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Ancestral sequence reconstruction as a tool to study the evolution of wood decaying fungi. 祖先序列重建作为研究木材腐朽真菌进化的工具。
Q3 MYCOLOGY Pub Date : 2022-10-14 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.1003489
Iván Ayuso-Fernández, Gonzalo Molpeceres, Susana Camarero, Francisco Javier Ruiz-Dueñas, Angel T Martínez

The study of evolution is limited by the techniques available to do so. Aside from the use of the fossil record, molecular phylogenetics can provide a detailed characterization of evolutionary histories using genes, genomes and proteins. However, these tools provide scarce biochemical information of the organisms and systems of interest and are therefore very limited when they come to explain protein evolution. In the past decade, this limitation has been overcome by the development of ancestral sequence reconstruction (ASR) methods. ASR allows the subsequent resurrection in the laboratory of inferred proteins from now extinct organisms, becoming an outstanding tool to study enzyme evolution. Here we review the recent advances in ASR methods and their application to study fungal evolution, with special focus on wood-decay fungi as essential organisms in the global carbon cycling.

进化研究受到现有技术的限制。除了使用化石记录外,分子系统发育学还可以使用基因、基因组和蛋白质对进化史进行详细描述。然而,这些工具提供了感兴趣的生物体和系统的稀缺生物化学信息,因此在解释蛋白质进化时非常有限。在过去的十年里,祖先序列重建(ASR)方法的发展克服了这一限制。ASR允许从现已灭绝的生物体中推断出的蛋白质在实验室中复活,成为研究酶进化的杰出工具。本文综述了ASR方法的最新进展及其在真菌进化研究中的应用,特别关注木材腐朽真菌作为全球碳循环中的重要生物。
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引用次数: 1
Mycovirus-encoded suppressors of RNA silencing: Possible allies or enemies in the use of RNAi to control fungal disease in crops. 真菌病毒编码的RNA沉默抑制剂:利用RNAi控制作物真菌疾病的可能盟友或敌人。
Q3 MYCOLOGY Pub Date : 2022-10-10 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.965781
Lorena Rodriguez Coy, Kim M Plummer, Mahmoud E Khalifa, Robin M MacDiarmid

Plants, fungi, and many other eukaryotes have evolved an RNA interference (RNAi) mechanism that is key for regulating gene expression and the control of pathogens. RNAi inhibits gene expression, in a sequence-specific manner, by recognizing and deploying cognate double-stranded RNA (dsRNA) either from endogenous sources (e.g. pre-micro RNAs) or exogenous origin (e.g. viruses, dsRNA, or small interfering RNAs, siRNAs). Recent studies have demonstrated that fungal pathogens can transfer siRNAs into plant cells to suppress host immunity and aid infection, in a mechanism termed cross-kingdom RNAi. New technologies, based on RNAi are being developed for crop protection against insect pests, viruses, and more recently against fungal pathogens. One example, is host-induced gene silencing (HIGS), which is a mechanism whereby transgenic plants are modified to produce siRNAs or dsRNAs targeting key transcripts of plants, or their pathogens or pests. An alternative gene regulation strategy that also co-opts the silencing machinery is spray-induced gene silencing (SIGS), in which dsRNAs or single-stranded RNAs (ssRNAs) are applied to target genes within a pathogen or pest. Fungi also use their RNA silencing machinery against mycoviruses (fungal viruses) and mycoviruses can deploy virus-encoded suppressors of RNAi (myco-VSRs) as a counter-defence. We propose that myco-VSRs may impact new dsRNA-based management methods, resulting in unintended outcomes, including suppression of management by HIGS or SIGS. Despite a large diversity of mycoviruses being discovered using high throughput sequencing, their biology is poorly understood. In particular, the prevalence of mycoviruses and the cellular effect of their encoded VSRs are under-appreciated when considering the deployment of HIGS and SIGS strategies. This review focuses on mycoviruses, their VSR activities in fungi, and the implications for control of pathogenic fungi using RNAi.

