292 results on '"Dan S. Tawfik"'
Search Results
2. The development of human sera tests for HDL-bound serum PON1 and its lipolactonase activitys⃞
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Leonid Gaidukov and Dan S. Tawfik
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blood tests ,lactones ,lipoproteins ,high density lipoprotein-bound enzymes ,enzyme stability ,atherosclerosis ,Biochemistry ,QD415-436 - Abstract
Serum paraoxonase (PON1) is a lipolactonase that associates with HDL-apolipoprotein A-I (HDL-apoA-I) and thereby plays a role in the prevention of atherosclerosis. Current sera tests make use of promiscuous substrates and provide no indications regarding HDL-PON1 complex formation. We developed new enzymatic tests that detect total PON1 levels, irrespective of HDL status and R/Q polymorphism, as well as the degree of catalytic stimulation and increased stability that follow PON1's tight binding to HDL-apoA-I. The tests are based on measuring total PON1 levels with a fluorogenic phosphotriester, measuring the lipolactonase activity with a chromogenic lactone, and assaying the enzyme's chelator-mediated inactivation rate. The latter two are affected by tight HDL binding and thereby derive the levels of the serum PON1-HDL complex. We demonstrate these new tests with a group of healthy individuals (n = 54) and show that the levels of PON1-HDL vary by a factor of 12. Whereas the traditionally applied paraoxonase and arylesterase tests weakly reflect PON1-HDL levels (R = 0.64), the lipolactonase test provides better correlation (R = 0.80). These new tests indicate the levels and activity of PON1 in a physiologically relevant context as well as the levels and quality of the HDL particles with which the enzyme is associated.
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- 2007
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3. The 192R/Q polymorphs of serum paraoxonase PON1 differ in HDL binding, lipolactonase stimulation, and cholesterol effluxs⃞
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Leonid Gaidukov, Mira Rosenblat, Michael Aviram, and Dan S. Tawfik
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paraoxonase isozymes ,polymorphism ,atherosclerosis ,lactones ,sera tests ,lipoproteins ,Biochemistry ,QD415-436 - Abstract
Serum paraoxonase (PON1) is a HDL-associated enzyme exhibiting potentially antiatherogenic properties. Here, we examined the common PON1-192R/Q human polymorphism. Despite numerous studies, the effect of this polymorphism on the antiatherogenic potential of PON1 is yet unresolved. Our structural model suggests that amino acid 192 constitutes part of the HDL-anchoring surface and active site of PON1. Based on our findings that PON1 is an interfacially activated lipolactonase that selectively binds HDL carrying apolipoprotein A-I (apoA-I) and is thereby greatly stabilized and catalytically activated, we examined the interaction of the PON1-192 isozymes with reconstituted HDL-apoA-I particles. We found that PON1 position 192 is indeed involved in HDL binding. The PON1-192Q binds HDL with a 3-fold lower affinity than the R isozyme and consequently exhibits significantly reduced stability, lipolactonase activity, and macrophage cholesterol efflux. We also observed the lower affinity and stability of the 192Q versus the 192R isozyme in sera of individuals belonging to the corresponding genotypes. The observed differences in the properties of PON1-192R/Q isozymes provide a basis for further analysis of the contribution of the 192R/Q polymorphism to the susceptibility to atherosclerosis, although other factors, such as the overall levels of PON1, may play a more significant role.
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- 2006
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4. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance
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Kaitlyn Tsai, Vanja Stojković, Lianet Noda-Garcia, Iris D Young, Alexander G Myasnikov, Jordan Kleinman, Ali Palla, Stephen N Floor, Adam Frost, James S Fraser, Dan S Tawfik, and Danica Galonić Fujimori
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Cfr ,directed evolution ,antibiotic resistance ,RNA modifications ,peptidyl transferase center ,cryoEM ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition of cfr results in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant that achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-electron microscopy structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr.
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- 2022
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5. Determining the interaction status and evolutionary fate of duplicated homomeric proteins.
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Saurav Mallik and Dan S. Tawfik
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- 2020
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6. On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment
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Liam M Longo, Jagoda Jabłońska, Pratik Vyas, Manil Kanade, Rachel Kolodny, Nir Ben-Tal, and Dan S Tawfik
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protein evolution ,enzyme evolution ,last universal common ancestor ,ancient peptide ,P-loop ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
This article is dedicated to the memory of Michael G. Rossmann. Dating back to the last universal common ancestor, P-loop NTPases and Rossmanns comprise the most ubiquitous and diverse enzyme lineages. Despite similarities in their overall architecture and phosphate binding motif, a lack of sequence identity and some fundamental structural differences currently designates them as independent emergences. We systematically searched for structure and sequence elements shared by both lineages. We detected homologous segments that span the first βαβ motif of both lineages, including the phosphate binding loop and a conserved aspartate at the tip of β2. The latter ligates the catalytic metal in P-loop NTPases, while in Rossmanns it binds the nucleotide’s ribose moiety. Tubulin, a Rossmann GTPase, demonstrates the potential of the β2-Asp to take either one of these two roles. While convergence cannot be completely ruled out, we show that both lineages likely emerged from a common βαβ segment that comprises the core of these enzyme families to this very day.
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- 2020
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7. On the Origins of Enzymes: Phosphate-Binding Polypeptides Mediate Phosphoryl Transfer to Synthesize Adenosine Triphosphate
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Pratik Vyas, Sergey Malitsky, Maxim Itkin, and Dan S. Tawfik
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Colloid and Surface Chemistry ,General Chemistry ,Biochemistry ,Catalysis - Published
- 2023
8. Local fitness landscape of the green fluorescent protein.
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Karen S. Sarkisyan, Dmitry Bolotin, Margarita V. Meer, Dinara R. Usmanova, Alexander S. Mishin, George V. Sharonov, Dmitry N. Ivankov, Nina G. Bozhanova, Mikhail S. Baranov, Onuralp Soylemez, Natalya S. Bogatyreva, Peter K. Vlasov, Evgeny S. Egorov, Maria D. Logacheva, Alexey S. Kondrashov, Dmitry M. Chudakov, Ekaterina V. Putintseva, Ilgar Z. Mamedov, Dan S. Tawfik, Konstantin A. Lukyanov, and Fyodor A. Kondrashov
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- 2016
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9. Dimethyl sulfide mediates microbial predator–prey interactions between zooplankton and algae in the ocean
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Daniella Schatz, Ron Rotkopf, Flora Vincent, Adva Shemi, Viviana Farstey, Assaf Vardi, Shifra Ben-Dor, Uria Alcolombri, Dan S. Tawfik, and Miguel J. Frada
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Microbiology (medical) ,biology ,Ecology ,fungi ,Immunology ,Thalassiosira pseudonana ,Cell Biology ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Microbiology ,Zooplankton ,Oxyrrhis marina ,chemistry.chemical_compound ,Diatom ,chemistry ,Algae ,Phytoplankton ,Genetics ,Dimethyl sulfide ,Trophic level - Abstract
Phytoplankton are key components of the oceanic carbon and sulfur cycles1. During bloom events, some species can emit large amounts of the organosulfur volatile dimethyl sulfide (DMS) into the ocean and consequently the atmosphere, where it can modulate aerosol formation and affect climate2,3. In aquatic environments, DMS plays an important role as a chemical signal mediating diverse trophic interactions. Yet, its role in microbial predator–prey interactions remains elusive with contradicting evidence for its role in either algal chemical defence or in the chemo-attraction of grazers to prey cells4,5. Here we investigated the signalling role of DMS during zooplankton–algae interactions by genetic and biochemical manipulation of the algal DMS-generating enzyme dimethylsulfoniopropionate lyase (DL) in the bloom-forming alga Emiliania huxleyi6. We inhibited DL activity in E. huxleyi cells in vivo using the selective DL-inhibitor 2-bromo-3-(dimethylsulfonio)-propionate7 and overexpressed the DL-encoding gene in the model diatom Thalassiosira pseudonana. We showed that algal DL activity did not serve as an anti-grazing chemical defence but paradoxically enhanced predation by the grazer Oxyrrhis marina and other microzooplankton and mesozooplankton, including ciliates and copepods. Consumption of algal prey with induced DL activity also promoted O. marina growth. Overall, our results demonstrate that DMS-mediated grazing may be ecologically important and prevalent during prey–predator dynamics in aquatic ecosystems. The role of algal DMS revealed here, acting as an eat-me signal for grazers, raises fundamental questions regarding the retention of its biosynthetic enzyme through the evolution of dominant bloom-forming phytoplankton in the ocean. Algal production of dimethyl sulfide plays a role in attracting predators and enhancing predation by zooplankton, thus mediating predator–prey relationships in the ocean.
