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Yang S, Qu G, Fu B, Yang F, Zeng W, Cai Y, Ye T, Yang Y, Deng X, Xiang W, Peng D, Zhou B. The function of KptA/Tpt1 gene - a minor review. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:577-591. [PMID: 32438974 DOI: 10.1071/fp19159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 02/06/2020] [Indexed: 06/11/2023]
Abstract
Rapid response of uni- and multicellular organisms to environmental changes and their own growth is achieved through a series of molecular mechanisms, often involving modification of macromolecules, including nucleic acids, proteins and lipids. The ADP-ribosylation process has ability to modify these different macromolecules in cells, and is closely related to the biological processes, such as DNA replication, transcription, signal transduction, cell division, stress, microbial aging and pathogenesis. In addition, tRNA plays an essential role in the regulation of gene expression, as effector molecules, no-load tRNA affects the overall gene expression level of cells under some nutritional stress. KptA/Tpt1 is an essential phosphotransferase in the process of pre-tRNA splicing, releasing mature tRNA and participating in ADP-ribose. The objective of this review is concluding the gene structure, the evolution history and the function of KptA/Tpt1 from prokaryote to eukaryote organisms. At the same time, the results of promoter elements analysis were also shown in the present study. Moreover, the problems in the function of KptA/Tpt1 that have not been clarified at the present time are summarised, and some suggestions to solve those problems are given. This review presents no only a summary of clear function of KptA/Tpt1 in the process of tRNA splicing and ADP-ribosylation of organisms, but also gives some proposals to clarify unclear problems of it in the future.
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Affiliation(s)
- Shiquan Yang
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Gaoyi Qu
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Bixia Fu
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Feng Yang
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Weixian Zeng
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Yunzhang Cai
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | - Tao Ye
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China
| | | | - Xiangwen Deng
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha, Hunan, 410004, China
| | - Wenhua Xiang
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China; and Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China; and National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha, Hunan, 410004, China
| | - Dan Peng
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China; and Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China; and Forestry Biotechnology Hunan Key Laboratories, Changsha, Hunan, 410004, China
| | - Bo Zhou
- Faculty of Bioscience and Biotechnology of Central South University of Forestry and Technology,410004, Changsha, China; and Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province, Huitong 438107, China; and National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Changsha, Hunan, 410004, China; and Forestry Biotechnology Hunan Key Laboratories, Changsha, Hunan, 410004, China; and Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China; and Corresponding author.
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Yang KJ, Guo L, Hou XL, Gong HQ, Liu CM. ZYGOTE-ARREST 3 that encodes the tRNA ligase is essential for zygote division in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:680-692. [PMID: 28631407 DOI: 10.1111/jipb.12561] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/16/2017] [Indexed: 05/28/2023]
Abstract
In sexual organisms, division of the zygote initiates a new life cycle. Although several genes involved in zygote division are known in plants, how the zygote is activated to start embryogenesis has remained elusive. Here, we showed that a mutation in ZYGOTE-ARREST 3 (ZYG3) in Arabidopsis led to a tight zygote-lethal phenotype. Map-based cloning revealed that ZYG3 encodes the transfer RNA (tRNA) ligase AtRNL, which is a single-copy gene in the Arabidopsis genome. Expression analyses showed that AtRNL is expressed throughout zygotic embryogenesis, and in meristematic tissues. Using pAtRNL::cAtRNL-sYFP-complemented zyg3/zyg3 plants, we showed that AtRNL is localized exclusively in the cytoplasm, suggesting that tRNA splicing occurs primarily in the cytoplasm. Analyses using partially rescued embryos showed that mutation in AtRNL compromised splicing of intron-containing tRNA. Mutations of two tRNA endonuclease genes, SEN1 and SEN2, also led to a zygote-lethal phenotype. These results together suggest that tRNA splicing is critical for initiating zygote division in Arabidopsis.
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Affiliation(s)
- Ke-Jin Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Nanyang Normal University, Nanyang 473061, China
| | - Lei Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiu-Li Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua-Qin Gong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Yukawa Y, Akama K, Noguchi K, Komiya M, Sugiura M. The context of transcription start site regions is crucial for transcription of a plant tRNALys(UUU) gene group both in vitro and in vivo. Gene 2013; 512:286-93. [DOI: 10.1016/j.gene.2012.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/22/2012] [Accepted: 10/18/2012] [Indexed: 10/27/2022]
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Englert M, Latz A, Becker D, Gimple O, Beier H, Akama K. Plant pre-tRNA splicing enzymes are targeted to multiple cellular compartments. Biochimie 2007; 89:1351-65. [PMID: 17698277 DOI: 10.1016/j.biochi.2007.06.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Accepted: 06/18/2007] [Indexed: 11/19/2022]
Abstract
Splicing of precursor tRNAs in plants requires the concerted action of three enzymes: an endonuclease to cleave the intron at the two splice sites, an RNA ligase for joining the resulting tRNA halves and a 2'-phosphotransferase to remove the 2'-phosphate from the splice junction. Pre-tRNA splicing has been demonstrated to occur exclusively in the nucleus of vertebrates and in the cytoplasm of budding yeast cells, respectively. We have investigated the subcellular localization of plant splicing enzymes fused to GFP by their transient expression in Allium epidermal and Vicia guard cells. Our results show that all three classes of splicing enzymes derived from Arabidopsis and Oryza are localized in the nucleus, suggesting that plant pre-tRNA splicing takes place preferentially in the nucleus. Moreover, two of the splicing enzymes, i.e., tRNA ligase and 2'-phosphotransferase, contain chloroplast transit signals at their N-termini and are predominantly targeted to chloroplasts and proplastids, respectively. The putative transit sequences are effective also in the heterologous context fused directly to GFP. Chloroplast genomes do not encode intron-containing tRNA genes of the nuclear type and consequently tRNA ligase and 2'-phosphotransferase are not required for classical pre-tRNA splicing in these organelles but they may play a role in tRNA repair and/or splicing of atypical group II introns. Additionally, 2'-phosphotransferase-GFP fusion protein has been found to be associated with mitochondria, as confirmed by colocalization studies with MitoTracker Red. In vivo analyses with mutated constructs suggest that alternative initiation of translation is one way utilized by tRNA splicing enzymes for differential targeting.