植物、真菌和许多其他真核生物已经进化出RNA干扰(RNAi)机制,这是调节基因表达和控制病原体的关键。RNAi通过识别和部署来自内源性来源(如前微RNA)或外源性来源(如病毒、dsRNA或小干扰RNA、siRNA)的同源双链RNA(dsRNA),以序列特异性方式抑制基因表达。最近的研究表明,真菌病原体可以将siRNA转移到植物细胞中,以抑制宿主免疫并帮助感染,其机制称为跨王国RNAi。基于RNAi的新技术正在开发中,用于作物抵御害虫、病毒,最近还用于抵御真菌病原体。一个例子是宿主诱导的基因沉默(HIGS),这是一种转基因植物被修饰以产生靶向植物或其病原体或害虫的关键转录物的siRNA或dsRNA的机制。另一种选择沉默机制的基因调控策略是喷雾诱导基因沉默(SIGS),其中将dsRNA或单链RNA(ssRNA)应用于病原体或害虫内的靶基因。真菌还利用其RNA沉默机制对抗真菌病毒(真菌病毒),真菌病毒可以部署病毒编码的RNAi抑制剂(myco-VSRs)作为防御。我们提出,分枝杆菌VSRs可能会影响新的基于dsRNA的管理方法,导致意想不到的结果,包括抑制HIGS或SIGS的管理。尽管使用高通量测序发现了大量多样的分枝杆菌病毒,但人们对其生物学知之甚少。特别是,在考虑HIGS和SIGS策略的部署时,真菌病毒的流行率及其编码的VSR的细胞效应被低估了。本文综述了真菌病毒及其在真菌中的VSR活性,以及利用RNAi控制病原真菌的意义。
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引用次数: 3
Fungal species associated with grapevine trunk diseases in Washington wine grapes and California table grapes, with novelties in the genera Cadophora, Cytospora, and Sporocadus. 华盛顿酿酒葡萄和加利福尼亚食用葡萄中与葡萄树干疾病有关的真菌种,在Cadphora属、Cytospora属和Sporocadus属中有新发现。
IF 2.1 Q3 MYCOLOGY Pub Date : 2022-10-07 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.1018140
Renaud Travadon, Daniel P Lawrence, Michelle M Moyer, Phillip T Fujiyoshi, Kendra Baumgartner

Grapevine trunk diseases cause serious economic losses to grape growers worldwide. The identification of the causal fungi is critical to implementing appropriate management strategies. Through a culture-based approach, we identified the fungal species composition associated with symptomatic grapevines from wine grapes in southeastern Washington and table grapes in the southern San Joaquin Valley of California, two regions with contrasting winter climates. Species were confirmed through molecular identification, sequencing two to six gene regions per isolate. Multilocus phylogenetic analyses were used to identify novel species. We identified 36 species from 112 isolates, with a combination of species that are new to science, are known causal fungi of grapevine trunk diseases, or are known causal fungi of diseases of other woody plants. The novel species Cadophora columbiana, Cytospora macropycnidia, Cytospora yakimana, and Sporocadus incarnatus are formally described and introduced, six species are newly reported from North America, and grape is reported as a new host for three species. Six species were shared between the two regions: Cytospora viticola, Diatrype stigma, Diplodia seriata, Kalmusia variispora, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. Dominating the fungal community in Washington wine grape vineyards were species in the fungal families Diatrypaceae, Cytosporaceae and Sporocadaceae, whereas in California table grape vineyards, the dominant species were in the families Diatrypaceae, Togniniaceae, Phaeomoniellaceae and Hymenochaetaceae. Pathogenicity tests demonstrated that 10 isolates caused wood discoloration similar to symptomatic wood from which they were originally isolated. Growth rates at temperatures from 5 to 35°C of 10 isolates per region, suggest that adaptation to local climate might explain their distribution.

