1
|
Thenmozhi Kulasekaran N, Sankara Subramanian SH, Thilakam ML, Gopal D, Lee JK, Marimuthu J. Functional analysis of a putative type III polyketide synthase from deep-sea sediment metagenome. J Biosci Bioeng 2024; 137:239-244. [PMID: 38307768 DOI: 10.1016/j.jbiosc.2023.12.019] [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: 08/22/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 02/04/2024]
Abstract
Type III polyketide synthases (type III PKSs) are single homodimeric enzymes that produce diverse products such as phloroglucinol, pyrones, resorcinols and chalcones which are biotechnologically important molecules. In an attempt to identify new type III PKS from extreme environments, the deep-sea sediment metagenome from Bay of Bengal was screened for type III PKS genes. BLASTX analyses of Nanopore sequence derived metagenome with the in-house created PKS database revealed a full length type III PKS from a 5 kb fragment. The annotated full length type III PKS, S9PKS showed 25-30 % sequence identity towards previously characterized enzymes. To functionally characterize the gene, it was synthesized, cloned into pET28a and pColdI vectors under T7 and csp promoters, respectively, and expressed in Escherichia coli Rosetta(DE3) pLysS. The optimized PKS (OptiPKS) was expressed as inclusion bodies under both promoters. The inclusion bodies were successfully solubilised using low concentration of urea, refolded and purified using Ni-NTA Agarose resin. The purified OptiPKS was tested for functionality using fatty acyl-CoA substrates at various temperatures. High performance liquid chromatography (HPLC) analyses revealed that OptiPKS produced tri and tetraketide pyrones using C4 to C10 acyl-CoA starter substrates. Further characterization and mutation of the enzyme would reveal its functional significance. Thus, the study could be a lead for the annotation and functional characterization of putative type III PKS from environmental metagenome data.
Collapse
Affiliation(s)
| | | | - Mary Leema Thilakam
- Marine Biotechnology Division, National Institute of Ocean Technology, Pallikaranai, Chennai-600100, Tamilnadu, India
| | - Dharani Gopal
- Marine Biotechnology Division, National Institute of Ocean Technology, Pallikaranai, Chennai-600100, Tamilnadu, India
| | - Jung Kul Lee
- Department of Chemical Engineering, Konkuk University, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jeya Marimuthu
- Marine Biotechnology Division, National Institute of Ocean Technology, Pallikaranai, Chennai-600100, Tamilnadu, India.
| |
Collapse
|
2
|
Abstract
Covering: 2020This review covers the literature published in 2020 for marine natural products (MNPs), with 757 citations (747 for the period January to December 2020) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1407 in 420 papers for 2020), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. A meta analysis of bioactivity data relating to new MNPs reported over the last five years is also presented.
Collapse
Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | |
Collapse
|
3
|
Zhu WZ, Wang SH, Gao HM, Ge YM, Dai J, Zhang XL, Yang Q. Characterization of Bioactivities and Biosynthesis of Angucycline/Angucyclinone Derivatives Derived from Gephyromycinifex aptenodytis gen. nov., sp. nov. Mar Drugs 2021; 20:md20010034. [PMID: 35049888 PMCID: PMC8779670 DOI: 10.3390/md20010034] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 12/30/2022] Open
Abstract
Strain NJES-13T is the type strain and currently the only species of the newly established actinobacteria genera Aptenodytes in the family Dermatophilaceae isolated from the gut microbiota of the Antarctic emperor penguin. This strain demonstrated excellent bioflocculation activity with bacteria-derived exopolysaccharides (EPSs). Moreover, it produced bioactive angucycline/angucyclinone derivatives (ADs) and contained one type III polyketide synthase (T3PKS), thus demonstrating great potential to produce novel bioactive compounds. However, the low productivity of the potential new AD metabolite was the main obstacle for its chemical structure elucidation. In this study, to increase the concentration of targeted metabolites, the influence of cellular morphology on AD metabolism in strain NJES-13T was determined using glass bead-enhanced fermentation. Based on the cellular ultra-structural observation driven by bacterial EPSs, and quantitative analysis of the targeted metabolites, the successful increasing of the productivity of three AD metabolites was achieved. Afterward, a new frigocyclinone analogue was isolated and then identified as 2-hydroxy-frigocyclinone, as well as two other known ADs named 2-hydroxy-tetrangomycin (2-HT) and gephyromycin (GPM). Three AD metabolites were found to demonstrate different bioactivities. Both C-2 hydroxyl substitutes, 2-hydroxy-tetrangomycin and 2-hydroxy-frigocyclinone, exhibited variable inhibitory activities against Staphylococcus aureus, Bacillus subtilis and Candida albicans. Moreover, the newly identified 2-hydroxy-frigocyclinone also showed significant cytotoxicity against three tested human-derived cancerous cell lines (HL-60, Bel-7402 and A549), with all obtained IC50 values less than 10 µM. Based on the genetic analysis after genomic mining, the plausible biogenetic pathway of the three bioactive ADs in strain NJES-13T was also proposed.