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- 2021
10. The evolutionary history of the HUP domain
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Jagoda Jabłońska, Liam M. Longo, Ita Gruić-Sovulj, and Dan S. Tawfik
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chemistry.chemical_classification ,Nucleotides ,Aminoacyl tRNA synthetase ,Ribose ,Last universal ancestor ,Computational biology ,Biochemistry ,HIGH motif, PP-ATPase, aminoacyl-tRNA synthetases, Rossmannoid, nucleotide binding domain, protein evolution, last universal common ancestor ,Amino Acyl-tRNA Synthetases ,Evolution, Molecular ,chemistry.chemical_compound ,Enzyme ,chemistry ,Cyclic nucleotide-binding domain ,Nucleotide ,Amino Acid Sequence ,NAD+ kinase ,Sequence Alignment ,Molecular Biology ,Adenylylation - Abstract
Among the enzyme lineages that undoubtedly emerged prior to the last universal common ancestor is the so-called HUP, which includes Class I aminoacyl tRNA synthetases (AARSs) as well as enzymes mediating NAD, FAD, and CoA biosynthesis. Here, we provide a detailed analysis of HUP evolution, from emergence to structural and functional diversification. The HUP is a nucleotide binding domain that uniquely catalyzes adenylation via the release of pyrophosphate. In contrast to other ancient nucleotide binding domains with the αβα sandwich architecture, such as P-loop NTPases, the HUP’s most conserved feature is not phosphate binding, but rather ribose binding by backbone interactions to the tips of β1 and/or β4. Indeed, the HUP exhibits unusual evolutionary plasticity and, while ribose binding is conserved, the location and mode of binding to the base and phosphate moieties of the nucleotide, and to the substrate(s) reacting with it, have diverged with time, foremost along the emergence of the AARSs. The HUP also beautifully demonstrates how a well- packed scaffold combined with evolvable surface elements promotes evolutionary innovation. Finally, we offer a scenario for the emergence of the HUP from a seed βαβ fragment, and suggest that despite an identical architecture, the HUP and the Rossmann represent independent emergences.
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- 2021
11. Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin
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Rosario Valenti, Jagoda Jabłońska, and Dan S. Tawfik
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Oxygen ,Manganese ,Superoxide Dismutase ,Superoxides ,Iron ,Metalloproteins ,Molecular Biology ,Biochemistry - Abstract
Superoxide dismutases (SODs) are critical metalloenzymes mitigating the damages of the modern oxygenated world. However, the emergence of one family of SODs, the Fe/Mn SOD, has been recurrently proposed to predate the great oxygenation event (GOE). This ancient family lacks metal binding selectivity, but displays strong catalytic selectivity. Therefore, some homologues would only be active when bound to Fe or Mn, although others, dubbed cambialistic, would function when loaded with either ion. This posed the longstanding question about the identity of the cognate metal ion of the first SODs to emerge. In this work, we utilize ancestral sequence reconstruction techniques to infer the earliest SODs. We show that the "ancestors" are active in vivo and in vitro. Further, we test their metal specificity and demonstrate that they are cambialistic in nature. Our findings shed light on how the predicted Last Common Universal Ancestor was capable of dealing with decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.
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- 2022
12. Utilization of diverse organophosphorus pollutants by marine bacteria
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Dragana Despotović, Einav Aharon, Olena Trofimyuk, Artem Dubovetskyi, Kesava Phaneendra Cherukuri, Yacov Ashani, Or Eliason, Martin Sperfeld, Haim Leader, Andrea Castelli, Laura Fumagalli, Alon Savidor, Yishai Levin, Liam M. Longo, Einat Segev, and Dan S. Tawfik
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Aquatic Organisms ,Multidisciplinary ,Bacteria ,anthropogenic organophosphorus compounds ,bioremediation ,marine bacteria ,phosphotriesterases ,Biodegradation, Environmental ,Escherichia coli ,Indian Ocean ,Mediterranean Sea ,Phosphorus ,Seawater ,Environmental Pollutants ,Organophosphorus Compounds ,Phosphoric Triester Hydrolases ,Settore CHIM/08 - Chimica Farmaceutica ,Environmental ,Biodegradation - Abstract
Anthropogenic organophosphorus compounds (AOPCs), such as phosphotriesters, are used extensively as plasticizers, flame retardants, nerve agents, and pesticides. To date, only a handful of soil bacteria bearing a phosphotriesterase (PTE), the key enzyme in the AOPC degradation pathway, have been identified. Therefore, the extent to which bacteria are capable of utilizing AOPCs as a phosphorus source, and how widespread this adaptation may be, remains unclear. Marine environments with phosphorus limitation and increasing levels of pollution by AOPCs may drive the emergence of PTE activity. Here, we report the utilization of diverse AOPCs by four model marine bacteria and 17 bacterial isolates from the Mediterranean Sea and the Red Sea. To unravel the details of AOPC utilization, two PTEs from marine bacteria were isolated and characterized, with one of the enzymes belonging to a protein family that, to our knowledge, has never before been associated with PTE activity. When expressed in Escherichia coli with a phosphodiesterase, a PTE isolated from a marine bacterium enabled growth on a pesticide analog as the sole phosphorus source. Utilization of AOPCs may provide bacteria a source of phosphorus in depleted environments and offers a prospect for the bioremediation of a pervasive class of anthropogenic pollutants.
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- 2022
13. Uniform binding and negative catalysis at the origin of enzymes
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Elad Noor, Avi I. Flamholz, Vijay Jayaraman, Brian L. Ross, Yair Cohen, Wayne M. Patrick, Ita Gruic‐Sovulj, and Dan S. Tawfik
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Kinetics ,Molecular Biology ,Biochemistry ,Catalysis ,Enzymes - Abstract
Enzymes are well known for their catalytic abilities, some even reaching "catalytic perfection" in the sense that the reaction they catalyze has reached the physical bound of the diffusion rate. However, our growing understanding of enzyme superfamilies has revealed that only some share a catalytic chemistry while others share a substrate-handle binding motif, for example, for a particular phosphate group. This suggests that some families emerged through a "substrate-handle-binding-first" mechanism ("binding-first" for brevity) instead of "chemistry-first" and we are, therefore, left to wonder what the role of non-catalytic binders might have been during enzyme evolution. In the last of their eight seminal, back-to-back articles from 1976, John Albery and Jeremy Knowles addressed the question of enzyme evolution by arguing that the simplest mode of enzyme evolution is what they defined as "uniform binding" (parallel stabilization of all enzyme-bound states to the same degree). Indeed, we show that a uniform-binding proto-catalyst can accelerate a reaction, but only when catalysis is already present, that is, when the transition state is already stabilized to some degree. Thus, we sought an alternative explanation for the cases where substrate-handle-binding preceded any involvement of a catalyst. We find that evolutionary starting points that exhibit negative catalysis can redirect the reaction's course to a preferred product without need for rate acceleration or product release; that is, if they do not stabilize, or even destabilize, the transition state corresponding to an undesired product. Such a mechanism might explain the emergence of "binding-first" enzyme families like the aldolase superfamily.
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- 2022
14. Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains
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Manas Seal, Orit Weil-Ktorza, Dragana Despotović, Dan S. Tawfik, Yaakov Levy, Norman Metanis, Liam M. Longo, and Daniella Goldfarb
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Colloid and Surface Chemistry ,Electron Spin Resonance Spectroscopy ,RNA ,Spin Labels ,General Chemistry ,Peptides ,Biochemistry ,Catalysis - Abstract
Peptide-RNA coacervates can result in the concentration and compartmentalization of simple biopolymers. Given their primordial relevance, peptide-RNA coacervates may have also been a key site of early protein evolution. However, the extent to which such coacervates might promote or suppress the exploration of novel peptide conformations is fundamentally unknown. To this end, we used electron paramagnetic resonance (EPR) spectroscopy to characterize the structure and dynamics of an ancient and ubiquitous nucleic acid binding element, the helix-hairpin-helix (HhH) motif, alone and in the presence of RNA, with which it forms coacervates. Double electron-electron resonance (DEER) spectroscopy applied to singly labeled peptides containing one HhH motif reveals the presence of dimers, even in the absence of RNA, and transient α-helical character. Moreover, dimer formation is promoted upon RNA binding and was detectable within peptide-RNA coacervates. The distance distributions between spin labels are consistent with the symmetric (HhH)2-Fold, which is generated upon duplication and fusion of a single HhH motif and traditionally associated with dsDNA binding. These results support the hypothesis that coacervates are a unique testing ground for peptide oligomerization and that phase-separating peptides could have been a resource for the construction of complex protein structures via common evolutionary processes, such as duplication and fusion.
