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Liew YJM, Chua KO, Yong HS, Song SL, Chan KG. Complete chloroplast genome of Boesenbergia rotunda and a comparative analysis with members of the family Zingiberaceae. Rev Bras Bot 2022; 45:1209-1222. [PMID: 36320930 PMCID: PMC9607705 DOI: 10.1007/s40415-022-00845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/15/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Boesenbergia rotunda (L.) Mansf. is a medically important ginger species of the family Zingiberaceae but its genomic information on molecular phylogeny and identification is scarce. In this work, the chloroplast genome of B. rotunda was sequenced, characterized and compared to the other Zingiberaceae species to provide chloroplast genetic resources and to determine its phylogenetic position in the family. The chloroplast genome of B. rotunda was 163,817 bp in length and consisted of a large single-copy (LSC) region of 88,302 bp, a small single-copy (SSC) region of 16,023 bp and a pair of inverted repeats (IRA and IRB) of 29,746 bp each. The chloroplast genome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Several genes had atypical start codons, while most amino acids exhibited biased usage of synonymous codons. Comparative analyses with various chloroplast genomes of Zingiberaceae taxa revealed several highly variable regions (psbK-psbI, trnT-GGU-psbD, rbcL-accD, ndhF-rpl32, and ycf1) in the LSC and SSC regions in the chloroplast genome of B. rotunda that could be utilized as molecular markers for DNA barcoding and species delimitation. Phylogenetic analyses based on shared protein-coding genes revealed that B. rotunda formed a distinct lineage with B. kingii Mood & L.M.Prince, in a subclade that also contained the genera Kaempferia and Zingiber. These findings constitute the first chloroplast genome information of B. rotunda that could be a reference for phylogenetic analysis and identification of genus Boesenbergia within the Zingiberaceae family. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s40415-022-00845-w.
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Affiliation(s)
- Yvonne Jing Mei Liew
- University of Malaya Centre for Proteomics Research, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
- Deputy Vice Chancellor’s Office (Research and Innovation), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kah-Ooi Chua
- Centre for Research in Biotechnology for Agriculture, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hoi-Sen Yong
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sze-Looi Song
- Institute for Advanced Studies, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Institute of Marine Sciences, Shantou University, Shantou, 515063 China
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Chua KO, Liew YJM, See-Too WS, Tan JY, Yong HS, Yin WF, Chan KG. Formicincola oecophyllae gen. nov. sp. nov., a novel member of the family Acetobacteraceae isolated from the weaver ant Oecophylla smaragdina. Antonie van Leeuwenhoek 2022; 115:995-1007. [DOI: 10.1007/s10482-022-01750-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
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Liew YJM, Ibrahim PAS, Ong HM, Chong CN, Tan CT, Schee JP, Gómez Román R, Cherian NG, Wong WF, Chang LY. The Immunobiology of Nipah Virus. Microorganisms 2022; 10:microorganisms10061162. [PMID: 35744680 PMCID: PMC9228579 DOI: 10.3390/microorganisms10061162] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 12/23/2022] Open
Abstract
Nipah virus (NiV) is a highly lethal zoonotic paramyxovirus that emerged in Malaysia in 1998. It is a human pathogen capable of causing severe respiratory infection and encephalitis. The natural reservoir of NiV, Pteropus fruit bats, remains a continuous virus source for future outbreaks, although infection in the bats is largely asymptomatic. NiV provokes serious disease in various mammalian species. In the recent human NiV outbreaks in Bangladesh and India, both bats-to-human and human-to-human transmissions have been observed. NiV has been demonstrated to interfere with the innate immune response via interferon type I signaling, promoting viral dissemination and preventing antiviral response. Studies of humoral immunity in infected NiV patients and animal models have shown that NiV-specific antibodies were produced upon infection and were protective. Studies on cellular immunity response to NiV infection in human and animal models also found that the adaptive immune response, specifically CD4+ and CD8+ T cells, was stimulated upon NiV infection. The experimental vaccines and therapeutic strategies developed have provided insights into the immunological requirements for the development of successful medical countermeasures against NiV. This review summarizes the current understanding of NiV pathogenesis and innate and adaptive immune responses induced upon infection.
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Affiliation(s)
- Yvonne Jing Mei Liew
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
- Deputy Vice Chancellor’s Office (Research & Innovation), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Puteri Ainaa S. Ibrahim
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
| | - Hui Ming Ong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
| | - Chee Ning Chong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
| | - Chong Tin Tan
- Division of Neurology, Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.T.T.); (J.P.S.)
| | - Jie Ping Schee
- Division of Neurology, Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (C.T.T.); (J.P.S.)
| | - Raúl Gómez Román
- Vaccine Research and Development, Coalition for Epidemic Preparedness Innovation (CEPI), Askekroken 11, 0277 Oslo, Norway; (R.G.R.); (N.G.C.)
| | - Neil George Cherian
- Vaccine Research and Development, Coalition for Epidemic Preparedness Innovation (CEPI), Askekroken 11, 0277 Oslo, Norway; (R.G.R.); (N.G.C.)
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
| | - Li-Yen Chang
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (Y.J.M.L.); (P.A.S.I.); (H.M.O.); (C.N.C.); (W.F.W.)
- Correspondence:
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Liew YJM, Lee YK, Khalid N, Rahman NA, Tan BC. Enhancing flavonoid production by promiscuous activity of prenyltransferase, BrPT2 from Boesenbergia rotunda. PeerJ 2020; 8:e9094. [PMID: 32391211 PMCID: PMC7197402 DOI: 10.7717/peerj.9094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/09/2020] [Indexed: 11/20/2022] Open
Abstract
Flavonoids and prenylated flavonoids are active components in medicinal plant extracts which exhibit beneficial effects on human health. Prenylated flavonoids consist of a flavonoid core with a prenyl group attached to it. This prenylation process is catalyzed by prenyltranferases (PTs). At present, only a few flavonoid-related PT genes have been identified. In this study, we aimed to investigate the roles of PT in flavonoid production. We isolated a putative PT gene (designated as BrPT2) from a medicinal ginger, Boesenbergia rotunda. The deduced protein sequence shared highest gene sequence homology (81%) with the predicted homogentisate phytyltransferase 2 chloroplastic isoform X1 from Musa acuminata subsp. Malaccensis. We then cloned the BrPT2 into pRI vector and expressed in B. rotunda cell suspension cultures via Agrobacterium-mediated transformation. The BrPT2-expressing cells were fed with substrate, pinostrobin chalcone, and their products were analyzed by liquid chromatography mass spectrometry. We found that the amount of flavonoids, namely alpinetin, pinostrobin, naringenin and pinocembrin, in BrPT2-expressing cells was higher than those obtained from the wild type cells. However, we were unable to detect any targeted prenylated flavonoids. Further in-vitro assay revealed that the reaction containing the BrPT2 protein produced the highest accumulation of pinostrobin from the substrate pinostrobin chalcone compared to the reaction without BrPT2 protein, suggesting that BrPT2 was able to accelerate the enzymatic reaction. The finding of this study implied that the isolated BrPT2 may not be involved in the prenylation of pinostrobin chalcone but resulted in high yield and production of other flavonoids, which is likely related to enzyme promiscuous activities.
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Affiliation(s)
- Yvonne Jing Mei Liew
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yean Kee Lee
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Norzulaani Khalid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,Center for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Boon Chin Tan
- Center for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
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