1
|
Hu Z, Liu Q, Ouyang B, Wang G, Wei C, Zhao X. Recent advances in genetic engineering to enhance plant-polysaccharide-degrading enzyme expression in Penicillium oxalicum: A brief review. Int J Biol Macromol 2024; 278:134775. [PMID: 39153674 DOI: 10.1016/j.ijbiomac.2024.134775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
With the depletion of non-renewable fossil fuels, there has been an increasing emphasis on renewable biomass. Penicillium oxalicum is notable for its exceptional capacity to secrete a diverse array of enzymes that degrade plant polysaccharides into monosaccharides. These valuable monosaccharides can be harnessed in the production of bioethanol and other sustainable forms of energy. By enhancing the production of plant-polysaccharide-degrading enzymes (PPDEs) in P. oxalicum, we can optimize the utilization of plant biomass. This paper presents recent advances in augmenting PPDE expression in P. oxalicum through genetic engineering strategies involving protoplast preparation, transformation, and factors influencing PPDE gene expression.
Collapse
Affiliation(s)
- Ziyan Hu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Qiling Liu
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Bei Ouyang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Guoping Wang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Chenyang Wei
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China.
| |
Collapse
|
2
|
Singh A, Anwer M, Israr J, Kumar A. Advances in CRISPR-Cas systems for fungal infections. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 208:83-107. [PMID: 39266189 DOI: 10.1016/bs.pmbts.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
Fungi contain a wide range of bioactive secondary metabolites (SMs) that have numerous applications in various fields, including agriculture, medicine, human health, and more. It is common for genes responsible for the production of secondary metabolites (SMs) to form biosynthetic gene clusters (BGCs). The identification and analysis of numerous unexplored gene clusters (BGCs) and their corresponding substances (SMs) has been significantly facilitated by the recent advancements in genomic and genetic technologies. Nevertheless, the exploration of secondary metabolites with commercial value is impeded by a variety of challenges. The emergence of modern CRISPR/Cas technologies has brought about a paradigm shift in fungal genetic engineering, significantly streamlining the process of discovering new bioactive compounds. This study begins with an examination of fungal biosynthetic gene clusters (BGCs) and their interconnections with the secondary metabolites (SMs) they generate. Following that, a brief summary of the conventional methods employed in fungal genetic engineering is provided. This study explores various sophisticated CRISPR/Cas-based methodologies and their utilization in examining the synthesis of secondary metabolites (SMs) in fungi. The chapter provides an in-depth analysis of the limitations and obstacles encountered in CRISPR/Cas-based systems when applied to fungal genetic engineering. It also proposes promising avenues for future research to optimize the efficiency of these systems.
Collapse
Affiliation(s)
- Avinash Singh
- Department of Biotechnology, Axis Institute of Higher Education, Kanpur, Uttar Pradesh, India
| | - Monisa Anwer
- Department of Biotechnology, Faculty of Engineering and Technology Rama University, Mandhana, Kanpur, Uttar Pradesh, India
| | - Juveriya Israr
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Lucknow, Barabanki, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology Rama University, Mandhana, Kanpur, Uttar Pradesh, India.
| |
Collapse
|
3
|
Zhao J, Zhao Y, Wu L, Yan N, Yang S, Xu L, He D, Li H, Bao X. Development of a Robust Saccharomyces cerevisiae Strain for Efficient Co-Fermentation of Mixed Sugars and Enhanced Inhibitor Tolerance through Protoplast Fusion. Microorganisms 2024; 12:1526. [PMID: 39203368 PMCID: PMC11356107 DOI: 10.3390/microorganisms12081526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 07/20/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
The economical and efficient commercial production of second-generation bioethanol requires fermentation microorganisms capable of entirely and rapidly utilizing all sugars in lignocellulosic hydrolysates. In this study, we developed a recombinant Saccharomyces cerevisiae strain, BLH510, through protoplast fusion and metabolic engineering to enhance its ability to co-ferment glucose, xylose, cellobiose, and xylooligosaccharides while tolerating various inhibitors commonly found in lignocellulosic hydrolysates. The parental strains, LF1 and BLN26, were selected for their superior glucose/xylose co-fermentation capabilities and inhibitor tolerance, respectively. The fusion strain BLH510 demonstrated efficient utilization of mixed sugars and high ethanol yield under oxygen-limited conditions. Under low inoculum conditions, strain BLH510 could completely consume all four kinds of sugars in the medium within 84 h. The fermentation produced 33.96 g/L ethanol, achieving 84.3% of the theoretical ethanol yield. Despite the challenging presence of mixed inhibitors, BLH510 successfully metabolized all four sugars above after 120 h of fermentation, producing approximately 30 g/L ethanol and reaching 83% of the theoretical yield. Also, strain BLH510 exhibited increased intracellular trehalose content, particularly under conditions with mixed inhibitors, where the intracellular trehalose reached 239.3 mg/g yeast biomass. This elevated trehalose content contributes to the enhanced stress tolerance of BLH510. The study also optimized conditions for protoplast preparation and fusion, balancing high preparation efficiency and satisfactory regeneration efficiency. The results indicate that BLH510 is a promising candidate for industrial second-generation bioethanol production from lignocellulosic biomass, offering improved performance under challenging fermentation conditions. Our work demonstrates the potential of combining protoplast fusion and metabolic engineering to develop superior S. cerevisiae strains for lignocellulosic bioethanol production. This approach can also be extended to develop robust microbial platforms for producing a wide array of lignocellulosic biomass-based biochemicals.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Hongxing Li
- Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, 3501 Daxue Road, Jinan 250353, China; (J.Z.); (Y.Z.); (L.W.); (N.Y.); (S.Y.); (L.X.); (D.H.); (X.B.)
