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Yang X, Chen Y, Zhang L, He J, Wu Q, Li S, Wang D, Gou J, Wu Z, Zhang K, Li S, Niu X. Melanin precursors mediated adaption to temperature changes in fungus and animal via inhibition of lipid-mediated ferroptosis. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1800-1817. [PMID: 36949229 DOI: 10.1007/s11427-022-2265-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/19/2022] [Indexed: 03/24/2023]
Abstract
The discovery of biological activities of natural products plays a vital part in drug development. The mechanism by which organisms respond to temperature changes via biosynthesis of natural products remained largely cryptic. A thermophilic fungus under cold stress turned black and accumulated a polyketide metabolite 1 and lipid mass. Deficiency in 1 caused melanin loss and accumulated extra lipid mass, unexpectedly leading to seriously damaged mitochondria diagnostic for ferroptosis. Further analysis revealed that lipid mass induced by cold stress intensively increased ferroptosis risk and 1 functioned as cell wall reinforcer against mass lipid accumulation and as reactive oxygen species scavenger against lipid peroxidation. We also found that melanin in mice lowered lipid level but enhanced animal resistance to cold stress. Treatment with melanin precursors significantly increased mouse cell survival rate under cold stress. Our results unveiled a metabolite-lipid-ferroptosis-cold relationship, which provided mechanistic insights into the functions of most common metabolites and into diseases related to cold stress. These findings opened a perspective for developing anti-cold and anti-ferroptosis therapeutics and agents.
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Affiliation(s)
- Xiaoyu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Yonghong Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Longlong Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Jiangbo He
- Kunming Key Laboratory of Respiratory Disease, Kunming University, Kunming, 650214, China
| | - Qunfu Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Shuhong Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Donglou Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Jianghui Gou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Zhuang Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Keqin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China
| | - Shenghong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Xuemei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, 650032, China.
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Pushparaj K, Meyyazhagan A, Bhotla HK, Arumugam VA, Pappuswamy M, Vadivalagan C, Hakeem KR, Balasubramanian B, Liu W, Mousavi Khaneghah A. The crux of bioactive metabolites in endophytic and thermophilic fungi and their proximal prospects in biotechnological and industrial domains. Toxicon 2023; 223:107007. [PMID: 36563862 DOI: 10.1016/j.toxicon.2022.107007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Fungi are ubiquitous in distribution and are found in grasses to hot springs. Their mode of nutrition provides sustenance for living and propagation. Ironically, varied fungal species have developed customized strategies for protection and survival by producing diverse secondary metabolites. The review aimed to project the contrasting potential features of the endophytic and thermophilic fungi groups. The metabolites and the enzymes of endophytic and thermophilic fungi served as the backbone to thrive and adapt within-host and in extreme conditions like higher pH, heat, and salinity, respectively. Identification, knowledge of their biochemistry and pathway, exploration, production, and utilization of these bioactive molecules in various commercial, industrial, and pharmaceutical domains were briefly discussed. The uniqueness of endophytes includes stress management and improved biomass production of the host, green fuel production, omnipresence, selected triple-symbiosis with the virus, synthesis of polyketides, and other active metabolites are widely used in biomedical applications and agriculture management. This review attempted to limelight the specific applications of thermophilic fungal metabolites and the roles of thermo-stable enzymes in bioprospecting. Moreover, probing the metabolites of thermophiles rendered novel antibiotic compounds, which were proven effective against multi-drug resistant bacteria and harboured the potential to curtail infectious diseases.
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Affiliation(s)
- Karthika Pushparaj
- Department of Zoology, School of Biosciences, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641 043, Tamil Nadu, India
| | - Arun Meyyazhagan
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | - Haripriya Kuchi Bhotla
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | - Vijaya Anand Arumugam
- Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, 641 046, Tamil Nadu, India
| | - Manikantan Pappuswamy
- Department of Life Science, CHRIST (Deemed to Be University), Bengaluru, Karnataka, 560076, India
| | | | - Khalid Rehman Hakeem
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | | | - Wenchao Liu
- Department of Animal Science, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China.
| | - Amin Mousavi Khaneghah
- Department of Fruit and Vegetable Product Technology, Prof. WacławDąbrowski Institute of Agricultural and Food Biotechnology - State Research Institute, 36 Rakowiecka St., 02-532, Warsaw, Poland; Department of Technology of Chemistry, Azerbaijan State Oil and Industry University, Baku, Azerbaijan.
