Neuroprotective phenylpropanoid esters of rhamnose isolated from roots of Scrophularia buergeriana

Four phenylpropanoid esters of rhamnose, buergerisides A1, B1, B2 and C1 were isolated from roots of Scrophularia huergeriana MIQ. (Scrophulariaceae), and were characterized as 2-O-acetyl-3,4-di-O-(E)-p-methoxycinnamoyl-alpha-L-rhamnopyranosid e, 2-O-acetyl-3-O-(E)-p-methoxycinnamoyl-alpha-L-rhamnopyranoside, 2-O-acetvl-3-O-(Z)-p-methoxycinnamoyl-alpha-L-rhamnopyranosi de and 4-O-(E)-p-methoxycinnamoyl-alpha-L-rhamnopyranoside, respectively. In addition, six known phenylpropanoids were authenticated as: (E)-cinnamic acid, (E)-p-methoxycinnamic acid, (E)-p-methoxycinnamic acid methyl ester, (E)-p-coumaric acid, (E)-caffeic acid, (E)-ferulic acid and a phenylalcohol, 2-(3-hydroxy-4-methoxyphenyl)ethanol. These ten phenylpropanoids all attenuated glutamate-induced neurotoxicity when added to primary cultures of rat cortical cells in a dose-dependent manner. These results demonstrate that phenylpropanoids isolated from S. buergeriana may exert significant protective effects against glutamate-induced neurodegeneration in primary cultures of cortical neurons.     

An unusual region of Paramecium mitochondrial DNA containing chloroplast-like genes

Based on DNA and amino acid comparisons with known genes and their products, a region of the Paramecium aurelia mitochondrial (mt) genome has been found to encode the following gene products: (1) photosystem II protein G (psbG); (2) a large open reading frame (ORF400) which is also found encoded in the chloroplast (cp) DNA of tobacco (as ORF393) and liverwort (as ORF392), and in the kinetoplast maxicircle DNA of Leishmania tarentolae (as ORFs 3 and 4); (3) ribosomal protein L2 (rpl2); (4) ribosomal protein S12 (rps12); (5) ribosomal protein S14 (rps14); and (6) NADH dehydrogenase subunit 2 (ndh2). All of these genes have been found in cp DNA, but the psbG gene has never been identified in a mt genome, and ribosomal protein genes have never been located in an animal or protozoan mitochondrion. The ndh2 gene has been found in both mitochondria and plastids. The Paramecium genes are among the most divergent of those sequenced to date. Two of the genes are encoded on the strand of DNA complementary to that encoding all other known Paramecium mt genes. No gene contains an identifiable intron. The rps12 and psbG genes are probably overlapping. It is not yet known whether these genes are transcribed or have functional gene products. The presence of these genes in the mt genome raises interesting questions concerning their evolutionary origin.     

The Chloroplast Genome Sequence of Mungbean (Vigna radiata) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships

Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between accD/rps16 and rbcL/trnK-UUU, and a 78-kb rearrangement between trnH/rpl14 and rps19/rps8. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species. Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.     

Do nonasterid holoparasitic flowering plants have plastid genomes?

Past work involving the plastid genome (plastome) of holoparasitic plants has been confined to Scrophulariaceae (or Orobanchaceae) which have truncated plastomes owing to loss of photosynthetic and other genes. Nonasterid holoparasites from Balanophoraceae (Corynaea), Hydnoraceae (Hydnora) and Cytinaceae (Cytinus) were tested for the presence of plastid genes and a plastome. Using PCR, plastid 16S rDNA was successfully amplified and sequenced from the above three holoparasites. The sequence of Cytinus showed 121 single base substitutions relative to Nicotiana (8% of the molecule) whereas higher sequence divergence was observed in Hydnora and Corynaea (287 and 513 changes, respectively). Secondary structural models for these 16S rRNAs show that most changes are compensatory, thus suggesting they are functional. Probes constructed for 16S rDNA and for four plastid-encoded ribosomal protein genes (rps2, rps4, rps7 and rpl16) were used in Southern blots of digested genomic DNA from the three holoparasites. Positive hybridizations were obtained using each of the five probes only for Cytinus. For SmaI digests, all plastid gene probes hybridized to a common fragment ca. 20 kb in length in this species. Taken together, these data provide preliminary evidence suggestive of the retention of highly diverged and truncated plastid genome in Cytinus. The greater sequence divergence for 16S rDNA and the negative hybridization results for Hydnora and Corynaea suggests two possibilities: the loss of typically conserved elements of their plastomes or the complete absence of a plastome.     

