Conservation of the structures of plant tRNAs and aminoacyl-tRNA synthetases

Regulation of tRNA biogenesis in plants and its link to plant growth and response to pathogens

The field of tRNA biology, encompassing the functional and structural complexity of tRNAs, has fascinated scientists over the years and is continuously growing. Besides their fundamental role in protein translation, new evidence indicates that tRNA-derived molecules also regulate gene expression and protein synthesis in all domains of life. This review highlights some of the recent findings linking tRNA transcription and modification with plant cell growth and response to pathogens. In fact, mutations in proteins directly involved in tRNA synthesis and modification most often lead to pleiotropic effects on plant growth and immunity. As plants need to optimize and balance their energy and nutrient resources towards growth and defense, regulatory pathways that play a central role in integrating tRNA transcription and protein translation with cell growth control and organ development, such as the auxin-TOR signaling pathway, also influence the plant immune response against pathogens. As a consequence, distinct pathogens employ an array of effector molecules including tRNA fragments to target such regulatory pathways to exploit the plant's translational capacity, gain access to nutrients and evade defenses. An example includes the RNA polymerase III repressor MAF1, a conserved component of the TOR signaling pathway that controls ribosome biogenesis and tRNA synthesis required for plant growth and which is targeted by a pathogen effector molecule to promote disease. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.

A critical role of water in the specific cleavage of the anticodon loop of some eukaryotic methionine initiator tRNAs

We have noticed that during a long storage and handling, the plant methionine initiator tRNA is spontaneously hydrolyzed within the anticodon loop at the C34-A35 phosphodiester bond. A literature search indicated that there is also the case for human initiator tRNA(Met) but not for yeast tRNA(i)Met or E. coli tRNA(f)Met. All these tRNAs have an identical nucleotide sequence of the anticodon stems and loops with only one difference at position 33 within the loop. It means that cytosine 33 (C33) makes the anticodon loop of plant and human tRNA(i)Met susceptible to the specific cleavage reaction. Using crystallographic data of tRNA(f)Met of E. coli with U33, we modeled the anticodon loop of this tRNA with C33. We found that C33 within the anticodon loop creates a pocket that can accomodate a hydrogen bonded water molecule that acts as a general base and catalyzes a hydrolysis of C-A bond. We conclude that a single nucleotide change in the primary structure of tRNA(i)Met made changes in hydration pattern and readjustment in hydrogen bonding which lead to a cleavage of the phosphodiester bond.

Higher plant 5S rRNAs share common secondary and tertiary structure. A new three domains model

A new model of secondary and tertiary structure of higher plant 5S RNA is proposed. It consists of three helical domains: domain alpha includes stem I; domain beta contains stems II and III and loops B and C; domain gamma consists of stems IV and V and loops D and E. Except for, presumably, a canonical RNA-A like domain alpha, the two remaining domains apparently adopt a perturbed RNA-A structure due to irregularities within internal loops B and E and three bulges occurring in the model. Bending of RNA could bring loops B and E and/or C and D closer making tertiary interactions likely. The model differs from that suggested for eukaryotic 5S rRNA, by organization of domain gamma. Our model is based on the results of partial digestion obtained with single- and double-strand RNA specific nucleases. The proposed secondary structure is strongly supported by the observation that crude plant 5S rRNA contains abundant RNA, identified as domain gamma of 5S rRNA. Presumably it is excised from the 5S rRNA molecule by a specific nuclease present in lupin seeds. Experimental results were confirmed by computer-aided secondary structure prediction analysis of all higher plant 5S rRNAs. Differences observed between earlier proposed models and our proposition are discussed.

The primary structure of lupin seed 5.8 S ribosomal RNA

The lack of colinearity between nucleotide sequence of the lupin 5.8 S rDNA gene (Rafalski, A.J., Wiewiórowski, M. and Soll, D. (1983) FEBS Lett. 152, 241-246) and 5.8 S rRNA of other plants (Erdmann, V.A. and Wolters, J. (1986) Nucleic Acids Res. 14, r1-r59.) prompted us to clarify this point by sequencing the native lupin 5.8 S rRNA. The sequence analysis was carried out using enzymatic and chemical methods. Lupin seed 5.8 S rRNA contains 164 nucleotides, including four modified ones: two residues of 2'-O-methylguanosine, one pseudouridine and one 2'-O-methyladenosine. The nucleotide sequence homology with the other plant 5.8 S rRNAs is approx. 88-96%.

