Showing papers by "Jeffrey D. Palmer published in 1997"

A Plastid of Probable Green Algal Origin in Apicomplexan Parasites

Abstract: Protozoan parasites of the phylum Apicomplexa contain three genetic elements: the nuclear and mitochondrial genomes characteristic of virtually all eukaryotic cells and a 35-kilobase circular extrachromosomal DNA. In situ hybridization techniques were used to localize the 35-kilobase DNA of Toxoplasma gondii to a discrete organelle surrounded by four membranes. Phylogenetic analysis of the tufA gene encoded by the 35-kilobase genomes of coccidians T. gondii and Eimeria tenella and the malaria parasite Plasmodium falciparum grouped this organellar genome with cyanobacteria and plastids, showing consistent clustering with green algal plastids. Taken together, these observations indicate that the Apicomplexa acquired a plastid by secondary endosymbiosis, probably from a green alga.

The origin of plastids and their spread via secondary symbiosis

Abstract: The endosymbiotic, cyanobacterial nature of plastids is clearly established, but several fundamental issues concerning the origin and early evolution of plastids remain unresolved. One key question is whether plastids are monophyletic (derived from a single cyanobacterial ancestor) or polyphyletic (derived from more than one ancestor). This issue is complicated by the presence in many photosynthetic eukaryotes of secondary plastids, acquired by ingestion of a eukaryote, itself already equipped with plastids, rather than by direct ingestion of a free-living cyanobacterium. A review of the phylogenetic evidence from plastid genes indicates that the three major lineages of primary plastids (red, green, and glaucocystophyte) are probably monophyletic. Mitochondrial data further support this conclusion for red and green plastids (but are unavailable for glaucocystophytes), while nuclear data are largely unresolved. If plastids are monophyletic, then the pigment diversity of plastids must postdate their status as endosymbiotic organelles, but whether this diversity arose primarily by acquisition or loss is nuclear. Secondary endosymbiosis has greatly multiplied the variety of photosynthetic eukaryotes. A secondary origin of plastids is unequivocal for cryptomonads and chlorarachniophytes, is likely for heterokonts, haptophytes, and euglenophytes, and is suggested for the nonphotosynthetic parasites of phylum Apicomplexa. The remarkable plastid diversity of dinoflagellates appears to be the result of multiple secondary and tertiary endosymbiotic events. A consistent feature of all plastid genomes is extreme reduction relative to their cyanobacterial progenitors via outright gene loss, transfer of genes to the nuclear genome, and substitution by genes of nuclear ancestry. Most of this reduction seems to have occurred relatively soon after primary endosymbiosis, before the emergence of the major lineages of plastids, yet recent data also reveal surprising diversity of gene content among these lineages. The rubisco genes (rbcLS) of primary plastids on the red lineage are not related to those of cyanobacteria and seem to have been acquired via horizontal gene transfer.

Implications for the Phylogeny, Classification, and Biogeography of Solanum from cpDNA Restriction Site Variation

Abstract: A phylogenetic analysis of Solanum based on chloroplast DNA restriction site variation confirms previous findings that Lycopersicon and Cyphomandra are derived from within Solanum. Three out of four Solanum subgenera with more than one representative in this analysis (Minon, Potatoe, Solanum) are found to be polyphyletic, suggesting that the subgeneric classification of the genus needs revision. Subgenus Leptostemonum is monophyletic within the context of our sampling. Three primary clades can be distinguished within Solanum. Clade I includes representatives of sections Archaesolanum, Dulcamara, Holophylla, Jasminosola- num, and Solanum. Clade II includes members of subgenus Potatoe (sections Basarthrum, Lycopersicon, and Petota). Clade III includes all representatives sampled from subg. Leptostemonum, sects. Allophyllum, Brevan- therum, Gemninata, Pseduocapsicum, and Cyphomandropsis, and species formerly assigned to Cyphomandra. Solanum as a whole and each of the three primary clades apppear to be New World in origin. Within Leptostemonum, African and Australian members are derived from New World ancestors.

The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families

Abstract: Comprehensive gene mapping reveals that the chloroplast genome of Trachelium caeruleum is highly rearranged relative to those of other land plants. Evolutionary scenarios that consist of seven to ten inversions, one or two transpositions, both expansion and contraction of the typically size-conserved inverted repeat, a presumed gene loss, deletions within two large open reading frames and several insertions, are sufficient to derive the Trachelium arrangement from the ancestral angiosperm chloroplast DNA arrangement. Two of the rearrangements disrupt transcriptional units that are otherwise conserved among land plants. At least five families of small dispersed repeats exist in the Trachelium chloroplast genome. Most of the repeats are associated with inversion endpoints and may have facilitated inversions through recombination across homologous repeats.

Organelle Genomes--Going, Going, Gone

Abstract: The organelles of eukaryotic cells—chloroplasts and mitochondria—first arose as engulfed symbionts with their own genomes. They subsequently lost most of their genes to the nucleus, retaining a few that could not be transferred. In his Perspective, Palmer discusses recent evidence that suggests that another organelle, the hydrogenosome, is a highly modified mitochondrion that has lost all of its genetic material.

