RESUMEN
Chloroplasts play critical roles in land plant cells. Despite their importance and the availability of at least 200 sequenced chloroplast genomes, the number of known DNA regulatory sequences in chloroplast genomes are limited. In this paper, we designed computational methods to systematically study putative DNA regulatory sequences in intergenic regions near chloroplast genes in seven plant species and in promoter sequences of nuclear genes in Arabidopsis and rice. We found that -35/-10 elements alone cannot explain the transcriptional regulation of chloroplast genes. We also concluded that there are unlikely motifs shared by intergenic sequences of most of chloroplast genes, indicating that these genes are regulated differently. Finally and surprisingly, we found five conserved motifs, each of which occurs in no more than six chloroplast intergenic sequences, are significantly shared by promoters of nuclear-genes encoding chloroplast proteins. By integrating information from gene function annotation, protein subcellular localization analyses, protein-protein interaction data, and gene expression data, we further showed support of the functionality of these conserved motifs. Our study implies the existence of unknown nuclear-encoded transcription factors that regulate both chloroplast genes and nuclear genes encoding chloroplast protein, which sheds light on the understanding of the transcriptional regulation of chloroplast genes.
Asunto(s)
Proteínas de Cloroplastos/genética , ADN de Cloroplastos/genética , ADN de Plantas/genética , Genes del Cloroplasto/genética , Motivos de Nucleótidos/genética , Arabidopsis/genética , Secuencia de Bases , Núcleo Celular/genética , Análisis por Conglomerados , Secuencia Conservada/genética , ADN de Cloroplastos/clasificación , ADN Intergénico/genética , ADN de Plantas/clasificación , Regulación de la Expresión Génica de las Plantas , Lactuca/genética , Solanum lycopersicum/genética , Oryza/genética , Filogenia , Regiones Promotoras Genéticas/genética , Secuencias Reguladoras de Ácidos Nucleicos/genética , Solanum tuberosum/genética , Glycine max/genética , Especificidad de la Especie , Nicotiana/genéticaRESUMEN
Artemisia campestris L. (Compositae) occurs naturally along the coastline of the Ryukyu Islands and has been traditionally used as a folk medicine for the treatment of liver and kidney disorders. The authors obtained specimens from the Ishigaki and Kume Islands of the Ryukyu Islands, Japan, and from the USA. A survey of the literature revealed that the Japanese name for A. campestris is Niitaka-yomogi or Riukiu-yomogi. Two distinct overall plant-form phenotypes were identified: an erect phenotype with long, upright, and straight main axis and assurgent branches; and a prostrate phenotype, having branches that are longer than the main axis and which grow along the ground. Except for the number of ray flowers, most of the flower head characters in the erect phenotypes were significantly larger than those in the prostrate phenotypes. In this experiment, the flower heads contained only small amounts of either capillarisin (<0.01-0.11 of the dry weight, % DW) and 6,7-dimethylesculetin (<0.01-0.30% DW), or none at all. DNA polymorphisms at two sites of the rpl16-rpl14 spacer region (nucleotide position 181-189 and 291-300 from the 5' end) revealed the existence of four different haplotypes. The number of adenines at nucleotide positions 291-300 appeared to be polymorphic within A. campestris from the Ryukyu Islands. Conversely, geographic differences between specimens from the Ryukyu Islands and USA manifested as a nine-base deletion at nucleotide positions 181-189. From a pharmacognostical context, the use of A. campestris flower heads as a substitute for Artemisiae capillaris Flos is not effective.
Asunto(s)
Artemisia/clasificación , ADN de Cloroplastos/clasificación , ADN de Cloroplastos/genética , Inflorescencia/clasificación , Medicina Tradicional/métodos , Farmacognosia/métodos , Análisis de Secuencia de ADN/métodos , Artemisia/genética , Secuencia de Bases , ADN de Cloroplastos/farmacología , Geografía , Inflorescencia/genética , Japón , Datos de Secuencia Molecular , Plantas Medicinales/clasificación , Plantas Medicinales/genética , Proteínas Ribosómicas/genéticaRESUMEN
Swertia mussotii is an important species in Tibetan folk medicine. However, it is quite expensive and frequently adulterated, so reliable methods for authentication of putative specimens and preparations of the species are needed to protect consumers and to support conservation measures. We show here that the chloroplast (cp) DNA RPL16 intron has limited utility for differentiating S. mussotii from closely related species, since the cpDNA RPL16 sequences are identical in S. mussotii and two other species of Swertia. However, the rDNA internal transcribed spacer (ITS) sequences differ significantly between S. mussotii and all of 13 tested potential adulterants. Thus, the ITS region provides a robust molecular marker for differentiating the medicinal S. mussotii from related adulterants. Therefore, a pair of allele-specific diagnostic primers based on the divergent ITS region was designed to distinguish S. mussotii from the other species. Authentication by allele-specific diagnostic PCR using these primers is convenient, effective and both simpler and less time-consuming than sequencing the ITS region.