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Chen Y, Yang X, Zhang L, Wu Q, Li S, Gou J, He J, Zhang K, Li S, Niu X. Tryptophan-centered metabolic alterations coincides with lipid-mediated fungal response to cold stress. Heliyon 2023; 9:e13066. [PMID: 36747564 PMCID: PMC9898655 DOI: 10.1016/j.heliyon.2023.e13066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Tryptophan and its derived metabolites have been assumed to play important roles in the development and survival of organisms. However, the links of tryptophan and its derived metabolites to temperature change remained largely cryptic. Here we presented that a class of prenyl indole alkaloids biosynthesized from tryptophan dramatically accumulated in thermophilic fungus Thermomyces dupontii under cold stress, in which lipid droplets were also highly accumulated and whose conidiophores were highly build-up. Concurrently, disruption of the key NRPS gene involved in the biosynthesis of prenyl indole alkaloids, resulted in decreased lipid and shrunken mitochondria but enlarged vacuoles. Moreover, the Fe3+ and superoxide levels in ΔNRPS were significantly increased but the reactive oxygen species lipid peroxidation and autophagy levels decreased. Metabolomics study revealed that most enriched metabolites in ΔNRPS were mainly composed of tryptophan degraded metabolites including well known ROS scavenger kynurenamines, and lipid-inhibitors, anthranilic acid and indoleacetic acid, and free radical reaction suppressor free fatty acids. Transcriptomic analysis suggested that the key gene involved in tryptophan metabolism, coinciding with the lipid metabolic processes and ion transports were most up-regulated in ΔNRPS under stress. Our results confirmed a lipid-mediated fungal response to cold stress and unveiled a link of tryptophan-based metabolic reprogramming to the fungal cold adaption.
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Affiliation(s)
- Yonghong Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China
| | - Xiaoyu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China
| | - Longlong Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China
| | - Qunfu Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China
| | - Shuhong Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China
| | - Jianghui Gou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China
| | - Jiangbo He
- Kunming Key Laboratory of Respiratory Disease, Kunming University, Kunming 650214, China
| | - Keqin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China
| | - Shenghong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
- Corresponding author.
| | - Xuemei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming 650032, China
- Corresponding author.
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Verma J, Sourirajan A, Dev K. Bacterial diversity in 110 thermal hot springs of Indian Himalayan Region (IHR). 3 Biotech 2022; 12:238. [PMID: 36003895 PMCID: PMC9393120 DOI: 10.1007/s13205-022-03270-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022] Open
Abstract
Thermal hot springs are present throughout the world and constitute a unique habitat for microbial diversity. The current investigation is conducted to study the bacterial diversity of thermophilic microorganisms in thermal hot springs of the Indian Himalayan Region (IHR). As of today, 110 geothermal hot springs have been explored for microbial diversity. In this study, we observed that the growth of thermophilic bacteria isolated from thermal hot springs of IHR ranges between 40 and 100 °C, and pH of 3.5-8 have been reported in the literature. The major bacterial species reported from the thermal hot springs of IHR are Bacillus spp., Geobacillus spp., Paenibacillus spp., Pseudomonas spp., Anoxybacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Thermus aquaticus, Aquimonas, Flavobacterium, etc. Furthermore, bacterial isolates from thermal hot springs of IHR have been reported to produce various enzymes and metabolites such as amylase, β-galactosidase, cellulase, nitrate reductase, acetoin, caffeine degradation enzymes, lipase, urease, and laccase. Metagenomic study and the entire genomic shotgun project have established the impact of physicochemical parameters (temperature and pH) on developing the microbiome. We have discussed the discoveries of microbiological data on the hot springs of IHR until the end of year 2021. As a whole, the microbiome adapts themselves as successful inhabitants to extreme environmental conditions and also serves as a diverse resource for potential applications in health, food, and environment.
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Affiliation(s)
- Jagdish Verma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173212 Himachal Pradesh India
| | - Anuradha Sourirajan
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173212 Himachal Pradesh India
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, 173212 Himachal Pradesh India
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Naeem M, Manzoor S, Abid MUH, Tareen MBK, Asad M, Mushtaq S, Ehsan N, Amna D, Xu B, Hazafa A. Fungal Proteases as Emerging Biocatalysts to Meet the Current Challenges and Recent Developments in Biomedical Therapies: An Updated Review. J Fungi (Basel) 2022; 8:jof8020109. [PMID: 35205863 PMCID: PMC8875690 DOI: 10.3390/jof8020109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 02/07/2023] Open
Abstract
With the increasing world population, demand for industrialization has also increased to fulfill humans' living standards. Fungi are considered a source of essential constituents to produce the biocatalytic enzymes, including amylases, proteases, lipases, and cellulases that contain broad-spectrum industrial and emerging applications. The present review discussed the origin, nature, mechanism of action, emerging aspects of genetic engineering for designing novel proteases, genome editing of fungal strains through CRISPR technology, present challenges and future recommendations of fungal proteases. The emerging evidence revealed that fungal proteases show a protective role to many environmental exposures and discovered that an imbalance of protease inhibitors and proteases in the epithelial barriers leads to the protection of chronic eosinophilic airway inflammation. Moreover, mitoproteases recently were found to execute intense proteolytic processes that are crucial for mitochondrial integrity and homeostasis function, including mitochondrial biogenesis, protein synthesis, and apoptosis. The emerging evidence revealed that CRISPR/Cas9 technology had been successfully developed in various filamentous fungi and higher fungi for editing of specific genes. In addition to medical importance, fungal proteases are extensively used in different industries such as foods to prepare butter, fruits, juices, and cheese, and to increase their shelf life. It is concluded that hydrolysis of proteins in industries is one of the most significant applications of fungal enzymes that led to massive usage of proteomics.