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Affiliation(s)
- Markus Englert
- Institute of Biochemistry, Biocenter, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
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Englert M, Beier H. Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Nucleic Acids Res 2005; 33:388-99. [PMID: 15653639 PMCID: PMC546159 DOI: 10.1093/nar/gki174] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Pre-tRNA splicing is an essential process in all eukaryotes. It requires the concerted action of an endonuclease to remove the intron and a ligase for joining the resulting tRNA halves as studied best in the yeast Saccharomyces cerevisiae. Here, we report the first characterization of an RNA ligase protein and its gene from a higher eukaryotic organism that is an essential component of the pre-tRNA splicing process. Purification of tRNA ligase from wheat germ by successive column chromatographic steps has identified a protein of 125 kDa by its potentiality to covalently bind AMP, and by its ability to catalyse the ligation of tRNA halves and the circularization of linear introns. Peptide sequences obtained from the purified protein led to the elucidation of the corresponding proteins and their genes in Arabidopsis and Oryza databases. The plant tRNA ligases exhibit no overall sequence homologies to any known RNA ligases, however, they harbour a number of conserved motifs that indicate the presence of three intrinsic enzyme activities: an adenylyltransferase/ligase domain in the N-terminal region, a polynucleotide kinase in the centre and a cyclic phosphodiesterase domain at the C-terminal end. In vitro expression of the recombinant Arabidopsis tRNA ligase and functional analyses revealed all expected individual activities. Plant RNA ligases are active on a variety of substrates in vitro and are capable of inter- and intramolecular RNA joining. Hence, we conclude that their role in vivo might comprise yet unknown essential functions besides their involvement in pre-tRNA splicing.
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Affiliation(s)
| | - Hildburg Beier
- To whom correspondence should be addressed. Tel: +49 931 888 4031; Fax: +49 931 888 4028;
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Hasegawa K, Yukawa Y, Obokata J, Sugiura M. A tRNA(Leu)-like sequence located immediately upstream of an Arabidopsis clock-regulated gene is transcriptionally active: efficient transcription by an RNA polymerase III-dependent in vitro transcription system. Gene 2003; 307:133-9. [PMID: 12706895 DOI: 10.1016/s0378-1119(03)00452-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A tRNA(Leu)-like sequence is located within a probable enhancer region of the RNA polymerase II-dependent gene encoding an RNA-binding protein, Atgrp7, in Arabidopsis (Mol. Gen. Genet. 261 (1999) 811). To examine whether this sequence is transcribed, we used our in vitro transcription system from tobacco cell nuclei. In vitro assays demonstrated that this tRNA-like sequence is transcribed by RNA polymerase III and its transcript is processed into tRNA-size molecules. Transcription starts at the CAA motif, a transcription initiation site for many plant tRNA genes. Mutation analyses indicated that transcription of this sequence depends on promoter elements typical for plant tRNA genes. We therefore concluded that this is a transcriptionally active tRNA(Leu)(AAG) gene. Mutation of a basic promoter element of the tRNA gene exerted no influence on the transcription of the downstream protein-coding gene, suggesting that no apparent interference occurs between the two adjacent genes.
