The bacterial recA gene and its eukaryotic homolog RAD51 are important for DNA repair, homologous recombination, and genome stability. Members of the recA͞RAD51 family have functions that have differentiated during evolution. However, the evolutionary history and relationships of these members remains unclear. Homolog searches in prokaryotes and eukaryotes indicated that most eubacteria contain only one recA. However, many archaeal species have two recA͞RAD51 homologs (RADA and RADB), and eukaryotes possess multiple members (RAD51, RAD51B, RAD51C, RAD51D, DMC1, XRCC2, XRCC3, and recA). Phylogenetic analyses indicated that the recA͞RAD51 family can be divided into three subfamilies: (i) RAD␣, with highly conserved functions; (ii) RAD␤, with relatively divergent functions; and (iii) recA, functioning in eubacteria and eukaryotic organelles. The RAD␣ and RAD␤ subfamilies each contain archaeal and eukaryotic members, suggesting that a gene duplication occurred before the archaea͞eukaryote split. In the RAD␣ subfamily, eukaryotic RAD51 and DMC1 genes formed two separate monophyletic groups when archaeal RADA genes were used as an outgroup. This result suggests that another duplication event occurred in the early stage of eukaryotic evolution, producing the DMC1 clade with meiosisspecific genes. The RAD␤ subfamily has a basal archaeal clade and five eukaryotic clades, suggesting that four eukaryotic duplication events occurred before animals and plants diverged. The eukaryotic recA genes were detected in plants and protists and showed strikingly high levels of sequence similarity to recA genes from proteobacteria or cyanobacteria. These results suggest that endosymbiotic transfer of recA genes occurred from mitochondria and chloroplasts to nuclear genomes of ancestral eukaryotes.origins of meiosis and eukaryotes ͉ phylogenetic analysis ͉ recombination ͉ DNA repair ͉ organellar genes D NA double-strand breaks (DSBs) can occur either spontaneously during DNA replication or by exogenous DNAdamaging agents. Efficient repair of DSBs is critical for genomic stability and cellular viability (1). A major DSB repair pathway is homologous recombination, which is also critical for meiosis and generation of genetic diversity. Among the best known recombination genes are the Escherichia coli recA gene and its eukaryotic homologs RAD51s (2, 3). recA encodes a DNA-dependent ATPase that binds to single-stranded DNA and promotes strand invasion and exchange between homologous DNA molecules (4). The two eukaryotic recA homologs, RAD51 and DMC1, were first discovered in the budding yeast Saccharomyces cerevisiae and are structurally and functionally similar to the E. coli recA gene (5, 6).Homologs of recA and RAD51 have then been identified in many prokaryotes and eukaryotes. In eubacteria, only one recA gene has been previously reported in each species (7). Unlike eubacteria, several archaeal species have two recA͞RAD51-like genes, called RADA and RADB (Table 1, which is published as supporting information on the PNAS web site) (8, 9)....

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Chemical modification of transcripts with 5′ caps occurs in all organisms. Here, we report a systems-level mass spectrometry-based technique, CapQuant, for quantitative analysis of an organism's cap epitranscriptome. The method was piloted with 21 canonical caps—m7GpppN, m7GpppNm, GpppN, GpppNm, and m2,2,7GpppG—and 5 ‘metabolite’ caps—NAD, FAD, UDP-Glc, UDP-GlcNAc, and dpCoA. Applying CapQuant to RNA from purified dengue virus, Escherichia coli, yeast, mouse tissues, and human cells, we discovered new cap structures in humans and mice (FAD, UDP-Glc, UDP-GlcNAc, and m7Gpppm6A), cell- and tissue-specific variations in cap methylation, and high proportions of caps lacking 2′-O-methylation (m7Gpppm6A in mammals, m7GpppA in dengue virus). While substantial Dimroth-induced loss of m1A and m1Am arose with specific RNA processing conditions, human lymphoblast cells showed no detectable m1A or m1Am in caps. CapQuant accurately captured the preference for purine nucleotides at eukaryotic transcription start sites and the correlation between metabolite levels and metabolite caps.

