Plastid translation and transcription genes in a non-photosynthetic plant: intact, missing and pseudo genes.

Abstract

The non‐photosynthetic, parasitic flowering plant Epifagus virginiana has recently been shown to contain a grossly reduced plastid genome that has lost many photosynthetic and chloro‐respiratory genes. We have cloned and sequenced a 3.9 kb domain of plastid DNA from Epifagus to investigate the patterns of evolutionary change in such a reduced genome and to determine which genes are still present and likely to be functional. This 3.9 kb domain is colinear with a 35.4 kb region of tobacco chloroplast DNA, differing from it by a minimum of 11 large deletions varying in length from 354 bp to 11.5 kb, as well as by a number of small deletions and insertions. The nine genes retained in Epifagus encode seven tRNAs and two ribosomal proteins and are coextensive and highly conserved in sequence with homologs in photosynthetic plants. This suggests that these genes are functional in Epifagus and, together with evidence that the Epifagus plastid genome is transcribed, implies that plastid gene products play a role in processes other than photosynthesis and gene expression. Genes that are completely absent include not only photosynthetic genes, but surprisingly, genes encoding three subunits of RNA polymerase, four tRNAs and one ribosomal protein. In addition, only pseudogenes are found for two other tRNAs. Despite these defunct tRNA genes, codon and amino acid usage in Epifagus protein genes is normal. We therefore hypothesize that the expression of plastid genes in Epifagus relies on the import of nuclear encoded tRNAs and RNA polymerase from the cytoplasm.

pTAC2, -6, and -12 Are Components of the Transcriptionally Active Plastid Chromosome That Are Required for Plastid Gene Expression

“…In addition to PEP, the existence of NEP has already been suggested from studies with the parasite Epifagus virginiana, which lacks the plastid rpoBC operon (Morden et al, 1991). Similar results were obtained for the plastid ribosomedeficient barley (Hordeum vulgare) mutant albostrians (Hess et al, 1993) and tobacco (Nicotiana tabacum) rpo deletion mutants (Allison et al, 1996;Hajdukiewicz et al, 1997), both still synthesizing plastid transcripts.…”

Pharmacognostical Studies of Cistanchis Herba (III) Phylogenetic Relationship of the Cistanche Plants Based on Plastid rps2 Gene and rpl16-rpl14 Intergenic Spacer Sequences.

“…Several appropriate primers were designed based on the sequences of Nicotiana tabacum (tobacco) 6) and Epifagus verginiana 7) so that whole region of the rps2 gene could be amplified (Fig. 1).…”

The Chloroplast trnT–trnF Region in the Seed Plant Lineage Gnetales

“…Studies on the function of tRNA upstream sequences have shown that either they contain prokaryote-type promoters (Gruissem et al 1983;Steinmetz et al 1983;Wu et al 1997) or there are eukaryote-type internal promoters directly in the tRNA (Galli et al 1981;Gruissem et al 1986;Cheng et al 1997). The loss of promoter elements from the nonphotosynthetic Epifagus tRNA Glu (UUC) (Morden et al 1991) suggests, however, that prokaryote-type promoters are not always required for transcription of tRNA genes, and a few studies of tRNA transcription in lineages with functioning chloroplasts also suggest this (Gruissem et al 1986;Jahn 1992;Wu et al 1997). We therefore interpret the lack of promoter elements in the upstream regions of Gnetales tRNA Thr , tRNA Leu , and tRNA Phe genes as indicating that these genes have internal promoters, relieving their spacer regions from functional constraints that would come from harboring functional promoters.…”