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Sruthy KS, Shukla L, Kundu A, Singh SK, Abdulrahman Alodaini H, Hatamleh AA, Santoyo G, Kumar A. Effect of Microbial Consortium Constructed with Lignolytic Ascomycetes Fungi on Degradation of Rice Stubble. J Fungi (Basel) 2023; 9:jof9050567. [PMID: 37233278 DOI: 10.3390/jof9050567] [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: 03/07/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/27/2023] Open
Abstract
Microbial degradation is an effective, eco-friendly and sustainable approach for management of the rice residue. After harvesting a rice crop, removal of stubble from the ground is a challenging task, that forces the farmers to burn the residue in-situ. Therefore, accelerated degradation using an eco-friendly alternative is a necessity. White rot fungi are the most explored group of microbes for accelerated degradation of lignin but they are very slow in growth. The present investigation focuses on degradation of rice stubble using a fungal consortium constructed with highly sporulating ascomycetes fungi, namely, Aspergillus terreus, Aspergillus fumigatus and Alternaria spp. All three species were successful at colonizing the rice stubble. Periodical HPLC analysis of rice stubble alkali extracts revealed that incubation with ligninolytic consortium released various lignin degradation products such as vanillin, vanillic acid, coniferyl alcohol, syringic acid and ferulic acid. The efficiency of the consortium was further studied at different dosages on paddy straw. Maximum lignin degradation was observed when the consortium was applied at 15% volume by weight of rice stubble. Maximum activity of different lignolytic enzymes such as lignin peroxidase, laccase and total phenols was also found with the same treatment. FTIR analysis also supported the observed results. Hence, the presently developed consortium for degrading rice stubble was found to be effective in both laboratory and field conditions. The developed consortium or its oxidative enzymes can be used alone or combined with other commercial cellulolytic consortia to manage the accumulating rice stubble effectively.
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Affiliation(s)
- Kallinkal Sobha Sruthy
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Livleen Shukla
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Aditi Kundu
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sandeep Kumar Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
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Khan W, El-Shehawi AM, Ali F, Ali M, Alqurashi M, Althaqafi MM, Alharthi SB. A Genome-Wide Identification and Expression Pattern of LMCO Gene Family from Turnip ( Brassica rapa L.) under Various Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091904. [PMID: 37176963 PMCID: PMC10180887 DOI: 10.3390/plants12091904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
Laccase-like multi-copper oxidases (LMCOs) are a group of enzymes involved in the oxidation of numerous substrates. Recently, these enzymes have become extremely popular due to their practical applications in various fields of biology. LMCOs generally oxidize various substrates by linking four-electron reduction of the final acceptor, molecular oxygen (O2), to water. Multi-copper oxidases related to laccase are extensively distributed as multi-gene families in the genome sequences of higher plants. The current study thoroughly investigated the LMCO gene family (Br-Lac) and its expression pattern under various abiotic stresses in B. rapa L. A total of 18 Br-Lac gene family members located on five different chromosomes were identified. Phylogenetic analysis classified the documented Br-Lac genes into seven groups: Group-I (four genes), Group-II (nine genes), Group-III (eight genes), Group-IV (four genes), Group-V (six genes), and Group-VI and Group-VII (one gene each). The key features of gene structure and responsive motifs shared the utmost resemblance within the same groups. Additionally, a divergence study also assessed the evolutionary features of Br-Lac genes. The anticipated period of divergence ranged from 12.365 to 39.250 MYA (million years ago). We also identified the pivotal role of the 18 documented members of the LMCO (Br-lac) gene family using quantitative real-time qRT-PCR. Br-Lac-6, Br-Lac-7, Br-Lac-8, Br-Lac-16, Br-Lac-17, and Br-Lac-22 responded positively to abiotic stresses (i.e., drought, heat, and salinity). These findings set the stage for the functional diversity of the LMCO genes in B. rapa.
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Affiliation(s)
- Waqar Khan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ahmed M El-Shehawi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Fayaz Ali
- Department of Botany, Shaheed Benazir Bhutto University, Sheringal, Dir Upper P.O. Box 18050, Pakistan
| | - Murad Ali
- Department of Botany, Hazara University Mansehra, Mansehra P.O. Box 21300, Pakistan
| | - Mohammed Alqurashi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mohammed M Althaqafi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Siraj B Alharthi
- Department of Biological Sciences, King Abdulaziz University, P.O. Box 16834, Jeddah 21474, Saudi Arabia
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3
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Singh G, Kumar S, Afreen S, Bhalla A, Khurana J, Chandel S, Aggarwal A, Arya SK. Laccase mediated delignification of wasted and non-food agricultural biomass: Recent developments and challenges. Int J Biol Macromol 2023; 235:123840. [PMID: 36849073 DOI: 10.1016/j.ijbiomac.2023.123840] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
Utilization of microbial laccases is considered as the cleaner and target specific biocatalytic mechanism for the recovery of cellulose and hemicelluloses from nonfood and wasted agricultural, lignocellulosic biomass (LCB). The extent of lignin removal by laccase depends on the biochemical composition of biomass and the redox potential (E0) of the biocatalyst. Intensive research efforts are going on all over the world for the recognition of appropriate and easily available agricultural lignocellulosic feedstocks to exploit maximally for the production of value-added bioproducts and biofuels. In such circumstances, laccase can play a major role as a leading biocatalyst and potent substitute for chemical based deconstruction of the lignocellulosic materials. The limited commercialization of laccase at an industrial scale has been feasible due to its full working efficiency mostly expressed in the presence of cost intensive redox mediators only. Although, recently there are some reports that came on the mediator free biocatalysis of enzyme but still not considerably explored and neither understood in depth. The present review will address the various research gaps and shortcomings that acted as the big hurdles before the complete exploitation of laccases at an industrial scale. Further, this article also reveals insights on different microbial laccases and their diverse functional environmental conditions that affect the deconstruction process of LCB.
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Affiliation(s)
- Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Shiv Kumar
- Department of Microbiology, Guru Gobind Singh Medical College and Hospital, Baba Farid University of Health Sciences, Faridkot 151203, Punjab, India
| | - Sumbul Afreen
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Aditya Bhalla
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | - Jyoti Khurana
- Biotechnology Department, Arka Jain University, Jamshedpur, Jharkhand, India
| | - Sanjeev Chandel
- GHG College of Pharmacy, Raikot Road, Ludhiana, -141109, India
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Chen J, Ye Y, Chi Y, Hao X, Zhao Q. Transcriptomics and co-expression network analysis revealing candidate genes for the laccase activity of Trametes gibbosa. BMC Microbiol 2023; 23:29. [PMID: 36703110 PMCID: PMC9878871 DOI: 10.1186/s12866-022-02727-3] [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: 07/23/2022] [Accepted: 12/08/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Trametes gibbosa, which is a white-rot fungus of the Polyporaceae family found in the cold temperate zone, causes spongy white rot on wood. Laccase can oxidize benzene homologs and is one of the important oxidases for white rot fungi to degrade wood. However, the pathway of laccase synthesis in white rot fungi is unknown. RESULTS The peak value of laccase activity reached 135.75 U/min/L on the 9th day. For laccase activity and RNA-seq data, gene expression was segmented into 24 modules. Turquoise and blue modules had greater associations with laccase activity (positively 0.94 and negatively -0.86, respectively). For biology function, these genes were concentrated on the cell cycle, citrate cycle, nicotinate, and nicotinamide metabolism, succinate dehydrogenase activity, flavin adenine dinucleotide binding, and oxidoreductase activity which are highly related to the laccase synthetic pathway. Among them, gene_8826 (MW199767), gene_7458 (MW199766), gene_61 (MW199765), gene_1741 (MH257605), and gene_11087 (MK805159) were identified as central genes. CONCLUSION Laccase activity steadily increased in wood degradation. Laccase oxidation consumes oxygen to produce hydrogen ions and water during the degradation of wood. Some of the hydrogen ions produced can be combined by Flavin adenine dinucleotide (FAD) to form reduced Flavin dinucleotide (FADH2), which can be transmitted. Also, the fungus was starved of oxygen throughout fermentation, and the NADH and FADH2 are unable to transfer hydrogen under hypoxia, resulting in the inability of NAD and FAD to regenerate and inhibit the tricarboxylic acid cycle of cells. These key hub genes related to laccase activity play important roles in the molecular mechanisms of laccase synthesis for exploring industrial excellent strains.