葡萄树干病害给世界各地的葡萄种植者造成了严重的经济损失。病原真菌的鉴定对于实施适当的管理策略至关重要。通过基于培养的方法,我们从华盛顿东南部的酿酒葡萄和加利福尼亚州圣华金谷南部的食用葡萄中确定了与有症状葡萄藤相关的真菌物种组成,这两个地区的冬季气候截然不同。物种通过分子鉴定得到确认,每个分离株测序两到六个基因区域。多基因座系统发育分析用于鉴定新物种。我们从112个分离株中鉴定了36个物种,这些物种是科学上新发现的,是葡萄树干疾病的已知致病真菌,或是其他木本植物疾病的已知病原真菌。正式描述并介绍了新物种Cadphora columbiana、Cytospora macropycnidia、Cytosora yakimana和Sporocadus incarnatus,其中6种来自北美,葡萄是3种的新宿主。这两个地区共有六个物种:葡萄胞孢菌、Diatrype柱头、seriata Diplodia、变种Kalmusia varispora、最小Phaeoacremonium和厚垣Phaeomoniella chlamydospora。在华盛顿葡萄酒葡萄园中,真菌群落中占主导地位的是双锥菌科、胞孢菌科和孢子菌科,而在加利福尼亚葡萄园,真菌群落的主导物种是双锥虫科、番茄科、Phaeomonielaceae和膜壳菌科。致病性测试表明,10个分离株导致木材变色,与它们最初分离的有症状的木材相似。每个地区10个分离株在5至35°C温度下的生长率表明,适应当地气候可能解释了它们的分布。
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引用次数: 0
Genome mining as a biotechnological tool for the discovery of novel biosynthetic genes in lichens. 基因组挖掘作为在地衣中发现新的生物合成基因的生物技术工具。
Q3 MYCOLOGY Pub Date : 2022-10-03 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.993171
Garima Singh, Francesco Dal Grande, Imke Schmitt

Natural products (NPs) and their derivatives are a major contributor to modern medicine. Historically, microorganisms such as bacteria and fungi have been instrumental in generating drugs and lead compounds because of the ease of culturing and genetically manipulating them. However, the ever-increasing demand for novel drugs highlights the need to bioprospect previously unexplored taxa for their biosynthetic potential. Next-generation sequencing technologies have expanded the range of organisms that can be explored for their biosynthetic content, as these technologies can provide a glimpse of an organism's entire biosynthetic landscape, without the need for cultivation. The entirety of biosynthetic genes can be compared to the genes of known function to identify the gene clusters potentially coding for novel products. In this study, we mine the genomes of nine lichen-forming fungal species of the genus Umbilicaria for biosynthetic genes, and categorize the biosynthetic gene clusters (BGCs) as "associated product structurally known" or "associated product putatively novel". Although lichen-forming fungi have been suggested to be a rich source of NPs, it is not known how their biosynthetic diversity compares to that of bacteria and non-lichenized fungi. We found that 25%-30% of biosynthetic genes are divergent as compared to the global database of BGCs, which comprises 1,200,000 characterized biosynthetic genes from plants, bacteria, and fungi. Out of 217 BGCs, 43 were highly divergant suggesting that they potentially encode structurally and functionally novel NPs. Clusters encoding the putatively novel metabolic diversity comprise polyketide synthases (30), non-ribosomal peptide synthetases (12), and terpenes (1). Our study emphasizes the utility of genomic data in bioprospecting microorganisms for their biosynthetic potential and in advancing the industrial application of unexplored taxa. We highlight the untapped structural metabolic diversity encoded in the lichenized fungal genomes. To the best of our knowledge, this is the first investigation identifying genes coding for NPs with potentially novel properties in lichenized fungi.

