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Protein resurrection

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https://www.readbyqxmd.com/read/28494872/using-resurrected-ancestral-proviral-proteins-to-engineer-virus-resistance
#1
Asunción Delgado, Rocio Arco, Beatriz Ibarra-Molero, Jose M Sanchez-Ruiz
Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli...
May 9, 2017: Cell Reports
https://www.readbyqxmd.com/read/28466470/an-osmotin-from-the-resurrection-plant-tripogon-loliiformis-tlosm-confers-tolerance-to-multiple-abiotic-stresses-in-transgenic-rice
#2
Thi Thuy Trang Le, Brett Williams, Sagadevan Mundree
Osmotin is a key protein associated with abiotic and biotic stress response in plants. In this study, an osmotin from the resurrection plant Tripogon loliiformis (TlOsm) was characterized and functionally analyzed under abiotic stress conditions in T. loliiformis as well as in transgenic Nicotiana tabacum (tobacco) and Oryza sativa (rice) plants. Real-time PCR analysis on mixed elicitor cDNA libraries from T. loliiformis showed that TlOsm was upregulated a thousand-fold during the early stages of osmotic stresses (cold, drought, and salinity) in both shoots and roots but down-regulated in shoots during heat stress...
May 3, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28419658/ancestral-haloalkane-dehalogenases-show-robustness-and-unique-substrate-specificity
#3
Petra Babkova, Eva Sebestova, Jan Brezovsky, Radka Chaloupkova, Jiri Damborsky
Ancestral sequence reconstruction (ASR) represents a powerful approach for empirical testing structure-function relationships of diverse proteins. We employed ASR to predict sequences of five ancestral haloalkane dehalogenases (HLDs) from the HLD-II subfamily. Genes encoding the inferred ancestral sequences were synthesized and expressed in Escherichia coli and the resurrected ancestral enzymes AncHLD1-5 were experimentally characterized. Strikingly, the ancestral HLDs exhibited significantly enhanced thermodynamic stability compared to extant enzymes (ΔTm up to 24 °C)...
April 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28398197/emergence-and-evolution-of-an-interaction-between-intrinsically-disordered-proteins
#4
Greta Hultqvist, Emma Åberg, Carlo Camilloni, Gustav N Sundell, Eva Andersson, Jakob Dogan, Celestine N Chi, Michele Vendruscolo, Per Jemth
Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. However, it is not clear how such interactions emerge and evolve on a molecular level. We performed phylogenetic reconstruction, resurrection and biophysical characterization of two interacting disordered protein domains, CID and NCBD. CID appeared after the divergence of protostomes and deuterostomes 450-600 million years ago, while NCBD was present in the protostome/deuterostome ancestor...
April 11, 2017: ELife
https://www.readbyqxmd.com/read/28356519/structural-reconstruction-of-protein-ancestry
#5
Romain Rouet, David B Langley, Peter Schofield, Mary Christie, Brendan Roome, Benjamin T Porebski, Ashley M Buckle, Ben E Clifton, Colin J Jackson, Daniela Stock, Daniel Christ
Ancestral protein reconstruction allows the resurrection and characterization of ancient proteins based on computational analyses of sequences of modern-day proteins. Unfortunately, many protein families are highly divergent and not suitable for sequence-based reconstruction approaches. This limitation is exemplified by the antigen receptors of jawed vertebrates (B- and T-cell receptors), heterodimers formed by pairs of Ig domains. These receptors are believed to have evolved from an extinct homodimeric ancestor through a process of gene duplication and diversification; however molecular evidence has so far remained elusive...
April 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28351347/sporobolus-stapfianus-insights-into-desiccation-tolerance-in-the-resurrection-grasses-from-linking-transcriptomics-to-metabolomics
#6
Abou Yobi, Karen A Schlauch, Richard L Tillett, Won C Yim, Catherine Espinoza, Bernard W M Wone, John C Cushman, Melvin J Oliver
BACKGROUND: Understanding the response of resurrection angiosperms to dehydration and rehydration is critical for deciphering the mechanisms of how plants cope with the rigors of water loss from their vegetative tissues. We have focused our studies on the C4 resurrection grass, Sporobolus stapfianus Gandoger, as a member of a group of important forage grasses. METHODS: We have combined non-targeted metabolomics with transcriptomics, via a NimbleGen array platform, to develop an understanding of how gene expression and metabolite profiles can be linked to generate a more detailed mechanistic appreciation of the cellular response to both desiccation and rehydration...