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Affiliation(s)
- Jie Chen
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China ,grid.4818.50000 0001 0791 5666Wageningen University & Research, Wageningen, Netherlands
| | - Yi Ye
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China
| | - Yujie Chi
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China
| | - Xin Hao
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China
| | - Qingquan Zhao
- grid.412246.70000 0004 1789 9091Northeast Forestry University, Harbin, China
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Tang H, Wang MJ, Gan XF, Li YQ. Funneling lignin-derived compounds into polyhydroxyalkanoate by Halomonas sp. Y3. BIORESOURCE TECHNOLOGY 2022; 362:127837. [PMID: 36031122 DOI: 10.1016/j.biortech.2022.127837] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Lignin-derived compounds (LDCs) biological funneling for polyhydroxyalkanoate (PHA) synthesis has been attractive but elusive. Herein, the Halomonas sp. Y3 is isolated and developed for PHA production from LDCs. Of the tested 13 LDCs, 4-hydroxybenzoic acid (4-HBA), protocatechuate (PA), catechol (CAT), and vanillic acid (VA) exhibit a hyper-degradation and production with 87.2 %, 85.8 %, 84.7 %, and 83.4 % TOC removal rate and 535.2 mg/L, 506.5 mg/L, 435.6 mg/L, and 440.8 mg/L PHA concentration, respectively. The Halomonas sp. Y3 genome is sequenced by identifying numerous genes responsible for LDCs funneling, stress response, and PHA biosynthesis. An open unsterilized fermentation with optimal conditions of pH 9.0 and NaCl 60 g/L is investigated, achieving a completely aseptic effect and significantly improved PHA production from LDCs. Overall, the results indicate that the Halomonas sp. Y3 is an ideal candidate for LDC bioconversion and exhibits a great potential to realize black liquor valorization.
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Affiliation(s)
- Hao Tang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Ming-Jun Wang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Xiao-Feng Gan
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China
| | - Yuan-Qiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, Leshan 614000, China; College of Life Sciences, Capital Normal University, Beijing 100048, China.
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6
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Chi YJ, Zhang J. Gene expression of the white-rot fungus Lenzites gibbosa during wood degradation. Mycologia 2022; 114:841-856. [PMID: 35834675 DOI: 10.1080/00275514.2022.2072148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
To determine the wood degradation mechanism and its key genes and biological processes of Lenzites gibbosa, we sequenced 15 transcriptomes of mycelial samples under woody environment at 3, 5, 7, and 11 d (D3, D5, D7, and D11) and nonwoody environment (control). All the transcripts were annotated as much as possible in eight databases to determine their function. The key genes and biological processes relating to wood degradation were predicted and screened. The expression of 11 key genes during wood degradation after 5 d of sawdust treatment was detected by quantitative polymerase chain reaction (PCR). A total of 2069 differentially expressed genes (DEGs) were obtained in 10 differential groups. Comparing wood with nonwood treatment condition, the key genes were those participating in oxidation-reduction process, they were oxidoreductase and peroxidase genes and their regulator genes; these genes mainly focused on the three biological processes of carbohydrate metabolism, lignin catabolism, and secondary metabolite biosynthesis, transport, and catabolism. The mostly enriched subcategories in molecular function were oxidoreductase activity, peroxidase activity, and heme binding in Gene Ontology (GO) annotation. One cellulose and hemicellulose degradation pathway and seven pathways related to lignin-derived aromatic compound degradation or the later degradation of lignin were found. In conclusion, during the process of L. gibbosa growing on wood, gene expression at the transcriptional level indicated that lignin catabolism and hyphal growth were promoted, but the metabolism of carbon and carbohydrates including cellulose in lignocellulose in overall trend was inhibited to some extent. The results have important reference value for the study of degradation mechanism of wood white rot.
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Affiliation(s)
- Yu Jie Chi
- School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, Heilongjiang 150040, China
| | - Jian Zhang
- School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, Heilongjiang 150040, China
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7
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Recent advances in the treatment of lignin in papermaking wastewater. World J Microbiol Biotechnol 2022; 38:116. [PMID: 35593964 DOI: 10.1007/s11274-022-03300-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
More than 695.7 million m3 of papermaking wastewater is discharged globally. It contains a mixture of complex pollutants, of which lignin is the major constituent (600-1000 mg/L) of papermaking black liquor, making it the second-largest energy-containing biomass globally and accounting for 47.4% and 59.4% of chemical oxygen demand (16,400 ± 120 mg/L) and chroma (3100 ± 22.32 mg/L) of papermaking wastewater. The complex process and dissolved pollutants are responsible for high pH, biochemical oxygen demand, chemical oxygen demand, total suspended solids, dark color, and toxicity. Papermaking wastewater has emerged as a substantial source of environmental pollution as the conventional wastewater treatment processes are high cost and seldom efficacious. This work introduces the shortcomings of the common treatment methods for papermaking wastewater and lignin, focusing on lignin biodegradation and discussing the metabolic pathways and application prospects of lignin-degrading microbial species. A comprehensive review of the existing lignin treatment methods has proposed that the reasonable amalgamation of biodegradation and various physicochemical techniques are environmentally friendly, sustainable, and economical. Lignin extraction from papermaking wastewater by technology combination is an effective approach to recover valuable organic materials and detoxify wastewater. This review focuses on recent breakthroughs and future trends in papermaking wastewater treatment and lignin removal, with special emphasis on biodegradation, recovery, and utilization of lignin, providing guidance for the mechanism exploration of lignin-degrading microorganisms and the optimization of high-value chemical production.
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Ares A, Costa J, Joaquim C, Pintado D, Santos D, Messmer MM, Mendes-Moreira PM. Effect of Low-Input Organic and Conventional Farming Systems on Maize Rhizosphere in Two Portuguese Open-Pollinated Varieties (OPV), "Pigarro" (Improved Landrace) and "SinPre" (a Composite Cross Population). Front Microbiol 2021; 12:636009. [PMID: 33717028 PMCID: PMC7953162 DOI: 10.3389/fmicb.2021.636009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Maize is one of the most important crops worldwide and is the number one arable crop in Portugal. A transition from the conventional farming system to organic agriculture requires optimization of cultivars and management, the interaction of plant-soil rhizosphere microbiota being pivotal. The objectives of this study were to unravel the effect of population genotype and farming system on microbial communities in the rhizosphere of maize. Rhizosphere soil samples of two open-pollinated maize populations ("SinPre" and "Pigarro") cultivated under conventional and organic farming systems were taken during flowering and analyzed by next-generation sequencing (NGS). Phenological data were collected from the replicated field trial. A total of 266 fungi and 317 bacteria genera were identified in "SinPre" and "Pigarro" populations, of which 186 (69.9%) and 277 (87.4%) were shared among them. The microbiota of "Pigarro" showed a significant higher (P < 0.05) average abundance than the microbiota of "SinPre." The farming system had a statistically significant impact (P < 0.05) on the soil rhizosphere microbiota, and several fungal and bacterial taxa were found to be farming system-specific. The rhizosphere microbiota diversity in the organic farming system was higher than that in the conventional system for both varieties. The presence of arbuscular mycorrhizae (Glomeromycota) was mainly detected in the microbiota of the "SinPre" population under the organic farming systems and very rare under conventional systems. A detailed metagenome function prediction was performed. At the fungal level, pathotroph-saprotroph and pathotroph-symbiotroph lifestyles were modified by the farming system. For bacterial microbiota, the main functions altered by the farming system were membrane transport, transcription, translation, cell motility, and signal transduction. This study allowed identifying groups of microorganisms known for their role as plant growth-promoting rhizobacteria (PGPR) and with the capacity to improve crop tolerance for stress conditions, allowing to minimize the use of synthetic fertilizers and pesticides. Arbuscular mycorrhizae (phyla Glomeromycota) were among the most important functional groups in the fungal microbiota and Achromobacter, Burkholderia, Erwinia, Lysinibacillus, Paenibacillus, Pseudomonas, and Stenotrophomonas in the bacterial microbiota. In this perspective, the potential role of these microorganisms will be explored in future research.