天然产物及其衍生物是现代医学的主要贡献者。从历史上看,细菌和真菌等微生物在产生药物和铅化合物方面发挥了重要作用,因为它们易于培养和基因操纵。然而,对新药日益增长的需求突出表明,需要对以前未探索的分类群进行生物勘探,以了解其生物合成潜力。下一代测序技术扩大了可以探索其生物合成含量的生物体的范围,因为这些技术可以在不需要培养的情况下提供生物体整个生物合成景观的一瞥。可以将整个生物合成基因与具有已知功能的基因进行比较,以识别潜在编码新产品的基因簇。在这项研究中,我们挖掘了9种脐属地衣形成真菌的基因组中的生物合成基因,并将生物合成基因簇(BGCs)归类为“结构已知的相关产物”或“推定新颖的相关产物。尽管地衣形成真菌被认为是NP的丰富来源,但尚不清楚它们的生物合成多样性与细菌和非地衣化真菌相比如何。我们发现,与全球BGC数据库相比,25%-30%的生物合成基因是不同的,该数据库包括来自植物、细菌和真菌的1200000个特征生物合成基因。在217个BGC中,有43个是高度分化的,这表明它们可能编码结构和功能上新颖的NP。编码假定的新代谢多样性的簇包括聚酮合成酶(30)、非核糖体肽合成酶(12)和萜烯(1)。我们的研究强调了基因组数据在生物勘探微生物生物合成潜力和推进未探索分类群工业应用方面的实用性。我们强调了地衣化真菌基因组中编码的未开发的结构代谢多样性。据我们所知,这是首次在地衣化真菌中鉴定具有潜在新特性的NP编码基因。
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引用次数: 4
Assessing the intracellular primary metabolic profile of Trichoderma reesei and Aspergillus niger grown on different carbon sources. 评估在不同碳源上生长的里氏木霉和黑曲霉的细胞内初级代谢谱。
IF 2.1 Q3 MYCOLOGY Pub Date : 2022-09-27 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.998361
Gustavo Pagotto Borin, Juliana Velasco de Castro Oliveira

Trichoderma reesei and Aspergillus niger are efficient biological platforms for the production of various industrial products, including cellulases and organic acids. Nevertheless, despite the extensive research on these fungi, integrated analyses of omics-driven approaches are still missing. In this study, the intracellular metabolic profile of T. reesei RUT-C30 and A. niger N402 strains grown on glucose, lactose, carboxymethylcellulose (CMC), and steam-exploded sugarcane bagasse (SEB) as carbon sources for 48 h was analysed by proton nuclear magnetic resonance. The aim was to verify the changes in the primary metabolism triggered by these substrates and use transcriptomics data from the literature to better understand the dynamics of the observed alterations. Glucose and CMC induced higher fungal growth whereas fungi grown on lactose showed the lowest dry weight. Metabolic profile analysis revealed that mannitol, trehalose, glutamate, glutamine, and alanine were the most abundant metabolites in both fungi regardless of the carbon source. These metabolites are of particular interest for the mobilization of carbon and nitrogen, and stress tolerance inside the cell. Their concomitant presence indicates conserved mechanisms adopted by both fungi to assimilate carbon sources of different levels of recalcitrance. Moreover, the higher levels of galactose intermediates in T. reesei suggest its better adaptation in lactose, whereas glycolate and malate in CMC might indicate activation of the glyoxylate shunt. Glycerol and 4-aminobutyrate accumulated in A. niger grown on CMC and lactose, suggesting their relevant role in these carbon sources. In SEB, a lower quantity and diversity of metabolites were identified compared to the other carbon sources, and the metabolic changes and higher xylanase and pNPGase activities indicated a better utilization of bagasse by A. niger. Transcriptomic analysis supported the observed metabolic changes and pathways identified in this work. Taken together, we have advanced the knowledge about how fungal primary metabolism is affected by different carbon sources, and have drawn attention to metabolites still unexplored. These findings might ultimately be considered for developing more robust and efficient microbial factories.