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Affiliation(s)
- Muhammad Naeem
- College of Life Science, Hebei Normal University, Shijiazhuang 050025, China;
| | - Saba Manzoor
- Department of Zoology, University of Sialkot, Sialkot 51310, Pakistan;
| | | | | | - Mirza Asad
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Sajida Mushtaq
- Department of Zoology, Government College Women University, Sialkot 51040, Pakistan;
| | - Nazia Ehsan
- Department of Zoology, Wildlife and Fisheries, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Dua Amna
- Institute of Food Science & Nutrition, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Baojun Xu
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University (BNU-HKBU) United International College, Zhuhai 519087, China
- Correspondence: (B.X.); (A.H.)
| | - Abu Hazafa
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
- Correspondence: (B.X.); (A.H.)
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6
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Li XJ, Li Q, Zhan XX, Zhang YJ, Xiong GL, Zheng JY. Expression and characterization of a thermostable lipase from Thermomyces dupontii. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02068-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Antonelli MA, Gaglioti AL, Silva PRDA, Knob A. Thermophilic fungi in Araucaria Forest, Atlantic Forest Biome, Brazil. AN ACAD BRAS CIENC 2021; 93:e20210714. [PMID: 34706012 DOI: 10.1590/0001-3765202120210714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/31/2021] [Indexed: 11/21/2022] Open
Abstract
Thermophilic fungi constitute an ecologically well-defined group, commonly found in environments wherever decomposition of organic matter takes place, making them self-heating. The importance of thermophilic fungus in ecosystems contrasts with the incompleteness of our understanding of the group's biogeography patterns, phylogenies and coevolution relationships. Actually, the lack of data about thermophilic fungi from the Brazil is a limiting factor that also contributes for this scenario. In order to reduce this gap of knowledge, we aimed to characterize thermophilic filamentous fungi in Araucaria Forest, Atlantic Forest biome. Species identification was achieved by using internal transcribed spacers (ITS) as molecular ribosomal markers. In total, 240 heat-tolerant fungal strains were isolated and identified as Thermothielavioides terrestris, Thielavia sp., Thermoascus crustaceus, Aspergillus fumigatus, Rhizomucor miehei, Rhizomucor pusillus, and Rhizopus microsporus. All thermophilic strains exhibited optimal growth at 45 °C. T. crustaceus, T. miehei e R. pusillus were the dominant species, with the frequencies of occurrence of 35.00%, 28.33% and 23.33%, respectively. Our data reveals the apparent diversity of the Neotropical realm and may serve as reference to future studies that will try to elucidate important aspects of group.
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Affiliation(s)
- Marcio André Antonelli
- Midwest State University State, Department of Biological Sciences, Alameda Élio Antonio Dalla Vecchia, 838, 85040-167 Guarapuava, PR, Brazil
| | - André Luiz Gaglioti
- Midwest State University State, Department of Biological Sciences, Alameda Élio Antonio Dalla Vecchia, 838, 85040-167 Guarapuava, PR, Brazil
| | - Paulo Roberto DA Silva
- Midwest State University State, Department of Biological Sciences, Alameda Élio Antonio Dalla Vecchia, 838, 85040-167 Guarapuava, PR, Brazil
| | - Adriana Knob
- Midwest State University State, Department of Biological Sciences, Alameda Élio Antonio Dalla Vecchia, 838, 85040-167 Guarapuava, PR, Brazil
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Agrawal S, Nandeibam J, Sarangthem I. Ultrastructural changes in methicillin-resistant Staphylococcus aureus (MRSA) induced by metabolites of thermophilous fungi Acrophialophora levis. PLoS One 2021; 16:e0258607. [PMID: 34648570 PMCID: PMC8516270 DOI: 10.1371/journal.pone.0258607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/30/2021] [Indexed: 12/02/2022] Open
Abstract
Staphylococcus aureus and Methicillin-resistant S. aureus (MRSA) remains one of the major concerns of healthcare associated and community-onset infections worldwide. The number of cases of treatment failure for infections associated with resistant bacteria is on the rise, due to the decreasing efficacy of current antibiotics. Notably, Acrophialophora levis, a thermophilous fungus species, showed antibacterial activity, namely against S. aureus and clinical MRSA strains. The ethyl acetate extract of culture filtrate was found to display significant activity against S. aureus and MRSA with a minimum inhibitory concentration (MIC) of 1 μg/mL and 4 μg/mL, respectively. Scanning electron micrographs demonstrated drastic changes in the cellular architecture of metabolite treated cells of S. aureus and an MRSA clinical isolate. Cell wall disruption, membrane lysis and probable leakage of cytoplasmic are hallmarks of the antibacterial effect of fungal metabolites against MRSA. The ethyl acetate extract also showed strong antioxidant activity using two different complementary free radicals scavenging methods, DPPH and ABTS with efficiency of 55% and 47% at 1 mg/mL, respectively. The total phenolic and flavonoid content was found to be 50 mg/GAE and 20 mg/CAE, respectively. More than ten metabolites from different classes were identified: phenolic acids, phenylpropanoids, sesquiterpenes, tannins, lignans and flavonoids. In conclusion, the significant antibacterial activity renders this fungal strain as a bioresource for natural compounds an interesting alternative against resistant bacteria.