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Affiliation(s)
- Aitana Ares
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Joana Costa
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra, Portugal
| | - Carolina Joaquim
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Duarte Pintado
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Daniela Santos
- Centro de Recursos Naturais, Ambiente e Sociedade (CERNAS), Coimbra, Portugal
| | - Monika M Messmer
- Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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Estrada-Rivera M, Hernández-Oñate MÁ, Dautt-Castro M, Gallardo-Negrete JDJ, Rebolledo-Prudencio OG, Uresti-Rivera EE, Arenas-Huertero C, Herrera-Estrella A, Casas-Flores S. IPA-1 a Putative Chromatin Remodeler/Helicase-Related Protein of Trichoderma virens Plays Important Roles in Antibiosis Against Rhizoctonia solani and Induction of Arabidopsis Systemic Disease Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:808-824. [PMID: 32101077 DOI: 10.1094/mpmi-04-19-0092-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichoderma spp. are filamentous fungi that colonize plant roots conferring beneficial effects to plants, either indirectly through the induction of their defense systems or directly through the suppression of phytopathogens in the rhizosphere. Transcriptomic analyses of Trichoderma spp. emerged as a powerful method for identifying the molecular events underlying the establishment of this beneficial relationship. Here, we focus on the transcriptomic response of Trichoderma virens during its interaction with Arabidopsis seedlings. The main response of T. virens to cocultivation with Arabidopsis was the repression of gene expression. The biological processes of transport and metabolism of carbohydrates were downregulated, including a set of cell wall-degrading enzymes putatively relevant for root colonization. Repression of such genes reached their basal levels at later times in the interaction, when genes belonging to the biological process of copper ion transport were induced, a necessary process providing copper as a cofactor for cell wall-degrading enzymes with the auxiliary activities class. RNA-Seq analyses showed the induction of a member of the SNF2 family of chromatin remodelers/helicase-related proteins, which was named IPA-1 (increased protection of Arabidopsis-1). Sequence analyses of IPA-1 showed its closest relatives to be members of the Rad5/Rad16 and SNF2 subfamilies; however, it grouped into a different clade. Although deletion of IPA-1 in T. virens did not affect its growth, the antibiotic activity of Δipa-1 culture filtrates against Rhizoctonia solani diminished but it remained unaltered against Botrytis cinerea. Triggering of the plant defense genes in plants treated with Δipa-1 was higher, showing enhanced resistance against Pseudomonas syringae but not against B. cinerea as compared with the wild type.
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Affiliation(s)
- Magnolia Estrada-Rivera
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - Miguel Ángel Hernández-Oñate
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, Carretera Gustavo Enrique Astiazarán Rosas No. 46, La Victoria, C.P. 83304. Hermosillo, Sonora, Mexico
| | - Mitzuko Dautt-Castro
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - José de Jesús Gallardo-Negrete
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | | | - Edith Elena Uresti-Rivera
- Facultad de Ciencias Químicas, Departamento de Inmunología y Biología Celular y Molecular, Universidad Autónoma de San Luis Potosí, Av. Salvador Nava s/n, Zona Universitaria, 78290, San Luis Potosí, Mexico
| | - Catalina Arenas-Huertero
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Chapultepec No. 1570. Priv. del Pedregal 78295, San Luis Potosí, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato, C.P. 36824, Irapuato, Gto., México
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
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10
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Riyadi FA, Tahir AA, Yusof N, Sabri NSA, Noor MJMM, Akhir FNMD, Othman N, Zakaria Z, Hara H. Enzymatic and genetic characterization of lignin depolymerization by Streptomyces sp. S6 isolated from a tropical environment. Sci Rep 2020; 10:7813. [PMID: 32385385 PMCID: PMC7210275 DOI: 10.1038/s41598-020-64817-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/23/2020] [Indexed: 11/13/2022] Open
Abstract
The conversion of lignocellulosic biomass into bioethanol or biochemical products requires a crucial pretreatment process to breakdown the recalcitrant lignin structure. This research focuses on the isolation and characterization of a lignin-degrading bacterial strain from a decaying oil palm empty fruit bunch (OPEFB). The isolated strain, identified as Streptomyces sp. S6, grew in a minimal medium with Kraft lignin (KL) as the sole carbon source. Several known ligninolytic enzyme assays were performed, and lignin peroxidase (LiP), laccase (Lac), dye-decolorizing peroxidase (DyP) and aryl-alcohol oxidase (AAO) activities were detected. A 55.3% reduction in the molecular weight (Mw) of KL was observed after 7 days of incubation with Streptomyces sp. S6 based on gel-permeation chromatography (GPC). Gas chromatography-mass spectrometry (GC-MS) also successfully highlighted the production of lignin-derived aromatic compounds, such as 3-methyl-butanoic acid, guaiacol derivatives, and 4,6-dimethyl-dodecane, after treatment of KL with strain S6. Finally, draft genome analysis of Streptomyces sp. S6 also revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin depolymerization, as well as for the mineralization of the lower molecular weight compounds, confirming the lignin degradation capability of the bacterial strain.
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Affiliation(s)
- Fatimah Azizah Riyadi
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Analhuda Abdullah Tahir
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Nurtasbiyah Yusof
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Nurul Syazwani Ahmad Sabri
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Megat Johari Megat Mohd Noor
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Fazrena Nadia M D Akhir
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Nor'azizi Othman
- Department of Mechanical Precision Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Zuriati Zakaria
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
| | - Hirofumi Hara
- Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia.
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11
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Ibarra Caballero JR, Ata JP, Leddy KA, Glenn TC, Kieran TJ, Klopfenstein NB, Kim MS, Stewart JE. Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, Phellinus noxius, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates. Fungal Biol 2020; 124:144-154. [PMID: 32008755 DOI: 10.1016/j.funbio.2019.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 11/25/2022]
Abstract
Phellinus noxius is a root-decay pathogen with a pan-tropical/subtropical distribution that attacks a wide range of tree hosts. For this study, genomic sequencing was conducted on P. noxius isolate P919-02W.7 from Federated States of Micronesia (Pohnpei), and its gene expression profile was analyzed using different host wood (Acer, Pinus, Prunus, and Salix) substrates. The assembled genome was 33.92 Mbp with 2954 contigs and 9389 predicted genes. Only small differences were observed in size and gene content in comparison with two other P. noxius genome assemblies (isolates OVT-YTM/97 from Hong Kong, China and FFPRI411160 from Japan, respectively). Genome analysis of P. noxius isolate P919-02W.7 revealed 488 genes encoding proteins related to carbohydrate and lignin metabolism, many of these enzymes are associated with degradation of plant cell wall components. Most of the transcripts expressed by P. noxius isolate P919-02W.7 were similar regardless of wood substrates. This study highlights the vast suite of decomposing enzymes produced by P. noxius, which suggests potential for degrading diverse wood substrates, even from temperate host trees. This information contributes to our understanding of pathogen ecology, mechanisms of wood decomposition, and pathogenic/saprophytic lifestyle.
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Affiliation(s)
- Jorge R Ibarra Caballero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Jessa P Ata
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA; Department of Forest Biological Sciences, University of the Philippines Los Baños, Laguna 4031, Philippines
| | - K A Leddy
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Ned B Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843, USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA.
| | - Jane E Stewart
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
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12
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Chaetomium as Potential Soft Rot Degrader of Woody and Papery Cultural Heritage. Fungal Biol 2020. [DOI: 10.1007/978-3-030-31612-9_15] [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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13
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Cellobiose dehydrogenase. FLAVIN-DEPENDENT ENZYMES: MECHANISMS, STRUCTURES AND APPLICATIONS 2020; 47:457-489. [DOI: 10.1016/bs.enz.2020.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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14
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Jain KK, Kumar A, Shankar A, Pandey D, Chaudhary B, Sharma KK. De novo transcriptome assembly and protein profiling of copper-induced lignocellulolytic fungus Ganoderma lucidum MDU-7 reveals genes involved in lignocellulose degradation and terpenoid biosynthetic pathways. Genomics 2020; 112:184-198. [DOI: 10.1016/j.ygeno.2019.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/07/2019] [Accepted: 01/20/2019] [Indexed: 12/23/2022]
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15
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Shin SK, Ko YJ, Hyeon JE, Han SO. Studies of advanced lignin valorization based on various types of lignolytic enzymes and microbes. BIORESOURCE TECHNOLOGY 2019; 289:121728. [PMID: 31277889 DOI: 10.1016/j.biortech.2019.121728] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
Lignin is a robust material that is considered useless because it has an inhibitory effect on microbes and acts as a physical barrier for cellulose degradation. Therefore, it has been removed from cellulosic biomass to produce high-value materials. However, lignin monomers can be converted to value-added chemicals such as biodegradable plastics and food additives by appropriately engineered microbes. Lignin degradation through peroxidase, laccase and other proteins with auxiliary activity is the first step in lignin valorization. Metabolic engineering of microorganisms for increased tolerance and production yield is the second step for lignin valorization. Here, this review offers a summary of current biotechnologies using various enzymatic activities, synergistic enzyme mixtures and metabolic engineering for lignin valorization in biorefinery.
