- THIS ARTICLE
-
Abstract
- Full Text (PDF)
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Lohan, A. J.
- Articles by Wolfe, K. H.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Lohan, A. J.
- Articles by Wolfe, K. H.
A Subset of Conserved tRNA Genes in Plastid DNA of Nongreen Plants
Amanda J. Lohana and Kenneth H. Wolfeaa Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
Corresponding author: Kenneth H. Wolfe, Department of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland., khwolfe{at}tcd.ie (E-mail).
Communicating editor: G. B. GOLDING
| ABSTRACT |
|---|
The plastid genome of the nonphotosynthetic parasitic plant Epifagus virginiana contains only 17 of the 30 tRNA genes normally found in angiosperm plastid DNA. Although this is insufficient for translation, the genome is functional, so import of cytosolic tRNAs into plastids has been suggested. This raises the question of whether the tRNA genes that remain in E. virginiana plastid DNA are active or have just fortuitously escaped deletion. We report the sequences of 20 plastid tRNA loci from Orobanche minor, which shares a nonphotosynthetic ancestor with E. virginiana. The two species have 9 intact tRNA genes in common, the others being defunct in one or both species. The intron-containing trnLUAA gene is absent from E. virginiana, but it is intact, transcribed, and spliced in O. minor. The shared intact genes are better conserved than intergenic sequences, which indicates that these genes are being maintained by natural selection and, therefore, must be functional. For the most part, the tRNA species conserved in nonphotosynthetic plastids are also those that have never been found to be imported in plant mitochondria, which suggests that the same rules may govern tRNA import in the two organelles. A small photosynthesis gene, psbI, is still intact in O. minor, and computer simulations show that some small nonessential genes have an appreciable chance of escaping deletion.
THE plastid genomes of photosynthetic angiosperms contain 30 different tRNA loci (![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
If tRNAs can be imported into plastids, one wonders why the E. virginiana plastid genome retains any tRNA genes at all. A special case can be made for one gene (trnEUUC) whose product is required for heme synthesis (![]()
![]()
![]()
In this study, we report the sequences of most of the plastid tRNA loci from a second holoparasitic plant, Orobanche minor (Orobanchaceae). Like E. virginiana, O. minor contains undifferentiated plastids lacking thylakoid stacks (A. J. LOHAN, unpublished data). Phylogenetic analysis of plastid rps2 showed that the common ancestor of the genera Orobanche and Epifagus was nonphotosynthetic (![]()
| MATERIALS AND METHODS |
|---|
O. minor var. compositarum was found growing on Senecio greyi plants on the campus of Trinity College Dublin, and was identified by Dr. MICHAEL WYSE-JACKSON. Total cellular DNA was extracted from above-ground tissue by the CTAB method (![]()
![]()
| RESULTS |
|---|
O. minor tRNA loci:
A total of 20 loci from O. minor were investigated. These are compared to their counterparts in E. virginiana (![]()
![]()
![]()
|
|
Expression of trnLUAA:
The gene encoding tRNALeu- (UAA) is apparently intact in O. minor (Figure 1F), and its group I intron can be folded into a normal secondary structure (with only minor length variations in unpaired loop regions, as compared to other species). This gene is absent from E. virginiana. Reverse transcriptase PCR showed that this gene is transcribed and the intron is spliced in O. minor (Figure 2A). The PCR product was sequenced and contains the expected splice junction (Figure 2B and Figure C).