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Affiliation(s)
- Shivankar Agrawal
- Indian Council of Medical Research (ICMR), Delhi, India
- Department of Microbiology, Institute of Bioresources and Sustainable Development, A National Institute of Department of Biotechnology, Government of India, Imphal, Manipur, India
- * E-mail: (SA); (IS)
| | - Jusna Nandeibam
- Department of Microbiology, Institute of Bioresources and Sustainable Development, A National Institute of Department of Biotechnology, Government of India, Imphal, Manipur, India
| | - Indira Sarangthem
- Department of Microbiology, Institute of Bioresources and Sustainable Development, A National Institute of Department of Biotechnology, Government of India, Imphal, Manipur, India
- * E-mail: (SA); (IS)
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Rocha Vieira F, Andrew Pecchia J. Fungal community assembly during a high-temperature composting under different pasteurization regimes used to elaborate the Agaricus bisporus substrate. Fungal Biol 2021; 125:826-833. [PMID: 34537178 DOI: 10.1016/j.funbio.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/10/2021] [Accepted: 05/24/2021] [Indexed: 01/04/2023]
Abstract
Agaricus bisporus cultivation is based on a selective substrate prepared by a meticulous composting process where thermophilic and/or thermotolerant fungi might play an important role in straw biomass depolymerization. Since fungi have physiological limitations to survive and grow in high-temperature environments, we set out different pasteurization regimes (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h) to evaluate the impact on the fungal community assembly. The fungal community profile generated by high-throughput sequencing showed shifts in community diversity and composition under different pasteurization regimes. Most of the recovered sequences belong to the Ascomycota phylum. Among 73 species detected, Mycothermus thermophilus, Talaromyces thermophilus, and Thermomyces lanuginosus were the most abundant. In the current study, we outlined that pasteurization regimes can reshape the fungal community in compost which can potentially impact the A. bisporus development.
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Affiliation(s)
- Fabricio Rocha Vieira
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.
| | - John Andrew Pecchia
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
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Seong J, Shin J, Kim K, Cho BK. Microbial production of nematicidal agents for controlling plant-parasitic nematodes. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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11
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Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method. Folia Microbiol (Praha) 2021; 66:457-468. [PMID: 33755859 DOI: 10.1007/s12223-021-00859-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
Fungi are considered to be the most resilient and economically important microbial community that can easily survive and optimally grow under a wide range of growth conditions. Thermophilic fungi from the geothermal sources have been less pondered upon and lie unexplored. Here, a microbiome approach was conducted to understand the concealed world of the environmental mycobiota from the two hot springs of North Sikkim district located in North-east India. The solfataric muds from the hot springs were analyzed. In both the samples, on the basis of genus level classification, genus Fusarium had the highest abundance followed by Colletotrichum, Pochonia, Pyricularia, Neurospora, etc. Analyzing the predicted genes, the functional proteins of New Yume Samdung mycobiome were found to be dominated by the genera Fusarium (22%), Trichoderma (12%), and Aspergillus (11%), whereas in the case of Old Yume Samdung, it was dominated by the genera Aspergillus (11%), Saccharomyces (6%), and Fusarium (5%). Interestingly, in the studied mycobiome, environmental yeasts were also detected. From the functional metagenomics, sulfate adenylatetransferase (SAT) proteins for sulfur assimilation were found in some of the fungal reads. Toxin protein reads such as AM-toxin biosynthesis proteins, AF-toxin biosynthesis proteins, Gliotoxin biosynthesis proteins, and aflatoxin biosynthesis proteins were detected in the mycobiomes.
