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Li C, Li Y, Guo J, Wang Y, Shi X, Zhang Y, Liang N, Ma H, Yuan J, Xu J, Chen H. Abundant mRNA m 1A modification in dinoflagellates: a new layer of gene regulation. EMBO Rep 2024:10.1038/s44319-024-00234-2. [PMID: 39223385 DOI: 10.1038/s44319-024-00234-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 08/01/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Dinoflagellates, a class of unicellular eukaryotic phytoplankton, exhibit minimal transcriptional regulation, representing a unique model for exploring gene expression. The biosynthesis, distribution, regulation, and function of mRNA N1-methyladenosine (m1A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study provides a comprehensive map of m1A in dinoflagellate mRNA and shows that m1A, rather than N6-methyladenosine (m6A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetric distribution along mature transcripts. In Amphidinium carterae, we identify 6549 m1A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many of which are involved in regulating carbon and nitrogen metabolism. Enriched within 3'UTRs, dinoflagellate mRNA m1A levels negatively correlate with translation efficiency. Nitrogen depletion further decreases mRNA m1A levels. Our data suggest that distinctive patterns of m1A modification might influence the expression of metabolism-related genes through translational control.
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Affiliation(s)
- Chongping Li
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, 518000, China
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China
| | - Ying Li
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, 518000, China
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China
- Shenzhen People's Hospital, 3046 Shennan E Rd, Shenzhen, 518020, China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518000, China
| | - Jia Guo
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, 450000, China
| | - Yuci Wang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, 518000, China
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518000, China
| | - Xiaoyan Shi
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, 518000, China
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China
| | - Yangyi Zhang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, 518000, China
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China
| | - Nan Liang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, 518000, China
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China
| | - Honghui Ma
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200000, China
| | - Jie Yuan
- Shenzhen People's Hospital, 3046 Shennan E Rd, Shenzhen, 518020, China.
| | - Jiawei Xu
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China.
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, 450000, China.
| | - Hao Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, 518000, China.
- The First Affiliated Hospital of Zhengzhou University & Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 450000, China.
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518000, China.
- NHC Key Laboratory of Birth Defects Prevention, Zhengzhou, 450000, China.
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Bowazolo C, Morse D. Ribosome profiling in the Symbiodiniacean dinoflagellate Fugacium kawagutii shows coordinated protein synthesis of enzymes in different pathways at different times of day. Mol Microbiol 2023; 120:462-471. [PMID: 37545098 DOI: 10.1111/mmi.15137] [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: 04/25/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/08/2023]
Abstract
Dinoflagellates respond to daily changes in light and dark by changes in cellular metabolism, yet the mechanisms used are still unclear. For example, Fugacium (previously Symbiodinium) kawagutii shows little difference in the transcriptome between day and night suggesting little transcriptional control over gene expression. Here, we have performed ribosome profiling at 2 h intervals over a daily light-dark cycle to assess the degree to which protein synthesis rates might change over the daily cycle. The number of F. kawagutii coding sequences with significant differences in the number of ribosome-protected fragments (RPF) over the 24-h cycle was 2923 using JTK_Cycle and 3655 using ECHO. The majority of the regulated transcripts showed peak translation at the onset of the dark period. The regulated sequences were assigned to different KEGG pathways and transcripts that were translated at roughly the same time were termed concurrently regulated. Both analyses revealed concurrent regulation of many transcripts whose gene products were involved in spliceosome or lysosome biogenesis with peak translation rates around the onset of the dark period, while others, involved in nitrate metabolism and ribosomal proteins, were preferentially translated around the onset of the day phase or the end of the night phase, respectively. In addition, some sequences involved in DNA synthesis were preferentially translated at the end of the day. We conclude that light-dark cycles seem able to synchronize translation of some transcripts encoding proteins involved in a range of different cellular processes, and propose that these changes may help the cells adapt and alter their metabolism as a function of the time of day.