|
Relative conservation of tRNA genes and intergenic spacers:
Because O. minor and E. virginiana are both nonphotosynthetic, as was their common ancestor (![]()
For eight loci that are intact in both O. minor and E. virginiana, it is possible to compare the level of sequence conservation in a tRNA gene to that in the neighboring noncoding or intronic DNA. At the ninth locus (trnFGAA), the pattern of deletion of intergenic DNA leaves no noncoding DNA available for comparison (Figure 1G). At all six usable loci that are located in the large single-copy region of the genome, the tRNA gene is conserved appreciably more strongly (
15% higher sequence identity) than the flanking DNA; these loci are trnQUUG, trnSGCU, trnDGUC, trnYGUA, trnEUUC, and trnfMCAU (Figure 1, AD). The two intact tRNA genes located in the IR also show conservation, but to a lesser extent (10 and 1% excess conservation for trnLCAA and trnNGUU, respectively; Figure 1H and Figure J). The overall levels of noncoding sequence divergence in the IR are reduced in comparison to the large single-copy region, an observation that concurs with other studies on ptDNA (![]()
88% for genes intact in both species), and trnSGGA is no better conserved than its flanking DNA. This implies that these genes are not under selection in at least one of the species; it is not possible to say for certain that they are nonessential in both. The only piece of data that is inconsistent with the general pattern of conservation of intact genes and divergence of noncoding and pseudogene sequences is the greater conservation of
trnAUGC exon 2 (95%) than its intron (89%; Figure 1I). This exon is short (22 bp compared), and the introns are so badly damaged that the gene cannot be functional in either species, so its conservation is either accidental or possibly connected to processing of the downstream 23S rRNA.
Other genes present in O. minor ptDNA:
The sequenced regions include several genes in addition to tRNA loci. The O. minor plastid 16S rRNA gene appears normal. In phylogenetic trees of angiosperm plastid 16S sequences, the Orobanchaceae were weakly monophyletic (4050% bootstrap support by different methods) and E. virginiana clustered with C. americana (98100% bootstrap support), with O. minor outside (results not shown). This is consistent with other phylogenetic analyses (![]()
![]()
The O. minor rps4 gene, encoding ribosomal protein S4, is intact. When compared to its E. virginiana homolog, there is an excess of synonymous over nonsynonymous nucleotide substitutions in codons (KS = 0.366 ± 0.067, KA = 0.126 ± 0.018; method of ![]()
An intact open reading frame was found corresponding to the small (111-bp) gene psbI, which codes for the PSII-I polypeptide of photosystem II (a reaction center component; ![]()
![]()
Simulation of DNA deletion:
The number of DNA deletions in the E. virginiana plastid genome, after it became nonphotosynthetic, is estimated to be in the hundreds (![]()
![]()
![]()
![]()
![]()
![]()
We explored this by making a computer simulation in which the photosynthetic constraint on tobacco ptDNA (131 kb of unique sequence) was removed. Possible deletion endpoints in the circular genome were chosen at random, and deletions were permitted if they did not damage any essential genes. The genes designated as essential were the protein-coding genes that are present in E. virginiana, the ribosomal RNAs, and trnEUUC (because of its role in heme synthesis). Deletions were made successively until the genome size fell below that of E. virginiana ptDNA (47 kb of unique sequence). Each locus in the genome was then examined to see if it was still intact, and the simulation was repeated 1000 times (Figure 3).
|
In the simulations, the average number of tRNA genes (including trnEUUC) surviving was 7.4 (standard deviation 1.8). None of the 1000 replicates had >13 tRNAs (as compared to 17 in E. virginiana). This suggests that about half the plastid tRNA genes in E. virginiana are retained by chance and half are maintained by selection; some of those retained by selection have been identified in Figure 1. The frequency of survival varies enormously from gene to gene, ranging from <1% in trnLUAG, trnGUCC, and trnVUAC to >60% in trnYGUA, trnICAU, trnRACG, and trnNGUU, which are "sheltered" from deletion by virtue of their proximity to essential genes (Figure 3). The mean frequency of accidental survival for the 16 tRNA genes retained in E. virginiana (30.0%; excluding trnEUUC) is higher than that in the 13 defunct genes (20.7%). The survival frequency of psbI is only 1.2%, but if the flanking tRNA genes (trnSGCU and trnQUUG, which are conserved between O. minor and E. virginiana) are designated as essential, this increases to 68%.
| DISCUSSION |
|---|
Our computer simulations (Figure 3), as well as the discovery that five tRNA genes and one photosynthesis gene are intact in O. minor but not in E. virginiana, show clearly that some genes can remain undeleted even where they are not essential. However, the sequence comparisons (Figure 1) indicate that at least six, possibly eight, tRNA genes have not only escaped deletion in both parasites, but also have been conserved in sequence in a manner that shows that they are not pseudogenes. One of these, trnEUUC, was expected to be conserved because of its role in heme synthesis, but there is no reason why the genes coding for other tRNAs should be conserved in sequence (despite divergence of flanking DNA), unless they are being used in translation.