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12
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Halophilic Fungal Communities: Current Research and Future Challenges. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Bioprospecting of Thermophilic Fungal Enzymes and Potential Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Huang WP, Du YJ, Yang Y, He JN, Lei Q, Yang XY, Zhang KQ, Niu XM. Two CRISPR/Cas9 Systems Developed in Thermomyces dupontii and Characterization of Key Gene Functions in Thermolide Biosynthesis and Fungal Adaptation. Appl Environ Microbiol 2020; 86:e01486-20. [PMID: 32769197 PMCID: PMC7531979 DOI: 10.1128/aem.01486-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/23/2020] [Indexed: 11/20/2022] Open
Abstract
Thermomyces dupontii, a widely distributed thermophilic fungus, is an ideal organism for investigating the mechanism of thermophilic fungal adaptation to diverse environments. However, genetic analysis of this fungus is hindered by a lack of available and efficient gene-manipulating tools. In this study, two different Cas9 proteins from mesophilic and thermophilic bacteria, with in vivo expression of a single guide RNA (sgRNA) under the control of tRNAGly, were successfully adapted for genome editing in T. dupontii We demonstrated the feasibility of applying these two gene editing systems to edit one or two genes in T. dupontii The mesophilic CRISPR/Cas9 system displayed higher editing efficiency (50 to 86%) than the thermophilic CRISPR/Cas9 system (40 to 67%). However, the thermophilic CRISPR/Cas9 system was much less time-consuming than the mesophilic CRISPR/Cas9 system. Combining the CRISPR/Cas9 systems with homologous recombination, a constitutive promoter was precisely knocked in to activate a silent polyketide synthase-nonribosomal peptide synthase (PKS-NRPS) biosynthetic gene, leading to the production of extra metabolites that did not exist in the parental strains. Metabolic analysis of the generated biosynthetic gene mutants suggested that a key biosynthetic pathway existed for the biosynthesis of thermolides in T. dupontii, with the last two steps being different from those in the heterologous host Aspergillus Further analysis suggested that these biosynthetic genes might be involved in fungal mycelial growth, conidiation, and spore germination, as well as in fungal adaptation to osmotic, oxidative, and cell wall-perturbing agents.IMPORTANCE Thermomyces represents a unique ecological taxon in fungi, but a lack of flexible genetic tools has greatly hampered the study of gene function in this taxon. The biosynthesis of potent nematicidal thermolides in T. dupontii remains largely unknown. In this study, mesophilic and thermophilic CRISPR/Cas9 gene editing systems were successfully established for both disrupting and activating genes in T. dupontii In this study, a usable thermophilic CRISPR/Cas9 gene editing system derived from bacteria was constructed in thermophilic fungi. Chemical analysis of the mutants generated by these two gene editing systems identified the key biosynthetic genes and pathway for the biosynthesis of nematocidal thermolides in T. dupontii Phenotype analysis and chemical stress experiments revealed potential roles of secondary metabolites or their biosynthetic genes in fungal development and adaption to chemical stress conditions. These two genomic editing systems will not only accelerate investigations into the biosynthetic mechanisms of unique natural products and functions of cryptic genes in T. dupontii but also offer an example for setting up CRISPR/Cas9 systems in other thermophilic fungi.
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Affiliation(s)
- Wei-Ping Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Yuan-Jiang Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Yun Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Jia-Ning He
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Qian Lei
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Xiao-Yu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Xue-Mei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
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15
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Sokolyanskaya LO, Ivanov MV, Ikkert OP, Kalinina AE, Evseev VA, Glukhova LB, Karnachuk OV. Copper Precipitation as Insoluble Oxalates by Thermotolerant Aspergillus spp. from Burning Wastes of Coal Mining. Microbiology (Reading) 2020. [DOI: 10.1134/s002626172004013x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Dos Santos Gomes AC, Casciatori FP, Gomes E, da Costa Carreira Nunes C, Moretti MMS, Thoméo JC. Growth kinetics of Myceliophthora thermophila M.7·7 in solid-state cultivation. J Appl Microbiol 2020; 130:90-99. [PMID: 32640074 DOI: 10.1111/jam.14774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 01/19/2023]
Abstract
AIMS This work aimed to estimate the growth of Myceliophthora thermophila M.7·7 in solid-state cultivation (SSC) through quantification of N-acetyl-d-glucosamine (NAG) and enzyme activity. METHODS AND RESULTS The fungus was cultivated in sugarcane bagasse and wheat bran. A consistent statistical analysis was done to assess the reliability of experimental data. Logistic model equation was fitted to experimental data and growth parameters were estimated. The results showed strong influence of the sample size on NAG and a minimum recommended sample size was identified. Scanning electron microscopy (SEM) was used to identify the strategy of substrate colonization. Wheat bran was attacked firstly, while sugarcane bagasse was consumed after wheat bran depletion. The biomass growth was poorly estimated by secretion kinetics of α-amylase, endoglucanase, protease and xylanase, but enzyme kinetics were important for understanding substrate colonization. CONCLUSIONS In conclusion, the NAG concentration was strongly affected by the sample size and sampling procedure. The strategy of fungal colonization on the substrates was well characterized through SEM analysis. The colonization strategy has direct influence on the kinetic parameters of the logistic model. Myceliophthora thermophila has a well-defined dynamic of enzyme secretion to degrade the substrate, although the kinetics of enzyme secretion has shown not adequate to characterize the kinetics of fungal growth. SIGNIFICANCE AND IMPACT OF THE STUDY The paper provides reliable growth kinetic parameters in the SSC of the cellulase producer fungus M. thermophila M.7·7, as well as a robust analysis on three indirect methods (NAG, enzymes and SEM) for estimation of fungal development.