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Affiliation(s)
- Sang Kyu Shin
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jeong Eun Hyeon
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea; Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul 01133, Republic of Korea; Department of Food and Nutrition, College of Health & Wellness, Sungshin Women's University, Seoul 01133, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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16
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Brink DP, Ravi K, Lidén G, Gorwa-Grauslund MF. Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. Appl Microbiol Biotechnol 2019; 103:3979-4002. [PMID: 30963208 PMCID: PMC6486533 DOI: 10.1007/s00253-019-09692-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 12/18/2022]
Abstract
Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.
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Affiliation(s)
- Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Krithika Ravi
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, Lund, Sweden
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
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17
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Liu D, Yan X, Si M, Deng X, Min X, Shi Y, Chai L. Bioconversion of lignin into bioplastics by Pandoraea sp. B-6: molecular mechanism. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:2761-2770. [PMID: 30484053 DOI: 10.1007/s11356-018-3785-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Lignin is a byproduct in the pulp and paper industry and is considered as a promising alternative for the provision of energy and chemicals. Currently, the efficient valorization of lignin is a challenge owing to its polymeric structure complexity. Here, we present a platform for bio-converting Kraft lignin (KL), to polyhydroxyalkanoate (PHA) by Pandoraea sp. B-6 (hereafter B-6). Depolymerization of KL by B-6 was first confirmed, and > 40% KL was degraded by B-6 in the initial 4 days. Characterization of PHA showed that up to 24.7% of PHA accumulated in B-6 grown in 6-g/L KL mineral medium. The composition, structure, and thermal properties of the produced PHA were analyzed, revealing that 3-hydroxybutyrate was the only monomer and that PHA was comparable with the commercially available bioplastics. Moreover, the genomic analysis illustrated three core enzymatic systems for lignin depolymerization including laccases, peroxidases, and Fenton-reaction enzymes; five catabolic pathways for LDAC degradation and a gene cluster consisting of bktB, phaR, phaB, phaA, and phaC genes involved in PHA biosynthesis. Accordingly, a basic model for the process from lignin depolymerization to PHA production was constructed. Our findings provide a comprehensive perspective for lignin valorization and bio-material production from waste.
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Affiliation(s)
- Dan Liu
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
| | - Xu Yan
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
| | - Mengying Si
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
| | - Xinhui Deng
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
| | - Xiaobo Min
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China
| | - Yan Shi
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China.
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China.
| | - Liyuan Chai
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, China.
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha, 410083, China.
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18
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Fungal Enzymes for the Textile Industry. RECENT ADVANCEMENT IN WHITE BIOTECHNOLOGY THROUGH FUNGI 2019. [DOI: 10.1007/978-3-030-10480-1_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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19
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Kirtzel J, Madhavan S, Wielsch N, Blinne A, Hupfer Y, Linde J, Krause K, Svatoš A, Kothe E. Enzymatic Bioweathering and Metal Mobilization From Black Slate by the Basidiomycete Schizophyllum commune. Front Microbiol 2018; 9:2545. [PMID: 30405590 PMCID: PMC6207625 DOI: 10.3389/fmicb.2018.02545] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 10/05/2018] [Indexed: 11/21/2022] Open
Abstract
Schizophyllum commune is a filamentous basidiomycete causing white-rot in many wood species with the help of a broad range of enzymes including multicopper oxidases such as laccases and laccase-like oxidases. Since these enzymes exhibit a broad substrate range, their ability to oxidatively degrade black slate was investigated. Both haploid monokaryotic, and mated dikaryotic strains were able to grow on black slate rich in organic carbon as sole carbon source. On defined media, only the monokaryon showed growth promotion by addition of slate. At the same time, metals were released from the slate and, after reaching a threshold concentration, inhibited further growth of the fungus. The proteome during decomposition of the black slate showed induction of proteins potentially involved in rock degradation and stress resistance, and the gene for laccase-like oxidase mco2 was up-regulated. Specifically in the dikaryon, the laccase gene lcc1 was induced, while lcc2 as well as mco1, mco3, and mco4 expression levels remained similar. Spectrophotometric analysis revealed that both life forms were able to degrade the rock and produce smaller particles.
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Affiliation(s)
- Julia Kirtzel
- Microbial Communication, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Soumya Madhavan
- Microbial Communication, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Natalie Wielsch
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Yvonne Hupfer
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Katrin Krause
- Microbial Communication, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Erika Kothe
- Microbial Communication, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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20
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Gu Q, Wu Q, Zhang J, Guo W, Ding Y, Wang J, Wu H, Sun M, Hou L, Wei X, Zhang Y. Isolation and Transcriptome Analysis of Phenol-Degrading Bacterium From Carbon-Sand Filters in a Full-Scale Drinking Water Treatment Plant. Front Microbiol 2018; 9:2162. [PMID: 30298058 PMCID: PMC6160575 DOI: 10.3389/fmicb.2018.02162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/23/2018] [Indexed: 02/03/2023] Open
Abstract
Phenol is a typical organic contaminant in the environment. To date, the biodegradation of phenol by microorganisms remains the preferred method for its removal and remediation, but data on phenol removal by drinking water biofilters are lacking. In this study, we used high-throughput sequencing to investigate the microbial community structure in a carbon-sand biofilter. The results indicated that the predominant bacterial group was Bacilli, followed by Gammaproteobacteria, Clostridia, and Alphaproteobacteria. In addition, a strain was capable of degrading phenol at low concentrations of 500 μg/L within 100 min was isolated and identified as Rhodococcus sp. CS-1. Transcriptome analysis results showed that Rhodococcus sp. CS-1 was able to degrade phenol via both the catechol and protocatechuate branch of the β-ketoadipate pathway. Furthermore, some novel candidate biomarkers (copper oxidase, copper chaperone, and MarR/DeoR/TetR family transcriptional regulators) were successfully identified to be potentially involved in phenol biodegradation. This study indicates that carbon-sand filters have the potential for remediation of phenol. The application of native microorganisms to drinking water treatment system is an adaptive strategy in oligotrophic water environments.
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Affiliation(s)
- Qihui Gu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Weipeng Guo
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Yu Ding
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Juan Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Huiqing Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Ming Sun
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Luanfeng Hou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Xianhu Wei
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Youxiong Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
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21
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Ceapă CD, Vázquez-Hernández M, Rodríguez-Luna SD, Cruz Vázquez AP, Jiménez Suárez V, Rodríguez-Sanoja R, Alvarez-Buylla ER, Sánchez S. Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions. PLoS One 2018; 13:e0192618. [PMID: 29447216 PMCID: PMC5813959 DOI: 10.1371/journal.pone.0192618] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/27/2018] [Indexed: 12/17/2022] Open
Abstract
Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S. scabrisporus NF3 genome is larger than the average Streptomyces genome and not structured for an obligate endosymbiotic lifestyle; this and the fact that can grow in R2YE media implies that it could include a soil-living stage. The genome displays an enrichment of genes associated with amino acid production, protein secretion, secondary metabolite and antioxidants production and xenobiotic degradation, indicating that S. scabrisporus NF3 could contribute to the metabolic enrichment of soil microbial communities and of its hosts. Importantly, besides its metabolic advantages, the genome showed evidence for differential functional specificity and diversification of plant interaction molecules, including genes for the production of plant hormones, stress resistance molecules, chitinases, antibiotics and siderophores. Given the diversity of S. scabrisporus mechanisms for host upkeep, we propose that these strategies were necessary for its adaptation to plant hosts and to face changes in environmental conditions.