The plastid tRNA genes of O. minor and E. virginiana can be classified into three groups (horizontal rows in Figure 4). The first group, those that are conserved in sequence and therefore functional, comprises 6 genes (trnEUUC, trnfMCAU, trnQUUG, trnYGUA, trnDGUC, and trnSGCU) plus possibly two others (trnNGUU and trnLCAA) that are conserved but have low sequence divergence in the adjacent noncoding DNA because of their location in the IR (Figure 1). The second group comprises 14 genes that are not intact in one or both species and are, therefore, nonessential and presumed to be compensated for by imported tRNAs. The third group comprises the remaining 8 genes, which are intact in E. virginiana, but there is no data from O. minor (or, in the case of trnFGAA, there is no alignable flanking DNA).
|
In plant mitochondria, only a few "native" mitochondrial tRNA genes are present in all species examined (![]()
![]()
![]()
![]()
![]()
![]()
![]()
Loss of tRNA genes from ptDNA has been documented in three holoparasitic species in the family Orobanchaceae (![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
Why would a plastid require a functioning nucleic acid import system? One possibility is simply that the apparatus for importing tRNAs into mitochondria also operates at low efficiency on plastids. Another is that the mechanisms for importing the (disputed) RNA component of plastid RNAse P (![]()
![]()
![]()
![]()
![]()
| FOOTNOTES |
|---|
1 We have followed ![]()
C stem, and one of these is shared with E. virginiana. ![]()
| ACKNOWLEDGMENTS |
|---|
This study was supported by Forbairt scientific awards SC/92/158 and SC/94/101. We thank Drs. DAN NICKRENT and JOACHIM MARIENFELD for unpublished information, and we are very grateful to Dr. KEVIN DEVINE and his research group for hosting A.J.L. after the demolition of our laboratory.
Manuscript received March 2, 1998; Accepted for publication June 5, 1998.
| LITERATURE CITED |
|---|
BAUM, M., A. CORDIER, and A. SCHON, 1996 RNase P from a photosynthetic organelle contains an RNA homologous to the cyanobacterial counterpart. J. Mol. Biol. 257:43-52[Medline].
BÖMMER, D., G. HABERHAUSEN, and K. ZETSCHE, 1993 A large deletion in the plastid DNA of the holoparasitic flowering plant Cuscuta reflexa concerning two ribosomal proteins (rpl2, rpl23), one transfer RNA (trnI) and an ORF 2280 homologue. Curr. Genet. 24:171-176[Medline].
COLWELL, A. E., 1994 Genome evolution in a non-photosynthetic plant. Ph.D. thesis. Washington University, St. Louis.
DELAVAULT, P., V. SAKANYAN, and P. THALOUARN, 1995 Divergent evolution of two plastid genes, rbcL and atpB, in a non-photosynthetic parasitic plant. Plant Mol. Biol. 29:1071-1079[Medline].
DEPAMPHILIS, C. W. and J. D. PALMER, 1990 Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature 348:337-339[Medline].
DEPAMPHILIS, C. W., N. D. YOUNG, and A. D. WOLFE, 1997 Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: many losses of photosynthesis and complex patterns of rate variation. Proc. Natl. Acad. Sci. USA 94:7367-7372
DIETRICH, A., J. H. WEIL, and L. MARÉCHAL-DROUARD, 1992 Nuclear-encoded transfer RNAs in plant mitochondria. Annu. Rev. Cell Biol. 8:115-131.
DIETRICH, A., I. SMALL, A. COSSET, J. H. WEIL, and L. MARÉCHAL-DROUARD, 1996 Editing and import: strategies for providing plant mitochondria with a complete set of functional transfer RNAs. Biochimie 78:518-529[Medline].
DOWNIE, S. R., D. S. KATZ-DOWNIE, K. H. WOLFE, P. J. CALIE, and J. D. PALMER, 1994 Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution. Curr. Genet. 25:367-378[Medline].