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Affiliation(s)
- A C Dos Santos Gomes
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto São Paulo, Brazil
| | - F P Casciatori
- Chemical Engineering Department, Graduate Program of Chemical Engineering, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, Brazil
| | - E Gomes
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto São Paulo, Brazil
| | - C da Costa Carreira Nunes
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto São Paulo, Brazil
| | - M M S Moretti
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto São Paulo, Brazil
| | - J C Thoméo
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), Rua Cristóvão Colombo 2265, São José do Rio Preto São Paulo, Brazil
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17
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Ibrar M, Ullah MW, Manan S, Farooq U, Rafiq M, Hasan F. Fungi from the extremes of life: an untapped treasure for bioactive compounds. Appl Microbiol Biotechnol 2020; 104:2777-2801. [DOI: 10.1007/s00253-020-10399-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/02/2020] [Accepted: 01/20/2020] [Indexed: 01/01/2023]
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18
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Zhang JM, Wang HH, Liu X, Hu CH, Zou Y. Heterologous and Engineered Biosynthesis of Nematocidal Polyketide–Nonribosomal Peptide Hybrid Macrolactone from Extreme Thermophilic Fungi. J Am Chem Soc 2020; 142:1957-1965. [DOI: 10.1021/jacs.9b11410] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jin-Mei Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Hang-Hang Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Xuan Liu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Chang-Hua Hu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
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19
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Molecular Approaches for Analyzing Environmental Chaetomium Diversity and Exploitation of Chaetomium thermophilum for Biochemical Analyses. Fungal Biol 2020. [DOI: 10.1007/978-3-030-31612-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Diversity and ecology of cultivable fungi isolated from the thermal soil gradients in Deception Island, Antarctica. Extremophiles 2019; 24:219-225. [DOI: 10.1007/s00792-019-01146-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/05/2019] [Indexed: 10/25/2022]
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21
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Thomas S, Sanya DRA, Fouchard F, Nguyen HV, Kunze G, Neuvéglise C, Crutz-Le Coq AM. Blastobotrys adeninivorans and B. raffinosifermentans, two sibling yeast species which accumulate lipids at elevated temperatures and from diverse sugars. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:154. [PMID: 31249618 PMCID: PMC6587252 DOI: 10.1186/s13068-019-1492-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/09/2019] [Indexed: 06/08/2023]
Abstract
BACKGROUND In the context of sustainable development, yeast are one class of microorganisms foreseen for the production of oil from diverse renewable feedstocks, in particular those that do not compete with the food supply. However, their use in bulk production, such as for the production of biodiesel, is still not cost effective, partly due to the possible poor use of desired substrates or poor robustness in the practical bioconversion process. We investigated the natural capacity of Blastobotrys adeninivorans, a yeast already used in biotechnology, to store lipids under different conditions. RESULTS The genotyping of seven strains showed the species to actually be composed of two different groups, one that (including the well-known strain LS3) could be reassigned to Blastobotrys raffinosifermentans. We showed that, under nitrogen limitation, strains of both species can synthesize lipids to over 20% of their dry-cell weight during shake-flask cultivation in glucose or xylose medium for 96 h. In addition, organic acids were excreted into the medium. LS3, our best lipid-producing strain, could also accumulate lipids from exogenous oleic acid, up to 38.1 ± 1.6% of its dry-cell weight, and synthesize lipids from various sugar substrates, up to 36.6 ± 0.5% when growing in cellobiose. Both species, represented by LS3 and CBS 8244T, could grow with little filamentation in the lipogenic medium from 28 to 45 °C and reached lipid titers ranging from 1.76 ± 0.28 to 3.08 ± 0.49 g/L in flasks. Under these conditions, the maximum bioconversion yield (Y FA/S = 0.093 ± 0.017) was obtained with LS3 at 37 °C. The presence of genes for predicted subunits of an ATP citrate lyase in the genome of LS3 reinforces its oleaginous character. CONCLUSIONS Blastobotrys adeninivorans and B. raffinosifermentans, which are known to be xerotolerant and genetically-tractable, are promising biotechnological yeasts of the Saccharomycotina that could be further developed through genetic engineering for the production of microbial oil. To our knowledge, this is the first report of efficient lipid storage in yeast when cultivated at a temperature above 40 °C. This paves the way to help reducing costs through consolidated bioprocessing.
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Affiliation(s)
- Stéphane Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Daniel R. A. Sanya
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Florian Fouchard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Huu-Vang Nguyen
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstr. 3, 06466 Gatersleben, Germany
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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22
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Takahashi S, Osugi K, Shimekake Y, Shinbo A, Abe K, Kera Y. Characterization and improvement of substrate-binding affinity of D-aspartate oxidase of the thermophilic fungus Thermomyces dupontii. Appl Microbiol Biotechnol 2019; 103:4053-4064. [PMID: 30937498 DOI: 10.1007/s00253-019-09787-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/05/2019] [Accepted: 03/19/2019] [Indexed: 12/23/2022]
Abstract
D-Aspartate oxidase (DDO) is a valuable enzyme that can be utilized in the determination of acidic D-amino acids and the optical resolution of a racemic mixture of acidic amino acids, which require its higher stability, higher catalytic activity, and higher substrate-binding affinity. In the present study, we identified DDO gene (TdDDO) of a thermophilic fungus, Thermomyces dupontii, and characterized the recombinant enzyme expressed in Escherichia coli. In addition, we generated a variant that has a higher substrate-binding affinity. The recombinant TdDDO expressed in E. coli exhibited oxidase activity toward acidic D-amino acids and a neutral D-amino acid, D-Gln, with the highest activity toward D-Glu. The Km and kcat values for D-Glu were 2.16 mM and 217 s-1, respectively. The enzyme had an optimum pH and temperature 8.0 and 60 °C, respectively, and was stable between pH 5.0 and 10.0, with a T50 of ca. 51 °C, which was much higher than that in DDOs from other origins. Enzyme stability decreased following a decrease in protein concentration, and externally added FAD could not repress the destabilization. The mutation of Phe248, potentially located in the active site of TdDDO, to Tyr residue, conserved in DDOs and D-amino acid oxidases, markedly increased substrate-binding affinity. The results showed the great potential of TdDDO and the variant for practical applications.
