters obtained for wild-type ISU1 (δ = 0.31 ± 0.05 mm/s; ΔEQ = 0.64 ± 0.05 mm/s) were similar to those obtained for the D37A derivative. Cluster transfer from ISU1 to apo Fd is demonstrated: the first example of transfer from an ISU-type protein. A lower limit for k2 of 80 M-1 min-1 was established for WT cluster transfer and a value of 18 M-1 min-1 for the D37A derivative. Finally, we have demonstrated through cross-linking studies that ferredoxin, an electron-transport protein, forms a complex with ISU1 in both apo and holo states. Cross-linking of holo ISU1 with holo Fd is consistent with a role for redox chemistry in cluster assembly and may mimic the intramolecular complex already defined in NifU.
The crystal structure of Chromatium vinosum C77S HiPIP has been determined and is compared with that of wild type. This is the first reported crystal structure of a Ser ligated [4Fe-4S] cluster and reveals a 0.11 Å shortening of the Fe−O bond (relative to Fe−S), but only minor structural alterations of the overall tertiary structure. Coordination changes are corroborated by resonance Raman spectroscopy. Comparison of the crystal and solution structures for HiPIPs identifies Phe48 as the main controller of solvent access to the Fe−S cluster; however, there is no significant change in cluster solvation of the C77S mutant relative to WT HiPIP. Ser ligation ultimately results in decreased cluster stability due to increased sensitivity to proton mediated degradation.
The FixL proteins are biological oxygen sensors that restrict the expression of specific genes to hypoxic conditions. FixL’s oxygen-detecting domain is a heme binding region that controls the activity of an attached histidine kinase. The FixL switch is regulated by binding of oxygen and other strong-field ligands. In the absence of bound ligand, the heme domain permits kinase activity. In the presence of bound ligand, this domain turns off kinase activity. Comparison of the structures of two forms of the Bradyrhizobium japonicum FixL heme domain, one in the “on” state without bound ligand and one in the “off” state with bound cyanide, reveals a mechanism of regulation by a heme that is distinct from the classical hemoglobin models. The close structural resemblance of the FixL heme domain to the photoactive yellow protein confirms the existence of a PAS structural motif but reveals the presence of an alternative regulatory gateway.
The FixL heme-based sensor, despite its low affinity for oxygen, is much more reactive than myoglobin toward the large polar ligand imidazole. To determine which features of a myoglobin heme pocket favor binding of imidazole, we have measured binding of this ligand to the FixL heme domain, elephant myoglobin, wild-type sperm whale myoglobin, and sperm whale myoglobins having alanine, valine, threonine, glutamine, leucine, phenylalanine, or tryptophan substitutions of the distal (E7) histidine residue. Except for histidine, the association rate constants dropped more than 3000-fold as the volume of the E7 side chain, at position 64, was expanded from alanine (10(6) M-1 s-1) to phenylalanine (10(3) M-1 s-1). There was inhibition of imidazole binding due to displacement of coordinated water from H64 and H64Q sperm whale myoglobins, where the E7 side chain hydrogen bonds directly to the bound ligand. The imidazole dissociation rate constants varied less dramatically and less consistently with any single factor, though they were measurably decreased by hydrogen bonding to an E7 glutamine or histidine. On the whole, the results for the sperm whale myoglobin E7 substitutions show that the rate constants for imidazole binding are useful and sensitive indicators of steric hindrance and polar interactions in the distal pockets of myoglobins. The combined effects of the glutamine 64 and phenylalanine 29 in elephant myoglobin largely account for its increased imidazole association and dissociation rate constants, respectively, compared to those of sperm whale myoglobin. An unhindered distal pocket not competent to stabilize positive poles is indicated by the large imidazole association (>/=10(4) M-1 s-1) and dissociation (>/=50 s-1) rate constants, parameters that are characteristic of FixL.