| | | |
Collapse
|
4
|
Cai R, Xiao Y, Xing J, Yu K, Li X, Chai Y. Establishment of a genetic transformation system for cordycipitoid fungus Cordyceps chanhua. Front Microbiol 2024; 15:1333793. [PMID: 38993492 PMCID: PMC11236535 DOI: 10.3389/fmicb.2024.1333793] [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: 11/06/2023] [Accepted: 05/01/2024] [Indexed: 07/13/2024] Open
Abstract
Cordyceps chanhua is a well-known edible and medicinal mushroom with a long history of use in China, and it contains a variety of secondary metabolites with interesting bioactive ingredients. However, recent researches have mainly focused on cultivation conditions, secondary metabolite compositions and pharmacological activities of C. chanhua, the lack of an efficient and stable genetic transformation system has largely limited further research on the relationship between secondary metabolites and biosynthetic gene clusters in C. chanhua. In this study, single-factor experiments were used to compare the effects of different osmotic stabilizers, enzyme concentrations and enzyme digestion times on protoplast yield, and we found that the highest yield of 5.53 × 108 protoplasts/mL was obtained with 0.7 M mannitol, 6 mg/mL snail enzyme and 4 h of enzyme digestion time, and the regeneration rate of protoplasts was up to approximately 30% using 0.7 M mannitol as an osmotic stabilizer. On this basis, a PEG-mediated genetic transformation system of C. chanhua was successfully established for the first time, which lays the foundation for further genetic transformation of C. chanhua.
Collapse
Affiliation(s)
- Ruihang Cai
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Yu Xiao
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiajia Xing
- College of Environmental and Resource Sciences, Zhejiang A&F University, Hangzhou, China
| | - Kongjian Yu
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xiaola Li
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Yiqiu Chai
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| |
Collapse
|
5
|
Coca-Ruiz V, Cabrera-Gómez N, Collado IG, Aleu J. Improved Protoplast Production Protocol for Fungal Transformations Mediated by CRISPR/Cas9 in Botrytis cinerea Non-Sporulating Isolates. PLANTS (BASEL, SWITZERLAND) 2024; 13:1754. [PMID: 38999594 PMCID: PMC11244380 DOI: 10.3390/plants13131754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
Botrytis cinerea is a necrotrophic fungus that causes considerable economic losses in commercial crops. Fungi of the genus Botrytis exhibit great morphological and genetic variability, ranging from non-sporogenic and non-infective isolates to highly virulent sporogenic ones. There is growing interest in the different isolates in terms of their methodological applications aimed at gaining a deeper understanding of the biology of these fungal species for more efficient control of the infections they cause. This article describes an improvement in the protoplast production protocol from non-sporogenic isolates, resulting in viable protoplasts with regenerating capacity. The method improvements consist of a two-day incubation period with mycelium plugs and orbital shaking. Special mention is made of our preference for the VinoTaste Pro enzyme in the KC buffer as a replacement for Glucanex, as it enhances the efficacy of protoplast isolation in B459 and B371 isolates. The methodology described here has proven to be very useful for biotechnological applications such as genetic transformations mediated by the CRISPR/Cas9 tool.