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Affiliation(s)
- Shouji Takahashi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan.
| | - Kohei Osugi
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Yuya Shimekake
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Akira Shinbo
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Katsumasa Abe
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
| | - Yoshio Kera
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, 940-2188, Japan
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Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity. Sci Rep 2019; 9:3674. [PMID: 30842513 PMCID: PMC6403320 DOI: 10.1038/s41598-019-40213-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/23/2019] [Indexed: 12/28/2022] Open
Abstract
Thermophilic fungi can represent a rich source of industrially relevant enzymes. Here, 105 fungal strains capable of growing at 50 °C and pH 2.0 were isolated from compost and decaying plant matter. Maximum growth temperatures of the strains were in the range 50 °C to 60 °C. Sequencing of the internal transcribed spacer (ITS) regions indicated that 78 fungi belonged to 12 species of Ascomycota and 3 species of Zygomycota, while no fungus of Basidiomycota was detected. The remaining 27 strains could not be reliably assigned to any known species. Phylogenetically, they belonged to the genus Thielavia, but they represented 23 highly divergent genetic groups different from each other and from the closest known species by 12 to 152 nucleotides in the ITS region. Fungal secretomes of all 105 strains produced during growth on untreated rice straw were studied for lignocellulolytic activity at different pH and temperatures. The endoglucanase and xylanase activities differed substantially between the different species and strains, but in general, the enzymes produced by the novel Thielavia spp. strains exhibited both higher thermal stability and tolerance to acidic conditions. The study highlights the vast potential of an untapped diversity of thermophilic fungi in the tropics.
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Li L, Ma Z(S. Global Microbiome Diversity Scaling in Hot Springs With DAR (Diversity-Area Relationship) Profiles. Front Microbiol 2019; 10:118. [PMID: 30853941 PMCID: PMC6395440 DOI: 10.3389/fmicb.2019.00118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/18/2019] [Indexed: 11/20/2022] Open
Abstract
The spatial distribution of biodiversity (i.e., the biogeography) of the hot-spring microbiome is critical for understanding the microbial ecosystems in hot springs. We investigated the microbiome diversity scaling (changes) over space by analyzing the diversity-area relationship (DAR), which is an extension to classic SAR (species-area relationship) law in biogeography. We built DAR models for archaea and bacteria with 16S-rRNA sequencing datasets from 165 hot springs globally. From the DAR models, we sketch out the biogeographic maps of hot-spring microbiomes by constructing: (i) DAR profile-measuring the archaea or bacteria diversity scaling over space (areas); (ii) PDO (pair-wise diversity overlap or similarity) profile-estimating the PDO between two hot springs; (iii) MAD (maximal accrual diversity) profile-predicting the global MAD; (iv) LRD/LGD (ratio of local diversity to regional or global diversity) profile. We further investigated the differences between archaea and bacteria in their biogeographic maps. For example, the comparison of DAR-profile maps revealed that the archaea diversity is more heterogeneous (i.e., more diverse) or scaling faster than the bacterial diversity does in terms of species numbers (species richness), but is less heterogeneous (i.e., less diverse) or scaling slower than bacteria when the diversity (Hill numbers) were weighted in favor of more abundant dominant species. When the diversity is weighted equally in terms of species abundances, archaea, and bacteria are equally heterogeneous over space or scaling at the same rate. Finally, unified DAR models (maps) were built with the combined datasets of archaea and bacteria.
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Affiliation(s)
- Lianwei Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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25
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Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors. Extremophiles 2018; 22:525-535. [DOI: 10.1007/s00792-018-1014-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/11/2018] [Indexed: 10/18/2022]
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26
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Genome mining for peptidases in heat-tolerant and mesophilic fungi and putative adaptations for thermostability. BMC Genomics 2018; 19:152. [PMID: 29463214 PMCID: PMC5819190 DOI: 10.1186/s12864-018-4549-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/13/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Peptidases (EC 3.4) consist of a large group of hydrolytic enzymes that catalyze the hydrolysis of proteins accounting for approximately 65% of the total worldwide enzyme production. Peptidases from thermophilic fungi have adaptations to high temperature that makes them adequate for biotechnological application. In the present study, we profiled the genomes of heat-tolerant fungi and phylogenetically related mesophilic species for genes encoding for peptidases and their putative adaptations for thermostability. RESULTS We generated an extensive catalogue of these enzymes ranging from 241 to 820 peptidase genes in the genomes of 23 fungi. Thermophilic species presented the smallest number of peptidases encoding genes in relation to mesophilic species, and the peptidases families with a greater number of genes were the most affected. We observed differences in peptidases in thermophilic species in comparison to mesophilic counterparts, at (i) the genome level: a great reduction in the number of peptidases encoding genes that harbored a higher number of copies; (ii) in the primary protein structure: shifts in proportion of single or groups of amino acids; and (iii) in the three-dimensional structure: reduction in the number of internal cavities. Similar results were reported for extremely thermophilic proteins, but here we show for the first time that several changes also occurred on the moderate thermophilic enzymes of fungi. In regards to the amino acids composition, peptidases from thermophilic species in relation to the mesophilic ones, contained a larger proportion of Ala, Glu, Gly, Pro, Arg and Val residues and a lower number of Cys, His, Ile, Lys, Met, Asn, Gln, Ser, Thr and Trp residues (P < 0.05). Moreover, we observed an increase in the proportion of hydrophobic and charged amino acids and a decrease in polar amino acids. CONCLUSIONS Although thermophilic fungi present less genes encoding for peptidases, these have adaptations that could play a role in thermal resistance from genome to protein structure level.
