scholarly journals The molecular signal for the adaptation to cold temperature during early life on Earth

2013 ◽  
Vol 9 (5) ◽  
pp. 20130608 ◽  
Author(s):  
Mathieu Groussin ◽  
Bastien Boussau ◽  
Sandrine Charles ◽  
Samuel Blanquart ◽  
Manolo Gouy
Keyword(s):  
Phylogenetic Trees ◽  
Large Scale ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Optimal Growth ◽  
Ancestral Sequence ◽  
Rate Variation ◽  
Last Common Ancestor ◽  
Ancestral Sequence Reconstruction ◽  
Sequence Reconstruction

Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of single enzymes or large protein concatenations support the conclusion that the ancestors of the bacterial and archaeal domains were thermophilic organisms which were adapted to hot environments during the early stages of the Earth. A parsimonious reasoning would therefore suggest that the last universal common ancestor (LUCA) was also thermophilic. Various authors have used branch-wise non-homogeneous evolutionary models that better capture the variation of molecular compositions among lineages to accurately reconstruct the ancestral G + C contents of ribosomal RNAs and the ancestral amino acid composition of highly conserved proteins. They confirmed the thermophilic nature of the ancestors of Bacteria and Archaea but concluded that LUCA, their last common ancestor, was a mesophilic organism having a moderate optimal growth temperature. In this letter, we investigate the unknown nature of the phylogenetic signal that informs ancestral sequence reconstruction to support this non-parsimonious scenario. We find that rate variation across sites of molecular sequences provides information at different time scales by recording the oldest adaptation to temperature in slow-evolving regions and subsequent adaptations in fast-evolving ones.

scholarly journals Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase

2019 ◽  
Vol 400 (3) ◽  
pp. 367-381 ◽  
Author(s):  
Kristina Straub ◽  
Mona Linde ◽  
Cosimo Kropp ◽  
Samuel Blanquart ◽  
Patrick Babinger ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Specific Property ◽  
Ancestral Sequence ◽  
Rational Approach ◽  
Ancestral Sequence Reconstruction ◽  
Representative Sequence ◽  
Sequence Selection ◽  
Sequence Reconstruction ◽  
Phosphate Synthase

Abstract For evolutionary studies, but also for protein engineering, ancestral sequence reconstruction (ASR) has become an indispensable tool. The first step of every ASR protocol is the preparation of a representative sequence set containing at most a few hundred recent homologs whose composition determines decisively the outcome of a reconstruction. A common approach for sequence selection consists of several rounds of manual recompilation that is driven by embedded phylogenetic analyses of the varied sequence sets. For ASR of a geranylgeranylglyceryl phosphate synthase, we additionally utilized FitSS4ASR, which replaces this time-consuming protocol with an efficient and more rational approach. FitSS4ASR applies orthogonal filters to a set of homologs to eliminate outlier sequences and those bearing only a weak phylogenetic signal. To demonstrate the usefulness of FitSS4ASR, we determined experimentally the oligomerization state of eight predecessors, which is a delicate and taxon-specific property. Corresponding ancestors deduced in a manual approach and by means of FitSS4ASR had the same dimeric or hexameric conformation; this concordance testifies to the efficiency of FitSS4ASR for sequence selection. FitSS4ASR-based results of two other ASR experiments were added to the Supporting Information. Program and documentation are available at https://gitlab.bioinf.ur.de/hek61586/FitSS4ASR.

scholarly journals Divergent evolution of a protein-protein interaction revealed through ancestral sequence reconstruction and resurrection

2020 ◽  
Author(s):  
Louise Laursen ◽  
Jelena Čalyševa ◽  
Toby J. Gibson ◽  
Per Jemth
Keyword(s):  
Protein Interaction ◽  
Postsynaptic Density ◽  
Ancestral Sequence ◽  
Scaffolding Protein ◽  
Divergent Evolution ◽  
Last Common Ancestor ◽  
Interaction Domain ◽  
Protein Protein Interaction ◽  
Ancestral Sequence Reconstruction ◽  
Sequence Reconstruction

AbstractThe postsynaptic density extends across the postsynaptic dendritic spine with Discs large (DLG) as the most abundant scaffolding protein. DLG dynamically alters the structure of the postsynaptic density, thus controlling the function and distribution of specific receptors at the synapse. PDZ domains make up one of the most abundant protein interaction domain families in animals. One important interaction governing postsynaptic architecture is that between the PDZ3 domain from DLG and cysteine-rich interactor of PDZ3 (CRIPT). However, little is know regarding functional evolution of the PDZ3:CRIPT interaction. Here, we subjected PDZ3 and CRIPT to ancestral sequence reconstruction, resurrection and biophysical experiments. We show that the PDZ3:CRIPT interaction is an ancient interaction, which was present in the last common ancestor of Eukaryotes, and that high affinity is maintained in most extant animal phyla. However, affinity is low in nematodes and insects, raising questions about the physiological function of the interaction in species from these animal groups. Our findings demonstrate how an apparently established protein-protein interaction involved in cellular scaffolding in bilaterians can suddenly be subject to dynamic evolution including possible loss of function.