Collapse
Affiliation(s)
- Víctor Coca-Ruiz
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Nuria Cabrera-Gómez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Isidro G Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| |
Collapse
|
6
|
Ning Y, Gu Q, Zheng T, Xu Y, Li S, Zhu Y, Hu B, Yu H, Liu X, Zhang Y, Jiao B, Lu X. Genome Mining Leads to Diverse Sesquiterpenes with Anti-inflammatory Activity from an Arctic-Derived Fungus. JOURNAL OF NATURAL PRODUCTS 2024; 87:1426-1440. [PMID: 38690764 DOI: 10.1021/acs.jnatprod.4c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
With the advancement of bioinformatics, the integration of genome mining with efficient separation technology enables the discovery of a greater number of novel bioactive compounds. The deletion of the key gene responsible for triterpene cyclase biosynthesis in the polar strain Eutypella sp. D-1 instigated metabolic shunting, resulting in the activation of dormant genes and the subsequent production of detectable, new compounds. Fifteen sesquiterpenes were isolated from the mutant strain, with eight being new compounds. The structural elucidation of these compounds was obtained through a combination of HRESIMS, NMR spectroscopy, and ECD calculations, revealing six distinct skeleton types. Compound 7 possessed a unique skeleton of 5/10 macrocyclic ether structure. Based on the gene functions and newly acquired secondary metabolites, the metabolic shunting pathway in the mutant strain was inferred. Compounds 6, 8, 11, 14, and 15 exhibited anti-inflammatory effects without cytotoxicity through the release of nitric oxide from lipopolysaccharide-stimulated RAW264.7 cells. Notably, acorane-type sesquiterpene 8 inhibited nitric oxide production and modulated the MAPK and NLRP3/caspase-1 signaling pathways. Compound 8 also alleviated the CuSO4-induced systemic neurological inflammation symptoms in a transgenic fluorescent zebrafish model.
Collapse
Affiliation(s)
- Yaodong Ning
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Qinwufeng Gu
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China
| | - Te Zheng
- Biology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250000, People's Republic of China
| | - Yao Xu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Song Li
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Yuping Zhu
- College of Basic Medical Sciences, Experimental Teacher Center, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Bo Hu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Haobing Yu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Xiaoyu Liu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Yun Zhang
- Biology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250000, People's Republic of China
| | - Binghua Jiao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Xiaoling Lu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, People's Republic of China
| |
Collapse
|
7
|
Tian YH, Liu M, Tang L, Zhang YJ, Hang Y, Shangguan LY, Zhang YQ, Zhang MS. Establishment of protoplasts transient expression system in Pinellia ternata (Thunb.) Breit. Biotechnol Lett 2023; 45:1381-1391. [PMID: 37589824 DOI: 10.1007/s10529-023-03420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/27/2023] [Accepted: 06/26/2023] [Indexed: 08/18/2023]
Abstract
OBJECTIVE In this study, we established an efficient and rapid transient expression system in the protoplasts of Pinellia ternata (Thunb.) Breit. (P. ternata). RESULTS The protoplasts of P. ternata were prepared from plant leaves as the source material by digesting them with the combination of 20 g·l-1 cellulase and 15 g·l-1 macerozyme for 6 h. Based on the screening of PEG concentration, the conditions for PEG-mediated protoplast transformation were improved, and the highest transformation efficiency was found for 40% PEG 4000. Furthermore, we used the subcellular protein localization technique in P. ternata protoplasts to allow further validation of transient expression system. CONCLUSIONS We present the method that can be applicable for studying both gene verification and expression in P. ternata protoplasts, thus allowing for engineering the improved varieties of P. ternata through molecular plant breeding techniques. This method can also be widely applicable for analyzing protein interactions, detecting promoter activity, for somatic cell fusion in plant breeding, as well as for other related studies.