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- 2022
15. The evolutionary history of class I aminoacyl-tRNA synthetases indicates early statistical translation
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Jagoda Jabłońska, Yao Chun-Chen, Liam M. Longo, Dan S. Tawfik, and Ita Gruic-Sovulj
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How protein translation evolved from a simple beginning to its complex and accurate contemporary state is unknown. Aminoacyl-tRNA synthetases (AARSs) define the genetic code by activating amino acids and loading them onto cognate tRNAs. As such, their evolutionary history can shed light on early translation. Using structure-based alignments of the conserved core of Class I AARSs, we reconstructed their phylogenetic tree and ancestral states. Unexpectedly, AARSs charging amino acids that are assumed to have emerged later – such as TrpRS and TyrRS or LysRS and CysRS – appear as the earliest splits in the tree; conversely, those AARSs charging abiotic, early-emerging amino acids, e.g. ValRS, seem to have diverged most recently. Furthermore, the inferred Class I ancestor (excluding TrpRS and TyrRS) lacks the residues that mediate selectivity in contemporary AARSs, and appears to be a generalist that could charge a wide range of amino acids. This ancestor subsequently diverged to two clades: “charged” (which gave rise to ArgRS, GluRS, and GlnRS) and “hydrophobics”, which includes CysRS and LysRS as its outgroups. The ancestors of both clades maintain a wide-accepting pocket that could readily diverge to the contemporary, specialized families. Overall, our findings suggest a “generalist-maintaining” model of class I AARS evolution, in which early statistical translation was kept active by a generalist AARS while the evolution of a specialized, accurate translation system took place.SignificanceAminoacyl-tRNA synthetases (AARS) define the genetic code by linking amino acids with their cognate tRNAs. While contemporary AARSs leverage exquisite molecular recognition and proofreading to ensure translational fidelity, early translation was likely less stringent and operated on a different pool of amino acids. The co-emergence of translational fidelity and the amino acid alphabet, however, is poorly understood. By inferring the evolutionary history of Class I AARSs we found seemingly conflicting signals: Namely, the oldest AARSs apparently operate on the youngest amino acids. We also observed that the early ancestors had broad amino acid specificities, consistent with a model of statistical translation. Our data suggests that a generalist AARS was actively maintained until complete specialization, thereby resolving the age paradox.
- Published
- 2022
16. How gene duplication diversifies the landscape of protein oligomeric state and function
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Saurav Mallik, Dan S Tawfik, and Emmanuel D Levy
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Evolution, Molecular ,Gene Duplication ,Genetics ,Biological Evolution ,Developmental Biology - Abstract
Oligomeric proteins are central to cellular life and the duplication and divergence of their genes is a key driver of evolutionary innovations. The duplication of a gene coding for an oligomeric protein has numerous possible outcomes, which motivates questions on the relationship between structural and functional divergence. How do protein oligomeric states diversify after gene duplication? In the simple case of duplication of a homo-oligomeric protein gene, what properties can influence the fate of descendant paralogs toward forming independent homomers or maintaining their interaction as a complex? Furthermore, how are functional innovations associated with the diversification of oligomeric states? Here, we review recent literature and present specific examples in an attempt to illustrate and answer these questions.
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- 2022
17. The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation
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Jagoda Jabłońska and Dan S. Tawfik
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0301 basic medicine ,Ecology ,Phylogenetic tree ,Great Oxygenation Event ,Last universal ancestor ,Biosphere ,chemistry.chemical_element ,Biology ,010502 geochemistry & geophysics ,Geologic record ,01 natural sciences ,Oxygen ,03 medical and health sciences ,030104 developmental biology ,chemistry ,Phylogenetics ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Ancestor - Abstract
Production of molecular oxygen was a turning point in the Earth’s history. The geological record indicates the Great Oxidation Event, which marked a permanent transition to an oxidizing atmosphere around 2.4 Ga. However, the degree to which oxygen was available to life before oxygenation of the atmosphere remains unknown. Here, phylogenetic analysis of all known oxygen-utilizing and -producing enzymes (O2-enzymes) indicates that oxygen became widely available to living organisms well before the Great Oxidation Event. About 60% of the O2-enzyme families whose birth can be dated appear to have emerged at the separation of terrestrial and marine bacteria (22 families, compared to two families assigned to the last universal common ancestor). This node, dubbed the last universal oxygen ancestor, coincides with a burst of emergence of both oxygenases and other oxidoreductases, thus suggesting a wider availability of oxygen around 3.1 Ga. Phylogenetic dating of O2-utilizing enzymes indicates a burst of emergence several hundred million years before the Great Oxidation Event.
- Published
- 2021
18. Quinone Methide‐Based Organophosphate Hydrolases Inhibitors: Trans Proximity Labelers versus Cis Labeling Activity‐Based Probes
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Dan S. Tawfik, Laura Fumagalli, Gili Ben-Nissan, Anna Meshcheriakova, Artem Dubovetskyi, Eitan Reuveny, Kesava Phaneendra Cherukuri, Michal Sharon, and Yacov Ashani
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chemistry.chemical_classification ,010405 organic chemistry ,Stereochemistry ,Hydrolysis ,Organic Chemistry ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Quinone methide ,Organophosphates ,Phosphoric Monoester Hydrolases ,0104 chemical sciences ,Turn (biochemistry) ,chemistry.chemical_compound ,Enzyme ,chemistry ,Covalent bond ,Enzymatic hydrolysis ,Phosphodiester bond ,Electrophile ,Molecular Medicine ,Enzyme Inhibitors ,Indolequinones ,Molecular Biology ,Cis–trans isomerism - Abstract
Quinone methide (QM) chemistry is widely applied including in enzyme inhibitors. Typically, enzyme-mediated bond breaking releases a phenol product that rearranges into an electrophilic QM that in turn covalently modifies protein side chains. However, the factors that govern the reactivity of QM-based inhibitors and their mode of inhibition have not been systematically explored. Foremost, enzyme inactivation might occur in cis, whereby a QM molecule inactivates the very same enzyme molecule that released it, or by trans if the released QMs diffuse away and inactivate other enzyme molecules. We examined QM-based inhibitors for enzymes exhibiting phosphoester hydrolase activity. We tested different phenolic substituents and benzylic leaving groups, thereby modulating the rates of enzymatic hydrolysis, phenolate-to-QM rearrangement, and the electrophilicity of the resulting QM. By developing assays that distinguish between cis and trans inhibition, we have identified certain combinations of leaving groups and phenyl substituents that lead to inhibition in the cis mode, while other combinations gave trans inhibition. Our results suggest that cis-acting QM-based substrates could be used as activity-based probes to identify various phospho- and phosphono-ester hydrolases, and potentially other hydrolases.
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- 2020
19. Polyamines Mediate Folding of Primordial Hyperacidic Helical Proteins
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Liam M. Longo, Dragana Despotovic, Dan S. Tawfik, Tali Scherf, Einav Aharon, Ita Gruić-Sovulj, and Amit Kahana
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Protein Folding ,Circular dichroism ,Glutamic Acid ,Context (language use) ,Biochemistry ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Polyamines ,Nuclear Magnetic Resonance, Biomolecular ,030304 developmental biology ,0303 health sciences ,Circular Dichroism ,Lysine ,030302 biochemistry & molecular biology ,Proteins ,Hydrogen-Ion Concentration ,Folding (chemistry) ,Amino Acid Substitution ,chemistry ,Phosphodiester bond ,Nucleic acid ,Protein folding ,Chemical chaperone ,Polyamine ,Peptides and proteins, Amines, Monomers, Organic polymers, Titration - Abstract
Polyamines are known to mediate diverse biological processes, and specifically to bind and stabilize compact conformations of nucleic acids, acting as chemical chaperones that promote folding by offsetting the repulsive negative charges of the phosphodiester backbone. However, whether and how polyamines modulate the structure and function of proteins remain unclear. In particular, early proteins are thought to have been highly acidic, like nucleic acids, due to a scarcity of basic amino acids in the prebiotic context. Perhaps polyamines, the abiotic synthesis of which is simple, could have served as chemical chaperones for such primordial proteins? We replaced all lysines of an ancestral 60-residue helix-bundle protein with glutamate, resulting in a disordered protein with 21 glutamates in total. Polyamines efficiently induce folding of this hyperacidic protein at submillimolar concentrations, and their potency scaled with the number of amine groups. Compared to cations, polyamines were several orders of magnitude more potent than Na+, while Mg2+ and Ca2+ had an effect similar to that of a diamine, inducing folding at approximately seawater concentrations. We propose that (i) polyamines and dications may have had a role in promoting folding of early proteins devoid of basic residues and (ii) coil–helix transitions could be the basis of polyamine regulation in contemporary proteins.