里氏木霉和黑曲霉是生产各种工业产品的有效生物平台,包括纤维素酶和有机酸。尽管如此,尽管对这些真菌进行了广泛的研究,但对组学驱动的方法的综合分析仍然缺失。在本研究中,通过质子核磁共振分析了里氏木霉RUT-C30和黑曲霉N402菌株在葡萄糖、乳糖、羧甲基纤维素(CMC)和蒸汽爆破甘蔗渣(SEB)作为碳源上生长48小时的细胞内代谢谱。目的是验证这些底物引发的初级代谢的变化,并使用文献中的转录组学数据来更好地了解观察到的变化的动力学。葡萄糖和CMC诱导了更高的真菌生长,而在乳糖上生长的真菌显示出最低的干重。代谢谱分析显示,无论碳源如何,甘露醇、海藻糖、谷氨酸、谷氨酰胺和丙氨酸都是这两种真菌中最丰富的代谢产物。这些代谢产物对碳和氮的动员以及细胞内的应激耐受性特别感兴趣。它们的同时存在表明,这两种真菌吸收不同顽抗水平的碳源所采用的保守机制。此外,里氏木霉中半乳糖中间体的较高水平表明其在乳糖中具有更好的适应能力,而CMC中的乙醇酸盐和苹果酸盐可能表明乙醛酸分流的激活。甘油和4-氨基丁酸盐在CMC和乳糖上生长的黑曲霉中积累,表明它们在这些碳源中的相关作用。在SEB中,与其他碳源相比,代谢产物的数量和多样性较低,代谢变化和较高的木聚糖酶和pNPGase活性表明黑曲霉更好地利用了蔗渣。转录组学分析支持了这项工作中观察到的代谢变化和途径。总之,我们已经深入了解了真菌初级代谢如何受到不同碳源的影响,并引起了人们对尚未探索的代谢产物的关注。这些发现可能最终被考虑用于开发更强大、更高效的微生物工厂。
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引用次数: 0
Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome. 呼吸可能是危险的:机会性真菌病原体和小型哺乳动物肺部真菌生物群落的多样性。
Q3 MYCOLOGY Pub Date : 2022-09-26 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.996574
Paris S Salazar-Hamm, Kyana N Montoya, Liliam Montoya, Kel Cook, Schuyler Liphardt, John W Taylor, Joseph A Cook, Donald O Natvig

Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus. Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.

人类肺部真菌生物群系研究通常以支气管肺泡灌洗或痰液为样本,可能忽略了组织中嵌入的真菌。利用来自生物库的超冷冻肺组织,我们从39个物种的199种小型哺乳动物中获得了真菌核糖体RNA ITS2序列。我们记录了多种真菌,包括常见的环境真菌,如青霉和曲霉菌,人类真菌生物群落的伙伴,如马拉色菌和念珠菌,以及其他专门适应肺部的真菌(球虫、芽孢菌和肺孢子虫)。肺孢子虫序列在83%的样本中被检测到,并且通常表现出与宿主的系统发育一致性。在尾根菌中来自不同机会病原体的序列中,12%的样本中出现了球虫类,85%的样本中发生了芽酵母类。球虫类序列出现在14种哺乳动物中。虽然有一些迹象表明真菌群落可能受到高水平烟曲霉的影响,但球虫类和烟曲霉的存在都与整个真菌生物群落的实质性变化无关。尽管Onygenales成员在肺部样本中很常见(92%),但在环境调查中并不常见。我们的研究结果表明,肺孢子虫和某些Onygenals是肺真菌生物群中常见的共生成员。这些结果为栖息在肺部的真菌的生物学提供了新的见解,并将小型哺乳动物标记为新出现的真菌病原体的潜在宿主。
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引用次数: 7
Mixed infections of fungal trunk pathogens and induced systemic phenolic compound production in grapevines. 葡萄树干真菌病原体的混合感染和诱导系统酚类化合物的产生。
Q3 MYCOLOGY Pub Date : 2022-09-15 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.1001143
Christopher M Wallis, Zachary Gorman, Erin R-A Galarneau, Kendra Baumgartner

