抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.

/pdf/selection-of-conserved-blocks-from-multiple-alignments-for-i0qfazjwh5.pdf

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

http://bio.gsnu.ac.kr/research/miRNA/RNAss/Mfold/miRNAss_JMB_1999_Mathews.pdf

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.

/pdf/phylogenetic-structure-of-the-prokaryotic-domain-the-primary-5c5cftso21.pdf

Phylogenetic structure of the prokaryotic domain: The primary kingdoms

Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.

Ribosomal Database Project: data and tools for high throughput rRNA analysis

▪ Abstract Recent results from ancestral (minimally derived) protists testify to the tremendous diversity of the mitochondrial genome in various eukaryotic lineages, but also reinforce the view that mitochondria, descendants of an endosymbiotic α-Proteobacterium, arose only once in evolution. The serial endosymbiosis theory, currently the most popular hypothesis to explain the origin of mitochondria, postulates the capture of an α-proteobacterial endosymbiont by a nucleus-containing eukaryotic host resembling extant amitochondriate protists. New sequence data have challenged this scenario, instead raising the possibility that the origin of the mitochondrion was coincident with, and contributed substantially to, the origin of the nuclear genome of the eukaryotic cell. Defining more precisely the α-proteobacterial ancestry of the mitochondrial genome, and the contribution of the endosymbiotic event to the nuclear genome, will be essential for a full understanding of the origin and evolution of the eukaryoti...

Mitochondrial Genome Evolution and the Origin of Eukaryotes

Mitochondria, organelles specialized in energy conservation reactions in eukaryotic cells, have evolved from eubacteria-like endo-symbionts 1–3 whose closest known relatives are the rickettsial group of α-proteobacteria 4,5. Because characterized mitochondrial genomes vary markedly in structure3, it has been impossible to infer from them the initial form of the proto-mitochondrial genome. This would require the identification of minimally derived mitochondrial DNAs that better reflect the ancestral state. Here we describe such a primitive mitochondrial genome, in the freshwater protozoon Reclinomonas americana6. This protist displays ultrastructural characteristics that ally it with the retortamonads7,8, a protozoan group that lacks mitochondria8,9. R. americana mtDNA (69,034 base pairs) contains the largest collection of genes (97) so far identified in any mtDNA, including genes for 5S ribosomal RNA, the RNA component of RNase P, and at least 18 proteins not previously known to be encoded in mitochondria. Most surprising are four genes specifying a multisubunit, eubacterial-type RNA polymerase. Features of gene content together with eubacterial characteristics of genome organization and expression not found before in mitochondrial genomes indicate that R. americana mtDNA more closely resembles the ancestral proto-mitochondrial genome than any other mtDNA investigated to date.

An ancestral mitochondrial DNA resembling a eubacterial genome in miniature

Recent advances in resolving the tree of eukaryotes are converging on a model composed of a few large hypothetical 'supergroups', each comprising a diversity of primarily microbial eukaryotes (protists, or protozoa and algae). The process of resolving the tree involves the synthesis of many kinds of data, including single-gene trees, multigene analyses, and other kinds of molecular and structural characters. Here, we review the recent progress in assembling the tree of eukaryotes, describing the major evidence for each supergroup, and where gaps in our knowledge remain. We also consider other factors emerging from phylogenetic analyses and comparative genomics, in particular lateral gene transfer, and whether such factors confound our understanding of the eukaryotic tree.

/pdf/the-tree-of-eukaryotes-12vtscov0y.pdf

The tree of eukaryotes

Mitochondrial genomes: anything goes.

Publisher Summary This chapter highlights endosymbiont hypothesis. All contemporary genomes (including those of plastids and mitochondria) ultimately derive from a single genome—the genome of a single, presumably cellular, entity which was the ancestor of all surviving forms of live. The construction and interpretation of phylogenetic trees based on small subunit (SSU, or 16S-like) and large subunit (LSU, or 23S-like) rRNA sequences have proven especially informative in instances where morphological diversity tends to confound traditional methods of phylogenetic analysis. In addition to ribosomal RNA (rRNA) sequence, there are a number of traits that characterize the archaebacteria as a distinct group of organisms, separate from all other prokaryotes. These include (1) cell walls that, when present, lack peptidoglycan and muramic acid; (2) the presence of lipids containing phytanyl side groups in ether linkage; and (3) the presence of RNA polymerases that are distinct from those of eubacteria in subunit composition, response to RNA synthesis inhibitors or stimulators, immunological reactivity, and gene sequence. Two major divisions of archaebacteria include (1) sulfur-dependent, extreme thermophiles; and (2) methane-producers (methanogens) and their relatives, including the extreme halophiles.

Michael W. Gray

Papers

Mitochondrial Genome Evolution and the Origin of Eukaryotes

An ancestral mitochondrial DNA resembling a eubacterial genome in miniature

The tree of eukaryotes

Mitochondrial genomes: anything goes.

The endosymbiont hypothesis revisited.