- Published
- 2020
20. Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes
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Liam M. Longo, Dušan Petrović, Dan S. Tawfik, and Shina Caroline Lynn Kamerlin
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Stereochemistry ,Protein domain ,Ligands ,010402 general chemistry ,01 natural sciences ,Evolution, Molecular ,03 medical and health sciences ,Protein Domains ,Moiety ,Amino Acid Sequence ,Binding site ,Databases, Protein ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Binding Sites ,Multidisciplinary ,Chemistry ,Biological Sciences ,Phosphate-Binding Proteins ,Small molecule ,Enzymes ,0104 chemical sciences ,Amino acid ,N-terminus ,Enzyme ,Structural biology ,Protein Binding - Abstract
The ubiquity of phospho-ligands suggests that phosphate binding emerged at the earliest stage of protein evolution. To evaluate this hypothesis and unravel its details, we identified all phosphate-binding protein lineages in the Evolutionary Classification of Protein Domains database. We found at least 250 independent evolutionary lineages that bind small molecule cofactors and metabolites with phosphate moieties. For many lineages, phosphate binding emerged later as a niche functionality, but for the oldest protein lineages, phosphate binding was the founding function. Across some 4 billion y of protein evolution, side-chain binding, in which the phosphate moiety does not interact with the backbone at all, emerged most frequently. However, in the oldest lineages, and most characteristically in αβα sandwich enzyme domains, N-helix binding sites dominate, where the phosphate moiety sits atop the N terminus of an α-helix. This discrepancy is explained by the observation that N-helix binding is uniquely realized by short, contiguous sequences with reduced amino acid diversity, foremost Gly, Ser, and Thr. The latter two amino acids preferentially interact with both the backbone amide and the side-chain hydroxyl (bidentate interaction) to promote binding by short sequences. We conclude that the first αβα sandwich domains emerged from shorter and simpler polypeptides that bound phospho-ligands via N-helix sites.
- Published
- 2020
21. How evolution shapes enzyme selectivity – lessons from aminoacyl‐tRNA synthetases and other amino acid utilizing enzymes
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Ita Gruić-Sovulj and Dan S. Tawfik
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0301 basic medicine ,Stereochemistry ,Biochemistry ,Substrate Specificity ,Amino Acyl-tRNA Synthetases ,Evolution, Molecular ,03 medical and health sciences ,chemistry.chemical_compound ,Negative selection ,0302 clinical medicine ,Molecular recognition ,Moiety ,Amino Acids ,Molecular Biology ,chemistry.chemical_classification ,biology ,Aminoacyl tRNA synthetase ,Active site ,Cell Biology ,Amino acid ,030104 developmental biology ,Enzyme ,chemistry ,030220 oncology & carcinogenesis ,Transfer RNA ,biology.protein ,amino acid selectivity, aminoacyl-tRNA synthetases, editing, enzyme specificity, negative selection - Abstract
Aminoacyl‐tRNA synthetases (AARSs) charge tRNA with their cognate amino acids. Many other enzymes use amino acids as substrates, yet discrimination against noncognate amino acids that threaten the accuracy of protein translation is a hallmark of AARSs. Comparing AARSs to these other enzymes allowed us to recognize patterns in molecular recognition and strategies used by evolution for exercising selectivity. Overall, AARSs are 2–3 orders of magnitude more selective than most other amino acid utilizing enzymes. AARSs also reveal the physicochemical limits of molecular discrimination. For example, amino acids smaller by a single methyl moiety present a discrimination ceiling of ~200, while larger ones can be discriminated by up to 105‐fold. In contrast, substrates larger by a hydroxyl group challenge AARS selectivity, due to promiscuous H‐ bonding with polar active site groups. This ‘hydroxyl paradox’ is resolved by editing. Indeed, when the physicochemical discrimination limits are reached, post‐transfer editing – hydrolysis of tRNAs charged with noncognate amino acids, evolved. The editing site often selectively recognizes the edited noncognate substrate using the very same feature that the synthetic site could not efficiently discriminate against. Finally, the comparison to other enzymes also reveals that the selectivity of AARSs is an explicitly evolved trait, showing some clear examples of how selection acted not only to optimize catalytic efficiency with the target substrate, but also to abolish activity with noncognate threat substrates (‘negative selection’).
- Published
- 2020
22. Innovation and tinkering in the evolution of oxidases
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Jagoda Jabłońska and Dan S. Tawfik
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Oxygen ,Catalytic Domain ,Oxidoreductases ,Molecular Biology ,Biochemistry ,Catalysis - Abstract
Although molecular oxygen is a relative newcomer to the biosphere, it has had a profound impact on metabolism. About 700 oxygen-dependent enzymatic reactions are known, the vast majority of which emerged only after the appearance of oxygen in the biosphere, circa 3 billion years ago. Oxygen was a major driving force for evolutionary innovation-~60% of all known oxygen-dependent enzyme families emerged as such; that is, the founding ancestor was an O
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- 2022
23. Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance
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Adam Frost, Iris D. Young, Kleinman J, James S. Fraser, Stojković, Stephen N. Floor, K. Tsai, Dan S. Tawfik, Danica Galonić Fujimori, Palla A, Alexander G. Myasnikov, and Lianet Noda-García
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Peptidyl transferase ,Adenosine ,antibiotic resistance ,Structural Biology and Molecular Biophysics ,Antibiotics ,Drug Resistance ,Ribosome ,Microbial ,structural biology ,directed evolution ,Biology (General) ,Genetics ,biology ,Escherichia coli Proteins ,General Neuroscience ,Drug Resistance, Microbial ,Methylation ,General Medicine ,Anti-Bacterial Agents ,peptidyl transferase center ,cryoEM ,Infectious Diseases ,Medicine ,Infection ,Research Article ,Cfr ,medicine.drug_class ,QH301-705.5 ,Science ,chemical biology ,RRNA methylation ,General Biochemistry, Genetics and Molecular Biology ,Vaccine Related ,Antibiotic resistance ,RNA modifications ,Biochemistry and Chemical Biology ,molecular biophysics ,medicine ,Escherichia coli ,biochemistry ,Ribosomal ,Binding Sites ,General Immunology and Microbiology ,E. coli ,Methyltransferases ,Ribosomal RNA ,biology.organism_classification ,coli ,RNA, Ribosomal ,biology.protein ,RNA ,Biochemistry and Cell Biology ,Antimicrobial Resistance ,Directed Molecular Evolution ,Bacteria - Abstract
Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition of cfr results in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant that achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-electron microscopy structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr., eLife digest Antibiotics treat or prevent infections by killing bacteria or slowing down their growth. A large proportion of these drugs do this by disrupting an essential piece of cellular machinery called the ribosome which the bacteria need to make proteins. However, over the course of the treatment, some bacteria may gain genetic alterations that allow them to resist the effects of the antibiotic. Antibiotic resistance is a major threat to global health, and understanding how it emerges and spreads is an important area of research. Recent studies have discovered populations of resistant bacteria carrying a gene for a protein named chloramphenicol-florfenicol resistance, or Cfr for short. Cfr inserts a small modification in to the ribosome that prevents antibiotics from inhibiting the production of proteins, making them ineffective against the infection. To date, Cfr has been found to cause resistance to eight different classes of antibiotics. Identifying which mutations enhance its activity and protect bacteria is vital for designing strategies that fight antibiotic resistance. To investigate how the gene for Cfr could mutate and make bacteria more resistant, Tsai et al. performed a laboratory technique called directed evolution, a cyclic process which mimics natural selection. Genetic changes were randomly introduced in the gene for the Cfr protein and bacteria carrying these mutations were treated with tiamulin, an antibiotic rendered ineffective by the modification Cfr introduces into the ribosome. Bacteria that survived were then selected and had more mutations inserted. By repeating this process several times, Tsai et al. identified ‘super’ variants of the Cfr protein that lead to greater resistance. The experiments showed that these variants boosted resistance by increasing the proportion of ribosomes that contained the protective modification. This process was facilitated by mutations that enabled higher levels of Cfr protein to accumulate in the cell. In addition, the current study allowed, for the first time, direct visualization of how the Cfr modification disrupts the effect antibiotics have on the ribosome. These findings will make it easier for clinics to look out for bacteria that carry these ‘super’ resistant mutations. They could also help researchers design a new generation of antibiotics that can overcome resistance caused by the Cfr protein.
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- 2022
24. Protein engineers turned evolutionists—the quest for the optimal starting point
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Devin L. Trudeau and Dan S. Tawfik
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0106 biological sciences ,0303 health sciences ,Computer science ,Biomedical Engineering ,Computational Biology ,Proteins ,food and beverages ,Bioengineering ,Protein Engineering ,Directed evolution ,01 natural sciences ,Enzymes ,Evolution, Molecular ,03 medical and health sciences ,Natural sequence ,Molecular evolution ,010608 biotechnology ,Computational design ,Evolutionism ,Biochemical engineering ,Directed Molecular Evolution ,Phylogeny ,030304 developmental biology ,Biotechnology - Abstract
The advent of laboratory directed evolution yielded a fruitful crosstalk between the disciplines of molecular evolution and bio-engineering. Here, we outline recent developments in both disciplines with respect to how one can identify the best starting points for directed evolution, such that highly efficient and robust tailor-made enzymes can be obtained with minimal optimization. Directed evolution studies have highlighted essential features of engineer-able enzymes: highly stable, mutationally robust enzymes with the capacity to accept a broad range of substrates. Robust, evolvable enzymes can be inferred from the natural sequence record. Broad substrate spectrum relates to conformational plasticity and can also be predicted by phylogenetic analyses and/or by computational design. Overall, an increasingly powerful toolkit is becoming available for identifying optimal starting points including network analyses of enzyme superfamilies and other bioinformatics methods.