To understand the evolutionary process of the DNA mismatch repair system, we conducted systematic phylogenetic analysis of its key components, the bacterial MutS and MutL genes and their eukaryotic homologs. Based on genome-wide homolog searches, we identified three new MutS subfamilies (MutS3-5) in addition to the previously studied MutS1 and MutS2 subfamilies. Detailed evolutionary analysis strongly suggests that frequent ancient horizontal gene transfer (HGT) occurred with both MutS and MutL genes from bacteria to eukaryotes and/or archaea. Our results further imply that the origins of mismatch repair system in eukaryotes and archaea are largely attributed to ancient HGT from bacteria instead of vertical evolution. Specifically, the eukaryotic MutS and MutL homologs likely originated from endosymbiotic ancestors of mitochondria or chloroplasts, indicating that not only archaea, but also bacteria are important sources of eukaryotic DNA metabolic genes. The archaeal MutS1 and MutL homologs were also acquired from bacteria simultaneously through HGT. Moreover, the distribution and evolution profiles of the MutS1 and MutL genes suggest that they have undergone long-term coevolution. Our work presents an overall portrait of the evolution of these important genes in DNA metabolism and also provides further understanding about the early evolution of cellular organisms.

Meiotic prophase I is a complex process involving homologous chromosome (homolog) pairing, synapsis, and recombination. The budding yeast (Saccharomyces cerevisiae) RAD51 gene is known to be important for recombination and DNA repair in the mitotic cell cycle. In addition, RAD51 is required for meiosis and its Arabidopsis (Arabidopsis thaliana) ortholog is important for normal meiotic homolog pairing, synapsis, and repair of double-stranded breaks. In vertebrate cell cultures, the RAD51 paralog RAD51C is also important for mitotic homologous recombination and maintenance of genome integrity. However, the function of RAD51C in meiosis is not well understood. Here we describe the identification and analysis of a mutation in the Arabidopsis RAD51C ortholog, AtRAD51C. Although the atrad51c-1 mutant has normal vegetative and flower development and has no detectable abnormality in mitosis, it is completely male and female sterile. During early meiosis, homologous chromosomes in atrad51c-1 fail to undergo synapsis and become severely fragmented. In addition, analysis of the atrad51c-1 atspo11-1 double mutant showed that fragmentation was nearly completely suppressed by the atspo11-1 mutation, indicating that the fragmentation largely represents a defect in processing double-stranded breaks generated by AtSPO11-1. Fluorescence in situ hybridization experiments suggest that homolog juxtaposition might also be abnormal in atrad51c-1 meiocytes. These results demonstrate that AtRAD51C is essential for normal meiosis and is probably required for homologous synapsis.Meiosis is essential for eukaryotic sexual reproduction, allowing the production of haploid gametes. In addition, meiotic recombination during the early stages of meiosis allows the exchange of genetic information, serving as an important source of genetic diversity. The success of meiosis depends on a complex and prolonged prophase I that involves homologous chromosome (homolog) pairing, synapsis, and recombination (Zickler and Kleckner, 1999;Page and Hawley, 2003;Schwarzacher, 2003). After pairing, the homologs continue to associate and this interaction has been referred to as homolog juxtaposition (Zickler and Kleckner, 1999). Recombination results in crossover events that correspond to cytologically observed chiasmata, which, in combination with sister chromatid cohesion, maintain the association between homologs in the form of bivalents, ensuring proper segregation of homologs at anaphase I. Synapsis, the formation of synaptonemal complexes (SCs) between closely associated chromosomes, has also been implicated to play important roles in meiotic prophase I, although its relationship with recombination differs among organisms.Cytological and molecular genetic studies support the idea that homolog pairing, synapsis, and recombination are closely coupled events in normal meiosis. In particular, recombination and synapsis are often interdependent. In fact, a number of meiotic genes are required for both normal synapsis and recombination in yeast (Saccharomyces cer...