Collapse
Affiliation(s)
- Wen-Zhuo Zhu
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (W.-Z.Z.); (S.-H.W.); (H.-M.G.)
| | - Shu-Heng Wang
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (W.-Z.Z.); (S.-H.W.); (H.-M.G.)
| | - Hui-Min Gao
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (W.-Z.Z.); (S.-H.W.); (H.-M.G.)
| | - Ya-Ming Ge
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316021, China;
| | - Jun Dai
- Natural “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), College of Bioengineering, Hubei University of Technology, Wuhan 430068, China;
| | - Xiao-Ling Zhang
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (W.-Z.Z.); (S.-H.W.); (H.-M.G.)
- ABI Group, Zhejiang Ocean University, Zhoushan 316022, China
- Correspondence: (X.-L.Z.); (Q.Y.)
| | - Qiao Yang
- Department of Marine Chemistry, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (W.-Z.Z.); (S.-H.W.); (H.-M.G.)
- ABI Group, Zhejiang Ocean University, Zhoushan 316022, China
- Department of Environment Science and Engineering, Zhejiang Ocean University, Zhoushan 316022, China
- Correspondence: (X.-L.Z.); (Q.Y.)
| |
Collapse
|
4
|
Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin. Mar Drugs 2021; 19:md19080458. [PMID: 34436297 PMCID: PMC8400323 DOI: 10.3390/md19080458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/13/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
A new versatile actinobacterium designated as strain NJES-13 was isolated from the feces of the Antarctic emperor penguin. This new isolate was found to produce two active gephyromycin analogues and bioflocculanting exopolysaccharides (EPS) metabolites. Phylogenetic analysis based on pairwise comparison of 16S rRNA gene sequences showed that strain NJES-13 was closely related to Mobilicoccus pelagius Aji5-31T with a gene similarity of 95.9%, which was lower than the threshold value (98.65%) for novel species delineation. Additional phylogenomic calculations of the average nucleotide identity (ANI, 75.9–79.1%), average amino acid identity (AAI, 52.4–66.9%) and digital DNA–DNA hybridization (dDDH, 18.6–21.9%), along with the constructed phylogenomic tree based on the up-to-date bacterial core gene (UBCG) set from the bacterial genomes, unequivocally separated strain NJES-13 from its close relatives within the family Dermatophilaceae. Hence, it clearly indicated that strain NJES-13 represented a putative new actinobacterial species isolated from the gut microbiota of mammals inhabiting the Antarctic. The obtained complete genome of strain NJES-13 consisted of a circular 3.45 Mb chromosome with a DNA G+C content of 67.0 mol%. Furthering genome mining of strain NJES-13 showed the presence of five biosynthetic gene clusters (BGCs) including one type III PKS responsible for the biosynthesis of the core of gephyromycins, and a series of genes encoding for bacterial EPS biosynthesis. Thus, based on the combined phylogenetic and active metabolites characterization presented in this study, we confidently conclude that strain NJES-13 is a novel, fresh actinobacterial candidate to produce active gephyromycins and microbial bioflocculanting EPS, with potential pharmaceutical, environmental and biotechnological implications.
Collapse
|