- Published
- 2019
25. Author response: Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance
- Author
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Kaitlyn Tsai, Vanja Stojković, Lianet Noda-Garcia, Iris D Young, Alexander G Myasnikov, Jordan Kleinman, Ali Palla, Stephen N Floor, Adam Frost, James S Fraser, Dan S Tawfik, and Danica Galonić Fujimori
- Published
- 2021
26. Correction to 'Peptide-RNA Coacervates as a Cradle for the Evolution of Folded Domains'
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Manas Seal, Orit Weil-Ktorza, Dragana Despotović, Dan S. Tawfik, Yaakov Levy, Norman Metanis, Liam M. Longo, and Daniella Goldfarb
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Colloid and Surface Chemistry ,General Chemistry ,Biochemistry ,Catalysis - Published
- 2022
27. Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations.
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Liat Rockah-Shmuel, ágnes Tóth-Petróczy, and Dan S. Tawfik
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- 2015
- Full Text
- View/download PDF
28. Widespread Utilization of Diverse Organophosphate Pollutants by Marine Bacteria
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Alon Savidor, Olena Trofimyuk, Andrea Castelli, Dan S. Tawfik, Yishai Levin, Artem Dubovetskyi, Liam M. Longo, Yacov Ashani, Dragana Despotovic, Einat Segev, Einav Aharon, Laura Fumagalli, Haim Leader, and Kesava Phaneendra Cherukuri
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Pollutant ,biology ,Phosphorus ,Organophosphate ,chemistry.chemical_element ,Pesticide ,biology.organism_classification ,chemistry.chemical_compound ,Marine bacteriophage ,Bioremediation ,chemistry ,Environmental chemistry ,Environmental science ,Anthropogenic pollutants ,Bacteria - Abstract
Anthropogenic organophosphates (AOPs), such as phosphotriesters, are used extensively as plasticizers, flame retardants, nerve agents and pesticides. Soil bacteria bearing a phosphotriesterase (PTE) can degrade AOPs, but whether bacteria are capable of utilizing AOPs as a phosphorus source, and how widespread PTEs are in nature, remains unclear. Here, we report the utilization of diverse AOPs by four model marine bacteria and seventeen bacterial isolates from seawater samples. To unravel the details of AOP utilization, two novel PTEs from marine bacteria were isolated and characterized. When expressed in E. coli, these PTEs enabled growth on a pesticide analog as the sole phosphorus source. Utilization of AOPs provides bacteria with a source of phosphorus in depleted environments and offers a new prospect for the bioremediation of a pervasive class of anthropogenic pollutants.One sentence summaryWidespread utilization of diverse organophosphate pollutants by over 20 marine bacterial strains represents a new hope for ocean bioremediation.
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- 2021
29. The Evolutionary Potential of Phenotypic Mutations.
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Hayato Yanagida, Ariel Gispan, Noam Kadouri, Shelly Rozen, Michal Sharon, Naama Barkai, and Dan S Tawfik
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Genetics ,QH426-470 - Abstract
Errors in protein synthesis, so-called phenotypic mutations, are orders-of-magnitude more frequent than genetic mutations. Here, we provide direct evidence that alternative protein forms and phenotypic variability derived from translational errors paved the path to genetic, evolutionary adaptations via gene duplication. We explored the evolutionary origins of Saccharomyces cerevisiae IDP3 - an NADP-dependent isocitrate dehydrogenase mediating fatty acids ß-oxidation in the peroxisome. Following the yeast whole genome duplication, IDP3 diverged from a cytosolic ancestral gene by acquisition of a C-terminal peroxisomal targeting signal. We discovered that the pre-duplicated cytosolic IDPs are partially localized to the peroxisome owing to +1 translational frameshifts that bypass the stop codon and unveil cryptic peroxisomal targeting signals within the 3'-UTR. Exploring putative cryptic signals in all 3'-UTRs of yeast genomes, we found that other enzymes related to NADPH production such as pyruvate carboxylase 1 (PYC1) might be prone to peroxisomal localization via cryptic signals. Using laboratory evolution we found that these translational frameshifts are rapidly imprinted via genetic single base deletions occurring within the very same gene location. Further, as exemplified here, the sequences that promote translational frameshifts are also more prone to genetic deletions. Thus, genotypes conferring higher phenotypic variability not only meet immediate challenges by unveiling cryptic 3'-UTR sequences, but also boost the potential for future genetic adaptations.
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- 2015
- Full Text
- View/download PDF
30. A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis
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Dan S. Tawfik, Michal Sharon, Jayaraman, James S. Fraser, Shay Vimer, Lee Dj, and Nadav Elad
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Enzymologic ,Enzyme complex ,Biochemistry & Molecular Biology ,Glutamic Acid ,Bacillus subtilis ,Gene Expression Regulation, Enzymologic ,Medicinal and Biomolecular Chemistry ,Bacterial Proteins ,Glutamate Dehydrogenase ,In vivo ,Glutamate synthase ,Molecular Biology ,chemistry.chemical_classification ,biology ,Chemistry ,Glutamate dehydrogenase ,Glutamate Synthase ,Glutamate receptor ,Bacterial ,Cell Biology ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,In vitro ,Enzyme ,Biochemistry ,Gene Expression Regulation ,biology.protein ,Biochemistry and Cell Biology - Abstract
SummaryMulti-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite rather than sequential reactions (“counter-enzymes”): glutamate synthase (GltAB), and glutamate dehydrogenase (GudB), that make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit GudB’s activity as this enzyme is constitutively expressed including in glutamate-limiting conditions. Using cryo-electron microscopy, we elucidated the structure of the complex and the basis of GudB’s inhibition. Finally, we show that this complex that exhibits unusual oscillatory progress curves is a necessity for planktonic growth in glutamate-limiting conditions, but is also essential for biofilm growth in glutamate-rich media, suggesting a regulatory role at fluctuating glutamate concentrations.
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- 2021
31. On the evolution of chaperones and cochaperones and the expansion of proteomes across the Tree of Life
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Pierre Goloubinoff, Dan S. Tawfik, Mathieu E. Rebeaud, and Saurav Mallik
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cochaperones ,Protein Folding ,Proteome ,core chaperones ,Gene Expression ,Computational biology ,Biology ,Evolution, Molecular ,Protein Aggregates ,Adenosine Triphosphate ,Heat shock protein ,Gene duplication ,Animals ,Protein Isoforms ,HSP70 Heat-Shock Proteins ,RNA, Messenger ,Gene ,Phylogeny ,Mammals ,Multidisciplinary ,Bacteria ,Adenosine Triphosphate/metabolism ,Archaea/genetics ,Archaea/metabolism ,Bacteria/genetics ,Bacteria/metabolism ,Fungi/genetics ,Fungi/metabolism ,Gene Ontology ,HSP70 Heat-Shock Proteins/genetics ,HSP70 Heat-Shock Proteins/metabolism ,Molecular Sequence Annotation ,Plants/genetics ,Plants/metabolism ,Protein Aggregates/genetics ,Protein Isoforms/genetics ,Protein Isoforms/metabolism ,Proteome/genetics ,Proteome/metabolism ,RNA, Messenger/genetics ,RNA, Messenger/metabolism ,Tree of Life ,chaperone network ,expansion of proteomes ,Fungi ,Biological Sciences ,Plants ,biology.organism_classification ,Hsp90 ,Archaea ,Hsp70 ,Biophysics and Computational Biology ,biology.protein ,HSP60 ,Function (biology) - Abstract
Significance Across the Tree of Life, life’s phenotypic diversity has been accompanied by a massive expansion of the protein universe. Compared with simple prokaryotes that harbor thousands of proteins, plants and animals harbor hundreds of thousands of proteins that are also longer, multidomain, and comprise a variety of folds and fold combinations, repeated segments, and beta-rich architectures that make them prone to misfolding and aggregation. Surprisingly, the relative representation of core chaperones, those dedicated to maintaining the folding quality of these increasingly complex proteomes, did not change from prokaryotic to mammalian genomes. To reconcile the expanding proteomes, core chaperones have rather increased in cellular abundance and evolved to function cooperatively as a network, combined with their supporting workforce, the cochaperones., Across the Tree of Life (ToL), the complexity of proteomes varies widely. Our systematic analysis depicts that from the simplest archaea to mammals, the total number of proteins per proteome expanded ∼200-fold. Individual proteins also became larger, and multidomain proteins expanded ∼50-fold. Apart from duplication and divergence of existing proteins, completely new proteins were born. Along the ToL, the number of different folds expanded ∼5-fold and fold combinations ∼20-fold. Proteins prone to misfolding and aggregation, such as repeat and beta-rich proteins, proliferated ∼600-fold and, accordingly, proteins predicted as aggregation-prone became 6-fold more frequent in mammalian compared with bacterial proteomes. To control the quality of these expanding proteomes, core chaperones, ranging from heat shock proteins 20 (HSP20s) that prevent aggregation to HSP60, HSP70, HSP90, and HSP100 acting as adenosine triphosphate (ATP)-fueled unfolding and refolding machines, also evolved. However, these core chaperones were already available in prokaryotes, and they comprise ∼0.3% of all genes from archaea to mammals. This challenge—roughly the same number of core chaperones supporting a massive expansion of proteomes—was met by 1) elevation of messenger RNA (mRNA) and protein abundances of the ancient generalist core chaperones in the cell, and 2) continuous emergence of new substrate-binding and nucleotide-exchange factor cochaperones that function cooperatively with core chaperones as a network.