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Thermophilic Fungi to Dominate Aflatoxigenic/Mycotoxigenic Fungi on Food under Global Warming. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14020199. [PMID: 28218685 PMCID: PMC5334753 DOI: 10.3390/ijerph14020199] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/09/2017] [Accepted: 02/13/2017] [Indexed: 11/16/2022]
Abstract
Certain filamentous fungi produce mycotoxins that contaminate food. Mycotoxin contamination of crops is highly influenced by environmental conditions and is already affected by global warming, where there is a succession of mycotoxigenic fungi towards those that have higher optimal growth temperatures. Aflatoxigenic fungi are at the highest limit of temperature although predicted increases in temperature are beyond that constraint. The present paper discusses what will succeed these fungi and represents the first such consideration. Aflatoxins are the most important mycotoxins and are common in tropical produce, much of which is exported to temperate regions. Hot countries may produce safer food under climate change because aflatoxigenic fungi will be inhibited. The same situation will occur in previously temperate regions where these fungi have recently appeared, although decades later. Existing thermotolerant and thermophilic fungi (TTF) will dominate, in contrast to the conventional mycotoxigenic fungi adapting or mutating, as it will be quicker. TTF produce a range of secondary metabolites, or potential mycotoxins and patulin which may become a new threat. In addition, Aspergillus fumigatus will appear more frequently, a serious human pathogen, because it is (a) thermotolerant and (b) present on crops: hence this is an even greater problem. An incubation temperature of 41 °C needs employing forthwith to detect TTF. Finally, TTF in crops requires study because of the potential for diseases in humans and animals under climate change.
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Oliveira TBD, Lopes VCP, Barbosa FN, Ferro M, Meirelles LA, Sette LD, Gomes E, Rodrigues A. Fungal communities in pressmud composting harbour beneficial and detrimental fungi for human welfare. MICROBIOLOGY-SGM 2016; 162:1147-1156. [PMID: 27170376 DOI: 10.1099/mic.0.000306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pressmud is a substrate derived from sugarcane juice filtrate, and around 26-40 kg of this residue are produced per ton of sugarcane. It is mainly used as fertilizer in crops, and its application in the field is often made without any prior treatment, but, in this research, it was studied for the risk this practice poses for human health. This research was stimulated by previous results indicating the presence of opportunistic pathogens in residues used in various composting systems and the extensive use of fresh pressmud in agriculture. Here, It was assessed the fungal diversity present in both fresh and composting pressmud using 454 pyrosequencing. In addition, heat-tolerant fungi were isolated and surveyed for their enzymatic repertoire of biomass-degrading enzymes (cellulase, xylanase, laccase and polygalacturonase). A wide range of opportunistic pathogens was found among the most abundant taxa in the fresh pressmud, such as Lomentospora prolificans (43.13 %), Trichosporon sp. (10.07 %), Candida tropicalis (7.91 %), and Hormographiella aspergillata (8.19 %). This indicates that fresh pressmud might be a putative source of human pathogenic fungi, presenting a potential threat to human health if applied as fertilizer without any treatment. With regard to the heat-tolerant fungi found in this substrate, all the 110 isolates screened were able to produce at least one of the tested enzymes. The pressmud composting process not only effectively reduces the load of pathogenic fungi, but also creates an interesting environment for fungi able to produce thermostable hydrolytic and oxidative enzymes with biotechnological applications.
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Affiliation(s)
- Tássio Brito de Oliveira
- Department of Biochemistry and Microbiology, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil
| | | | | | - Milene Ferro
- Center for the Study of Social Insects, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil
| | - Lucas Andrade Meirelles
- Department of Biochemistry and Microbiology, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil.,Division of Biology and Biological Engineering, Caltech - California Institute of Technology, Pasadena, CA, USA
| | - Lara Durães Sette
- Department of Biochemistry and Microbiology, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil
| | - Eleni Gomes
- Department of Biology, UNESP - Univ Estadual Paulista, Sao Jose do Rio Preto, SP, Brazil
| | - Andre Rodrigues
- Department of Biochemistry and Microbiology, UNESP - Univ Estadual Paulista, Rio Claro, SP, Brazil
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Gomes E, de Souza AR, Orjuela GL, Da Silva R, de Oliveira TB, Rodrigues A. Applications and Benefits of Thermophilic Microorganisms and Their Enzymes for Industrial Biotechnology. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_21] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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