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Affiliation(s)
- Corina Diana Ceapă
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Melissa Vázquez-Hernández
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Stefany Daniela Rodríguez-Luna
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Angélica Patricia Cruz Vázquez
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
- Instituto Tecnológico de Tuxtla Gutiérrez,Tuxtla, Gutiérrez, Chiapas, México
| | - Verónica Jiménez Suárez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Romina Rodríguez-Sanoja
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Elena R. Alvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Sergio Sánchez
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
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22
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Kumar VP, Kolte AP, Dhali A, Naik C, Sridhar M. Enhanced delignification of lignocellulosic substrates by Pichia GS115 expressed recombinant laccase. J GEN APPL MICROBIOL 2018; 64:180-189. [DOI: 10.2323/jgam.2017.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Vidya Pradeep Kumar
- Bioenergetics and Environmental Sciences Division, National Institute of Animal Nutrition and Physiology
| | - Atul P. Kolte
- Animal Nutrition Division, National Institute of Animal Nutrition and Physiology
| | - Arindam Dhali
- Bioenergetics and Environmental Sciences Division, National Institute of Animal Nutrition and Physiology
| | | | - Manpal Sridhar
- Bioenergetics and Environmental Sciences Division, National Institute of Animal Nutrition and Physiology
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23
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Sista Kameshwar AK, Qin W. Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi. Mycology 2017; 9:93-105. [PMID: 30123665 PMCID: PMC6059041 DOI: 10.1080/21501203.2017.1419296] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/15/2017] [Indexed: 12/12/2022] Open
Abstract
We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, Canada
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24
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Janusz G, Pawlik A, Sulej J, Swiderska-Burek U, Jarosz-Wilkolazka A, Paszczynski A. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiol Rev 2017; 41:941-962. [PMID: 29088355 PMCID: PMC5812493 DOI: 10.1093/femsre/fux049] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022] Open
Abstract
Extensive research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.
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Affiliation(s)
- Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Pawlik
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Justyna Sulej
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Urszula Swiderska-Burek
- Department of Botany and Mycology, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Anna Jarosz-Wilkolazka
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka 19 St., 20-033 Lublin, Poland
| | - Andrzej Paszczynski
- School of Food Science, Food Research Center, Room 103, University of Idaho, Moscow, ID 83844, USA
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Kameshwar AKS, Qin W. Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation. Int J Biol Sci 2017; 13:85-99. [PMID: 28123349 PMCID: PMC5264264 DOI: 10.7150/ijbs.17390] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/10/2016] [Indexed: 01/04/2023] Open
Abstract
In literature, extensive studies have been conducted on popular wood degrading white rot fungus, Phanerochaete chrysosporium about its lignin degrading mechanisms compared to the cellulose and hemicellulose degrading abilities. This study delineates cellulose and hemicellulose degrading mechanisms through large scale metadata analysis of P. chrysosporium gene expression data (retrieved from NCBI GEO) to understand the common expression patterns of differentially expressed genes when cultured on different growth substrates. Genes encoding glycoside hydrolase classes commonly expressed during breakdown of cellulose such as GH-5,6,7,9,44,45,48 and hemicellulose are GH-2,8,10,11,26,30,43,47 were found to be highly expressed among varied growth conditions including simple customized and complex natural plant biomass growth mediums. Genes encoding carbohydrate esterase class enzymes CE (1,4,8,9,15,16) polysaccharide lyase class enzymes PL-8 and PL-14, and glycosyl transferases classes GT (1,2,4,8,15,20,35,39,48) were differentially expressed in natural plant biomass growth mediums. Based on these results, P. chrysosporium, on natural plant biomass substrates was found to express lignin and hemicellulose degrading enzymes more than cellulolytic enzymes except GH-61 (LPMO) class enzymes, in early stages. It was observed that the fate of P. chrysosporium transcriptome is significantly affected by the wood substrate provided. We believe, the gene expression findings in this study plays crucial role in developing genetically efficient microbe with effective cellulose and hemicellulose degradation abilities.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada
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Franco Cairo JPL, Carazzolle MF, Leonardo FC, Mofatto LS, Brenelli LB, Gonçalves TA, Uchima CA, Domingues RR, Alvarez TM, Tramontina R, Vidal RO, Costa FF, Costa-Leonardo AM, Paes Leme AF, Pereira GAG, Squina FM. Expanding the Knowledge on Lignocellulolytic and Redox Enzymes of Worker and Soldier Castes from the Lower Termite Coptotermes gestroi. Front Microbiol 2016; 7:1518. [PMID: 27790186 PMCID: PMC5061848 DOI: 10.3389/fmicb.2016.01518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/12/2016] [Indexed: 11/13/2022] Open
Abstract
Termites are considered one of the most efficient decomposers of lignocelluloses on Earth due to their ability to produce, along with its microbial symbionts, a repertoire of carbohydrate-active enzymes (CAZymes). Recently, a set of Pro-oxidant, Antioxidant, and Detoxification enzymes (PAD) were also correlated with the metabolism of carbohydrates and lignin in termites. The lower termite Coptotermes gestroi is considered the main urban pest in Brazil, causing damage to wood constructions. Recently, analysis of the enzymatic repertoire of C. gestroi unveiled the presence of different CAZymes. Because the gene profile of CAZy/PAD enzymes endogenously synthesized by C. gestroi and also by their symbiotic protists remains unclear, the aim of this study was to explore the eukaryotic repertoire of these enzymes in worker and soldier castes of C. gestroi. Our findings showed that worker and soldier castes present similar repertoires of CAZy/PAD enzymes, and also confirmed that endo-glucanases (GH9) and beta-glucosidases (GH1) were the most important glycoside hydrolase families related to lignocellulose degradation in both castes. Classical cellulases such as exo-glucanases (GH7) and endo-glucanases (GH5 and GH45), as well as classical xylanases (GH10 and GH11), were found in both castes only taxonomically related to protists, highlighting the importance of symbiosis in C. gestroi. Moreover, our analysis revealed the presence of Auxiliary Activity enzyme families (AAs), which could be related to lignin modifications in termite digestomes. In conclusion, this report expanded the knowledge on genes and proteins related to CAZy/PAD enzymes from worker and soldier castes of lower termites, revealing new potential enzyme candidates for second-generation biofuel processes.
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Affiliation(s)
- João P L Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Flávia C Leonardo
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil; Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Luciana S Mofatto
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil; Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Lívia B Brenelli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Thiago A Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Cristiane A Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Romênia R Domingues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBIO), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Thabata M Alvarez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Robson Tramontina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM)Campinas, Brazil; Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas (UNICAMP)Campinas, Brazil
| | - Ramon O Vidal
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Fernando F Costa
- Centro de Hematologia e Hemoterapia (Hemocentro), Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Ana M Costa-Leonardo
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP) Rio Claro, Brazil
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBIO), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
| | - Gonçalo A G Pereira
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas (UNICAMP) Campinas, Brazil
| | - Fabio M Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas, Brazil
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Activities of Secreted Aryl Alcohol Quinone Oxidoreductases from Pycnoporus cinnabarinus Provide Insights into Fungal Degradation of Plant Biomass. Appl Environ Microbiol 2016; 82:2411-2423. [PMID: 26873317 DOI: 10.1128/aem.03761-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/08/2016] [Indexed: 11/20/2022] Open
Abstract
Auxiliary activities family 3 subfamily 2 (AA3_2) from the CAZy database comprises various functions related to ligninolytic enzymes, such as fungal aryl alcohol oxidases (AAO) and glucose oxidases, both of which are flavoenzymes. The recent study of the Pycnoporus cinnabarinus CIRM BRFM 137 genome combined with its secretome revealed that four AA3_2 enzymes are secreted during biomass degradation. One of these AA3_2 enzymes, scf184803.g17, has recently been produced heterologously in Aspergillus niger Based on the enzyme's activity and specificity, it was assigned to the glucose dehydrogenases (PcinnabarinusGDH [PcGDH]). Here, we analyze the distribution of the other three AA3_2 enzymes (scf185002.g8, scf184611.g7, and scf184746.g13) to assess their putative functions. These proteins showed the highest homology with aryl alcohol oxidase from Pleurotus eryngii Biochemical characterization demonstrated that they were also flavoenzymes harboring flavin adenine dinucleotide (FAD) as a cofactor and able to oxidize a wide variety of phenolic and nonphenolic aryl alcohols and one aliphatic polyunsaturated primary alcohol. Though presenting homology with fungal AAOs, these enzymes exhibited greater efficiency in reducing electron acceptors (quinones and one artificial acceptor) than molecular oxygen and so were defined as aryl-alcohol:quinone oxidoreductases (AAQOs) with two enzymes possessing residual oxidase activity (PcAAQO2 and PcAAQO3). Structural comparison of PcAAQO homology models with P. eryngii AAO demonstrated a wider substrate access channel connecting the active-site cavity to the solvent, explaining the absence of activity with molecular oxygen. Finally, the ability of PcAAQOs to reduce radical intermediates generated by laccase from P. cinnabarinus was demonstrated, shedding light on the ligninolytic system of this fungus.