scholarly journals Divergent Evolution of a Protein–Protein Interaction Revealed through Ancestral Sequence Reconstruction and Resurrection

2020 ◽  
Vol 38 (1) ◽  
pp. 152-167
Author(s):  
Louise Laursen ◽  
Jelena Čalyševa ◽  
Toby J Gibson ◽  
Per Jemth
Keyword(s):  
Protein Interaction ◽  
Postsynaptic Density ◽  
Ancestral Sequence ◽  
Scaffolding Protein ◽  
Divergent Evolution ◽  
Last Common Ancestor ◽  
Loss Of Function ◽  
Protein Protein Interaction ◽  
Ancestral Sequence Reconstruction ◽  
Sequence Reconstruction

Abstract The postsynaptic density extends across the postsynaptic dendritic spine with discs large (DLG) as the most abundant scaffolding protein. DLG dynamically alters the structure of the postsynaptic density, thus controlling the function and distribution of specific receptors at the synapse. DLG contains three PDZ domains and one important interaction governing postsynaptic architecture is that between the PDZ3 domain from DLG and a protein called cysteine-rich interactor of PDZ3 (CRIPT). However, little is known regarding functional evolution of the PDZ3:CRIPT interaction. Here, we subjected PDZ3 and CRIPT to ancestral sequence reconstruction, resurrection, and biophysical experiments. We show that the PDZ3:CRIPT interaction is an ancient interaction, which was likely present in the last common ancestor of Eukaryotes, and that high affinity is maintained in most extant animal phyla. However, affinity is low in nematodes and insects, raising questions about the physiological function of the interaction in species from these animal groups. Our findings demonstrate how an apparently established protein–protein interaction involved in cellular scaffolding in bilaterians can suddenly be subject to dynamic evolution including possible loss of function.

Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the ‘retro’ approach to protein engineering

2016 ◽  
Vol 474 (1) ◽  
pp. 1-19 ◽  
Author(s):  
Yosephine Gumulya ◽  
Elizabeth M.J. Gillam
Keyword(s):  
Protein Engineering ◽  
Protein Evolution ◽  
Phylogenetic Trees ◽  
Ancestral Sequence ◽  
Novel Proteins ◽  
Ancestral Sequence Reconstruction ◽  
Ancestral Sequences ◽  
Sequence Reconstruction ◽  
Ancient Proteins ◽  
Life On Earth

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. Recently, however, ASR has developed from a tool for testing hypotheses about protein evolution to a useful means for designing novel proteins. The strength of this approach lies in the ability to infer ancestral sequences encoding proteins that have desirable properties compared with contemporary forms, particularly thermostability and broad substrate range, making them good starting points for laboratory evolution. Developments in technologies for DNA sequencing and synthesis and computational phylogenetic analysis have led to an escalation in the number of ancient proteins resurrected in the last decade and greatly facilitated the use of ASR in the burgeoning field of synthetic biology. However, the primary challenge of ASR remains in accurately inferring ancestral states, despite the uncertainty arising from evolutionary models, incomplete sequences and limited phylogenetic trees. This review will focus, firstly, on the use of ASR to uncover links between sequence and phenotype and, secondly, on the practical application of ASR in protein engineering.

scholarly journals Response to Comment on “Ancient origins of allosteric activation in a Ser-Thr kinase”

Science ◽  
2020 ◽  
Vol 370 (6519) ◽  
pp. eabd0364
Author(s):  
Christopher Wilson ◽  
Dorothee Kern
Keyword(s):  
Common Ancestor ◽  
Species Tree ◽  
Ancestral Sequence ◽  
Gene Trees ◽  
Allosteric Activation ◽  
Ancestral Sequence Reconstruction ◽  
Sequence Reconstruction

Park et al. question one out of seven findings from Hadzipasic et al.: whether TPX2 allosterically regulates the oldest Aurora. We had already addressed the two concerns raised—sparse sequence sampling and not forcing the gene to the species tree—before publication. Moreover, we believe their ancestral sequence reconstruction would be consistent with a nonallosteric common ancestor, and we show large sequence differences caused by species tree–enforced gene trees.

scholarly journals Accounting for ambiguity in ancestral sequence reconstruction

2019 ◽  
Vol 35 (21) ◽  
pp. 4290-4297 ◽  
Author(s):  
A Oliva ◽  
S Pulicani ◽  
V Lefort ◽  
L Bréhélin ◽  
O Gascuel ◽  
...  
Keyword(s):  
Amino Acid ◽  
Large Scale ◽  
Amino Acid Sequences ◽  
Ancestral Sequence ◽  
Tuning Parameters ◽  
Ancestral Sequence Reconstruction ◽  
Sequence Reconstruction ◽  
Phylogenetic Framework ◽  
Genetic Sequences ◽  
New Criterion