DOYLE, J. J. and J. L. DOYLE, 1987 A rapid DNA isolation for small quantities of fresh tissue. Phytochem. Bull. 19:11-15.
EMS, S. C., C. W. MORDEN, C. K. DIXON, K. H. WOLFE, and C. W. DEPAMPHILIS et al., 1995 Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Mol. Biol. 29:721-733[Medline].
FREYER, R., K. NECKERMANN, R. M. MAIER, and H. KÖSSEL, 1995 Structural and functional analysis of plastid genomes from parasitic plants: loss of an intron within the genus Cuscuta. Curr. Genet. 27:580-586[Medline].
HABERHAUSEN, G. and K. ZETSCHE, 1994 Functional loss of all ndh genes in an otherwise relatively unaltered plastid genome of the holoparasitic flowering plant Cuscuta reflexa. Plant Mol. Biol. 24:217-222[Medline].
HABERHAUSEN, G., K. VALENTIN, and K. ZETSCHE, 1992 Organization and sequence of photosynthetic genes from the plastid genome of the holoparasitic flowering plant Cuscuta reflexa. Mol. Gen. Genet. 232:154-161[Medline].
HEDTKE, B., T. BÖRNER, and A. WEIHE, 1997 Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis. Science 277:809-811
HOWE, C. J. and A. L. SMITH, 1991 Plants without chlorophyll. Nature 349:109[Medline].
IKEUCHI, M. and Y. INOUE, 1988 A new photosystem II reaction center component (4.8 kDa protein) encoded by chloroplast genome. FEBS Lett. 241:99-104[Medline].
KUMAR, R., L. MARÉCHAL-DROUARD, K. AKAMA, and I. SMALL, 1996 Striking differences in mitochondrial tRNA import between different plant species. Mol. Gen. Genet. 252:404-411[Medline].
LI, W. H., C. I. WU, and C. C. LUO, 1985 A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174[Abstract].
LYNCH, M., 1997 Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes. Mol. Biol. Evol. 14:914-925[Abstract].
MARÉCHAL-DROUARD, L., P. GUILLEMAUT, A. COSSET, M. ARBOGAST, and F. WEBER et al., 1990 Transfer RNAs of potato (Solanum tuberosum) mitochondria have different genetic origins. Nucleic Acids Res. 18:3689-3696
MARÉCHAL-DROUARD, L., J.-H. WEIL, and A. DIETRICH, 1993 Transfer RNAs and transfer RNA genes in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 44:13-32.
MICHEL, F., K. UMESONO, and H. OZEKI, 1989 Comparative and functional anatomy of group II catalytic intronsa review. Gene 82:5-30[Medline].
MORDEN, C. W., K. H. WOLFE, C. W. DEPAMPHILIS, and J. D. PALMER, 1991 Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes. EMBO J. 10:3281-3288[Medline].
NICKRENT, D. L., Y. OUYANG, R. J. DUFF, and C. W. DEPAMPHILIS, 1997 Do nonasterid holoparasitic flowering plants have plastid genomes? Plant Mol. Biol. 34:717-729[Medline].
NICKRENT, D. L., R. J. DUFF, A. E. COLWELL, A. D. WOLFE, N. D. YOUNG et al., 1998 Molecular phylogenetic and evolutionary studies of parasitic plants, pp. 211241 in Molecular Systematics of Plants, Ed. 2, edited by D. E. SOLTIS, P. S. SOLTIS and J. J. DOYLE. Chapman & Hall, New York.
PACKER, J. C. and C. J. HOWE, 1998 Algal plastid genomes encode homologues of the SRP-associated RNA. Mol. Microbiol. 27:508-510[Medline].
PFITZINGER, H., J. H. WEIL, D. T. PILLAY, and P. GUILLEMAUT, 1990 Codon recognition mechanisms in plant chloroplasts. Plant Mol. Biol. 14:805-814[Medline].