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Kameshwar AKS, Qin W. Lignin Degrading Fungal Enzymes. PRODUCTION OF BIOFUELS AND CHEMICALS FROM LIGNIN 2016. [DOI: 10.1007/978-981-10-1965-4_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Kameshwar AKS, Qin W. Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms. Int J Biol Sci 2016; 12:156-71. [PMID: 26884714 PMCID: PMC4737673 DOI: 10.7150/ijbs.13537] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/03/2015] [Indexed: 01/23/2023] Open
Abstract
Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada
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Tian BY, Cao Y, Zhang KQ. Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots. Sci Rep 2015; 5:17087. [PMID: 26603211 PMCID: PMC4658523 DOI: 10.1038/srep17087] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/23/2015] [Indexed: 11/09/2022] Open
Abstract
Endophytes are known to play important roles in plant’s health and productivity. In this study, we investigated the root microbiome of tomato in association with infection by root knot nematodes. Our objectives were to observe the effects and response of the bacterial endophytes before nematode attacks and to reveal the functional attributes of microbes in plant health and nematode pathogenesis. Community analysis of root-associated microbiomes in healthy and nematode-infected tomatoes indicated that nematode infections were associated with variation and differentiation of the endophyte and rhizosphere bacterial populations in plant roots. The community of the resident endophytes in tomato root was significantly affected by nemato-pathogenesis. Remarkably, some bacterial groups in the nematode feeding structure, the root gall, were specifically enriched, suggesting an association with nematode pathogenesis. Function-based metagenomic analysis indicated that the enriched bacterial populations in root gall harbored abundant genes related to degradation of plant polysaccharides, carbohydrate and protein metabolism, and biological nitrogen fixation. Our data indicated that some of the previously assumed beneficial endophytes or bacterial associates with nematode might be involved in nematode infections of the tomato roots.
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Affiliation(s)
- Bao-Yu Tian
- College of Life Science, Fujian Normal University, Fuzhou, Fujian, 350108, China
| | - Yi Cao
- Key Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China.,Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, 550081, China
| | - Ke-Qin Zhang
- Key Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan, 650091, China
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Manoharan L, Kushwaha SK, Hedlund K, Ahrén D. Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils. DNA Res 2015; 22:451-60. [PMID: 26490729 PMCID: PMC4675713 DOI: 10.1093/dnares/dsv026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/28/2015] [Indexed: 01/09/2023] Open
Abstract
Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances.
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Affiliation(s)
| | - Sandeep K Kushwaha
- Department of Biology, Lund University, Lund 223 62, Sweden Bioinformatics Infrastructure for Life Sciences (BILS), Lund University, Lund, Sweden PlantLink, Swedish University of Agriculture Sciences, Alnarp, Sweden
| | | | - Dag Ahrén
- Department of Biology, Lund University, Lund 223 62, Sweden Bioinformatics Infrastructure for Life Sciences (BILS), Lund University, Lund, Sweden
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De novo transcriptome analysis of Inonotus baumii by RNA-seq. J Biosci Bioeng 2015; 121:380-4. [PMID: 26493632 DOI: 10.1016/j.jbiosc.2015.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 08/24/2015] [Accepted: 09/05/2015] [Indexed: 01/24/2023]
Abstract
Inonotus baumii, a basidiomycete white rot fungus, has been widely used as traditional herbal medicine in China, Korea, Japan and other Asian countries for many years. Its extract is of great medicinal importance and plays a valuable role in the immune response and disease resistance. However, limited genetic resources for I. baumii have hindered exploration of this species. In order to gain a molecular understanding of this fungus, Illumina high-throughput technology was used to sequence and analyze the transcriptome of I. baumii, and 280,691 contigs, 43,890 scaffolds and 30,051 unigenes were obtained. Additionally, based on similarity search with known proteins, unigenes were annotated with gene descriptions, gene ontology (GO), clusters of orthologous group (COG), and database of protein families (Pfam) terms. According to the annotation of unigenes, a total of 12 candidate genes involved in the triterpenoid biosynthesis pathway and 21 putative FOLymes (fungal oxidative lignin enzymes) and 176 CAZymes (carbohydrate-active enzymes) were obtained using homology-based BlastX. Moreover, for better understanding of the transcripts function, the BlastX algorithm was used to search for homologous sequences against the Yeast genome. This is the first study on transcriptome analyses of I. baumii, which provided a dataset for functional gene mining and laid a basis for further functional genomics studies of I. baumii.
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Al-Maali G. The influence of metal citrates obtained by aquananotechnology on growth of the strains of medical macromycetes Ganoderma lucidum 1900 and Trametes versicolor 353. UKRAINIAN BOTANICAL JOURNAL 2015. [DOI: 10.15407/ukrbotj72.04.393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Aylward FO, Khadempour L, Tremmel DM, McDonald BR, Nicora CD, Wu S, Moore RJ, Orton DJ, Monroe ME, Piehowski PD, Purvine SO, Smith RD, Lipton MS, Burnum-Johnson KE, Currie CR. Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants. PLoS One 2015; 10:e0134752. [PMID: 26317212 PMCID: PMC4552819 DOI: 10.1371/journal.pone.0134752] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/13/2015] [Indexed: 11/18/2022] Open
Abstract
Leaf-cutter ants are prolific and conspicuous constituents of Neotropical ecosystems that derive energy from specialized fungus gardens they cultivate using prodigious amounts of foliar biomass. The basidiomycetous cultivar of the ants, Leucoagaricus gongylophorus, produces specialized hyphal swellings called gongylidia that serve as the primary food source of ant colonies. Gongylidia also contain plant biomass-degrading enzymes that become concentrated in ant digestive tracts and are deposited within fecal droplets onto fresh foliar material as ants incorporate it into the fungus garden. Although the enzymes concentrated by L. gongylophorus within gongylidia are thought to be critical to the initial degradation of plant biomass, only a few enzymes present in these hyphal swellings have been identified. Here we use proteomic methods to identify proteins present in the gongylidia of three Atta cephalotes colonies. Our results demonstrate that a diverse but consistent set of enzymes is present in gongylidia, including numerous plant biomass-degrading enzymes likely involved in the degradation of polysaccharides, plant toxins, and proteins. Overall, gongylidia contained over three quarters of all biomass-degrading enzymes identified in the L. gongylophorus genome, demonstrating that the majority of the enzymes produced by this fungus for biomass breakdown are ingested by the ants. We also identify a set of 40 of these enzymes enriched in gongylidia compared to whole fungus garden samples, suggesting that certain enzymes may be particularly important in the initial degradation of foliar material. Our work sheds light on the complex interplay between leaf-cutter ants and their fungal symbiont that allows for the host insects to occupy an herbivorous niche by indirectly deriving energy from plant biomass.
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Affiliation(s)
- Frank O Aylward
- Department of Bacteriology, University of Wisconson-Madison, Madison, Wisconsin, United States of America; Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Lily Khadempour
- Department of Bacteriology, University of Wisconson-Madison, Madison, Wisconsin, United States of America; Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Daniel M Tremmel
- Department of Bacteriology, University of Wisconson-Madison, Madison, Wisconsin, United States of America; Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconson-Madison, Madison, Wisconsin, United States of America; Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Si Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Samuel O Purvine
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mary S Lipton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kristin E Burnum-Johnson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconson-Madison, Madison, Wisconsin, United States of America; Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
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Breitenbach M, Weber M, Rinnerthaler M, Karl T, Breitenbach-Koller L. Oxidative stress in fungi: its function in signal transduction, interaction with plant hosts, and lignocellulose degradation. Biomolecules 2015; 5:318-42. [PMID: 25854186 PMCID: PMC4496675 DOI: 10.3390/biom5020318] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 12/29/2022] Open
Abstract
In this review article, we want to present an overview of oxidative stress in fungal cells in relation to signal transduction, interaction of fungi with plant hosts, and lignocellulose degradation. We will discuss external oxidative stress which may occur through the interaction with other microorganisms or plant hosts as well as internally generated oxidative stress, which can for instance originate from NADPH oxidases or “leaky” mitochondria and may be modulated by the peroxiredoxin system or by protein disulfide isomerases thus contributing to redox signaling. Analyzing redox signaling in fungi with the tools of molecular genetics is presently only in its beginning. However, it is already clear that redox signaling in fungal cells often is linked to cell differentiation (like the formation of perithecia), virulence (in plant pathogens), hyphal growth and the successful passage through the stationary phase.