Isolation and characterization of rad51 orthologs from Coprinus cinereus and Lycopersicon esculentum, and phylogenetic analysis of eukaryotic recA homologs.

Abstract: In eubacteria, the recA gene has long been recognized as essential for homologous recombination and DNA repair. Recent work has identified recA homologs in archaebacteria and eukaryotes, thus emphasizing the universal role this gene plays in DNA metabolism. We have isolated and characterized two new recA homologs, one from the basidiomycete Coprinus cinereus and the other from the angiosperm Lycopersicon esculentum. Like the RAD51 gene of Saccharomyces cerevisiae, the Coprinus gene is highly induced by gamma irradiation and during meiosis. Phylogenetic analyses of eukarotic recA homologs reveal a gene duplication early in eukaryotic evolution which gave rise to two putatively monophyletic groups of recA-like genes. One group of 11 characterized genes, designated the rad51 group, is orthologous to the Saccharomyces RAD51 gene and also contains the Coprinus and Lycopersicon genes. The other group of seven genes, designated the dmc1 group, is orthologous to the Saccharomyces DMC1 gene. Sequence comparisons and phylogenetic analysis reveal extensive lineage- and gene-specific differences in rates of RecA protein evolution. Dmc1 consistently evolves faster than Rad51, and fungal proteins of both types, especially those of Saccharomyces, change rapidly, particularly in comparison to the slowly evolving vertebrate proteins. The Drosophila Rad51 protein has undergone remarkably rapid sequence divergence.

Mergers of Botany and Biology Departments

Abstract: In the article “Biology departments restructure” by Wade Roush (News & Comment, [14 Mar., p. 1556][1]), Rytas Vilgalys of Duke University is quoted as saying that botany at several schools, including Indiana University (IU), has “gone into eclipse” or has lost influence as a result of its merger with zoology. Although the merger of taxon-based departments may have injured botanical studies at other universities, botany at IU has been strengthened by its integration with other disciplines after the interdepartmental merger in 1978. The merged department was replaced by the Plant Sciences Graduate Program, which currently includes 18 faculty members, representing an increase of four plant scientists since the merger. Faculty hires since the merger represent all levels of analysis, ranging from molecular to organismal. In addition, IU plant sciences faculty do not appear to have lost influence in the Department of Biology. The department chair and directors of three of the six graduate programs in biology are plant science faculty. Further evidence of continued excellence in botanical studies at IU includes a recent graduate research traineeship award in the plant sciences from the U.S. Department of Agriculture and a “top 10%” ranking by the 1996 Gourman Report. The continued success of botany at IU suggests that departmental realignments need not weaken taxon-specific disciplines, but that instead they may serve to invigorate research areas that might otherwise decline. # Mergers of Botany and Biology Departments {#article-title-2} Vilgalys is quoted as saying that, at schools “where botany and zoology have merged,” including at the University of Michigan, “botany has gone into eclipse.” In fact, it may be argued that the botanical sciences at the University of Michigan have never been stronger. In 1974, shortly before the two departments merged, 27% of the biologists in the departments of botany and zoology were plant scientists. Today that figure is 31%. Of course, I am including in “botanical sciences” such disciplines as plant ecology and plant physiology, whereas Vilgalys appears to define botany as the traditional fields of plant taxonomy and systematics. But even in 1974, a minority of the faculty in the botany department fell into those categories. From the mid-1960s until 1974, the botany department had in place a progressive faculty hiring program; during this time only two “traditional” botanists (out of a total of 12) were hired. The rewards of the foresight of the early administrators of botany may be seen today in the University of Michigan’s thriving programs in such fields as plant ecology, plant molecular biology, and cell and molecular biology in general. # Mergers of Botany and Biology Departments {#article-title-3} In this era of increasing budget constraints and forced restructuring of academic departments as reported by Roush, one wonders whether graduate education and graduate students will be lost in the shuffle. Because graduate students represent an investment, and many of the solutions seem to depend on economics, their worth needs to be clearly defined and reinforced among administrators, faculty, and the students themselves. Graduate students are the life force of an academic department: they perform most of the hands-on research that goes on in research universities; their use as teaching assistants allows faculty the time to pursue research-related activities; and they are routinely called on to provide data and conceptual background to grant proposals “written” by their mentors. Published research done by graduate students is often co-authored by faculty, thus bolstering publication records; presentations of such research at meetings provides critical “advertising” for a laboratory, department, or university. All this while they are paid a minimal salary with few benefits, no sick leave or compensation, and often with no guarantees of funding for the next year. The lack of recognition of such contributions has led graduate students at some schools to unionize. When graduate students are empowered with the attention and respect they deserve, however, the intellectual and economic returns a university can expect far outweigh the original investment. [1]: /lookup/doi/10.1126/science.275.5306.1556