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Kim W, Jeong MH, Yun SH, Hur JS. Transcriptome Analysis Identifies a Gene Cluster for the Biosynthesis of Biruloquinone, a Rare Phenanthraquinone, in a Lichen-Forming Fungus Cladonia macilenta. J Fungi (Basel) 2021; 7:398. [PMID: 34065383 PMCID: PMC8161216 DOI: 10.3390/jof7050398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/03/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022] Open
Abstract
Lichens are prolific producers of natural products of polyketide origin. We previously described a culture of lichen-forming fungus (LFF) Cladonia macilenta that produces biruloquinone, a purple pigment that is a phenanthraquinone rarely found in nature. However, there was no genetic information on the biosynthesis of biruloquinone. To identify a biosynthetic gene cluster for biruloquinone, we mined polyketide synthase (PKS) genes from the genome sequence of a LFF isolated from thalli of C. macilenta. The 38 PKS in C. macilenta are highly diverse, many of which form phylogenetic clades with PKS previously characterized in non-lichenized fungi. We compared transcriptional profiles of the 38 PKS genes in two chemotypic variants, one producing biruloquinone and the other producing no appreciable metabolite in vitro. We identified a PKS gene (hereafter PKS21) that was highly upregulated in the LFF that produces biruloquinone. The boundaries of a putative biruloquinone gene cluster were demarcated by co-expression patterns of six clustered genes, including the PKS21. Biruloquinone gene clusters exhibited a high degree of synteny between related species. In this study we identified a novel PKS family responsible for the biosynthesis of biruloquinone through whole-transcriptome analysis.
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Affiliation(s)
- Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, Korea;
| | - Min-Hye Jeong
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, Korea;
| | - Sung-Hwan Yun
- Department of Medical Sciences, Soonchunhyang University, Asan 31538, Korea;
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon 57922, Korea;
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Jia SL, Chi Z, Chen L, Liu GL, Hu Z, Chi ZM. Molecular evolution and regulation of DHN melanin-related gene clusters are closely related to adaptation of different melanin-producing fungi. Genomics 2021; 113:1962-1975. [PMID: 33901575 DOI: 10.1016/j.ygeno.2021.04.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/31/2021] [Accepted: 04/20/2021] [Indexed: 12/31/2022]
Abstract
Many genes responsible for melanin biosynthesis in fungi were physically linked together. The PKS gene clusters in most of the melanin-producing fungi were regulated by the Cmr1. It was found that a close rearrangement of the PKS gene clusters had evolved in most of the melanin-producing fungi and various functions of melanin in them were beneficial to their adaptation to the changing environments. The melanin-producing fungi had undergone at least five large-scale differentiations, making their PKS gene clusters be quickly evolved and the fungi be adapted to different harsh environments. The recent gene losses and expansion were remarkably frequent in the PKS gene clusters, leading to their rapid evolution and adaptation of their hosts to different environments. The PKS gene and the CMR1 gene in them were subject to a strong co-evolution, but the horizontal gene transfer events might have occurred in the genome-duplicated species, Aspergillus and Penicillium.
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Affiliation(s)
- Shu-Lei Jia
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266003 Qingdao, China
| | - Lu Chen
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266003 Qingdao, China
| | - Guang-Lei Liu
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266003 Qingdao, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou 515063, China
| | - Zhen-Ming Chi
- College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266003 Qingdao, China.
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A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi. J Ind Microbiol Biotechnol 2018; 45:1067-1081. [PMID: 30206732 DOI: 10.1007/s10295-018-2080-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022]
Abstract
Lichens are fungi that form symbiotic partnerships with algae. Although lichens produce diverse polyketides, difficulties in establishing and maintaining lichen cultures have prohibited detailed studies of their biosynthetic pathways. Creative, albeit non-definitive, methods have been developed to assign function to biosynthetic gene clusters in lieu of techniques such as gene knockout and heterologous expressions that are commonly applied to easily cultivatable organisms. We review a total of 81 completely sequenced polyketide synthase (PKS) genes from lichenizing fungi, comprising to our best efforts all complete and reported PKS genes in lichenizing fungi to date. This review provides an overview of the approaches used to locate and sequence PKS genes in lichen genomes, current approaches to assign function to lichen PKS gene clusters, and what polyketides are proposed to be biosynthesized by these PKS. We conclude with remarks on prospects for genomics-based natural products discovery in lichens. We hope that this review will serve as a guide to ongoing research efforts on polyketide biosynthesis in lichenizing fungi.
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Both a PKS and a PPTase are involved in melanin biosynthesis and regulation of Aureobasidium melanogenum XJ5-1 isolated from the Taklimakan desert. Gene 2017; 602:8-15. [DOI: 10.1016/j.gene.2016.11.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 11/19/2022]
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Deduke C, Piercey-Normore MD. Substratum preference of two species of Xanthoparmelia. Fungal Biol 2015; 119:812-22. [PMID: 26321730 DOI: 10.1016/j.funbio.2015.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 03/22/2015] [Accepted: 05/14/2015] [Indexed: 11/17/2022]
Abstract
The distribution of established saxicolous lichens has been previously studied but substratum preference and elemental composition has been relatively unexplored. The objectives of this study were to compare ascospore germination and growth for two species of Xanthoparmelia using media supplemented with pulverized rock and to explore photobiont selectivity relative to ecological guilds. Mature apothecia from X. cumberlandia and X. viriduloumbrina were subjected to five treatments, which include water agar supplemented with crushed granodiorite, basalt, mica schist, dolostone, and malt yeast agar as the control. The algal actin gene was sequenced and the closest algal matches were retrieved from GenBank and analysed to produce a haplotype network. X. cumberlandia exhibited substratum preference for the mica schist treatment, while X. viriduloumbrina grew better on granodiorite and malt yeast agar relative to dolostone. Ascospore germination for both species failed to progress beyond the initial swelling and protrusion stage on the dolostone treatment. The actin gene sequences for the algae were most similar to those of Trebouxia jamesii. The rock substrates did not correspond with the photobiont haplotypes, which does not support the ecological guild hypothesis. This study provided insights into substratum preference and the suitability of the substratum for algal selection.
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Affiliation(s)
- Chris Deduke
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada.
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