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Affiliation(s)
- Michael Breitenbach
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg 5020, Austria.
| | - Manuela Weber
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg 5020, Austria.
| | - Mark Rinnerthaler
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg 5020, Austria.
| | - Thomas Karl
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg 5020, Austria.
| | - Lore Breitenbach-Koller
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg 5020, Austria.
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Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D. MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics. BMC Bioinformatics 2015; 16:65. [PMID: 25880302 PMCID: PMC4355349 DOI: 10.1186/s12859-015-0501-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 02/19/2015] [Indexed: 12/15/2022] Open
Abstract
Background Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. Results In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 300,000 probes that match more than 400,000 publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/. Conclusion MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0501-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandeep K Kushwaha
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
| | | | | | - Katarina Hedlund
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
| | - Dag Ahrén
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden. .,Bioinformatics Infrastructure for Life Sciences (BILS), Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
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Wibberg D, Jelonek L, Rupp O, Kröber M, Goesmann A, Grosch R, Pühler A, Schlüter A. Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs). Fungal Biol 2014; 118:800-13. [PMID: 25209639 DOI: 10.1016/j.funbio.2014.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/27/2014] [Accepted: 06/27/2014] [Indexed: 10/25/2022]
Abstract
Rhizoctonia solani is a soil-borne plant pathogenic fungus of the phylum Basidiomycota. It affects a wide range of agriculturally important crops and hence is responsible for economically relevant crop losses. Transcriptome analysis of the bottom rot pathogen R. solani AG1-1B (isolate 7/3/14) by applying high-throughput sequencing and bioinformatics methods addressing Expressed Sequence Tag (EST) data interpretation provided new insights in expressed genes of this fungus. Two normalized cDNA libraries representing different cultivation conditions of the fungus were sequenced on the 454 FLX (Roche) system. Subsequent to cDNA sequence assembly and quality control, ESTs were analysed applying advanced bioinformatics methods. More than 14 000 transcript isoforms originating from approximately 10 000 predictable R. solani AG1-IB 7/3/14 genes are represented in each dataset. Comparative analyses revealed several differentially expressed genes depending on the growth conditions applied. Determinants with predicted functions in recognition processes between the fungus and the host plant were identified. Moreover, many R. solani AG1-IB ESTs were predicted to encode putative cellulose, pectin, and lignin degrading enzymes. Furthermore, genes playing a possible role in mitogen-activated protein (MAP) kinase cascades, 4-aminobutyric acid (GABA) metabolism, melanin synthesis, plant defence antagonism, phytotoxin, and mycotoxin synthesis were detected.
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Affiliation(s)
- Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Magdalena Kröber
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Gießen University, D-35392 Gießen, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetables and Ornamental Crops (IGZ), D-14979 Großbeeren, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501 Bielefeld, Germany.
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Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One 2014; 9:e93560. [PMID: 24714189 PMCID: PMC3979922 DOI: 10.1371/journal.pone.0093560] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/07/2014] [Indexed: 12/27/2022] Open
Abstract
Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.
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Xie S, Syrenne R, Sun S, Yuan JS. Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel--from systems biology to synthetic design. Curr Opin Biotechnol 2014; 27:195-203. [PMID: 24657913 DOI: 10.1016/j.copbio.2014.02.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 12/24/2022]
Abstract
Efficient degradation and utilization of lignocellulosic biomass remains a challenge for sustainable and affordable biofuels. Various natural biomass utilization systems (NBUS) evolved the capacity to combat the recalcitrance of plant cell walls. The study of these NBUS could enable the development of efficient and cost-effective biocatalysts, microorganisms, and bioprocesses for biofuels and bioproducts. Here, we reviewed the recent research progresses for several NBUS, ranging from single cell microorganisms to consortiums such as cattle rumen and insect guts. These studies aided the discovery of biomass-degrading enzymes and the elucidation of the evolutionary and functional relevance in these systems. In particular, advances in the next generation 'omics' technologies offered new opportunities to explore NBUS in a high-throughput manner. Systems biology helped to facilitate the rapid biocatalyst discovery and detailed mechanism analysis, which could in turn guide the reverse design of engineered microorganisms and bioprocesses for cost-effective and efficient biomass conversion.
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Affiliation(s)
- Shangxian Xie
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States
| | - Ryan Syrenne
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States; Molecular & Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, United States
| | - Su Sun
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States
| | - Joshua S Yuan
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, United States.
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40
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Baldrian P, López-Mondéjar R. Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods. Appl Microbiol Biotechnol 2014; 98:1531-7. [PMID: 24384749 DOI: 10.1007/s00253-013-5457-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/30/2013] [Accepted: 12/05/2013] [Indexed: 11/28/2022]
Abstract
Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Vídeňská 1083, 14220, Prague 4, Czech Republic,
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41
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Daniel G. Fungal and Bacterial Biodegradation: White Rots, Brown Rots, Soft Rots, and Bacteria. ACS SYMPOSIUM SERIES 2014. [DOI: 10.1021/bk-2014-1158.ch002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Geoffrey Daniel
- Department of Forest Products/Wood Science, Swedish University of Agricultural Sciences, Box 7008, Uppsala, Sweden
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D'haeseleer P, Gladden JM, Allgaier M, Chain PSG, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolić L, Hugenholtz P, Simmons BA, Singer SW. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One 2013; 8:e68465. [PMID: 23894306 PMCID: PMC3716776 DOI: 10.1371/journal.pone.0068465] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 05/29/2013] [Indexed: 12/02/2022] Open
Abstract
Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.
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Affiliation(s)
- Patrik D'haeseleer
- Joint BioEnergy Institute, Emeryville, California, United States of America.
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Wong KS, Cheung MK, Au CH, Kwan HS. A novel Lentinula edodes laccase and its comparative enzymology suggest guaiacol-based laccase engineering for bioremediation. PLoS One 2013; 8:e66426. [PMID: 23799101 PMCID: PMC3683064 DOI: 10.1371/journal.pone.0066426] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/09/2013] [Indexed: 11/18/2022] Open
Abstract
Laccases are versatile biocatalysts for the bioremediation of various xenobiotics, including dyes and polyaromatic hydrocarbons. However, current sources of new enzymes, simple heterologous expression hosts and enzymatic information (such as the appropriateness of common screening substrates on laccase engineering) remain scarce to support efficient engineering of laccase for better "green" applications. To address the issue, this study began with cloning the laccase family of Lentinula edodes. Three laccases perfectio sensu stricto (Lcc4A, Lcc5, and Lcc7) were then expressed from Pichia pastoris, characterized and compared with the previously reported Lcc1A and Lcc1B in terms of kinetics, stability, and degradation of dyes and polyaromatic hydrocarbons. Lcc7 represented a novel laccase, and it exhibited both the highest catalytic efficiency (assayed with 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) [ABTS]) and thermostability. However, its performance on "green" applications surprisingly did not match the activity on the common screening substrates, namely, ABTS and 2,6-dimethoxyphenol. On the other hand, correlation analyses revealed that guaiacol is much better associated with the decolorization of multiple structurally different dyes than are the two common screening substrates. Comparison of the oxidation chemistry of guaiacol and phenolic dyes, such as azo dyes, further showed that they both involve generation of phenoxyl radicals in laccase-catalyzed oxidation. In summary, this study concluded a robust expression platform of L. edodes laccases, novel laccases, and an indicative screening substrate, guaiacol, which are all essential fundamentals for appropriately driving the engineering of laccases towards more efficient "green" applications.