Immunochemical properties of elongation factors 1 of plant origin

Elongation factors 1 (EF-1) have been isolated from different plants: wheat, yellow lupine, blue lupine, Chinese cabbage and Norway maple. Antibodies for EF-1 from yellow lupine have been obtained in rabbits; antibodies for wheat EF-1 were elicited in mice. The immunological properties of EF-1 were assayed by the following methods: western blotting, double immunodiffusion and rocket immunoelectrophoresis. Our results suggest that one antigenic site is similar for all plant elongation binding factors tested. This epitope probably overlaps the centre of biological activity of EF-1, as was shown for wheat EF-1. The hypothesis concerning the potential presence of plant EF-1 as a subunit of turnip yellow mosaic virus RNA replicase (similar to prokaryotic EF-Tu in the Q beta RNA replicase system) has also been tested using immunotechniques as well as tests of biological activity, but has not been confirmed.

Yellow lupin cytoplasmic tRNAGlu is not a cofactor in chlorophyll biosynthesis

Yellow lupin seeds (Lupinus luteus) cytoplasmic tRNAGlu was isolated and the primary structure was determined to be: (sequence in text) AGU CCCGGCGACGGAACCAOH. It is 76 nucleotides long and contains 8 modified nucleosides: 2 residues of pseudouridine, ribothymidine, 3 dihydrouridines, 5-methylcytosine and 1-methyladenosine. This tRNAGlu assayed in delta-aminolevulinic acid synthesis was shown to be inactive. Its structural features are discussed.

Phenylalanyl-tRNA synthetases as an example for comparative and evolutionary aspects of aminoacyl-tRNA synthetases

Aminoacyl-tRNA synthetases are indispensable components of protein synthesis in all three lines of evolutionary descent, eubacteria, archaebacteria and eukaryotes. Furthermore they are also present in the translational apparatus of the semi-autonomous organelles, mitochondria and chloroplasts, of the eukaryotic cell. Therefore aminoacyl-tRNA synthetases are appropriate objects for comparative molecular biology in order to obtain a comprehensive picture of the evolution of the translational process. The analysis of the phenylalanyl-tRNA synthetase in a large variety of organisms and organelles in this respect is the most advanced. In addition to comparison of quaternary structure, analysis includes functional aspects of accuracy mechanisms (proofreading) and comparison of structural features by means of substrate analogs. Evolutionary relationships are furthermore elucidated using the immunological approach and heterologous aminoacylation.

Conservation of plant cytoplasmic tRNA structure. Nucleotide sequence of rape tRNAPhe

The primary structure of rape seeds tRNAPhe has been determined. It is identical to that of wheat germ, pea and barley tRNAsPhe, and of the minor tRNAPhe species of yellow lupin seeds.

The nucleotide sequence of methionine elongator tRNA from wheat germ

Wheat germ methionine elongator tRNA (tRNAmMet) was purified by three column chromatogaphies followed by electrophoresis on polyacrylamide gel. Its sequence is pG-G-G-G-U-G-G-U-m1G-m2G-C-G-C-A-G-D-D-G-G-C-acp3U-A-G-C-G-C-m22G-psi-A-G-G- psi-C-U-Cm-A-U-mt6A-A-psi-C-C-U-G-A-G-m7G-D-m5C-G-A-G-A-T-psi-C-G-m1A-G2-C-C-U- C-U-C-U-C-A-C-C-C-C-A-C-C-A. Two hypermodified nucleosides, methylthreoninocarbonyladenosine (mt6A) and 3(3-amino-3-carboxypropyl)uridine (acp3U), are present in this tRNA.

