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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

Small design from big alignment: engineering proteins with multiple sequence alignment as the starting point.

Tianwen Wang¹, Chen Liang², Yajing Hou²

¹College of Life Sciences, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China. tianwenw@gmail.com.

Biotechnology Letters

|May 21, 2020

Summary

This summary is machine-generated.

Multiple sequence alignment (MSA) aids protein engineering by revealing evolutionary relationships. This review highlights how MSA advances protein thermostability, solubility, and function through methods like consensus sequencing and ancestral sequence reconstruction.

Keywords:

Ancestral sequence reconstruction Coevolutionary analysis Comparative structure modeling Consensus sequence Multiple sequence alignment Protein engineering

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Area of Science:

Biochemistry and Molecular Biology
Bioinformatics
Protein Engineering

Background:

Multiple sequence alignment (MSA) is crucial for understanding evolutionary relationships between protein sequences.
Analyzing individual sequences is insufficient; MSA provides comparative insights into sequence-function correlations.
MSA serves as a foundational reference for advanced protein engineering strategies.

Purpose of the Study:

To review recent advancements in protein engineering that leverage multiple sequence alignment (MSA).
To elucidate how MSA-derived information enhances protein properties and enables novel engineering approaches.

Main Methods:

Engineering protein thermostability and solubility by mutating sequences towards the alignment consensus.
Structure-based protein engineering utilizing comparative modeling informed by MSA.
Reconstructing ancestral protein sequences from MSA to create thermostable and promiscuous paleoenzymes.
Identifying and targeting evolutionarily coupled sites within MSA for site-specific mutations.

Main Results:

MSA enables targeted mutations to improve protein stability and solubility.
Comparative modeling, guided by MSA, facilitates structure-based protein design.
Ancestral sequence reconstruction from MSA yields enzymes with enhanced thermostability and promiscuity.
Targeting co-evolving sites identified via MSA leads to functional protein improvements.

Conclusions:

Multiple sequence alignment is a powerful tool that significantly benefits protein engineering.
MSA-driven strategies offer diverse approaches to enhance protein function, stability, and create novel biocatalysts.