The sequences of two nuclear genes and a pseudogene for tRNA(Pro) from the higher plant Phaseolus vulgaris

The tRNA(Ser)-isoacceptors and their genes in Nicotiana rustica: genome organization, expression in vitro and sequence analyses

The existence of six serine codons results in a complex pattern of tRNA(Ser) isoacceptors in organisms and organelles. According to the original wobble hypothesis, a minimum of three isoacceptors should be sufficient to read the six serine codons. We have isolated five cytoplasmic tRNAs(Ser) from leaves of Nicotiana rustica. Their nucleotide sequences identify them as four different isoacceptors with the anticodons cm5UGA, CGA, IGA and GCU. For tRNA(Ser) with IGA anticodon, two species have been detected which vary only by one nucleotide in the long extra arm. The first three isoacceptors recognize codons of the type UCN whereas the fourth isoacceptor reads the two serine codons AGC and AGU. The tRNA(Ser) sequences were used to design appropriate primers for the amplification of Nicotiana nuclear tRNA(Ser) genes by the polymerase chain reaction (PCR). A total number of eight tRNA(Ser) genes differing in the coding region were thus identified. Selected PCR DNA fragments were then employed as probes for the isolation of the corresponding genes from a nuclear DNA library of N. rustica. Sequence analyses revealed that five of the isolated seven clones contained tRNA(Ser) genes which are identical in sequence with the five cytoplasmic tRNAs(Ser) mentioned above. None of them contains an intervening sequence. This is the first time that all putative cellular tRNA(Ser) isoacceptors and their corresponding genes have been characterized in an eukaryotic organism. Most of the tRNA(Ser) genes are functional as deduced from in vitro transcription and processing studies. Two of the genes yield pre-tRNAs(Ser) which are not or poorly converted to mature tRNA in a plant extract. The approximate tRNA(Ser) gene number was estimated by hybridization of specific DNA probes to Eco RI-cleaved Nicotiana nuclear DNA. The overall hybridization pattern indicates that members of each particular tRNA(Ser) gene family do not appear to be clustered but distributed randomly throughout the Nicotiana genome.

Expression of variant nuclear Arabidopsis tRNA(Ser) genes and pre-tRNA maturation differ in HeLa, yeast and wheat germ extracts

We have recently identified a tRNA gene cluster in the Arabidopsis nuclear genome. One tRNA(Ser) (AGA) gene and two tRNA(Tyr) (GTA) genes occur in tandem arrangement on a 1.5 kb unit that is amplified about 20-fold at a single chromosomal site. Here we have studied the in vitro expression of seven individually cloned tRNA(Ser) genes (pAtS1 to pAtS7) derived from this cluster. Five out of the seven tRNA(Ser) genes contain point mutations in the coding region which have in part adverse effects on the expression of these genes in different cell-free systems: (i) C10 and A62 in plant tRNA(Ser) genes, which correspond to G10 and C62, respectively, in all known vertebrate tRNA genes, result in a reduced transcription efficiency in HeLa but not in yeast extract. This indicates that yeast RNA polymerase III tolerates nucleotide substitutions at positions 10 [5' internal control region (ICR)] and 62 (3' ICR), whereas the vertebrate RNA polymerase III requires a more stringent consensus sequence. (ii) Processing of a pre-tRNA(Ser) with a mismatch in the aminoacyl stem is impaired in HeLa, yeast and wheat germ extracts, however, a mismatch in the anticodon stem is deleterious for HeLa and wheat germ but not for yeast processing enzymes. The unexpectedly high number of potential tRNA(Ser) pseudogenes in the cluster - quite in contrast to the tRNA(Ser) genes which mainly code for functional tRNAs - suggested that tRNA(Ser) (AGA) genes also occur elsewhere in the genome. We present evidence that single copies of tRNA(Ser) (AGA) genes do indeed exist outside the tRNA gene cluster.

Genomic amplification in the cotyledon parenchyma of common bean

The cotyledon parenchyma cells of common bean (Phaseolus vulgaris L.) produce large quantities of storage proteins during embryo maturation; throughout this period, these cells also accumulate nuclear DNA (nDNA). To investigate the basis of this nDNA accumulation, we have measured storage protein mRNA pools, nDNA mass, and gene copy number at specific stages of cotyledon development. RNA blotting and hybridization show that transcripts encoding the major embryo-specific storage proteins are present very early in cotyledon development, accumulate in coordinate fashion to peak during mid-maturation, and fall in abundance prior to the onset of dormancy. During this same period, nDNA mass per parenchyma cell nucleus, as measured by Feulgen microspectrophotometry, increases from 2C-4C to about 64C (C being the haploid germ cell genomic complement). The nDNA values do not cluster around integral multiples of the diploid 2C amount. DNA blotting and hybridization are used to evaluate the relative representations of different classes of the bean genome in DNA samples isolated from vegetative tissues, from cotyledons beginning to accumulate storage proteins, and from cotyledons of late maturation embryos entering dormancy. The results demonstrate that the observed DNA accumulation in the cotyledon parenchyma is due to overlapping rounds of replication of the complete genome and not to disproportionate amplification of specific sequences nor to random DNA synthesis.

A nuclear-encoded potato (Solanum tuberosum) mitochondrial tRNA(Leu) and its cytosolic counterpart have identical nucleotide sequences

Sequencing of potato mitochondrial (mt) tRNA(Leu)(NAA) and of its cytosolic (cyt) counterpart revealed that these tRNAs are identical, except for a post-transcriptional modification: a Gm is present at position 18 in mt tRNA(Leu), instead of a G in cyt tRNA(Leu). Hybridization studies have shown that potato mt tRNA(Leu)(NAA) has a nuclear origin and must therefore be imported from the cytosol.

A nuclear tRNA(UGASer) gene from the wheat Triticum vulgare var. Aria

The nucleotide sequence of a wheat nuclear tRNA(UGASer) gene from Triticum vulgare var. Aria has been determined. It has a typical intragenic promoter with boxA and boxB elements and a putative termination signal 12 nucleotides downstream from the last tRNA-coding nucleotide. The region upstream from the coding segment contains a G + C-rich sequence with a symmetrical element. The sequence described is the first nuclear tRNA gene from a monocotyledonous plant.

Localization, sequence and expression of the gene coding for tRNA(Pro) (UGG) in plant mitochondria

The four Sal I fragments of wheat mitochondrial DNA containing the 18S and 5S ribosomal RNA genes were screened for the presence of tRNA genes. Upon sequencing, a tRNA(Pro) (UGG) gene was found in two of these four fragments. The localization of the corresponding gene on the maize mitochondrial genome was established. Transcriptional studies have shown that this gene is transcribed in wheat and maize mitochondria. The sequence of the corresponding tRNA(Pro) (UGG) of bean mitochondria was determined using in vitro post-labeling techniques.

APhaseolus vulgaris mitochondrial tRNA(Leu) is identical to its cytoplasmic counterpart: sequencing andin vivo transcription of the gene corresponding to the cytoplasmic tRNA(Leu.)

We report here that the sequence ofP. vulgaris mitochondrial and cytoplasmic tRNA(Leu) (NAA) are identical except for a post-transcriptional modification. There is an unidentified modification at the "wobble" position which, from the sequence of the nuclear tRNA(Leu) gene, we identify as a derivative of C. We also show that thisP. vulgaris nuclear gene is functional by demonstrating its transcription in anin vivo eukaryotic transcription system.