Straub, Kristina and Linde, Mona and Kropp, Cosimo and Blanquart, Samuel and Babinger, Patrick and Merkl, Rainer (2019) Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase. BIOLOGICAL CHEMISTRY, 400 (3). pp. 367-381. ISSN 1431-6730, 1437-4315
Full text not available from this repository. (Request a copy)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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | LONG-BRANCH ATTRACTION; PHYLOGENETIC ANALYSES; MAXIMUM-LIKELIHOOD; PROTEIN; EVOLUTIONARY; ENZYME; ALIGNMENT; TAXA; DATABASE; SPECIFICITY; common ancestors; oligomerization; protein design; protein evolution; sequence space |
| Subjects: | 500 Science > 570 Life sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Rainer Merkl |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 16 Apr 2020 08:15 |
| Last Modified: | 16 Apr 2020 08:15 |
| URI: | https://pred.uni-regensburg.de/id/eprint/27467 |
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