Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants?

Scossa, Federico; Fernie, Alisdair R.

doi:10.1016/j.csbj.2021.03.008

Cited by 13 publications

(9 citation statements)

References 231 publications

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“…There are challenges to examining these timelines experimentally. 102,103 However, with increased taxa sampling and increasingly sophisticated phylogenomic methods, we are beginning to piece together how BGCs emerged and diversied.…”

Section: Cluster Evolutionmentioning

confidence: 99%

“…Attempts to understand the birth of a BGC may involve identifying the ancestral gene composition of relevant loci using comparative genomics, and predicting the activities of ancestral genes using phylogenetics, annotation or experimentation. The BGC responsible for nepetalactone biosynthesis in Nepeta was investigated using such an approach, including ancestral sequence reconstruction 100,103 (Fig. 7).…”

Section: Tracking Cluster Originsmentioning

confidence: 99%

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Plant biosynthetic gene clusters in the context of metabolic evolution

Smit

Lichman

2022

Nat. Prod. Rep.

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Section: Cluster Evolutionmentioning

confidence: 99%

Section: Tracking Cluster Originsmentioning

confidence: 99%

Plant biosynthetic gene clusters in the context of metabolic evolution

Smit

Lichman

2022

Nat. Prod. Rep.

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“…A previous study that included a panel of 145 wild-type microbial esterases unambiguously concluded that there is a direct relationship between enzyme enantioselectivity and substrate specificity . In addition, ancestral enzymes are generally considered to have a broader substrate scope compared to enzymes sourced from extant genes . The enantioselectivity results of our 101-enzyme panel when tested with substrate 1a support this general scientific consensus.…”

Section: Results and Discussionmentioning

confidence: 99%

Ancestral Sequence Reconstruction Enhances Gene Mining Efforts for Industrial Ene Reductases by Expanding Enzyme Panels with Thermostable Catalysts

et al. 2023

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Ancestral sequence reconstruction (ASR) has been used to produce enzymes that exhibit enhanced stability, activity, and promiscuity compared to wild-type (WT) enzymes. In this work, we compiled a panel of 57 closely related wild-type ene reductases and 56 counterpart ancestral enzymes and statistically compared their biocatalytic properties. Enzyme activity, selectivity, thermostability, and expression level distributions were used to compare their performance. ASR and WT enzymes exhibited comparable activity and overexpression levels, but ASR enzymes displayed enhanced average thermostability (by 9 °C) compared to their wild-type counterparts. Our results demonstrate that ASR-derived ene reductase enzymes may be used as a complement to wild-type enzymes and may provide a superior source of biocatalysts for alkene reduction for industrial applications.

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“…Functional studies in emerging genetic models of extant streptophyte algae should help answer these questions (Zhou et al , 2020). Likewise, reconstructing ancestral proteins could help to understand the evolutionary trajectory that caused the auxin responses, protein structure, and function to diverge in the green lineages (Scossa & Fernie, 2021).…”

Section: Giant Steps…mentioning

confidence: 99%

The birth of a giant: evolutionary insights into the origin of auxin responses in plants

et al. 2023

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The plant signaling molecule auxin is present in multiple kingdoms of life. Since its discovery, a century of research has been focused on its action as a phytohormone. In land plants, auxin regulates growth and development through transcriptional and non‐transcriptional programs. Some of the molecular mechanisms underlying these responses are well understood, mainly in Arabidopsis. Recently, the availability of genomic and transcriptomic data of green lineages, together with phylogenetic inference, has provided the basis to reconstruct the evolutionary history of some components involved in auxin biology. In this review, we follow the evolutionary trajectory that allowed auxin to become the “giant” of plant biology by focusing on bryophytes and streptophyte algae. We consider auxin biosynthesis, transport, physiological, and molecular responses, as well as evidence supporting the role of auxin as a chemical messenger for communication within ecosystems. Finally, we emphasize that functional validation of predicted orthologs will shed light on the conserved properties of auxin biology among streptophytes.

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Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants?

Abstract: Graphical abstract

Cited by 13 publications

References 231 publications

Plant biosynthetic gene clusters in the context of metabolic evolution

Plant biosynthetic gene clusters in the context of metabolic evolution

Ancestral Sequence Reconstruction Enhances Gene Mining Efforts for Industrial Ene Reductases by Expanding Enzyme Panels with Thermostable Catalysts

The birth of a giant: evolutionary insights into the origin of auxin responses in plants

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