Complete nucleotide sequence of the S10-spc operon of phytoplasma: gene organization and genetic code resemble those of Bacillus subtilis

An 11.4-kbp region of genomic DNA containing the complete S10-spc operon was constructed by an integrative mapping technique with eight plasmid vectors carrying ribosomal protein sequences from onion yellows phytoplasma. Southern hybridization analysis indicated that phytoplasmal S10-spc is a single-copy operon. This is the first complete S10-spc operon of a phytoplasma to be reported, although only a part of six serial genes of the S10 operon is reported previously. The operon has a context of 5'-rps10, rpl3, rpl4, rpl23, rpl2, rps19, rpl22, rps3, rpl16, rpl29, rps17, rpl14, rpl24, rpl5, rps14, rps8, rpl6, rpl18, rps5, rpl30, rpl15, SecY-3', and is composed of 21 ribosomal protein subunit genes and a SecY protein translocase subunit gene. Resembling Bacillus, this operon contains an rpl30 gene that other mollicutes (Mycoplasma genitalium, M. pneumoniae, and M. pulmonis) lack. A phylogenetic tree based on the rps3 sequence showed that phytoplasmas are phylogenetically closer to acholeplasmas and bacillus than to mycoplasmas. In the S10-spc operon, translation may start from either a GTG codon or an ATG codon, and stop at a TGA codon, as has been reported for acholeplasmas and bacillus. However, in mycoplasmas, GTG was found as a start codon, and TGA was found not as a stop codon, but instead as a tryptophan codon. These data derived from the gene organization, and the genetic code deviation support the hypothesis that phytoplasmal genes resemble those of acholeplasmas and Bacillus more than those of other mollicutes.     

Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus

Gene transfer events from organelle genomes (mitochondria and chloroplasts in plants) to the nuclear genome are important processes in the evolution of the eukaryotic cell. It is highly likely that the gene transfer event is still an ongoing process in higher plant mitochondria and chloroplasts. The number and order of genes encoded in the chloroplast genome of higher plants are highly conserved. Recently, several exceptional cases of gene loss from the chloroplast genome have been discovered as the number of complete chloroplast genome sequences has increased. The Populus chloroplast genome has lost the rpl32 gene, while the corresponding the chloroplast rpl32 (cp rpl32) gene has been identified in the nuclear genome. Nuclear genes transferred from the chloroplast genome need to gain a sequence that encodes a transit peptide. Here, we revealed that the nuclear cp rpl32 gene has acquired the exon sequence, which is highly homologous to a transit peptide derived from the chloroplast Cu-Zn superoxide dismutase (cp sod-1) gene. The cp rpl32 gene has acquired the sequence that encodes not only for the transit peptide, but also for the conserved N-terminal portion of the mature SOD protein from the cp sod-1 gene, suggesting the occurrence of DNA sequence duplication. Unlike cp SOD-1, cp RPL32 did not show biased localization in the chloroplasts. This difference may be caused by mutations accumulated in the sequence of the SOD domain on the cp rpl32 gene. We provide new insight into the fate of the inherent sequence derived from a transit peptide.     