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Affiliation(s)
- Keiko Hasegawa
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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Akama K, Beier H. Translational nonsense codon suppression as indicator for functional pre-tRNA splicing in transformed Arabidopsis hypocotyl-derived calli. Nucleic Acids Res 2003; 31:1197-207. [PMID: 12582239 PMCID: PMC150238 DOI: 10.1093/nar/gkg220] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transient expression of three novel plant amber suppressors derived from a cloned Nicotiana tRNA(Ser)(CGA), an Arabidopsis intron-containing tRNA(Tyr)(GTA) and an Arabidopsis intron-containing tRNA(Met)(CAT) gene, respectively, was studied in a homologous plant system that utilized the Agro bacterium-mediated gene transfer to Arabidopsis hypocotyl explants. This versatile system allows the detection of beta-glucuronidase (GUS) activity by histochemical and enzymatic analyses. The activity of the suppressors was demonstrated by the ability to suppress a premature amber codon in a modified GUS gene. Co-transformation of Arabidopsis hypocotyls with the amber suppressor tRNA(Ser) gene and the GUS reporter gene resulted in approximately 10% of the GUS activity found in the same tissue transformed solely with the functional control GUS gene. Amber suppressor tRNAs derived from intron-containing tRNA(Tyr) or tRNA(Met) genes were functional in vivo only after some additional gene manipulations. The G3:C70 base pair in the acceptor stem of tRNA(Met)(CUA) had to be converted to a G3:U70 base pair, which is the major determinant for alanine tRNA identity. The inability of amber suppressor tRNA(Tyr) to show any activity in vivo predominantly results from a distorted intron secondary structure of the corresponding pre-tRNA that could be cured by a single nucleotide exchange in the intervening sequence. The improved amber suppressors tRNA(Tyr) and tRNA(Met) were subsequently employed for studying various aspects of the plant-specific mechanism of pre-tRNA splicing as well as for demonstrating the influence of intron-dependent base modifications on suppressor activity.
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MESH Headings
- Arabidopsis/genetics
- Base Sequence
- Codon, Nonsense/genetics
- Culture Techniques
- Glucuronidase/genetics
- Glucuronidase/metabolism
- Hypocotyl/genetics
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Plants, Genetically Modified
- Protein Biosynthesis/genetics
- RNA Precursors/genetics
- RNA Splicing
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Tyr/chemistry
- RNA, Transfer, Tyr/genetics
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Suppression, Genetic
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Affiliation(s)
- Kazuhito Akama
- Department of Biological Science, Shimane University, Matsue, 690-8504, Japan.
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Yukawa Y, Fan H, Akama K, Beier H, Gross HJ, Sugiura M. A tobacco nuclear extract supporting transcription, processing, splicing and modification of plant intron-containing tRNA precursors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2001; 28:583-94. [PMID: 11849597 DOI: 10.1046/j.1365-313x.2001.01172.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nuclear tRNA genes are transcribed by RNA polymerase III (Pol III) and pre-tRNAs are processed into mature tRNAs via complex processes in the nucleus. We have developed an in vitro Pol III-dependent transcription system derived from tobacco cultured cells, which supports efficiently not only transcription of a variety of plant tRNA genes but also 5'-and 3'-end processing, nucleotide modification and splicing of intron-containing pre-tRNAs. The structures of in vitro transcripts have been confirmed by primer extension analysis and by RNase T1 fingerprinting. The optimal Mg2+ concentration differed for each step so that each reaction can be controlled by adjusting the Mg2+ concentration. At 1 mm Mg2+, only transcription occurs so that pre-tRNAs accumulate. The splicing reaction can be initiated by raising Mg2+ ions (> 5 mm) and enhanced by adding 1 mm hexamminecobalt chloride. Using the optimized system for the Nicotiana intron-containing tRNATyr gene, the precise initiation and termination sites of transcription and the splice sites were determined. The presence of 1 mm NAD+ in the reaction mixture leads to the removal of the 2' phosphate at the splice junction of tRNATyr, demonstrating the activity of a 2'-phosphotransferase in the tobacco nuclear extract. Many modified nucleosides such as m2G, m22G, m1A, phi27 and phi35 are introduced in either of the studied transcripts. As shown in other systems, the conversion of U35 to phi requires an intron-containing substrate.
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Affiliation(s)
- Y Yukawa
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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Akama K, Junker V, Beier H. Identification of two catalytic subunits of tRNA splicing endonuclease from Arabidopsis thaliana. Gene 2000; 257:177-85. [PMID: 11080584 DOI: 10.1016/s0378-1119(00)00408-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
tRNA splicing endonuclease is essential for the correct removal of introns from precursor tRNA molecules of Archaea and Eucarya. The only well-characterized eucaryotic enzyme until now is the endonuclease from yeast (Saccharomyces cerevisiae). This protein has a heterotetrameric structure. Two of the four subunits, i.e. Sen34 and Sen44, contain the active sites for cleavage at the 3'- and 5'-splice sites, respectively. We have identified three novel genes from Arabidopsis thaliana, encoding putative subunits of tRNA splicing endonuclease. They are designated as AtSen1, AtSen2, and AtpsSen1. Both genes AtSen1 and AtSen2 seem to be functionally active, as deduced from corresponding cDNA sequences. Comparison of the amino acid sequences of the these two Arabidopsis proteins revealed 72% identity. However, AtpsSen1 is more similar to AtSen1, but is very likely a pseudogene, as concluded from extended stretches of deletions and the presence of in-frame stop codons. All putative proteins contain a conserved domain at their C-terminus common to counterparts from other organisms. Interestingly, they are more similar to the yeast catalytic subunit Sen44 than to Sen34. Southern analysis with various probes revealed that each gene is present as single copies in the nuclear genome. The evolutionary implications of these findings are discussed.
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Affiliation(s)
- K Akama
- Department of Biological Science, Shimane University, 690-8504, Matsue, Japan.
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