植物分解の新手法を開発(How plants rot: New method decodes hidden decomposers of wood and leaves)

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2025-08-28 ゲーテ大学

Web要約 の発言:
フランクフルト大学の研究チームは、木材や落ち葉を分解する生物の酵素を網羅的に探索する新手法「fDOG」を開発した。これは18,000種以上のDNAデータから、機能的に対応するオーソログ遺伝子を同定し、タンパク質ドメイン構造も考慮して精度を高める。解析により、従来は分解者とされていた菌類や細菌に加え、昆虫やダニなど節足動物も植物細胞壁分解酵素を持つ可能性が示された。これらの酵素は水平遺伝子移転で獲得したと考えられ、従来想定されていた腸内細菌依存を超えた能力を持つことが浮上。また、菌類では腐生から寄生への生活様式の変化に伴い分解酵素を失った例も確認された。成果は植物分解者の多様性を再評価し、炭素循環理解に新たな視点を提供する。

<関連情報>

fDOGを用いた特徴構造認識型オルソログ検索が明らかにする、植物細胞壁分解酵素の生命圏における分布 Feature Architecture-Aware Ortholog Search With fDOG Reveals the Distribution of Plant Cell Wall-Degrading Enzymes Across Life

Vinh Tran , Felix Langschied , Hannah Muelbaier , Julian Dosch , Freya Arthen , Miklos Balint , Ingo Ebersberger
Molecular Biology and Evolution  Published:09 June 2025
DOI:https://doi.org/10.1093/molbev/msaf120

Feature-aware phylogenetic profiling with fDOG. pHMM Training phase: fDOG extracts the core orthologs used for pHMM training from a set of primer taxa that are ordered according to increasing taxonomic distance to the seed taxon from which the seed protein was taken from (left tree). A minimum and a maximum taxonomic distance of the primer taxa from the seed taxon can be specified to control the diversity of the training data (subtree in black). During pHMM training, fDOG iteratively compiles the core ortholog group and re-trains the pHMM. In each iteration, fDOG uses the current pHMM to identify orthologs across the primer taxa (Ci, …, Cm), it infers their feature architecture similarities (FAS) to the seed protein and orders them according to decreasing similarity of both amino acid sequence and feature architecture to the seed. The highest-ranking sequence is added to the core ortholog set. At the end of each iteration, the core orthologs are aligned and the pHMM is re-trained. Full ortholog search: The final pHMM is used for a profile-based ortholog search across all taxa from a proteome collection. The feature architecture of each detected ortholog is compared to that of the seed protein, and a similarity score (FAS score) is computed. This obtains the feature architecture aware phylogenetic profile of the seed protein (right tree). The color represents the FAS score ranging from 0 (orange; no shared features) to1 (blue; identical feature architectures). See main text for further information. The full workflow is shown in supplementary fig. S1, Supplementary Material online.

Abstract

The decomposition of plant material is a key driver of the global carbon cycle, traditionally attributed to fungi and bacteria. However, some invertebrates also possess orthologs to bacterial or fungal cellulolytic enzymes, likely acquired via horizontal gene transfer. This reticulated mode of evolution necessitates ortholog searches in large taxon sets to comprehensively map the repertoire of plant cell wall-degrading enzymes (PCDs) across the tree of life, a task surpassing capacities of current software. Here, we use fDOG, a novel profile-based ortholog search tool to trace 235 potential PCDs across more than 18,000 taxa. fDOG allows to start the ortholog search from a single protein sequence as a seed, it performs on par with state-of-the-art software that require the comparison of entire proteomes, and it is unique in routinely scoring protein feature architecture differences between the seed protein and its orthologs. Visualizing the presence–absence patterns of PCD orthologs using a Uniform Manifold Approximation and Projection highlights taxa where recent changes in the enzyme repertoire indicate a change in lifestyle. Three invertebrates have a particularly rich set of PCD orthologs encoded in their genome. Only few of the orthologs show differing protein feature architectures relative to the seed that suggest functional modifications. Thus, the corresponding species represent lineages within the invertebrates that may contribute to the global carbon cycle. This study shows how fDOG can be used to create a multi-scale view on the taxonomic distribution of a metabolic capacity that ranges from tree of life-wide surveys to individual feature architecture changes within a species.

生物化学工学
fDOGフランクフルト大学植物分解酵素水平遺伝子移転炭素循環節足動物
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