As grapevines mature in California vineyards they accumulate chronic wood infections by the Ascomycete fungi that cause trunk diseases, including Botryosphaeria dieback (caused by Diplodia seriata and Neofusicoccum parvum) and Esca (caused by Phaeomoniella chlamydospora). It is thought that such mixed infections become localized to separate internal lesions/cankers of the permanent, woody structure of an individual vine, but nonetheless the fungi all colonize the same vascular system. In response to infection by one pathogen, the host may initiate systemic biochemical changes, which in turn may affect the extent of subsequent infections by other pathogens. To test this hypothesis, we measured changes in phenolic compounds in the wood and lesion lengths of the pathogens, during sequential co-inoculations with different or identical pair-wise sequences of infection by D. seriata, N. parvum, or P. chlamydospora. Prior fungal infections only affected the development of subsequent D. seriata infections. Effects of fungal infections on phenolic compounds were variable, yet initial infection by D. seriata was associated with significantly higher concentrations of most phenolic compounds distally, compared to all other initial inoculation treatments. It was hypothesized that pre-existing phenolic levels can slow initial lesion development of fungal trunk pathogens, especially for D. seriata, but over time the pathogens appeared to overcome or neutralize phenolic compounds and grow unimpeded. These results demonstrate that effects of one fungal trunk pathogen infection is generally unable to distally affect another long-term, albeit shifts in host phenolics and other plant defenses do occur.

随着葡萄藤在加州葡萄园成熟,它们会积累由子囊菌引起的慢性木材感染,子囊菌会导致树干疾病,包括由Diplodia seriata和Neofusicoccum parvum引起的Botryosphaeria dieback和由Phaeomoniella chlamydospora引起的Esca。人们认为,这种混合感染会局限于单个葡萄藤的永久性木质结构的内部病变/溃疡,但尽管如此,真菌都在同一血管系统中定植。作为对一种病原体感染的反应,宿主可能会引发全身生化变化,进而影响其他病原体随后感染的程度。为了验证这一假设,我们测量了木材中酚类化合物的变化和病原体的病变长度,在连续联合接种不同或相同的序列感染的D.seriata、N.parvum或P.chlamydospora的过程中。先前的真菌感染只会影响随后的串联D.seriata感染的发展。真菌感染对酚类化合物的影响是可变的,但与所有其他初始接种处理相比,严重念珠菌的初始感染与远端大多数酚类化合物浓度显著较高有关。据推测,预先存在的酚类水平可以减缓真菌主干病原体的初始病变发展,尤其是对D.seriata而言,但随着时间的推移,病原体似乎会克服或中和酚类化合物,并不受阻碍地生长。这些结果表明,一种真菌树干病原体感染的影响通常不会长期影响另一种,尽管宿主酚类物质和其他植物防御确实发生了变化。
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引用次数: 0
Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture. 木霉-基因组学和基因组学是生物学、生物技术和农业研究的宝库。
IF 2.1 Q3 MYCOLOGY Pub Date : 2022-09-14 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.1002161
Miriam Schalamun, Monika Schmoll

The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.