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Affiliation(s)
- Kin-Sing Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Man-Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chun-Hang Au
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hoi-Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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44
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Ekwe E, Morgenstern I, Tsang A, Storms R, Powlowski J. Non-Hydrolytic Cellulose Active Proteins: Research Progress and Potential Application in Biorefineries. Ind Biotechnol (New Rochelle N Y) 2013. [DOI: 10.1089/ind.2013.0010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Enongene Ekwe
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
| | - Ingo Morgenstern
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Reginald Storms
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada
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45
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Yakovlev IA, Hietala AM, Courty PE, Lundell T, Solheim H, Fossdal CG. Genes associated with lignin degradation in the polyphagous white-rot pathogen Heterobasidion irregulare show substrate-specific regulation. Fungal Genet Biol 2013; 56:17-24. [PMID: 23665189 DOI: 10.1016/j.fgb.2013.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 11/15/2022]
Abstract
The pathogenic white-rot basidiomycete Heterobasidion irregulare is able to remove lignin and hemicellulose prior to cellulose during the colonization of root and stem xylem of conifer and broadleaf trees. We identified and followed the regulation of expression of genes belonging to families encoding ligninolytic enzymes. In comparison with typical white-rot fungi, the H. irregulare genome has exclusively the short-manganese peroxidase type encoding genes (6 short-MnPs) and thereby a slight contraction in the pool of class II heme-containing peroxidases, but an expansion of the MCO laccases with 17 gene models. Furthermore, the genome shows a versatile set of other oxidoreductase genes putatively involved in lignin oxidation and conversion, including 5 glyoxal oxidases, 19 quinone-oxidoreductases and 12 aryl-alcohol oxidases. Their genetic multiplicity and gene-specific regulation patterns on cultures based on defined lignin, cellulose or Norway spruce lignocellulose substrates suggest divergent specificities and physiological roles for these enzymes. While the short-MnP encoding genes showed similar transcript levels upon fungal growth on heartwood and reaction zone (RZ), a xylem defense tissue rich in phenolic compounds unique to trees, a subset of laccases showed higher gene expression in the RZ cultures. In contrast, other oxidoreductases depending on initial MnP activity showed generally lower transcript levels on RZ than on heartwood. These data suggest that the rate of fungal oxidative conversion of xylem lignin differs between spruce RZ and heartwood. It is conceivable that in RZ part of the oxidoreductase activities of laccases are related to the detoxification of phenolic compounds involved in host-defense. Expression of the several short-MnP enzymes indicated an important role for these enzymes in effective delignification of wood by H. irregulare.
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Affiliation(s)
- Igor A Yakovlev
- Norwegian Forest and Landscape Institute, PO Box 115, N-1431 Ås, Norway
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46
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Garcia-Ubasart J, Vidal T, Torres AL, Rojas OJ. Laccase-Mediated Coupling of Nonpolar Chains for the Hydrophobization of Lignocellulose. Biomacromolecules 2013; 14:1637-44. [DOI: 10.1021/bm400291s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jordi Garcia-Ubasart
- Textile and Paper
Engineering
Department, ETSEIAT, Universitat Politècnica de Catalunya, E-08222 Terrassa, Spain
| | - Teresa Vidal
- Textile and Paper
Engineering
Department, ETSEIAT, Universitat Politècnica de Catalunya, E-08222 Terrassa, Spain
| | - Antonio L. Torres
- Textile and Paper
Engineering
Department, ETSEIAT, Universitat Politècnica de Catalunya, E-08222 Terrassa, Spain
| | - Orlando J. Rojas
- Departments of Forest Biomaterials
and Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-8005,
United States
- School of Science
and Technology,
Department of Forest Products Technology, Aalto University, 00076 Aalto, Finland
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47
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Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Appl Environ Microbiol 2013; 79:3770-8. [PMID: 23584789 DOI: 10.1128/aem.03833-12] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plants represent a large reservoir of organic carbon comprised primarily of recalcitrant polymers that most metazoans are unable to deconstruct. Many herbivores gain access to nutrients in this material indirectly by associating with microbial symbionts, and leaf-cutter ants are a paradigmatic example. These ants use fresh foliar biomass as manure to cultivate gardens composed primarily of Leucoagaricus gongylophorus, a basidiomycetous fungus that produces specialized hyphal swellings that serve as a food source for the host ant colony. Although leaf-cutter ants are conspicuous herbivores that contribute substantially to carbon turnover in Neotropical ecosystems, the process through which plant biomass is degraded in their fungus gardens is not well understood. Here we present the first draft genome of L. gongylophorus, and, using genomic and metaproteomic tools, we investigate its role in lignocellulose degradation in the gardens of both Atta cephalotes and Acromyrmex echinatior leaf-cutter ants. We show that L. gongylophorus produces a diversity of lignocellulases in ant gardens and is likely the primary driver of plant biomass degradation in these ecosystems. We also show that this fungus produces distinct sets of lignocellulases throughout the different stages of biomass degradation, including numerous cellulases and laccases that likely play an important role in lignocellulose degradation. Our study provides a detailed analysis of plant biomass degradation in leaf-cutter ant fungus gardens and insight into the enzymes underlying the symbiosis between these dominant herbivores and their obligate fungal cultivar.
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48
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Levasseur A, Drula E, Lombard V, Coutinho PM, Henrissat B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:41. [PMID: 23514094 PMCID: PMC3620520 DOI: 10.1186/1754-6834-6-41] [Citation(s) in RCA: 762] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 03/11/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Since its inception, the carbohydrate-active enzymes database (CAZy; http://www.cazy.org) has described the families of enzymes that cleave or build complex carbohydrates, namely the glycoside hydrolases (GH), the polysaccharide lyases (PL), the carbohydrate esterases (CE), the glycosyltransferases (GT) and their appended non-catalytic carbohydrate-binding modules (CBM). The recent discovery that members of families CBM33 and family GH61 are in fact lytic polysaccharide monooxygenases (LPMO), demands a reclassification of these families into a suitable category. RESULTS Because lignin is invariably found together with polysaccharides in the plant cell wall and because lignin fragments are likely to act in concert with (LPMO), we have decided to join the families of lignin degradation enzymes to the LPMO families and launch a new CAZy class that we name "Auxiliary Activities" in order to accommodate a range of enzyme mechanisms and substrates related to lignocellulose conversion. Comparative analyses of these auxiliary activities in 41 fungal genomes reveal a pertinent division of several fungal groups and subgroups combining their phylogenetic origin and their nutritional mode (white vs. brown rot). CONCLUSIONS The new class introduced in the CAZy database extends the traditional CAZy families, and provides a better coverage of the full extent of the lignocellulose breakdown machinery.
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Affiliation(s)
- Anthony Levasseur
- INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, ESIL Polytech Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Aix-Marseille Université, 163 Avenue de Luminy, Marseille, 13288, France
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49
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Kuramae EE, Hillekens RHE, de Hollander M, van der Heijden MGA, van den Berg M, van Straalen NM, Kowalchuk GA. Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf. FEMS Microbiol Ecol 2013; 84:519-31. [PMID: 23360493 DOI: 10.1111/1574-6941.12080] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 01/11/2013] [Accepted: 01/23/2013] [Indexed: 11/27/2022] Open
Abstract
Soil fungi are key players in the degradation of recalcitrant organic matter in terrestrial ecosystems. To examine the organisms and genes responsible for complex organic matter degradation in soil, we tracked changes in fungal community composition and expressed genes in soil adjacent to mesh bags containing maize leaves undergoing decomposition. Using high-throughput sequencing approaches, changes in fungal community composition were determined by targeting 18S rRNA gene sequences, whereas community gene expression was examined via a metatranscriptomic approach. The majority of the 93 000 partial 18S rRNA gene sequences generated, were affiliated with the Ascomycota and Basidiomycota. Fungal diversity was at least 224 operational taxonomic units at the 97% similarity cutoff level. During litter degradation, the relative proportion of Basidiomycota increased, with a decrease in Ascomycota : Basidiomycota ratios over time. The most commonly detected decomposition-associated fungi included Agaricomycetes and Tremellales as well as unclassified Mucoromycotina. The majority of protein families found in the metatranscriptomic data were affiliated to fungal groups described to degrade plant-derived cellulose, such as Mucoraceae, Chaetomiaceae, Sordariaceae, Sebacinaceae, Tremellaceae, Psathyrellaceae and Schizophyllaceae. The combination of high-throughput rRNA gene-based and metatranscriptomic approaches provided perspectives into the organisms and genes involved in complex organic matter in soil.
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Affiliation(s)
- Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
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50
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Mathieu Y, Gelhaye E, Dumarçay S, Gérardin P, Harvengt L, Buée M. Selection and validation of enzymatic activities as functional markers in wood biotechnology and fungal ecology. J Microbiol Methods 2013. [DOI: 10.1016/j.mimet.2012.11.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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