Genetic improvement of low-lignin poplars: a new strategy based on molecular recognition, chemical reactions and empirical breeding.

IF 5.4 2区 生物学 Q1 PLANT SCIENCES Physiologia plantarum Pub Date : 2025-01-01 DOI:10.1111/ppl.70011
Huaichuan Duan, Siyao Li, Xin Wang, Yutong Ge, Yuting Song, Dongling Hu, Wei Liu, Jianping Hu, Hubing Shi
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Abstract

As an important source of pollution in the papermaking process, the presence of lignin in poplar can seriously affect the quality and process of pulping. During lignin synthesis, Caffeoyl-CoA-O methyltransferase (CCoAOMT), as a specialized catalytic transferase, can effectively regulate the methylation of caffeoyl-coenzyme A (CCoA) to feruloyl-coenzyme A. Targeting CCoAOMT, this study investigated the substrate recognition mechanism and the possible reaction mechanism, the key residues of lignin binding were mutated and the lignin content was validated by deep convolutional neural-network model based on genome-wide prediction (DCNGP). The molecular mechanics results indicate that the binding of S-adenosyl methionine (SAM) and CCoA is sequential, with SAM first binding and inducing inward constriction of the CCoAOMT; then CCoA binds to the pocket, and this process closes the outer channel, preventing contamination by impurities and ensuring that the reaction proceeds. Next, the key residues in the recognition process of SAM (F69 and D91) and CCoA (I40, N170, Y188 and D218) were analyzed, and we identified that K146 as a base catalyst is important for inducing the methylation reaction. Immediately after that, the possible methylation reaction mechanism was deduced by the combination of Restrained Electrostatic Potential (RESP) and Independent Gradient Model (IGM) analysis, focusing on the catalytic center electron cloud density and RESP charge distribution. Finally, the DCNGP results verified that the designed mutant groups were all able to effectively reduce the lignin content and increase the S-lignin content/ G-lignin content ratio, which was beneficial for the subsequent lignin removal. Multifaceted consideration of factors that reduce lignin content and combined deep learning to screen for favorable mutations in target traits provides new ideas for targeted breeding of low-lignin poplars.

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低木质素杨树遗传改良:基于分子识别、化学反应和经验育种的新策略。
作为造纸过程中的重要污染源,木质素的存在会严重影响制浆质量和制浆过程。在木质素合成过程中,咖啡酰基辅酶a - o甲基转移酶(CCoAOMT)作为一种专门的催化转移酶,可以有效调节咖啡酰基辅酶a (CCoA)甲基化为阿铁酰辅酶a。本研究针对CCoAOMT,研究了底物识别机制和可能的反应机制,突变了木质素结合的关键残基,并通过基于全基因组预测(DCNGP)的深度卷积神经网络模型验证了木质素含量。分子力学结果表明,s -腺苷蛋氨酸(SAM)与CCoA的结合是顺序的,SAM首先结合并诱导CCoAOMT向内收缩;然后CCoA结合在口袋上,这个过程关闭了外部通道,防止了杂质的污染,确保了反应的进行。接下来,我们分析了SAM (F69和D91)和CCoA (I40, N170, Y188和D218)识别过程中的关键残基,我们发现K146作为碱基催化剂对诱导甲基化反应很重要。随后,结合抑制静电势(RESP)和独立梯度模型(IGM)分析,重点分析了催化中心电子云密度和RESP电荷分布,推导了可能的甲基化反应机理。最后,DCNGP结果验证了所设计的突变体组均能有效降低木质素含量,提高s -木质素含量/ g -木质素含量比,有利于后续的木质素脱除。从多方面考虑降低木质素含量的因素,结合深度学习筛选目标性状的有利突变,为低木质素杨树的定向育种提供了新的思路。
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来源期刊
Physiologia plantarum
Physiologia plantarum 生物-植物科学
CiteScore
11.00
自引率
3.10%
发文量
224
审稿时长
3.9 months
期刊介绍: Physiologia Plantarum is an international journal committed to publishing the best full-length original research papers that advance our understanding of primary mechanisms of plant development, growth and productivity as well as plant interactions with the biotic and abiotic environment. All organisational levels of experimental plant biology – from molecular and cell biology, biochemistry and biophysics to ecophysiology and global change biology – fall within the scope of the journal. The content is distributed between 5 main subject areas supervised by Subject Editors specialised in the respective domain: (1) biochemistry and metabolism, (2) ecophysiology, stress and adaptation, (3) uptake, transport and assimilation, (4) development, growth and differentiation, (5) photobiology and photosynthesis.
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