Chemical probes for tRNA tertiary structure. Comparative alkylation of tRNA with methylnitrosourea, ethylnitrosourea and dimethylsulfate

The tertiary structure of tRNA in solution can be proved by chemical modification experiments. Three reagents, N-ethyl-N-nitrosourea, N-methyl-N-nitrosourea and dimethylsulfate which are known to alkylate nucleic acids at nucleophilic centers were compared. It is found that N-ethyl-N-nitrosourea and N-methyl-N-nitrosourea mainly react with phosphate residues and dimethylsulfate only with the bases. With dimethylsulfate the extent of alkylation of guanosines is about one order of magnitude higher than that of the phosphates by the nitroso compounds.

Organization and nucleotide sequence of nuclear 5S rRNA genes in yellow lupin (Lupinus luteus)

Genomic blots of yellow lupin (Lupinus luteus) DNA digested with restriction nucleases and probed with 32P-labelled Lupinus 5S RNA reveal that 5S DNA is organized as tandemly repeated sequences of one size class, 342 bp. The DNA is extensively methylated. Two cloned BamHI ribosomal repeats were sequenced, revealing sequence divergence within both the coding and spacer regions.

Interaction of alkaloids with plant transfer ribonucleic acids. Effect of sparteine on lupin arginyl-tRNA formation

The effect of the alkaloid sparteine on arginyl-tRNA formation was studied. It was demonstrated that sparteine sulfate in the concentration range 10-60 mM inhibits the charging reaction when amino acid, ATP and tRNA are used as variable substrates. The mode of action is different for all pattern of inhibition for all varied substrates is generally uncompetitive. A pattern of inhibition for all varied substrates is generally uncompetitive. A non-competitive mechanism for amino acid and tRNA was observed at low sparteine concentration, but in the case of ATP it is also uncompetitive.

The evolving tRNA molecule

The study of tRNA molecular evolution is crucial to understanding the origin and establishment of the genetic code as well as the differentiation and refinement of the machinery of protein synthesis in prokaryotes, eukaryotes, organelles, and phage systems. The small size of the molecule and its critical involvement in a multiplicity of roles distinguish its study from classical protein molecular evolution with respect to goals and methods. Here, the authors assess available and missing data, existing and needed methodology, and the impact of tRNA studies on current theories both of genetic code evolution and of the evolution of species. They analyze mutational "hot spots", the role of base modification, synthetase recognition, codon-anticodon interactions and the status of organelle tRNA.

Method for detection of enzymatic activities which use aminoacyl-tRNA as a substrate

A method for detection of enzymatic activities which use aminoacyl-tRNA is described. It is based on the synthesis of aminoacyl-tRNA in the reaction mixture (in situ) without additional purification. The results are the same as when using purified AA-tRNA.

The nucleotide sequences of the initiator transfer RNAs from bean cytoplasm and chloroplasts

The initiator tRNAsMet from the cytoplasm and chloroplasts of Phaseolus vulgaris have been purified and sequenced. The sequence of bean cytoplasmic initiator tRNAiMet is : pA-U-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-C-G-G-A-A-G-C-G-U-m2G-G-U-G-G-G2-C-C-C-A-U-t6A-A-C-C-C-A-C-A-G-m7G-D-m5C-C-C-A-G-G-A-psi-C-G-m1A-A-A-C-C-U-Gm-G-C-U-C-U-G-A-U-A-C-C-AOH. The sequence of bean cytoplasmic tRNAiMet is almost identical to that of wheat germ and shows a high degree of homology with other cytoplasmic initiator tRNAs. The sequence of bean chloroplast initiator tRNAfMet is : pC-G-C-G-G-A-G-U-A-G-A-G-C-A-A-C-U-U-Gm-G-D-A-G-C-U-C-G-C-A-A-G-G-C-U-C-A-U-A-A-C-C-U-U-G-A-A-m7G-acp3U-U-A-C-G-G-G-T-psi-C-A-A-A-U-C-C-C-G-U-C-U-C-C-G-C-A-A- C-C-AOH. Bean chloroplast initiator tRNAfMet sequence shows procaryotic characteristics at the 5' end of the acceptor stem and in the TpsiC loop, but also contains some distinctive features.