March 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28337996/protein-interaction-evolution-from-promiscuity-to-specificity-with-reduced-flexibility-in-an-increasingly-complex-network
#7
T Alhindi, Z Zhang, P Ruelens, H Coenen, H Degroote, N Iraci, K Geuten
A key question regarding protein evolution is how proteins adapt to the dynamic environment in which they function and how in turn their evolution shapes the protein interaction network. We used extant and resurrected ancestral plant MADS-domain transcription factors to understand how SEPALLATA3, a protein with hub and glue properties, evolved and takes part in network organization. Although the density of dimeric interactions was saturated in the network, many new interactions became mediated by SEPALLATA3 after a whole genome triplication event...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265281/chloroplast-genome-analysis-of-resurrection-tertiary-relict-haberlea-rhodopensis-highlights-genes-important-for-desiccation-stress-response
#8
Zdravka Ivanova, Gaurav Sablok, Evelina Daskalova, Gergana Zahmanova, Elena Apostolova, Galina Yahubyan, Vesselin Baev
Haberlea rhodopensis is a paleolithic tertiary relict species, best known as a resurrection plant with remarkable tolerance to desiccation. When exposed to severe drought stress, H. rhodopensis shows an ability to maintain the structural integrity of its photosynthetic apparatus, which re-activates easily upon rehydration. We present here the results from the assembly and annotation of the chloroplast (cp) genome of H. rhodopensis, which was further subjected to comparative analysis with the cp genomes of closely related species...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28008088/exploring-the-past-and-the-future-of-protein-evolution-with-ancestral-sequence-reconstruction-the-retro-approach-to-protein-engineering
#9
REVIEW
Yosephine Gumulya, Elizabeth M J Gillam
A central goal in molecular evolution is to understand the ways in which genes and proteins evolve in response to changing environments. In the absence of intact DNA from fossils, ancestral sequence reconstruction (ASR) can be used to infer the evolutionary precursors of extant proteins. To date, ancestral proteins belonging to eubacteria, archaea, yeast and vertebrates have been inferred that have been hypothesized to date from between several million to over 3 billion years ago. ASR has yielded insights into the early history of life on Earth and the evolution of proteins and macromolecular complexes...
January 1, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/27930710/urb-rip-an-adaptable-and-efficient-approach-for-immunoprecipitation-of-rnas-and-associated-rnas-proteins
#10
Kyle A Cottrell, Sergej Djuranovic
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application...
2016: PloS One
https://www.readbyqxmd.com/read/27899133/adaptively-introgressed-neandertal-haplotype-at-the-oas-locus-functionally-impacts-innate-immune-responses-in-humans
#11
Aaron J Sams, Anne Dumaine, Yohann Nédélec, Vania Yotova, Carolina Alfieri, Jerome E Tanner, Philipp W Messer, Luis B Barreiro
BACKGROUND: The 2'-5' oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. RESULTS: Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus...
November 29, 2016: Genome Biology
https://www.readbyqxmd.com/read/27863072/when-directed-evolution-met-ancestral-enzyme-resurrection
#12
Miguel Alcalde
The directed evolution of ancestral -resurrected- enzymes can give a new twist in protein engineering approaches towards more versatile and robust biocatalysts.
January 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/27846568/predictable-convergence-in-hemoglobin-function-has-unpredictable-molecular-underpinnings
#13
Chandrasekhar Natarajan, Federico G Hoffmann, Roy E Weber, Angela Fago, Christopher C Witt, Jay F Storz
To investigate the predictability of genetic adaptation, we examined the molecular basis of convergence in hemoglobin function in comparisons involving 56 avian taxa that have contrasting altitudinal range limits. Convergent increases in hemoglobin-oxygen affinity were pervasive among high-altitude taxa, but few such changes were attributable to parallel amino acid substitutions at key residues. Thus, predictable changes in biochemical phenotype do not have a predictable molecular basis. Experiments involving resurrected ancestral proteins revealed that historical substitutions have context-dependent effects, indicating that possible adaptive solutions are contingent on prior history...
October 21, 2016: Science
https://www.readbyqxmd.com/read/27825296/resurrecting-ancestral-structural-dynamics-of-an-antiviral-immune-receptor-adaptive-binding-pocket-reorganization-repeatedly-shifts-rna-preference
#14
Charles Pugh, Oralia Kolaczkowski, Austin Manny, Bryan Korithoski, Bryan Kolaczkowski
BACKGROUND: Although resurrecting ancestral proteins is a powerful tool for understanding the molecular-functional evolution of gene families, nearly all studies have examined proteins functioning in relatively stable biological processes. The extent to which more dynamic systems obey the same 'rules' governing stable processes is unclear. Here we present the first detailed investigation of the functional evolution of the RIG-like receptors (RLRs), a family of innate immune receptors that detect viral RNA in the cytoplasm...