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- 2021
32. The number and type of oxygen-utilizing enzymes indicates aerobic vs. anaerobic phenotype
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Dan S. Tawfik and Jagoda Jabłońska
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0301 basic medicine ,Cytochrome ,chemistry.chemical_element ,Electrons ,Biochemistry ,Oxygen ,Xenobiotics ,03 medical and health sciences ,0302 clinical medicine ,Physiology (medical) ,Anaerobiosis ,Amino Acids ,chemistry.chemical_classification ,Reactive oxygen species ,biology ,Catalase ,Electron transport chain ,Phenotype ,Amino acid ,030104 developmental biology ,Enzyme ,chemistry ,biology.protein ,Metagenome ,Reactive Oxygen Species ,Oxidation-Reduction ,030217 neurology & neurosurgery - Abstract
Oxygen is a major metabolic driving force that enabled the expansion of metabolic networks including new metabolites and new enzymes. It had a dramatic impact on the primary electron transport chain where it serves as terminal electron acceptor, but oxygen is also used by many enzymes as electron acceptor for a variety of reactions. The organismal oxygen phenotype, aerobic vs. anaerobic, should be manifested in its O2-utilizing enzymes. Traditionally, enzymes involved in primary oxygen metabolism such as cytochrome c, and reactive oxygen species (ROS)-neutralizing enzymes (e.g. catalase), were used as identifiers of oxygen phenotype. However, these enzymes are often found in strict anaerobes. We aimed to identify the O2-utilizing enzymes that may distinguish between aerobes and anaerobes. To this end, we annotated the O2-utilizing enzymes across the prokaryotic tree of life. We recovered over 700 enzymes and mapped their presence/absence in 272 representative genomes. As seen before, enzymes mediating primary oxygen metabolism, and ROS neutralizing enzymes, could be found in both aerobes and anaerobes. However, there exists a subset of enzymes, primarily oxidases that catabolyze various substrates, including amino acids and xenobiotics, that are preferentially enriched in aerobes. Overall it appears that the total number of oxygen-utilizing enzymes, and the presence of enzymes involved in 'peripheral', secondary oxygen metabolism, can reliably distinguish aerobes from anaerobes based solely on genome sequences. These criteria can also indicate the oxygen phenotype in metagenomic samples.
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- 2019
33. A Personal Reflection on the Chemistry‐Biology Interface
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Dan S. Tawfik
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Chemistry ,Interface (computing) ,General Chemistry ,Chemistry (relationship) ,Reflection (computer graphics) ,Engineering physics - Published
- 2019
34. Helicase-like functions in phosphate loop containing beta-alpha polypeptides
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Michal Sharon, Fanindra Kumar Deshmukh, Pratik Vyas, Dan S. Tawfik, Liam M. Longo, and Olena Trofimyuk
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Models, Molecular ,Protein Conformation, alpha-Helical ,0301 basic medicine ,AAA Domain ,Amino Acid Motifs ,DNA, Single-Stranded ,01 natural sciences ,RNA Helicases ,Phosphates ,03 medical and health sciences ,chemistry.chemical_compound ,Recombinase ,Nucleotide ,Amino Acid Sequence ,chemistry.chemical_classification ,Multidisciplinary ,biology ,010405 organic chemistry ,Chemistry ,Walker motifs ,DNA Helicases ,Proteins ,Helicase ,RNA ,Biological Sciences ,Nucleoside-Triphosphatase ,Receptor–ligand kinetics ,0104 chemical sciences ,Rec A Recombinases ,Enzyme ,030104 developmental biology ,Biophysics ,biology.protein ,Protein Conformation, beta-Strand ,Peptides ,Function (biology) ,DNA - Abstract
The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple βα repeat proteins bind NTPs, but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one β-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes comprise a plausible description of the sequence, structure and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.Significance statementIt is widely assumed that today’s large and complex proteins emerged from much shorter and simpler polypeptides. Yet the nature of these early precursors remains enigmatic. We describe polypeptides that contain one of the earliest protein motifs, a phosphate-binding loop, or P-loop, embedded in a single beta-alpha element. These P-loop prototypes show intriguing characteristics of a primordial world comprised of nucleic acids and peptides. They are ‘generalists’ capable of binding different phospho-ligands, including inorganic polyphosphates and single-stranded DNA. Nonetheless, in promoting double-stranded DNA unwinding and strand-exchange they resemble modern P-loop helicases and recombinases. Our study describes a missing link in the evolution of complex proteins – simple polypeptides that tangibly relate to contemporary P-loop enzymes in sequence, structure and function.
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- 2021
35. Proto‐proteins in Protocells
- Author
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Dragana Despotovic and Dan S. Tawfik
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Protocell ,Abiogenesis ,Chemistry ,Mechanical Engineering ,Energy Engineering and Power Technology ,Management Science and Operations Research ,Protein evolution ,Cell biology - Published
- 2021
36. Bridging Themes: Short Protein Segments Found in Different Architectures
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Nir Ben-Tal, Rachel Kolodny, Sergey Nepomnyachiy, and Dan S. Tawfik
- Subjects
Bridging (networking) ,Domain level ,ancestral segments ,protein space ,Biology ,AcademicSubjects/SCI01180 ,Divergence (computer science) ,Homologous Sequences ,Protein evolution ,03 medical and health sciences ,0302 clinical medicine ,protein evolutionary patterns ,Genetics ,Molecular Biology ,Discoveries ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Sequence (medicine) ,bridging themes ,0303 health sciences ,AcademicSubjects/SCI01130 ,Common ancestry ,Sequence homology ,Evolutionary biology ,030217 neurology & neurosurgery ,Function (biology) - Abstract
The vast majority of theoretically possible polypeptide chains do not fold, let alone confer function. Hence, protein evolution from preexisting building blocks has clear potential advantages over ab initio emergence from random sequences. In support of this view, sequence similarities between different proteins is generally indicative of common ancestry, and we collectively refer to such homologous sequences as ‘themes’. At the domain level, sequence homology is routinely detected. However, short themes which are segments, or fragments of intact domains, are particularly interesting because they may provide hints about the emergence of domains, as opposed to divergence of preexisting domains, or their mixing-and-matching to form multi-domain proteins. Here we identified 525 representative short themes, comprising 20-to-80 residues, that are unexpectedly shared between domains considered to have emerged independently. Among these ‘bridging themes’ are ones shared between the most ancient domains, e.g., Rossmann, P-loop NTPase, TIM-barrel, Flavodoxin, and Ferredoxin-like. We elaborate on several particularly interesting cases, where the bridging themes mediate ligand binding. Ligand binding may have contributed to the stability and the plasticity of these building blocks, and to their ability to invade preexisting domains or serve as starting points for completely new domains.
- Published
- 2021
37. Dimethyl sulfide acts as eat-me signal during microbial predator-prey interactions in the ocean
- Author
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Assaf Vardi, Viviana Farstey, Daniella Schatz, Uria Alcolombri, Miguel J. Frada, Ron Rotkopf, Adva Shemi, Shifra Ben-Dor, and Dan S. Tawfik
- Subjects
chemistry.chemical_compound ,chemistry ,Ecology ,Dimethyl sulfide ,Signal ,Predation - Abstract
Phytoplankton are key components of the oceanic carbon and sulfur cycles 1. During bloom events, some species can emit massive amounts of the organosulfur volatile dimethyl sulfide (DMS) to the atmosphere, where it can modulate aerosol formation and affect climate. In aquatic environments, DMS plays an important role as a chemical signal mediating diverse trophic-level interactions. Yet its role in microbial predator-prey interactions remains elusive with contradicting evidence for its role in algal chemical defense and in grazer’s chemoattraction to prey cells. Here, we investigated the signaling role of DMS during zooplankton-algae interactions by genetic and biochemical manipulation of the algal DMS-generating enzyme (Dimethylsulfoniopropionate lyase, DL) from the bloom-forming alga Emiliania huxleyi. We inhibited DL activity in live E. huxleyi cells by the novel DL-inhibitor 2-bromo-3-(dimethylsulfonio)-propionate (Br-DMSP) , and overexpressed DL in the model diatom Thalassiosira pseudonana. We showed that algal DL activity did not serve as anti-grazing chemical defense, and paradoxically enhanced grazing by the model microzooplankton Oxyrrhis marina and other micro- and mesozooplankton, including ciliates and copepods. Consumption of algal prey with induced DL activity also promoted O. marina’s growth. Overall, our results demonstrate that DMS-mediated herbivory may be ecologically important and prevalent during prey-predator dynamics in oceanic ecosystems. The role of DMS as an appetizing signal to grazers revealed here raises fundamental questions regarding the retention of its biosynthetic enzyme through the evolution of dominant bloom-forming phytoplankton in the ocean.
