Journal of Microbiology

Journal Articles

Identification and heterologous reconstitution of a 5-alk(en)ylresorcinol synthase from endophytic fungus Shiraia sp. Slf14: Huiwen Yan , Lei Sun , Jinge Huang , Yixing Qiu , Fuchao Xu , Riming Yan , Du Zhu , Wei Wang , Jixun Zhan; J. Microbiol. 2018;56(11):805-812. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8278-x

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A new type III polyketide synthase gene (Ssars) was discovered from the genome of Shiraia sp. Slf14, an endophytic fungal strain from Huperzia serrata. The intron-free gene was cloned from the cDNA and ligated to two expression vectors pET28a and YEpADH2p-URA3 for expression in Escherichia coli BL21(DE3) and Saccharomyces cerevisiae BJ5464, respectively. SsARS was efficiently expressed in E. coli BL21(DE3), leading to the synthesis of a series of polyketide products. Six major products were isolated from the engineered E. coli and characterized as 1,3-dihydroxyphenyl- 5-undecane, 1,3-dihydroxyphenyl-5-cis-6􍿁-tridecene,1,3-dihydroxyphenyl- 5-tridecane, 1,3-dihydroxyphenyl-5-cis-8􍿁- pentadecene, 1,3-dihydroxyphenyl-5-pentadecane, and 1,3- dihydroxyphenyl-5-cis-10􍿁-heptadecene, respectively, based on the spectral data and biosynthetic origin. Expression of SsARS in the yeast also led to the synthesis of the same polyketide products, indicating that this enzyme can be reconstituted in both heterologous hosts. Supplementation of soybean oil into the culture of E. coli BL21(DE3)/SsARS increased the production titers of 1–6 and led to the synthesis of an additional product, which was identified as 5-(8􍿁Z,11􍿁Z-heptadecadienyl) resorcinol. This work thus allowed the identification of SsARS as a 5-alk(en)ylresorcinol synthase with flexible substrate specificity toward endogenous and exogenous fatty acids. Desired resorcinol derivatives may be synthesized by supplying corresponding fatty acids into the culture medium.

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Genetic Engineering of Filamentous Fungi: Prospects for Obtaining Fourth-Generation Biological Products
Lorena Resende Oliveira, Ariany Rosa Gonçalves, Eliane Dias Quintela, Leandro Colognese, Marcio Vinicius de C. Barros Cortes, Marta Cristina Corsi de Filippi
Applied Microbiology.2024; 4(2): 794. CrossRef
Genome-Based Analysis of Verticillium Polyketide Synthase Gene Clusters
Mohammad Sayari, Aria Dolatabadian, Mohamed El-Shetehy, Pawanpuneet Kaur Rehal, Fouad Daayf
Biology.2022; 11(9): 1252. CrossRef
Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts
Rosa Sagita, Wim J. Quax, Kristina Haslinger
Frontiers in Bioengineering and Biotechnology.2021;[Epub] CrossRef
Research on endophytic fungi for producing huperzine A on a large-scale
Xiao Sang, Minhe Yang, Jingqian Su
Critical Reviews in Microbiology.2020; 46(6): 654. CrossRef
Evolutionary Histories of Type III Polyketide Synthases in Fungi
Jorge Carlos Navarro-Muñoz, Jérôme Collemare
Frontiers in Microbiology.2020;[Epub] CrossRef
Transcriptional heterologous expression of two type III PKS from the lichen Cladonia uncialis
Robert L. Bertrand, John L. Sorensen
Mycological Progress.2019; 18(12): 1437. CrossRef
Advancement of Metabolic Engineering Assisted by Synthetic Biology
Hyang-Mi Lee, Phuong N. L. Vo, Dokyun Na
Catalysts.2018; 8(12): 619. CrossRef

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products: Marfil-Santana Miguel David , O’Connor-Sánchez Aileen , Ramírez-Prado Jorge Humberto , De los Santos-Briones Cesar , López- Aguiar , Lluvia Korynthia , Rojas-Herrera Rafael , Lago-Lestón Asunción , Prieto-Davó Alejandra; J. Microbiol. 2016;54(11):774-781. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6092-x

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Abstract

The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.