The cyanelle genome of Cyanophora paradoxa encodes ribosomal proteins not encoded by the chloroplasts genomes of higher plants

The rpl35, rpl20, rpl5, rps8, and a portion of the rpl6 genes of the cyanelle genome of Cyanophora paradoxa have been cloned, mapped and sequenced. Homologs of the rpl35, rpl5, and rpl6 genes are not found in the chloroplasts of higher plants. The rpl35 genes most likely form a dicistronic operon which is located upstream from the apcE-apcA-apcB locus of the cyanelle and which is divergently transcribed from this locus. The rpl5, rpl8, and rpl6 genes probably form a part of a larger cluster of genes encoding components of the cyanellar ribosomes. These genes are organized in a fashion similar to that observed in all procaryotes examined to date, with the exception that the rps14 gene is not found between the rpl5 and rps8 coding sequences. Hypotheses concerning the origins of cyanelles and chloroplasts are discussed.     

Gene clusters for ribosomal proteins in the mitochondrial genome of a liverwort, Marchantia polymorpha.

We detected 16 genes for ribosomal proteins in the complete sequence of the mitochondrial DNA from a liverwort, Marchantia polymorpha. The genes formed two major clusters, rps12-rps7 and rps10-rpl2-rps19-rps3-rpl16-rpl5- rps14-rps8- rpl6-rps13-rps11-rps1, very similar in organization to Escherichia coli ribosomal protein operons (str and S10-spc-alpha operons, respectively). In contrast, rps2 and rps4 genes were located separately in the liverwort mitochondrial genome (the latter was part of the alpha operon in E. coli). Furthermore, several ribosomal proteins encoded by the liverwort mitochondrial genome differed substantially in size from their counterparts in E. coli and liverwort chloroplast.     

Disintegration of the scrophulariaceae

A molecular systematic study of Scrophulariaceae sensu lato using DNA sequences of three plastid genes (rbcL, ndhF, and rps2) revealed at least five distinct monophyletic groups. Thirty-nine genera representing 24 tribes of the Scrophulariaceae s.l. (sensu lato) were analyzed along with representatives of 15 other families of Lamiales. The Scrophulariaceae s.s. (sensu stricto) include part or all of tribes Aptosimeae, Hemimerideae, Leucophylleae, Manuleae, Selagineae, and Verbasceae (= Scrophularieae) and the conventional families Buddlejaceae and Myoporaceae. Veronicaceae includes all or part of tribes Angelonieae, Antirrhineae, Cheloneae, Digitaleae, and Gratioleae and the conventional families Callitrichaceae, Globulariaceae, Hippuridaceae, and Plantaginaceae. The Orobanchaceae include tribes Buchnereae, Rhinantheae, and the conventional Orobanchaceae. All sampled members of Orobanchaceae are parasitic, except Lindenbergia, which is sister to the rest of the family. Family Calceolariaceae Olmstead is newly erected herein to recognize the phylogenetic distinctiveness of tribe Calceolarieae. The Calceolariaceae are close to the base of the Lamiales. The Stilbaceae are expanded by the inclusion of Halleria. Mimulus does not belong in any of these five groups.     

Nonessential plastid-encoded ribosomal proteins in tobacco: a developmental role for plastid translation and implications for reductive genome evolution

Plastid genomes of higher plants contain a conserved set of ribosomal protein genes. Although plastid translational activity is essential for cell survival in tobacco (Nicotiana tabacum), individual plastid ribosomal proteins can be nonessential. Candidates for nonessential plastid ribosomal proteins are ribosomal proteins identified as nonessential in bacteria and those whose genes were lost from the highly reduced plastid genomes of nonphotosynthetic plastid-bearing lineages (parasitic plants, apicomplexan protozoa). Here we report the reverse genetic analysis of seven plastid-encoded ribosomal proteins that meet these criteria. We have introduced knockout alleles for the corresponding genes into the tobacco plastid genome. Five of the targeted genes (ribosomal protein of the large subunit22 [rpl22], rpl23, rpl32, ribosomal protein of the small subunit3 [rps3], and rps16) were shown to be essential even under heterotrophic conditions, despite their loss in at least some parasitic plastid-bearing lineages. This suggests that nonphotosynthetic plastids show elevated rates of gene transfer to the nuclear genome. Knockout of two ribosomal protein genes, rps15 and rpl36, yielded homoplasmic transplastomic mutants, thus indicating nonessentiality. Whereas Δrps15 plants showed only a mild phenotype, Δrpl36 plants were severely impaired in photosynthesis and growth and, moreover, displayed greatly altered leaf morphology. This finding provides strong genetic evidence that chloroplast translational activity influences leaf development, presumably via a retrograde signaling pathway.     