- Published
- 2021
38. On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment
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Dan S. Tawfik, Nir Ben-Tal, Liam M. Longo, Pratik Vyas, Rachel Kolodny, and Jagoda Jabłońska
- Subjects
last universal common ancestor ,enzyme evolution ,QH301-705.5 ,Science ,AAA Proteins ,GTPase ,Biology ,ancient peptide ,P-loop ,Cofactor ,General Biochemistry, Genetics and Molecular Biology ,Evolution, Molecular ,chemistry.chemical_compound ,Catalytic metal ,None ,Ribose ,Nucleotide ,Biology (General) ,Beta (finance) ,protein evolution ,Sequence (medicine) ,chemistry.chemical_classification ,Evolutionary Biology ,Binding Sites ,General Immunology and Microbiology ,General Neuroscience ,Last universal ancestor ,General Medicine ,Sequence identity ,Protein Structure, Tertiary ,Enzyme ,Tubulin ,chemistry ,Evolutionary biology ,biology.protein ,Medicine ,Sequence Alignment ,Research Article - Abstract
Dating back to the last universal common ancestor (LUCA), the P-loop NTPases and Rossmanns now comprise the most ubiquitous and diverse enzyme lineages. Intriguing similarities in their overall architecture and phosphate binding motifs suggest common ancestry; however, due to a lack of sequence identity and some fundamental structural differences, these families are considered independent emergences. To address this longstanding dichotomy, we systematically searched for ‘bridge proteins’ with structure and sequence elements shared by both lineages. We detected homologous segments that span the first βαβ segment of both lineages and include two key functional motifs: (i) a phosphate binding loop – the ‘Walker A’ motif of P-loop NTPases or the Rossmann equivalent, both residing at the N-terminus of α1; and (ii) an Asp at the tip of β2. The latter comprises the ‘Walker B’ aspartate that chelates the catalytic metal in P-loop NTPases, or the canonical Rossmann β2-Asp that binds the cofactor’s ribose moiety. Tubulin, a Rossmann GTPase, demonstrates the potential of the β2-Asp to take either one of these two roles. We conclude that common P-loops/Rossmann ancestry is plausible, although convergence cannot be completely ruled out. Regardless, both lineages most likely emerged from a polypeptide comprising a βαβ segment carrying the above two functional motifs, a segment that comprises the core of both enzyme families to this very day.
- Published
- 2020
39. Author response: On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment
- Author
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Jagoda Jabłońska, Dan S. Tawfik, Liam M. Longo, Nir Ben-Tal, Rachel Kolodny, Pratik Vyas, and Manil Kanade
- Subjects
chemistry.chemical_classification ,Enzyme ,chemistry ,Fragment (computer graphics) ,Alpha (ethology) ,Beta (finance) ,Molecular biology - Published
- 2020
40. Author Reply to Peer Reviews of On the Emergence of P-Loop NTPase and Rossmann Enzymes from a Beta-Alpha-Beta Ancestral Fragment
- Author
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Dan S. Tawfik, Nir Ben-Tal, Rachel Kolodny, Manil Kanade, Pratik Vyas, Jagoda Jabłońska, and Liam M. Longo
- Published
- 2020
41. Polyamines Mediate Folding of Primordial Hyper-Acidic Helical Proteins
- Author
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Dragana Despotovic, Einav Aharon, Ita Gruić-Sovulj, Liam M. Longo, Tali Scherf, Amit Kahana, and Dan S. Tawfik
- Subjects
Folding (chemistry) ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Phosphodiester bond ,Glutamate receptor ,Nucleic acid ,Context (language use) ,Amine gas treating ,Chemical chaperone ,Polyamine - Abstract
Polyamines are known to mediate diverse biological processes, and specifically to bind and stabilize compact conformations of nucleic acids, acting as chemical chaperones that promote folding by offsetting the repulsive negative charges of the phosphodiester backbone. However, whether and how polyamines modulate the structure and function of proteins remains unclear. Further, early proteins are thought to have been highly acidic, like nucleic acids, due to a scarcity of basic amino acids in the prebiotic context. Perhaps polyamines, the abiotic synthesis of which is simple, could have served as chemical chaperones for such primordial proteins? We replaced all lysines of an ancestral 60-residue helix-bundle protein to glutamate, resulting in a disordered protein with 21 glutamates in total. Polyamines efficiently induce folding of this hyper-acidic protein at sub-millimolar concentrations, and their potency scaled with the number of amine groups. Compared to cations, polyamines were several orders of magnitude more potent than Na+, while Mg2+and Ca2+had an effect similar to a di-amine, inducing folding at approximately seawater concentrations. We propose that (i) polyamines and dications may have had a role in promoting folding of early proteins devoid of basic residues, and that (ii) coil-helix transitions could be the basis of polyamine regulation in contemporary proteins.
- Published
- 2020
42. Determining the interaction status and evolutionary fate of duplicated homomeric proteins
- Author
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Dan S. Tawfik and Saurav Mallik
- Subjects
0301 basic medicine ,Evolutionary Genetics ,Yeast and Fungal Models ,medicine.disease_cause ,Biochemistry ,0302 clinical medicine ,Gene Duplication ,Gene duplication ,Fungal Evolution ,Biology (General) ,Organism ,Crystallography ,Ecology ,biology ,Physics ,Escherichia coli Proteins ,Eukaryota ,Common ancestry ,Condensed Matter Physics ,Biological Evolution ,Computational Theory and Mathematics ,Experimental Organism Systems ,Modeling and Simulation ,Physical Sciences ,Crystal Structure ,Saccharomyces Cerevisiae ,Research Article ,Saccharomyces cerevisiae Proteins ,animal structures ,QH301-705.5 ,Protein domain ,Saccharomyces cerevisiae ,Paralogous Gene ,Mycology ,Research and Analysis Methods ,Protein–protein interaction ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Saccharomyces ,Model Organisms ,Protein Domains ,medicine ,Genetics ,Homomeric ,Solid State Physics ,Protein Interactions ,Escherichia coli ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Evolutionary Biology ,Human evolutionary genetics ,fungi ,Organisms ,Fungi ,Biology and Life Sciences ,Proteins ,biology.organism_classification ,Yeast ,030104 developmental biology ,Evolutionary biology ,Animal Studies ,030217 neurology & neurosurgery - Abstract
Oligomeric proteins are central to life. Duplication and divergence of their genes is a key evolutionary driver, also because duplications can yield very different outcomes. Given a homomeric ancestor, duplication can yield two paralogs that form two distinct homomeric complexes, or a heteromeric complex comprising both paralogs. Alternatively, one paralog remains a homomer while the other acquires a new partner. However, so far, conflicting trends have been noted with respect to which fate dominates, primarily because different methods and criteria are being used to assign the interaction status of paralogs. Here, we systematically analyzed all Saccharomyces cerevisiae and Escherichia coli oligomeric complexes that include paralogous proteins. We found that the proportions of homo-hetero duplication fates strongly depend on a variety of factors, yet that nonetheless, rigorous filtering gives a consistent picture. In E. coli about 50%, of the paralogous pairs appear to have retained the ancestral homomeric interaction, whereas in S. cerevisiae only ~10% retained a homomeric state. This difference was also observed when unique complexes were counted instead of paralogous gene pairs. We further show that this difference is accounted for by multiple cases of heteromeric yeast complexes that share common ancestry with homomeric bacterial complexes. Our analysis settles contradicting trends and conflicting previous analyses, and provides a systematic and rigorous pipeline for delineating the fate of duplicated oligomers in any organism for which protein-protein interaction data are available., Author summary About half of all proteins assemble as oligomers, either by self-interaction (homomers) or via interaction with another protein (heteromers). The latter can be unrelated, yet, quite commonly, the interacting proteins are paralogs, namely two genes that arose by gene duplication. Indeed, while a homomer is encoded by a single gene, heteromers demand two genes as a minimum. Duplication can therefore yield two discrete homomeric complexes or a single heteromer. Do paralogs tend to retain the ancestral homomeric interaction, or do they mostly diverge into heteromeric complexes? Despite several studies addressing this question, to date, we lack a systematic, rigorous approach for delineating the oligomeric fates of paralogs on an organism scale. To this end, we developed a new pipeline for analysis of molecular interaction databases that includes various filtering steps and unambiguous definitions of all possible oligomeric fates. Applying this method to Escherichia coli and Saccharomyces cerevisiae we noted that paralogous pairs tend to remain homomeric in the former while in the latter heteromeric complexes dominate. We consequently note a systematic trend of homomeric bacterial proteins diverging into heteromeric complexes in eukaryotes.