木霉属是研究最好的丝状真菌类群之一,这主要是因为它在从农业到酶生物合成再到生物燃料生产的应用中具有高度相关性。然而,从科学和生态学的角度来看,这些真菌的生理能力,导致了这些有益的应用,也是令人感兴趣的。因此,这篇综述总结了真菌基因组研究的最新进展、先前开始的基因组注释工作的更新和新发现,以及对酶和生物活性化合物(如纤维素酶、降解外源性物质的酶和具有潜在药用价值的代谢产物)的生物勘探工作。从而为木霉菌株的基因组、线粒体基因组和真菌病毒基因组提供了与酶生产、生物控制和真菌修复相关的见解。在某些情况下,生物活性化合物的产生可能与负责任的基因或簇有关,并且可以使用基因组信息来支持或预测生物修复能力。对木霉属进化的深入研究揭示了大规模的水平基因转移,主要是CAZyme基因,但也有次级代谢产物簇。对性发育的调查表明,木霉属物种具有重复诱导点突变(RIP)能力,在某些情况下,观察到节段性非整倍体。一些随机突变体最终放弃了它们的关键突变,如里氏木霉QM9978和QM9136,QM6a的育性缺陷可以追溯到其基因缺陷。木霉核心基因组被缩小到7000个基因,并在多个物种的基因组中进行了基因聚类研究。最后,重点介绍了CRISPR/Cas9在木霉中的应用、里氏木霉的克隆和表达策略以及利用基因组挖掘工具对木霉进行生物勘探的最新进展。关于进化、基因组学和生理学的有趣新发现突出了新趋势,并说明了木霉在不同研究领域的有价值的前景。
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引用次数: 0
Concepts and considerations for enhancing RNAi efficiency in phytopathogenic fungi for RNAi-based crop protection using nanocarrier-mediated dsRNA delivery systems. 利用纳米载体介导的dsRNA递送系统提高植物病原真菌RNAi效率以保护基于RNAi的作物的概念和考虑因素。
Q3 MYCOLOGY Pub Date : 2022-09-08 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.977502
Poonam Ray, Debashish Sahu, Raghavendra Aminedi, Divya Chandran

Existing, emerging, and reemerging strains of phytopathogenic fungi pose a significant threat to agricultural productivity globally. This risk is further exacerbated by the lack of resistance source(s) in plants or a breakdown of resistance by pathogens through co-evolution. In recent years, attenuation of essential pathogen gene(s) via double-stranded (ds) RNA-mediated RNA interference (RNAi) in host plants, a phenomenon known as host-induced gene silencing, has gained significant attention as a way to combat pathogen attack. Yet, due to biosafety concerns regarding transgenics, country-specific GMO legislation has limited the practical application of desirable attributes in plants. The topical application of dsRNA/siRNA targeting essential fungal gene(s) through spray-induced gene silencing (SIGS) on host plants has opened up a transgene-free avenue for crop protection. However, several factors influence the outcome of RNAi, including but not limited to RNAi mechanism in plant/fungi, dsRNA/siRNA uptake efficiency, dsRNA/siRNA design parameters, dsRNA stability and delivery strategy, off-target effects, etc. This review emphasizes the significance of these factors and suggests appropriate measures to consider while designing in silico and in vitro experiments for successful RNAi in open-field conditions. We also highlight prospective nanoparticles as smart delivery vehicles for deploying RNAi molecules in plant systems for long-term crop protection and ecosystem compatibility. Lastly, we provide specific directions for future investigations that focus on blending nanotechnology and RNAi-based fungal control for practical applications.

现有的、新出现的和重新出现的植物病原真菌菌株对全球农业生产力构成了重大威胁。植物缺乏抗性来源或病原体通过共同进化破坏抗性,进一步加剧了这种风险。近年来,通过双链(ds)RNA介导的RNA干扰(RNAi)在宿主植物中减弱基本病原体基因,这一现象被称为宿主诱导的基因沉默,作为对抗病原体攻击的一种方式,已引起了人们的极大关注。然而,由于对转基因生物安全的担忧,针对特定国家的转基因立法限制了理想特性在植物中的实际应用。dsRNA/siRNA通过喷雾诱导基因沉默(SIGS)靶向重要真菌基因在寄主植物上的局部应用为作物保护开辟了一条无转基因的途径。然而,有几个因素影响RNAi的结果,包括但不限于植物/真菌中的RNAi机制、dsRNA/siRNA吸收效率、dsRNA/siRNA设计参数、dsRNA稳定性和递送策略、脱靶效应等。这篇综述强调了这些因素的重要性,并提出了在开阔场地条件下设计成功RNAi的计算机和体外实验时应考虑的适当措施。我们还强调,纳米颗粒有望成为在植物系统中部署RNAi分子的智能递送载体,以实现长期作物保护和生态系统兼容性。最后,我们为未来的研究提供了具体的方向,重点是将纳米技术和基于RNAi的真菌控制结合起来进行实际应用。
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引用次数: 4
Experimental and in-host evolution of triazole resistance in human pathogenic fungi. 人类病原真菌对三唑耐药性的实验和宿主内进化。
Q3 MYCOLOGY Pub Date : 2022-08-23 eCollection Date: 2022-01-01 DOI: 10.3389/ffunb.2022.957577
Mariana Handelman, Nir Osherov

