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Matsuzawa A, Lee J, Nakagawa S, Itoh J, Takahashi Ueda M, Mitsuhashi S, Kochi Y, Kaneko-Ishino T, Ishino F. HERV-Derived Ervpb1 Is Conserved in Simiiformes, Exhibiting Expression in Hematopoietic Cell Lineages Including Macrophages. Int J Mol Sci 2021; 22:ijms22094504. [PMID: 33925887 PMCID: PMC8123466 DOI: 10.3390/ijms22094504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: The ERVPb1 gene in humans is derived from an envelope (Env) gene of a human endogenous retrovirus group, HERV-P(b). The ERVPb1 gene reportedly has a conserved open reading frame (ORF) in Old World monkeys. Although its forced expression led to cell-fusion in an ex vivo cell culture system, like other Env-derived genes such as syncytin-1 and -2, its mRNA expression is not placenta-specific, but almost ubiquitous, albeit being quite low in human tissues and organs, implying a distinct role for ERVPb1. (2) Methods: To elucidate the cell lineage(s) in which the ERVPb1 protein is translated in human development, we developed a novel, highly sensitive system for detecting HERV-derived proteins/peptides expressed in the tissue differentiation process of human induced pluripotent stem cells (iPSCs). (3) Results: We first determined that ERVPb1 is also conserved in New World monkeys. Then, we showed that the ERVPb1 protein is translated from a uniquely spliced ERVPb1 transcript in hematopoietic cell lineages, including a subset of macrophages, and further showed that its mRNA expression is upregulated by lipopolysaccharide (LPS) stimulation in primary human monocytes. (4) Conclusions: ERVPb1 is unique to Simiiformes and actually translated in hematopoietic cell lineages, including a subset of macrophages.
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Affiliation(s)
- Ayumi Matsuzawa
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (A.M.); (J.L.)
| | - Jiyoung Lee
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (A.M.); (J.L.)
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan;
| | - Johbu Itoh
- Department of Pathology, School of Medicine, Tokai University, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan;
| | - Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.T.U.); (S.M.); (Y.K.)
| | - Satomi Mitsuhashi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.T.U.); (S.M.); (Y.K.)
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.T.U.); (S.M.); (Y.K.)
| | - Tomoko Kaneko-Ishino
- Department of Nursing, School of Medicine, Tokai University, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan
- Correspondence: (T.K.-I.); (F.I.)
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (A.M.); (J.L.)
- Correspondence: (T.K.-I.); (F.I.)
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Sun Y, Xie M, Xu Z, Chan KC, Zhong JY, Fan K, Wong-Bajracharya J, Lam HM, Lim BL. Differential RNA Editing and Intron Splicing in Soybean Mitochondria during Nodulation. Int J Mol Sci 2020; 21:E9378. [PMID: 33317061 PMCID: PMC7764374 DOI: 10.3390/ijms21249378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022] Open
Abstract
Nitrogen fixation in soybean consumes a tremendous amount of energy, leading to substantial differences in energy metabolism and mitochondrial activities between nodules and uninoculated roots. While C-to-U RNA editing and intron splicing of mitochondrial transcripts are common in plant species, their roles in relation to nodule functions are still elusive. In this study, we performed RNA-seq to compare transcript profiles and RNA editing of mitochondrial genes in soybean nodules and roots. A total of 631 RNA editing sites were identified on mitochondrial transcripts, with 12% or 74 sites differentially edited among the transcripts isolated from nodules, stripped roots, and uninoculated roots. Eight out of these 74 differentially edited sites are located on the matR transcript, of which the degrees of RNA editing were the highest in the nodule sample. The degree of mitochondrial intron splicing was also examined. The splicing efficiencies of several introns in nodules and stripped roots were higher than in uninoculated roots. These include nad1 introns 2/3/4, nad4 intron 3, nad5 introns 2/3, cox2 intron 1, and ccmFc intron 1. A greater splicing efficiency of nad4 intron 1, a higher NAD4 protein abundance, and a reduction in supercomplex I + III2 were also observed in nodules, although the causal relationship between these observations requires further investigation.
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Affiliation(s)
- Yuzhe Sun
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Y.S.); (Z.X.); (K.C.C.); (J.Y.Z.)
| | - Min Xie
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (M.X.); (K.F.); (J.W.-B.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Zhou Xu
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Y.S.); (Z.X.); (K.C.C.); (J.Y.Z.)
| | - Koon Chuen Chan
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Y.S.); (Z.X.); (K.C.C.); (J.Y.Z.)
| | - Jia Yi Zhong
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Y.S.); (Z.X.); (K.C.C.); (J.Y.Z.)
| | - Kejing Fan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (M.X.); (K.F.); (J.W.-B.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Johanna Wong-Bajracharya
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (M.X.); (K.F.); (J.W.-B.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (M.X.); (K.F.); (J.W.-B.)
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; (Y.S.); (Z.X.); (K.C.C.); (J.Y.Z.)
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China; (M.X.); (K.F.); (J.W.-B.)
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