Abstract Motivation The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used to infer nucleotide, amino-acid or codon states at internal nodes of the tree, for every position along the sequence. These criteria generally select the state that maximizes (or minimizes) a given criterion. Although it is perfectly sensible from a statistical perspective, that strategy fails to convey useful information about the level of uncertainty associated to the inference. Results The present study introduces a new criterion for ancestral sequence reconstruction, the minimum posterior expected error (MPEE), that selects a single state whenever the signal conveyed by the data is strong, and a combination of multiple states otherwise. We also assess the performance of a criterion based on the Brier scoring scheme which, like MPEE, does not rely on any tuning parameters. The precision and accuracy of several other criteria that involve arbitrarily set tuning parameters are also evaluated. Large scale simulations demonstrate the benefits of using the MPEE and Brier-based criteria with a substantial increase in the accuracy of the inference of past sequences compared to the standard approach and realistic compromises on the precision of the solutions returned. Availability and implementation The software package PhyML (https://github.com/stephaneguindon/phyml) provides an implementation of the Maximum A Posteriori (MAP) and MPEE criteria for reconstructing ancestral nucleotide and amino-acid sequences.

scholarly journals Insertions and deletions as phylogenetic signal in alignment-free sequence comparison

2021 ◽  
Author(s):  
Niklas Birth ◽  
Thomas Dencker ◽  
Burkhard Morgenstern
Keyword(s):  
Sequence Comparison ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Last Common Ancestor ◽  
Amino Acid Residues ◽  
Tree Reconstruction ◽  
Sequence Alignments ◽  
Insertions And Deletions ◽  
Alignment Free

AbstractMost methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies based on aligned nucleotide or amino-acid residues. Gaps in alignments are usually not used as phylogenetic signal, even though they can, in principle, provide valuable information. In this paper, we explore an alignment-free approach to utilize insertions and deletions for phylogeny inference. We are using our previously developed approach Multi-SpaM, to generate local gap-free four-way alignments, so-called quartet blocks. For pairs of quartet blocks involving the same four sequences, we consider the distances between these blocks in the four sequences, to obtain hints about insertions or deletions that may have occurred since the four sequences evolved from their last common ancestor. This way, a pair of quartet blocks can support one of the three possible quartet topologies for the four involved sequences. We use this information as input for Maximum-Parsimony and for the software program Quartet MaxCut to reconstruct phylogenetic trees that are only based on insertions and deletions.

Ancestral sequence reconstruction for protein engineers

2021 ◽  
Vol 69 ◽  
pp. 131-141
Author(s):  
Matthew A. Spence ◽  
Joe A. Kaczmarski ◽  
Jake W. Saunders ◽  
Colin J. Jackson
Keyword(s):  
Ancestral Sequence ◽  
Ancestral Sequence Reconstruction ◽  
Sequence Reconstruction

scholarly journals Ancestral sequence reconstruction produces thermally stable enzymes with mesophilic enzyme-like catalytic properties

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ryutaro Furukawa ◽  
Wakako Toma ◽  
Koji Yamazaki ◽  
Satoshi Akanuma
Keyword(s):  
Low Temperature ◽  
Catalytic Properties ◽  
Amino Acid Sequences ◽  
Ancestral Sequence ◽  
Kinetic Properties ◽  
Reconstruction Technique ◽  
Thermally Stable ◽  
Ancestral Sequence Reconstruction ◽  
Ancestral Sequences ◽  
Sequence Reconstruction

Abstract Enzymes have high catalytic efficiency and low environmental impact, and are therefore potentially useful tools for various industrial processes. Crucially, however, natural enzymes do not always have the properties required for specific processes. It may be necessary, therefore, to design, engineer, and evolve enzymes with properties that are not found in natural enzymes. In particular, the creation of enzymes that are thermally stable and catalytically active at low temperature is desirable for processes involving both high and low temperatures. In the current study, we designed two ancestral sequences of 3-isopropylmalate dehydrogenase by an ancestral sequence reconstruction technique based on a phylogenetic analysis of extant homologous amino acid sequences. Genes encoding the designed sequences were artificially synthesized and expressed in Escherichia coli. The reconstructed enzymes were found to be slightly more thermally stable than the extant thermophilic homologue from Thermus thermophilus. Moreover, they had considerably higher low-temperature catalytic activity as compared with the T. thermophilus enzyme. Detailed analyses of their temperature-dependent specific activities and kinetic properties showed that the reconstructed enzymes have catalytic properties similar to those of mesophilic homologues. Collectively, our study demonstrates that ancestral sequence reconstruction can produce a thermally stable enzyme with catalytic properties adapted to low-temperature reactions.

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