The leading fungal pathogens causing systemic infections in humans are Candida spp., Aspergillus fumigatus, and Cryptococcus neoformans. The major class of antifungals used to treat such infections are the triazoles, which target the cytochrome P450 lanosterol 14-α-demethylase, encoded by the ERG11 (yeasts)/cyp51A (molds) genes, catalyzing a key step in the ergosterol biosynthetic pathway. Triazole resistance in clinical fungi is a rising concern worldwide, causing increasing mortality in immunocompromised patients. This review describes the use of serial clinical isolates and in-vitro evolution toward understanding the mechanisms of triazole resistance. We outline, compare, and discuss how these approaches have helped identify the evolutionary pathways taken by pathogenic fungi to acquire triazole resistance. While they all share a core mechanism (mutation and overexpression of ERG11/cyp51A and efflux transporters), their timing and mechanism differs: Candida and Cryptococcus spp. exhibit resistance-conferring aneuploidies and copy number variants not seen in A. fumigatus. Candida spp. have a proclivity to develop resistance by undergoing mutations in transcription factors (TAC1, MRR1, PDR5) that increase the expression of efflux transporters. A. fumigatus is especially prone to accumulate resistance mutations in cyp51A early during the evolution of resistance. Recently, examination of serial clinical isolates and experimental lab-evolved triazole-resistant strains using modern omics and gene editing tools has begun to realize the full potential of these approaches. As a result, triazole-resistance mechanisms can now be analyzed at increasingly finer resolutions. This newfound knowledge will be instrumental in formulating new molecular approaches to fight the rapidly emerging epidemic of antifungal resistant fungi.

引起人类全身感染的主要真菌病原体是念珠菌、烟曲霉和新型隐球菌。用于治疗此类感染的主要抗真菌药物是三唑类,其靶向ERG11(酵母)/cyp51A(霉菌)基因编码的细胞色素P450羊毛甾醇14-α-去甲基化酶,催化麦角甾醇生物合成途径的关键步骤。临床真菌对三唑的耐药性日益引起全世界的关注,导致免疫功能低下患者的死亡率不断上升。这篇综述描述了一系列临床分离株的使用和体外进化,以了解三唑耐药性的机制。我们概述、比较和讨论了这些方法如何帮助确定致病真菌获得三唑耐药性的进化途径。虽然它们都有一个共同的核心机制(ERG11/cyp51A和外排转运蛋白的突变和过表达),但它们的时间和机制不同:念珠菌和隐球菌表现出耐药性非整倍体和拷贝数变异,这在烟曲霉中没有发现。念珠菌有通过转录因子(TAC1、MRR1、PDR5)发生突变来增加外排转运蛋白表达而产生耐药性的倾向。烟曲霉在抗性进化的早期特别容易在cyp51A中积累抗性突变。最近,使用现代组学和基因编辑工具对一系列临床分离株和实验实验室进化的三唑耐药性菌株进行检查,已经开始意识到这些方法的全部潜力。因此,现在可以以越来越精细的分辨率分析三唑抗性机制。这一新发现的知识将有助于制定新的分子方法来对抗快速出现的抗真菌耐药性真菌。
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引用次数: 2
期刊
Frontiers in fungal biology
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