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Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications
Pablo Suárez‐Moo, Alejandra Prieto‐Davó
MicrobiologyOpen.2024;[Epub] CrossRef
Changes in the sediment microbial community structure of coastal and inland sinkholes of a karst ecosystem from the Yucatan peninsula
Pablo Suárez-Moo, Claudia A. Remes-Rodríguez, Norma A. Márquez-Velázquez, Luisa I. Falcón, José Q. García-Maldonado, Alejandra Prieto-Davó
Scientific Reports.2022;[Epub] CrossRef
Insights into the Chemical Diversity of Selected Fungi from the Tza Itzá Cenote of the Yucatan Peninsula
Carlos A. Fajardo-Hernández, Firoz Shah Tuglak Khan, Laura Flores-Bocanegra, Alejandra Prieto-Davó, Baojie Wan, Rui Ma, Mallique Qader, Rodrigo Villanueva-Silva, Anahí Martínez-Cárdenas, Marian A. López-Lobato, Shabnam Hematian, Scott G. Franzblau, Huzefa
ACS Omega.2022; 7(14): 12171. CrossRef

Research Support, Non-U.S. Gov'ts

Note] Analysis of a draft genome sequence of Kitasatospora cheerisanensis KCTC 2395 producing bafilomycin antibiotics: Jae Yoon Hwang , Soo Hee Kim , Hye Ryeung Oh , Eunju Kwon , Doo Hyun Nam; J. Microbiol. 2015;53(1):84-89. Published online December 4, 2014; DOI: https://doi.org/10.1007/s12275-015-4340-0

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Abstract

Kitasatospora cheerisanensis KCTC 2395, producing bafilomycin antibiotics belonging to plecomacrolide group, was isolated from a soil sample at Mt. Jiri, Korea. The draft genome sequence contains 8.04 Mb with 73.6% G+C content and 7,810 open reading frames. All the genes for aerial mycelium and spore formations were confirmed in this draft genome. In phylogenetic analysis of MurE proteins (UDPN- acetylmuramyl-L-alanyl-D-glutamate:DAP ligase) in a conserved dcw (division of cell wall) locus, MurE proteins of Kitasatospora species were placed in a separate clade between MurEs of Streptomyces species incorporating LL-diaminopimelic acid (DAP) and MurEs of Saccharopolyspora erythraea as well as Mycobacterium tuberculosis ligating meso- DAP. From this finding, it was assumed that Kitasatospora MurEs exhibit the substrate specificity for both LL-DAP and meso-DAP. The bafilomycin biosynthetic gene cluster was located in the left subtelomeric region. In 71.3 kb-long gene cluster, 17 genes probably involved in the biosynthesis of bafilomycin derivatives were deduced, including 5 polyketide synthase (PKS) genes comprised of 12 PKS modules.

Citations

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Genome-directed discovery of antiproliferative bafilomycins from a deepsea-derived Streptomyces samsunensis
Runyi Wang, Yilei Bao, Yujing Dong, Yun Dong, Huayue Li
Bioorganic Chemistry.2023; 138: 106599. CrossRef
Engineering Bafilomycin High-Producers by Manipulating Regulatory and Biosynthetic Genes in the Marine Bacterium Streptomyces lohii
Zhong Li, Shuai Li, Lei Du, Xingwang Zhang, Yuanyuan Jiang, Wenhua Liu, Wei Zhang, Shengying Li
Marine Drugs.2021; 19(1): 29. CrossRef
Genome based characterization of Kitasatospora sp. MMS16-BH015, a multiple heavy metal resistant soil actinobacterium with high antimicrobial potential
Bo-Ram Yun, Adeel Malik, Seung Bum Kim
Gene.2020; 733: 144379. CrossRef
Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential
Adeel Malik, Yu Ri Kim, Seung Bum Kim
Genes.2020; 11(10): 1166. CrossRef
Biosynthesis of 2-amino-3-hydroxycyclopent-2-enone moiety of bafilomycin in Kitasatospora cheerisanensis KCTC2395
Nguyen Phan Kieu Hanh, Jae Yoon Hwang, Hye Ryeung Oh, Geum Jin Kim, Hyukjae Choi, Doo Hyun Nam
Journal of Microbiology.2018; 56(8): 571. CrossRef
Genus Kitasatospora, taxonomic features and diversity of secondary metabolites
Yōko Takahashi
The Journal of Antibiotics.2017; 70(5): 506. CrossRef
Evolution of cyclizing 5-aminolevulinate synthases in the biosynthesis of actinomycete secondary metabolites: outcomes for genetic screening techniques
Kateřina Petříčková, Alica Chroňáková, Tomáš Zelenka, Tomáš Chrudimský, Stanislav Pospíšil, Miroslav Petříček, Václav Krištůfek
Frontiers in Microbiology.2015;[Epub] CrossRef