SHARMA, J., M. PANICO, J. BARBER, and H. R. MORRIS, 1997 Characterization of the low molecular weight photosystem II reaction center subunits and their light-induced modifications by mass spectrometry. J. Biol. Chem. 272:3935-3943
SHINOZAKI, K., M. OHME, M. TANAKA, T. WAKASUGI, and N. HAYASHIDA et al., 1986 The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:2043-2049[Medline].
SUGIURA, M., 1989 The chloroplast chromosomes in land plants. Annu. Rev. Cell Biol. 5:51-70.
SUGIURA, M., 1992 The chloroplast genome. Plant Mol. Biol. 19:149-168[Medline].
TAYLOR, G. W., K. H. WOLFE, C. W. MORDEN, C. W. DEPAMPHILIS, and J. D. PALMER, 1991 Lack of a functional plastid tRNA(Cys) gene is associated with loss of photosynthesis in a lineage of parasitic plants. Curr. Genet. 20:515-518[Medline].
THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON, 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680
UNSELD, M., J. R. MARIENFELD, P. BRANDT, and A. BRENNICKE, 1997 The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nature Genet. 15:57-61[Medline].
VERONICO, P., R. GALLERANI, and L. R. CECI, 1996 Compilation and classification of higher plant mitochondrial tRNA genes. Nucleic Acids Res. 24:2199-2203
WAKASUGI, T., M. OHME, K. SHINOZAKI, and M. SUGIURA, 1986 Structures of tobacco chloroplast genes for tRNA-Ile (CAU), tRNA-Leu (CAA), tRNA-Cys (GCA), tRNA-Ser (UGA) and tRNA-Thr (GGU): a compilation of tRNA genes from tobacco chloroplasts. Plant Mol. Biol. 7:385-392.
WIMPEE, C. F., R. MORGAN, and R. L. WROBEL, 1992 Loss of transfer RNA genes from the plastid 16S-23S ribosomal RNA gene spacer in a parasitic plant. Curr. Genet. 21:417-422[Medline].
WOLFE, A. D. and C. W. DEPAMPHILIS, 1997 Alternate paths of evolution for the photosynthetic gene rbcL in four nonphotosynthetic species of Orobanche. Plant Mol. Biol. 33:965-977[Medline].
WOLFE, K. H., W. H. LI, and P. M. SHARP, 1987 Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84:9054-9058
WOLFE, K. H., C. W. MORDEN, S. C. EMS, and J. D. PALMER, 1992a Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes. J. Mol. Evol. 35:304-317[Medline].
WOLFE, K. H., C. W. MORDEN, and J. D. PALMER, 1992b Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc. Natl. Acad. Sci. USA 89:10648-10652
This article has been cited by other articles:
![]() |
Z. Xia, Y.-Z. Wang, and J. F. Smith Familial placement and relations of Rehmannia and Triaenophora (Scrophulariaceae s.l.) inferred from five gene regions Am. J. Botany, February 1, 2009; 96(2): 519 - 530. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. W. Chumley, J. D. Palmer, J. P. Mower, H. M. Fourcade, P. J. Calie, J. L. Boore, and R. K. Jansen The Complete Chloroplast Genome Sequence of Pelargonium x hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants Mol. Biol. Evol., November 1, 2006; 23(11): 2175 - 2190. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. P. Randle and A. D. Wolfe The evolution and expression of RBCL in holoparasitic sister-genera Harveya and Hyobanche (Orobanchaceae) Am. J. Botany, September 1, 2005; 92(9): 1575 - 1585. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. A. Rosenblad and T. Samuelsson Identification of Chloroplast Signal Recognition Particle RNA Genes Plant Cell Physiol., November 15, 2004; 45(11): 1633 - 1639. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. L. Nickrent, M. A. Garcia, M. P. Martin, and R. L. Mathiasen A phylogeny of all species of Arceuthobium (Viscaceae) using nuclear and chloroplast DNA sequences Am. J. Botany, January 1, 2004; 91(1): 125 - 138. [Abstract] [Full Text] [PDF] |
||||
- THIS ARTICLE
-
Abstract
- Full Text (PDF)
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Lohan, A. J.
- Articles by Wolfe, K. H.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Lohan, A. J.
- Articles by Wolfe, K. H.