November 8, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27623311/phosphorylation-of-blar1-in-manifestation-of-antibiotic-resistance-in-methicillin-resistant-staphylococcus-aureus-and-its-abrogation-by-small-molecules
#15
Marc A Boudreau, Jennifer Fishovitz, Leticia I Llarrull, Qiaobin Xiao, Shahriar Mobashery
Methicillin-resistant Staphylococcus aureus (MRSA), an important human pathogen, has evolved an inducible mechanism for resistance to β-lactam antibiotics. We report herein that the integral membrane protein BlaR1, the β-lactam sensor/signal transducer protein, is phosphorylated on exposure to β-lactam antibiotics. This event is critical to the onset of the induction of antibiotic resistance. Furthermore, we document that BlaR1 phosphorylation and the antibiotic-resistance phenotype are both reversed in the presence of synthetic protein kinase inhibitors of our design, restoring susceptibility of the organism to a penicillin, resurrecting it from obsolescence in treatment of these intransigent bacteria...
October 9, 2015: ACS Infectious Diseases
https://www.readbyqxmd.com/read/27600879/rational-design-and-engineering-of-a-mutant-variant-of-urate-oxidase-as-a-therapeutic-enzyme-a-molecular-dynamics-simulation-approach
#16
Sajjad Ahrari, Fatemeh Dabbagh, Sobhan Ahrari, Younes Ghasemi, Navid Mogharrab, Yasser Riazalhosseini
BACKGROUND: Urate oxidase is absent in humans so the enzyme is considered as an important therapeutic agent to control hyperuricemic disorders. Currently available enzymes with pharmaceutical applications have adverse effects associated with allergic reactions and anaphylactic shocks, in case of chronic treatment. Therefore, developing variant forms of the enzyme, with lower immunogenicity and similar or higher activity, is of great importance. AIM: Here, we tried to improve the structure of a recently resurrected ancestral mammalian urate oxidase (which is claimed to have higher enzymatic activity compared to other mammalian counterparts) by introducing eight rational mutations and verified the consequence of these mutations on immunogenicity, stability and the affinity of protein to uric acid by computational techniques...
September 5, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27528732/engineering-ancestral-protein-hyperstability
#17
M Luisa Romero-Romero, Valeria A Risso, Sergio Martinez-Rodriguez, Beatriz Ibarra-Molero, Jose M Sanchez-Ruiz
Many experimental analyses and proposed scenarios support that ancient life was thermophilic. In congruence with this hypothesis, proteins encoded by reconstructed sequences corresponding to ancient phylogenetic nodes often display very high stability. Here, we show that such 'reconstructed ancestral hyperstability' can be further engineered on the basis of a straightforward approach that uses exclusively information afforded by the ancestral reconstruction process itself. Since evolution does not imply continuous progression, screening of the mutations between two evolutionarily related resurrected ancestral proteins may identify mutations that further stabilize the most stable one...
October 15, 2016: Biochemical Journal
https://www.readbyqxmd.com/read/27472806/phylobot-a-web-portal-for-automated-phylogenetics-ancestral-sequence-reconstruction-and-exploration-of-mutational-trajectories
#18
Victor Hanson-Smith, Alexander Johnson
The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and "resurrect" (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function...
July 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27403565/studying-the-supramolecular-organization-of-photosynthetic-membranes-within-freeze-fractured-leaf-tissues-by-cryo-scanning-electron-microscopy
#19
Dana Charuvi, Reinat Nevo, Ifat Kaplan-Ashiri, Eyal Shimoni, Ziv Reich
Cryo-scanning electron microscopy (SEM) of freeze-fractured samples allows investigation of biological structures at near native conditions. Here, we describe a technique for studying the supramolecular organization of photosynthetic (thylakoid) membranes within leaf samples. This is achieved by high-pressure freezing of leaf tissues, freeze-fracturing, double-layer coating and finally cryo-SEM imaging. Use of the double-layer coating method allows acquiring high magnification (>100,000X) images with minimal beam damage to the frozen-hydrated samples as well as minimal charging effects...
2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27352852/coevolution-of-urat1-and-uricase-during-primate-evolution-implications-for-serum-urate-homeostasis-and-gout
#20
Philip K Tan, Jennifer E Farrar, Eric A Gaucher, Jeffrey N Miner
Uric acid is the highly insoluble end-product of purine metabolism in humans. Serum levels exceeding the solubility threshold can trigger formation of urate crystals resulting in gouty arthritis. Uric acid is primarily excreted through the kidneys with 90% reabsorbed back into the bloodstream through the uric acid transporter URAT1. This reabsorption process is essential for the high serum uric acid levels found in humans. We discovered that URAT1 proteins from humans and baboons have higher affinity for uric acid compared with transporters from rats and mice...
September 2016: Molecular Biology and Evolution
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