Collapse
Affiliation(s)
- Yu-Hang Tian
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Miao Liu
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
- Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China
| | - Liu Tang
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Yu-Jin Zhang
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Ye Hang
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Li-Yang Shangguan
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Yin-Qun Zhang
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China
| | - Ming-Sheng Zhang
- College of Life Sciences, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| |
Collapse
|
8
|
Advances and Challenges in CRISPR/Cas-Based Fungal Genome Engineering for Secondary Metabolite Production: A Review. J Fungi (Basel) 2023; 9:jof9030362. [PMID: 36983530 PMCID: PMC10058990 DOI: 10.3390/jof9030362] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Fungi represent an important source of bioactive secondary metabolites (SMs), which have wide applications in many fields, including medicine, agriculture, human health, and many other industries. The genes involved in SM biosynthesis are usually clustered adjacent to each other into a region known as a biosynthetic gene cluster (BGC). The recent advent of a diversity of genetic and genomic technologies has facilitated the identification of many cryptic or uncharacterized BGCs and their associated SMs. However, there are still many challenges that hamper the broader exploration of industrially important secondary metabolites. The recent advanced CRISPR/Cas system has revolutionized fungal genetic engineering and enabled the discovery of novel bioactive compounds. In this review, we firstly introduce fungal BGCs and their relationships with associated SMs, followed by a brief summary of the conventional strategies for fungal genetic engineering. Next, we introduce a range of state-of-the-art CRISPR/Cas-based tools that have been developed and review recent applications of these methods in fungi for research on the biosynthesis of SMs. Finally, the challenges and limitations of these CRISPR/Cas-based systems are discussed and directions for future research are proposed in order to expand their applications and improve efficiency for fungal genetic engineering.
Collapse
|
9
|
Ning Y, Xu Y, Jiao B, Lu X. Application of Gene Knockout and Heterologous Expression Strategy in Fungal Secondary Metabolites Biosynthesis. Mar Drugs 2022; 20:705. [PMID: 36355028 PMCID: PMC9699552 DOI: 10.3390/md20110705] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
The in-depth study of fungal secondary metabolites (SMs) over the past few years has led to the discovery of a vast number of novel fungal SMs, some of which possess good biological activity. However, because of the limitations of the traditional natural product mining methods, the discovery of new SMs has become increasingly difficult. In recent years, with the rapid development of gene sequencing technology and bioinformatics, new breakthroughs have been made in the study of fungal SMs, and more fungal biosynthetic gene clusters of SMs have been discovered, which shows that the fungi still have a considerable potential to produce SMs. How to study these gene clusters to obtain a large number of unknown SMs has been a research hotspot. With the continuous breakthrough of molecular biology technology, gene manipulation has reached a mature stage. Methods such as gene knockout and heterologous expression techniques have been widely used in the study of fungal SM biosynthesis and have achieved good effects. In this review, the representative studies on the biosynthesis of fungal SMs by gene knockout and heterologous expression under the fungal genome mining in the last three years were summarized. The techniques and methods used in these studies were also briefly discussed. In addition, the prospect of synthetic biology in the future under this research background was proposed.
Collapse
Affiliation(s)
| | | | | | - Xiaoling Lu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
| |
Collapse
|
10
|
Gakuubi MM, Ching KC, Munusamy M, Wibowo M, Lim CT, Ma GL, Liang ZX, Kanagasundaram Y, Ng SB. CRISPR/Cas9 RNP-assisted validation of palmarumycin biosynthetic gene cluster in Lophiotrema sp. F6932. Front Microbiol 2022; 13:1012115. [PMID: 36246293 PMCID: PMC9556985 DOI: 10.3389/fmicb.2022.1012115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Lophiotrema is a genus of ascomycetous fungi within the family Lophiotremataceae. Members of this genus have been isolated as endophytes from a wide range of host plants and also from plant debris within terrestrial and marine habitats, where they are thought to function as saprobes. Lophiotrema sp. F6932 was isolated from white mangrove (Avicennia officinalis) in Pulau Ubin Island, Singapore. Crude extracts from the fungus exhibited strong antibacterial activity, and bioassay-guided isolation and structure elucidation of bioactive constituents led to the isolation of palmarumycin C8 and a new analog palmarumycin CP30. Whole-genome sequencing analysis resulted in the identification of a putative type 1 iterative PKS (iPKS) predicated to be involved in the biosynthesis of palmarumycins. To verify the involvement of palmarumycin (PAL) gene cluster in the biosynthesis of these compounds, we employed ribonucleoprotein (RNP)-mediated CRISPR-Cas9 to induce targeted deletion of the ketosynthase (KS) domain in PAL. Double-strand breaks (DSBs) upstream and downstream of the KS domain was followed by homology-directed repair (HDR) with a hygromycin resistance cassette flanked by a 50 bp of homology on both sides of the DSBs. The resultant deletion mutants displayed completely different phenotypes compared to the wild-type strain, as they had different colony morphology and were no longer able to produce palmarumycins or melanin. This study, therefore, confirms the involvement of PAL in the biosynthesis of palmarumycins, and paves the way for implementing a similar approach in the characterization of other gene clusters of interest in this largely understudied fungal strain.
Collapse
Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chun Teck Lim
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Siew Bee Ng,
| |
Collapse
|