The complete chloroplast genome sequence of the endangered species Syringa pinnatifolia (Oleaceae)

Syringa pinnatifolia is an endangered endemic species in China with important ornamental and medicinal value, and it needs urgent protection. Here, we report the complete chloroplast (cp) genome structure of S. pinnatifolia and its evolution is inferred through comparative studies with related species. The S. pinnatifolia cp genome was 155 326 bp and contained a large single copy region (LSC) of 86 167 bp and a small single copy region (SSC) of 17 775 bp, as well as a pair of inverted repeat regions (IRs) of 25 692 bp. A total of 113 unique genes were annotated, including 79 protein‐coding genes, 30 tRNA genes and four rRNA genes. The GC content of the S. pinnatifolia cp genome was 37.9%, and the corresponding values in the LSC, SSC and IR regions were 36.0, 32.1, 43.2% respectively. Repetitive sequences analysis revealed that the S. pinnatifolia cp genome contained 38 repeats. Microsatellite marker detection analysis identified 253 simple sequence repeats (SSRs), which provides opportunities for future studies of the population genetics and phylogenetic relationships of Syringa. Phylogenetic analysis of 29 selected cp genomes revealed that S. pinnatifolia is closely related to Syringa vulgaris and all 27 Lamiales species formed a clade separate from the two outgroup species. This newly characterized S. pinnatifolia chloroplast genome will provide a useful genomic resource of phylogenetic inference and the development of more genetic markers for species discrimination and population studies in the genus Syringa.     

The nucleotide sequence of five ribosomal protein genes from the cyanelles ofCyanophora paradoxa: Implications concerning the phylogenetic relationship between cyanelles and chloroplasts

Summary The nucleotide sequences of the ribosomal protein genesrps18, rps19, rpl2, rpl33, and partial sequence ofrpl22 from cyanelles, the photosynthetic organelles of the protistCyanophora paradoxa, have been determined. These genes form two clusters oriented in opposite and divergent directions. One cluster contains therpl33 andrps18 genes; the other contains therpl2, rps19, andrpl22 genes, in that order. Phylogenetic trees were constructed from both the DNA sequences and the deduced protein sequences of cyanelles,Euglena gracilis and land plant chloroplasts, andEscherichia coli, using parsimony or maximum likelihood methods. In addition, a phylogenetic tree was built from a distance matrix comparing the number of nucleotide substitutions per site. The phylogeny inferred from all these methods suggests that cyanelles fall within the chloroplast line of evolution and that the evolutionary distances between cyanelles and land plant chloroplasts are shorter than betweenE. gracilis chloroplasts and land plant chloroplasts.     

基于形态和cpDNA序列探讨柽柳和甘蒙柽柳的亲缘关系

柽柳科植物的系统学关系已初步明确,但部分种间的系统进化关系仍有待澄清。为明确中国黄河流域广泛分布的柽柳(Tamarix chinensis)和甘蒙柽柳(T. austromongolica)的亲缘关系,利用13个稳定的形态学性状和3个cpDNA间隔区片段(rpl20-5′-rps12, rps16, trn L-trn F)对柽柳科3属9种植物进行研究,结果表明3条序列的位点变异程度依次为trn L-trn F>rps16>rpl20-5′-rps12,柽柳和甘蒙柽柳群体共享有同一单倍型,表型和分子数据均支持柽柳和甘蒙柽柳为单系分支的近缘种,推测柽柳和甘蒙柽柳的分化大致发生在0.69Ma (0-1.93) Ma,与同属内其它物种相比,分化时间相对较晚。     

