1
|
YÜCEL H, EKİNCİ K. Carbohydrate active enzyme system in rumen fungi: a review. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2022. [DOI: 10.21448/ijsm.1075030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Hydrolysis and dehydration reactions of carbohydrates, which are used as energy raw materials by all living things in nature, are controlled by Carbohydrate Active Enzyme (CAZy) systems. These enzymes are also used in different industrial areas today. There are different types of microorganisms that have the CAZy system and are used in the industrial sector. Apart from current organisms, there are also rumen fungi within the group of candidate microorganisms with the CAZy system. It has been reported that xylanase (EC3.2.1.8 and EC3.2.1.37) enzyme, a member of the glycoside hydrolase enzyme family obtained from Trichoderma sp. and used especially in areas such as bread, paper, and feed industry, is more synthesized in rumen fungi such as Orpinomyces sp. and Neocallimastix sp. Therefore, this study reviews Neocallimastixsp., Orpinomyces sp., Caecomyces sp., Piromyces sp., and Anaeromyces sp., registered in the CAZy and Mycocosm database for rumen fungi to have both CAZy enzyme activity and to be an alternative microorganism in the industry. Furthermore the CAZy enzyme activities of the strains are investigated. The review shows thatNeocallimax sp. and Orpinomyces sp. areconsidered as candidate microorganisms.
Collapse
Affiliation(s)
- Halit YÜCEL
- KAHRAMANMARAŞ SÜTÇÜ İMAM ÜNİVERSİTESİ, ZİRAAT FAKÜLTESİ
| | | |
Collapse
|
2
|
Novel Monomeric Fungal Subtilisin Inhibitor from a Plant-Pathogenic Fungus, Choanephora cucurbitarum: Isolation and Molecular Characterization. Appl Environ Microbiol 2020; 86:AEM.01818-20. [PMID: 32887713 DOI: 10.1128/aem.01818-20] [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: 07/28/2020] [Accepted: 08/27/2020] [Indexed: 11/20/2022] Open
Abstract
The bacterial protease inhibitor domains known as Streptomyces subtilisin inhibitors (SSI) are rarely found in fungi. Genome analysis of a fungal pathogen, Choanephora cucurbitarum KUS-F28377, revealed 11 SSI-like domains that are horizontally transferred and sequentially diverged during evolution. We investigated the molecular function of fungal SSI-like domains of C. cucurbitarum, designated "choanepins." Among the proteins tested, only choanepin9 showed inhibitory activity against subtilisin as the target protease, accounting for 47% of the inhibitory activity of bacterial SSI. However, the binding affinity (expressed as the dissociation constant [Kd ]) of choanepin9 measured via microscale thermophoresis was 21 nM, whereas that for bacterial SSI is 34 nM. The trend of binding and inhibitory activity suggests that the two inhibitors exhibit different inhibitory mechanisms for subtilisin protease. Interestingly, choanepin9 was identified as a monomer in studies in vitro, whereas bacterial SSI is a homodimer. Based on these observations, we constructed a monomeric bacterial SSI protein with decreased binding affinity to abrogate its inhibitory activity. By altering the reactive sites of choanepin9 deduced from the P1 and P4 sites of bacterial SSI, we reestablished that these residues in choanepins are also crucial for modulating inhibitory activity. These findings suggest that the fungal SSI evolved to target specific cognate proteases by altering the residues involved in inhibitory reactivity (reactive sites) and binding affinity (structural integrity). The function of fungal SSI proteins identified in this study provides not only a clue to fungal pathogenesis via protease inhibition but also a template for the design of novel serine protease inhibitors.IMPORTANCE Until recently, Streptomyces subtilisin inhibitors (SSI) were reported and characterized only in bacteria. We found SSI-like domains in a plant-pathogenic fungus, Choanephora cucurbitarum KUS-F28377, which contains 11 sequentially diverged SSI-like domains. None of these fungal SSI-like domains were functionally characterized before. The active form of fungal SSI-like protein is a monomer, in contrast to the homodimeric bacterial SSI. We constructed a synthetic monomer of bacterial SSI to demonstrate the modulation of its activity based on structural integrity and not reactive sites. Our results suggest the duplication and divergence of SSI-like domains of C. cucurbitarum within the genome to inhibit various cognate proteases during evolution by modulating both binding and reactivity. The molecular functional characterization of fungal SSI-like domains will be useful in understanding their biological role and future biotechnological applications.
Collapse
|
3
|
Kameshwar AKS, Ramos LP, Qin W. CAZymes-based ranking of fungi (CBRF): an interactive web database for identifying fungi with extrinsic plant biomass degrading abilities. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0286-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractCarbohydrate-active enzymes (CAZymes) are industrially important enzymes, which are involved in synthesis and breakdown of carbohydrates. CAZymes secreted by microorganisms especially fungi are widely used in industries. However, identifying an ideal fungal candidate is costly and time-consuming process. In this regard, we have developed a web-database “CAZymes Based Ranking of Fungi (CBRF)”, for sorting and selecting an ideal fungal candidate based on their genome-wide distribution of CAZymes. We have retrieved the complete annotated proteomic data of 443 published fungal genomes from JGI-MycoCosm web-repository, for the CBRF web-database construction. CBRF web-database was developed using open source computing programing languages such as MySQL, HTML, CSS, bootstrap, jQuery, JavaScript and Ajax frameworks. CBRF web-database sorts complete annotated list of fungi based on three selection functionalities: (a) to sort either by ascending (or) descending orders; (b) to sort the fungi based on a selected CAZy group and class; (c) to sort fungi based on their individual lignocellulolytic abilities. We have also developed a simple and basic webpage “S-CAZymes” using HTML, CSS and Java script languages. The global search functionality of S-CAZymes enables the users to understand and retrieve information about a specific carbohydrate-active enzyme and its current classification in the corresponding CAZy family. The S-CAZymes is a supporting web page which can be used in complementary with the CBRF web-database (knowing the classification of specific CAZyme in S-CAZyme and use this information further to sort fungi using CBRF web-database). The CBRF web-database and S-CAZymes webpage are hosted through Amazon® Web Services (AWS) available at http://13.58.192.177/RankEnzymes/about. We strongly believe that CBRF web-database simplifies the process of identifying a suitable fungus both in academics and industries. In future, we intend to update the CBRF web-database with the public release of new annotated fungal genomes.
Collapse
|
4
|
Wijayawardene NN, Pawłowska J, Letcher PM, Kirk PM, Humber RA, Schüßler A, Wrzosek M, Muszewska A, Okrasińska A, Istel Ł, Gęsiorska A, Mungai P, Lateef AA, Rajeshkumar KC, Singh RV, Radek R, Walther G, Wagner L, Walker C, Wijesundara DSA, Papizadeh M, Dolatabadi S, Shenoy BD, Tokarev YS, Lumyong S, Hyde KD. Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0409-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
5
|
West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF. Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res 2018; 28:569-580. [PMID: 29496730 PMCID: PMC5880246 DOI: 10.1101/gr.228429.117] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/27/2018] [Indexed: 11/24/2022]
Abstract
Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.
Collapse
Affiliation(s)
- Patrick T West
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Igor V Grigoriev
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|