Whole genome structural predictions reveal hidden diversity in putative oxidative enzymes of the lignocellulose-degrading ascomycete Parascedosporium putredinis NO1.
Whole genome structural predictions reveal hidden diversity in putative oxidative enzymes of the lignocellulose-degrading ascomycete Parascedosporium putredinis NO1.
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DOI：
10.1128/spectrum.01035-23
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发表时间：
2023-12-12
影响因子：
3.7
通讯作者：
Cha, Chang-Jun
中科院分区：
文献类型：
--
作者：
Scott, Conor J. R.;Leadbeater, Daniel R.;Oates, Nicola C.;James, Sally R.;Newling, Katherine;Li, Yi;Mcgregor, Nicholas G. S.;Bird, Susannah;Bruce, Neil C.;Cha, Chang-Jun
关键词：
木质纤维素的经济定价对于实现真正的循环生物经济至关重要；然而，这需要开发系统和工艺，以扩大目前可再生燃料、化学品和可持续材料以外的生物产品的范围。腐烂副孢子菌1号是一种子囊菌，在麦秆堆肥群落培养的后期阶段蓬勃发展，表明有降解顽固的木质素丰富的生物量的倾向，但存在于代表性较低和未被开发的真菌谱系中。在最近发现了一种新的木质素β-乙醚键裂解酶后，该菌株已被证明是鉴定针对木质纤维素顽固组分的新酶的令人兴奋的候选菌株。对腐烂假单胞菌1号基因组进行了测序、组装和注释，得到了该属的第一个基因组。基因组大小为39Mb，由21个重叠群组成，包含9.998个蛋白质编码序列。碳水化合物活性酶(CAZyme)酶谱与2570个子囊菌基因组进行了比较，并详细地与里氏木霉、尖孢镰刀菌和姊妹种球生塞多孢霉进行了比较。在腐烂假单胞菌1号基因组中观察到CAZymes的氧化辅助活性类显著增加，这是由于编码可能的裂解多糖单加氧酶(LPMO)、LPMO氧化还原系统中的氧化酶和木质素降解漆酶的序列增加所致。腐烂假单胞菌1号在子囊菌门中AA基因密度的得分高于第95个百分位数，这表明木质纤维素的分解主要是氧化策略。采用了新的基于结构的搜索方法，发现了17个新的序列，它们与LPMO、漆酶和过氧化物酶序列具有结构相似性，是潜在的新的木质纤维素降解酶。一个注释的参考基因组揭示了腐烂假单胞菌No1是一个有用的资源，用于鉴定新的木质纤维素降解酶，用于木本植物生物量的生物精制。利用基于“结构组学”的搜索策略，我们确定了新的潜在的木质纤维素活性序列，这些序列可能被传统的序列搜索方法遗漏了。这些新的鉴定，加上从这一未被探索的谱系中发现的新的酶功能，以及最近发现的一种新的酚氧化酶，该酶能裂解腐臭假单胞菌1号木质素中的主要结构β-O-4连接，突出了未被探索和未被充分代表的微囊藻科植物是一个特别有趣的候选者，值得进一步探索高价值生物可再生产品的价态。
Economic valorization of lignocellulose is paramount to realizing a true circular bioeconomy; however, this requires the development of systems and processes to expand the repertoire of bioproducts beyond current renewable fuels, chemicals, and sustainable materials. Parascedosporium putredinis NO1 is an ascomycete that thrived at the later stages of a wheat-straw composting community culture, indicating a propensity to degrade recalcitrant lignin-enriched biomass, but exists within an underrepresented and underexplored fungal lineage. This strain has been proven to be an exciting candidate for the identification of new enzymes targeting recalcitrant components of lignocellulose following the recent discovery of a new lignin β-ether linkage cleaving enzyme. The first genome for the genus Parascedosporium for P. putredinis NO1 genome was sequenced, assembled, and annotated. The genome is 39 Mb in size, consisting of 21 contigs annotated to contain 9.998 protein-coding sequences. The carbohydrate-active enzyme (CAZyme) repertoire was compared to 2570 ascomycete genomes and in detail with Trichoderma reesei, Fusarium oxysporum, and sister taxa Scedosporium boydii. Significant expansion in the oxidative auxiliary activity class of CAZymes was observed in the P. putredinis NO1 genome, resulting from increased sequences encoding putative lytic polysaccharide monooxygenases (LPMOs), oxidative enzymes acting within LPMO redox systems, and lignin-degrading laccases. P. putredinis NO1 scored above the 95th percentile for AA gene density across the ascomycete phylum, suggesting a primarily oxidative strategy for lignocellulose breakdown. Novel structure-based searching approaches were employed, revealing 17 new sequences with structural similarity to LPMO, laccase, and peroxidase sequences and which are potentially new lignocellulose-degrading enzymes. An annotated reference genome has revealed P. putredinis NO1 as a useful resource for the identification of new lignocellulose-degrading enzymes for biorefining of woody plant biomass. Utilizing a “structure-omics”-based searching strategy, we identified new potentially lignocellulose-active sequences that would have been missed by traditional sequence searching methods. These new identifications, alongside the discovery of novel enzymatic functions from this underexplored lineage with the recent discovery of a new phenol oxidase that cleaves the main structural β-O-4 linkage in lignin from P. putredinis NO1, highlight the underexplored and poorly represented family Microascaceae as a particularly interesting candidate worthy of further exploration toward the valorization of high value biorenewable products.
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影响因子：
6.4
作者：
Craig JP;Coradetti ST;Starr TL;Glass NL
通讯作者：
Glass NL
影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
影响因子：
5.2
作者：
Anasontzis GE;Kourtoglou E;Villas-Boâs SG;Hatzinikolaou DG;Christakopoulos P
通讯作者：
Christakopoulos P
影响因子：
4.6
作者：
Pardo I;Rodríguez-Escribano D;Aza P;de Salas F;Martínez AT;Camarero S
通讯作者：
Camarero S
影响因子：
14.9
作者：
Drula E;Garron ML;Dogan S;Lombard V;Henrissat B;Terrapon N
通讯作者：
Terrapon N