The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms

Mahonia bealei (Berberidaceae) is a frequently-used traditional Chinese medicinal plant with efficient anti-inflammatory ability. This plant is one of the sources of berberine, a new cholesterol-lowering drug with anti-diabetic activity. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of M. bealei. The complete cp genome of M. bealei is 164,792 bp in length, and has a typical structure with large (LSC 73,052 bp) and small (SSC 18,591 bp) single-copy regions separated by a pair of inverted repeats (IRs 36,501 bp) of large size. The Mahonia cp genome contains 111 unique genes and 39 genes are duplicated in the IR regions. The gene order and content of M. bealei are almost unarranged which is consistent with the hypothesis that large IRs stabilize cp genome and reduce gene loss-and-gain probabilities during evolutionary process. A large IR expansion of over 12 kb has occurred in M. bealei, 15 genes (rps19, rpl22, rps3, rpl16, rpl14, rps8, infA, rpl36, rps11, petD, petB, psbH, psbN, psbT and psbB) have expanded to have an additional copy in the IRs. The IR expansion rearrangement occurred via a double-strand DNA break and subsequence repair, which is different from the ordinary gene conversion mechanism. Repeat analysis identified 39 direct/inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Analysis also revealed 75 simple sequence repeat (SSR) loci and almost all are composed of A or T, contributing to a distinct bias in base composition. Comparison of protein-coding sequences with ESTs reveals 9 putative RNA edits and 5 of them resulted in non-synonymous modifications in rpoC1, rps2, rps19 and ycf1. Phylogenetic analysis using maximum parsimony (MP) and maximum likelihood (ML) was performed on a dataset composed of 65 protein-coding genes from 25 taxa, which yields an identical tree topology as previous plastid-based trees, and provides strong support for the sister relationship between Ranunculaceae and Berberidaceae. Molecular dating analyses suggest that Ranunculaceae and Berberidaceae diverged between 90 and 84 mya, which is congruent with the fossil records and with recent estimates of the divergence time of these two taxa.     

Phylogenetics of early branching eudicots:Comparing phylogenetic signal across plastid introns,spacers,and genes

<正>Recent phylogenetic analyses revealed a grade with Ranunculales,Sabiales,Proteales,Trochodendrales, and Buxales as first branching eudicots,with the respective positions of Proteales and Sabiales still lacking statistical confidence.As previous analyses of conserved plastid genes remain inconclusive,we aimed to use and evaluate a representative set of plastid introns(group I:trnL;group II:petD,rpll6,trnK) and intergenic spacers(trnL-F,petB-petD, atpB-rbcL,rps3-rpl16) in comparison to the rapidly evolving matK and slowly evolving atpB and rbcL genes. Overall patterns of micro structural mutations converged across genomic regions,underscoring the existence of a general mutational pattern throughout the plastid genome.Phylogenetic signal differed strongly between functionally and structurally different genomic regions and was highest in matK,followed by spacers,then group II and group I introns.The more conserved atpB and rbcL coding regions showed distinctly lower phylogenetic information content.Parsimony,maximum likelihood,and Bayesian phylogenetic analyses based on the combined dataset of non-coding and rapidly evolving regions(14 000 aligned characters) converged to a backbone topology of eudicots with Ranunculales branching first,a Proteales-Sabiales clade second,followed by Trochodendrales and Buxales. Gunnerales generally appeared as sister to all remaining core eudicots with maximum support.Our results show that a small number of intron and spacer sequences allow similar insights into phylogenetic relationships of eudicots compared to datasets of many combined genes.The non-coding proportion of the plastid genome thus can be considered an important information source for plastid phylogenomics.