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- 2020
43. Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion
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Jagoda Jabłońska, Liam M. Longo, Matthew J. Walker, Orit Weil‐Ktorza, Yael Fridmann-Sirkis, Gabriele Varani, Norman Metanis, Dragana Despotovic, and Dan S. Tawfik
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Ornithine ,Arginine ,03 medical and health sciences ,chemistry.chemical_compound ,Protein biosynthesis ,Amino Acid Sequence ,Amino Acids ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Multidisciplinary ,030302 biochemistry & molecular biology ,RNA ,Proteins ,DNA ,Biological Sciences ,Amino acid ,DNA-Binding Proteins ,Nucleoproteins ,chemistry ,Biochemistry ,Nucleic acid ,Peptides ,Function (biology) - Abstract
De novo emergence demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can polypeptides confer functions of evolutionary relevance, and how might such polypeptides evolve into modern proteins? The earliest proteins present an even greater challenge, as they were likely based on abiotic, spontaneously synthesized amino acids. Here we asked whether a primordial function, such as nucleic acid binding, could emerge with ornithine, a basic amino acid that forms abiotically yet is absent in modern-day proteins. We combined ancestral sequence reconstruction and empiric deconstruction to unravel a gradual evolutionary trajectory leading from a polypeptide to a ubiquitous nucleic acid-binding protein. Intermediates along this trajectory comprise sequence-duplicated functional proteins built from 10 amino acid types, with ornithine as the only basic amino acid. Ornithine side chains were further modified into arginine by an abiotic chemical reaction, improving both structure and function. Along this trajectory, function evolved from phase separation with RNA (coacervates) to avid and specific double-stranded DNA binding. Our results suggest that phase-separating polypeptides may have been an evolutionary resource for the emergence of early proteins, and that ornithine, together with its postsynthesis modification to arginine, could have been the earliest basic amino acids.
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- 2020
44. The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation
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Jagoda, Jabłońska and Dan S, Tawfik
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Oxygen ,Atmosphere ,Humans ,Biological Evolution ,Oxidation-Reduction ,Phylogeny - Abstract
Production of molecular oxygen was a turning point in the Earth's history. The geological record indicates the Great Oxidation Event, which marked a permanent transition to an oxidizing atmosphere around 2.4 Ga. However, the degree to which oxygen was available to life before oxygenation of the atmosphere remains unknown. Here, phylogenetic analysis of all known oxygen-utilizing and -producing enzymes (O
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- 2020
45. Enzyme promiscuity and evolution in light of cellular metabolism
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Dan S. Tawfik
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0301 basic medicine ,Cognitive science ,Cellular metabolism ,biology ,Cells ,Context (language use) ,Cell Biology ,Biochemistry ,Enzymes ,Substrate Specificity ,Evolution, Molecular ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,030220 oncology & carcinogenesis ,Research community ,biology.protein ,Substrate specificity ,Enzyme promiscuity ,Sociology ,Molecular Biology ,Introductory Journal Article - Abstract
This Special Issue is composed of 10 reviews that delve into the intricacies behind enzyme promiscuity and evolution, an area that is of increasing interest in the biological research community. In particular, the reviews in this Special Issue explore enzyme promiscuity and evolution in the context of cellular metabolism, as discussed in this introductory Editorial. It is our hope that you enjoy these fascinating and informative reviews and we wish to thank the authors for their compelling contributions to The FEBS Journal. doi: 10.1111/febs.12650.
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- 2020
46. Enzyme evolution in natural products biosynthesis: target- or diversity-oriented?
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Lianet Noda-Garcia and Dan S. Tawfik
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0301 basic medicine ,chemistry.chemical_classification ,Models, Molecular ,Biological Products ,Natural product ,Bacteria ,Computational biology ,Biology ,Plants ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Analytical Chemistry ,Biosynthetic Pathways ,Enzymes ,Evolution, Molecular ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Enzyme ,chemistry ,Biosynthesis ,Chemical diversity ,Biocatalysis - Abstract
Natural product biosynthesis (NPB) is the Panda's Thumb of evolutionary biochemistry. Arm races between organisms, and ever-changing environments, result in relentless innovation. This review focusses on enzyme evolution in NPB. First, we review cases of de novo emergence, whereby a completely new enzymatic activity arose in a ligand-binding protein, or a new enzyme emerged including a completely new scaffold. Second, we briefly review the current models for enzyme evolution, and how they explain the inherent promiscuity of NPB enzymes and their tendency to produce multiple related products. We thus suggest that NPB enzymes a priori evolved to generate a specific product; they are, however, trapped in a multifunctional, generalist evolutionary state and thereby produce a diversity of products.
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- 2020
47. Primordial emergence of a nucleic acid binding protein via phase separation and statistical ornithine to arginine conversion
- Author
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Dragana Despotovic, Jagoda Jabłońska, Matthew J. Walker, Gabriele Varani, Yael Fridmann-Sirkis, Liam M. Longo, Dan S. Tawfik, Norman Metanis, and Orit Weil‐Ktorza
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chemistry.chemical_classification ,0303 health sciences ,Arginine ,010405 organic chemistry ,Chemistry ,RNA ,Chemical modification ,Sequence (biology) ,Ornithine ,01 natural sciences ,0104 chemical sciences ,Amino acid ,03 medical and health sciences ,chemistry.chemical_compound ,Biochemistry ,Nucleic acid ,Function (biology) ,030304 developmental biology - Abstract
De novo emergence, and emergence of the earliest proteins specifically, demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can peptides confer evolutionary relevant functions, let alone with minimal abiotic amino acid alphabets? How can such polypeptides evolve into mature proteins? Specifically, while nucleic acids binding is presumed a primordial function, it demands basic amino acids that do not readily form abiotically. To address these questions, we describe an experimentally-validated trajectory from a phase-separating polypeptide to a dsDNA-binding protein. The intermediates comprise sequence-duplicated, functional proteins made of only 10 amino acid types, with ornithine, which can form abiotically, as the only basic amino acid. Statistical, chemical modification of ornithine sidechains to arginine promoted structure and function. The function concomitantly evolved – from phase separation with RNA (coacervates) to avid and specific dsDNA binding – thereby demonstrating a smooth, gradual peptide-to-protein transition with respect to sequence, structure, and function.
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- 2020
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- View/download PDF
48. Preface
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Dan S, Tawfik
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- 2020
49. How Protein Stability and New Functions Trade Off.
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Nobuhiko Tokuriki, Francois Stricher, Luis Serrano, and Dan S. Tawfik
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- 2008
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50. Enzyme Evolution: An Epistatic Ratchet versus a Smooth Reversible Transition
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Kesava-Phaneendra Cherukuri, Misha Soskine, Dan S. Tawfik, Shina Caroline Lynn Kamerlin, Joel L. Sussman, Qinghua Liao, Klaudia Szeler, Orly Dym, Moshe Ben-David, and Artem Dubovetskyi
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Mutant ,Reversion ,010402 general chemistry ,01 natural sciences ,Evolution, Molecular ,03 medical and health sciences ,Hydrolase ,Genetics ,Lactonase ,Humans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,biology ,Transition (genetics) ,Aryldialkylphosphatase ,Active site ,Epistasis, Genetic ,Phosphoric Monoester Hydrolases ,0104 chemical sciences ,biology.protein ,Epistasis ,Directed Molecular Evolution ,Function (biology) - Abstract
Evolutionary trajectories are deemed largely irreversible. In a newly diverged protein, reversion of mutations that led to the functional switch typically results in loss of both the new and the ancestral functions. Nonetheless, evolutionary transitions where reversions are viable have also been described. The structural and mechanistic causes of reversion compatibility versus incompatibility therefore remain unclear. We examined two laboratory evolution trajectories of mammalian paraoxonase-1, a lactonase with promiscuous organophosphate hydrolase (OPH) activity. Both trajectories began with the same active-site mutant, His115Trp, which lost the native lactonase activity and acquired higher OPH activity. A neo-functionalization trajectory amplified the promiscuous OPH activity, whereas the re-functionalization trajectory restored the native activity, thus generating a new lactonase that lacks His115. The His115 revertants of these trajectories indicated opposite trends. Revertants of the neo-functionalization trajectory lost both the evolved OPH and the original lactonase activity. Revertants of the trajectory that restored the original lactonase function were, however, fully active. Crystal structures and molecular simulations show that in the newly diverged OPH, the reverted His115 and other catalytic residues are displaced, thus causing loss of both the original and the new activity. In contrast, in the re-functionalization trajectory, reversion compatibility of the original lactonase activity derives from mechanistic versatility whereby multiple residues can fulfill the same task. This versatility enables unique sequence-reversible compositions that are inaccessible when the active site was repurposed toward a new function.
- Published
- 2019
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