Cloning and Analysis of a Type II Polyketide Synthase Gene Cluster from Streptomyces toxytricini NRRL 15,443: Anna Yoo , Atanas V. Demirev , Ji Seon Lee , Sang Dal Kim , Doo Hyun Nam; J. Microbiol. 2006;44(6):649-654.; DOI: https://doi.org/2462 [pii]

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Abstract: A standard type II polyketide synthase (PKS) gene cluster was isolated while attempting to clone the biosynthetic gene for lipstatin from Streptomyces toxytricini NRRL 15,443. This result was observed using a Southern blot of a PstI-digested S. toxytricini chromosomal DNA library with a 444 bp amplified probe of a ketosynthase (KS) gene fragment. Four open reading frames [thioesterase (TE), β-ketoacyl systhase (KAS), chain length factor (CLF), and acyl carrier protein (ACP)], were identified through the nucleotide sequence determination and analysis of a 4.5 kb cloned DNA fragment. In order to confirm the involvement of a cloned gene in lipstatin biosynthesis, a gene disruption experiment for the KS gene was performed. However, the resulting gene disruptant did not show any significant difference in lipstatin production when compared to wild-type S. toxytricini. This result suggests that lipstatin may not be synthesized by a type II PKS.

Review

Genomics Reveals Traces of Fungal Phenylpropanoid-flavonoid Metabolic Pathway in the F ilamentous Fungus Aspergillus oryzae: Praveen Rao Juvvadi , Yasuyo Seshime , Katsuhiko Kitamoto; J. Microbiol. 2005;43(6):475-486.; DOI: https://doi.org/2302 [pii]

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Abstract: Fungal secondary metabolites constitute a wide variety of compounds which either play a vital role in agricultural, pharmaceutical and industrial contexts, or have devastating effects on agriculture, animal and human affairs by virtue of their toxigenicity. Owing to their beneficial and deleterious characteristics, these complex compounds and the genes responsible for their synthesis have been the subjects of extensive investigation by microbiologists and pharmacologists. A majority of the fungal secondary metabolic genes are classified as type I polyketide synthases (PKS) which are often clustered with other secondary metabolism related genes. In this review we discuss on the significance of our recent discovery of chalcone synthase (CHS) genes belonging to the type III PKS superfamily in an industrially important fungus, Aspergillus oryzae. CHS genes are known to play a vital role in the biosynthesis of flavonoids in plants. A comparative genome analyses revealed the unique character of A. oryzae with four CHS-like genes (csyA, csyB, csyC and csyD) amongst other Aspergilli (Aspergillus nidulans and Aspergillus fumigatus) which contained none of the CHS-like genes. Some other fungi such as Neurospora crassa, Fusarium graminearum, Magnaporthe grisea, Podospora anserina and Phanerochaete chrysosporium also contained putative type III PKSs, with a phylogenic distinction from bacteria and plants. The enzymatically active nature of these newly discovered homologues is expected owing to the conservation in the catalytic residues across the different species of plants and fungi, and also by the fact that a majority of these genes (csyA, csyB and csyD) were expressed in A. oryzae. While this finding brings filamentous fungi closer to plants and bacteria which until recently were the only ones considered to possess the type III PKSs, the presence of putative genes encoding other principal enzymes involved in the phenylpropanoid and flavonoid biosynthesis (viz., phenylalanine ammonia-lyase, cinnamic acid hydroxylase and p-coumarate CoA ligase) in the A. oryzae genome undoubtedly prove the extent of its metabolic diversity. Since many of these genes have not been identified earlier, knowledge on their corresponding products or activities remain undeciphered. In future, it is anticipated that these enzymes may be reasonable targets for metabolic engineering in fungi to produce agriculturally and nutritionally important metabolites.

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