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Affiliation(s)
- Carl Bowazolo
- Département de Sciences Biologiques, Institut de Recherche en biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - David Morse
- Département de Sciences Biologiques, Institut de Recherche en biologie Végétale, Université de Montréal, Montréal, Québec, Canada
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Orchestrated translation specializes dinoflagellate metabolism three times per day. Proc Natl Acad Sci U S A 2022; 119:e2122335119. [PMID: 35858433 PMCID: PMC9335273 DOI: 10.1073/pnas.2122335119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Many cells specialize for different metabolic tasks at different times over their normal ZT cycle by changes in gene expression. However, in most cases, circadian gene expression has been assessed at the mRNA accumulation level, which may not faithfully reflect protein synthesis rates. Here, we use ribosome profiling in the dinoflagellate Lingulodinium polyedra to identify thousands of transcripts showing coordinated translation. All of the components in carbon fixation are concurrently regulated at ZT0, predicting the known rhythm of carbon fixation, and many enzymes involved in DNA replication are concurrently regulated at ZT12, also predicting the known rhythm in this process. Most of the enzymes in glycolysis and the TCA cycle are also regulated together, suggesting rhythms in these processes as well. Surprisingly, a third cluster of transcripts show peak translation at approximately ZT16, and these transcripts encode enzymes involved in transcription, translation, and amino acid biosynthesis. The latter has physiological consequences, as measured free amino acid levels increase at night and thus represent a previously undocumented rhythm in this model. Our results suggest that ribosome profiling may be a more accurate predictor of changed metabolic state than transcriptomics.
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Zaheri B, Morse D. An overview of transcription in dinoflagellates. Gene 2022; 829:146505. [PMID: 35447242 DOI: 10.1016/j.gene.2022.146505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 02/18/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]
Abstract
Dinoflagellates are a vital diverse family of unicellular algae widespread in various aquatic environments. Typically large genomes and permanently condensed chromosomes without histones make these organisms unique among eukaryotes in terms of chromatin structure and gene expression. Genomic and transcriptomic sequencing projects have provided new insight into the genetic foundation of dinoflagellate behaviors. Genes in tandem arrays, trans-splicing of mRNAs and lower levels of transcriptional regulation compared to other eukaryotes all contribute to the differences seen. Here we present a general overview of transcription in dinoflagellates based on previously described work.
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Affiliation(s)
- Bahareh Zaheri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke est, Université de Montréal, Montréal H1X 2B2, Canada
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke est, Université de Montréal, Montréal H1X 2B2, Canada.
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Zaheri B, Veilleux-Trinh C, Morse D. A DINOFLAGELLATE TBP-LIKE FACTOR ACTIVATES TRANSCRIPTION FROM A TTTT-BOX IN YEAST. JOURNAL OF PHYCOLOGY 2022; 58:343-346. [PMID: 35146760 DOI: 10.1111/jpy.13243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/13/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Dinoflagellates do not have a typical TATA-binding protein (TBP), a subunit of the general transcription factor TFIID complex. Instead, they have a TBP-like factor (TLF) that has been shown to bind TTTT instead of TATA in vitro. The ability of TLF to act as a functional replacement of TBP in vivo has never been assessed, however. Here, we show that a dinoflagellate TLF can drive expression of a reporter gene controlled by a budding yeast promoter whose TATA box was mutated to TTTT. TLF is thus able to bind and activate the yeast RNA polymerase and appear to function normally in the TFIID complex.
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Affiliation(s)
- Bahareh Zaheri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, Canada
| | - Charlotte Veilleux-Trinh
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, Canada
| | - David Morse
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, Canada
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Lin S, Song B, Morse D. Spatial organization of dinoflagellate genomes: Novel insights and remaining critical questions. JOURNAL OF PHYCOLOGY 2021; 57:1674-1678. [PMID: 34389979 DOI: 10.1111/jpy.13206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
As is true for many other aspects, genome architecture, evolution, and function in dinoflagellates are enigmatic and, in the meantime, continuous inspiration for scientific quests. Recent third-generation sequencing and Hi-C linkage analyses brought new insights into the spatial organization of symbiodiniacean genomes, revealing the topologically associated domains, discrete gene clusters and their cis and trans orientations, and relationships with transcription. Where do these new findings bring us in dinoflagellate genomics? Here, we aim to place these new results in the backdrop of the long history of research on this topic and in the context of what critical questions remain to be pursued in the future. The new data suggest, pending verification of other complete chromosome assemblies, a potential evolutionary trend in chromosome number decrease and length increase within the Symbiodiniaceae. While questions remain about the mechanics of the three-dimensional chromosome structure and cell cycle-related DNA replication, the mechanisms of gene transcription and genome size evolution, these latest findings set new starting points for further inquiries.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - David Morse
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Quebec, H1X 2B2, Canada
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Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Int J Mol Sci 2021; 22:ijms222111311. [PMID: 34768741 PMCID: PMC8582858 DOI: 10.3390/ijms222111311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.
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