Why have organelles retained genomes?

The observation that chloroplasts and mitochondria have retained relics of eubacterial genomes and a protein-synthesizing machinery has long puzzled biologists. If most genes have been transferred from organelles to the nucleus during evolution, why not all? What selective pressure maintains genomes in organelles? Electron transport through the photosynthetic and respiratory membranes is a powerful - but dangerous - source of energy. Recent evidence suggests that organelle genomes have persisted because structural proteins that maintain redox balance within bioenergetic membranes must be synthesized when and where they are needed, to counteract the potentially deadly side effects of ATP-generating electron transport.     

Why are plastid genomes retained in non-photosynthetic organisms?

The evolution of the plastid from a photosynthetic bacterial endosymbiont involved a dramatic reduction in the complexity of the plastid genome, with many genes either discarded or transferred to the nucleus of the eukaryotic host. However, this evolutionary process has not gone to completion and a subset of genes remains in all plastids examined to date. The various hypotheses put forward to explain the retention of the plastid genome have tended to focus on the need for photosynthetic organisms to retain a genetic system in the chloroplast, and they fail to explain why heterotrophic plants and algae, and the apicomplexan parasites all retain a genome in their non-photosynthetic plastids. Here we consider two additional explanations: the 'essential tRNAs' hypothesis and the 'transfer-window' hypothesis.     

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags (‘barcodes’). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three ‘bait’ sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species ‘barcodes’ that currently use the cox1 gene only.     

Undetected antisense tRNAs in mitochondrial genomes?

Background  

The hypothesis that both mitochondrial (mt) complementary DNA strands of tRNA genes code for tRNAs (sense-antisense coding) is explored. This could explain why mt tRNA mutations are 6.5 times more frequently pathogenic than in other mt sequences. Antisense tRNA expression is plausible because tRNA punctuation signals mt sense RNA maturation: both sense and antisense tRNAs form secondary structures potentially signalling processing. Sense RNA maturation processes by default 11 antisense tRNAs neighbouring sense genes. If antisense tRNAs are expressed, processed antisense tRNAs should have adapted more for translational activity than unprocessed ones. Four tRNA properties are examined: antisense tRNA 5′ and 3′ end processing by sense RNA maturation and its accuracy, cloverleaf stability and misacylation potential.     

Why are there so many carbohydrate-active enzyme-related genes in plants?

Plants contain far more carbohydrate-active enzyme-encoding genes than any other organism sequenced to date. The extremely large number of glycosidase and glycosyltransferase-related genes in plant genomes can be explained by the complex structure of the plant cell wall, by ancient genome duplication and by recent local duplications, but also by the recent emergence of novel and unrelated protein functions based on widely available pre-existing scaffolds.     

Why does mitochondrial complex I have so many subunits?

The prokaryotic and eukaryotic homologues of complex I (proton-pumping NADH:quinone oxidoreductase) perform the same function in energy transduction, but the eukaryotic enzymes are twice as big as their prokaryotic cousins, and comprise three times as many subunits. Fourteen core subunits are conserved in all complexes I, and are sufficient for catalysis - so why are the eukaryotic enzymes embellished by so many supernumerary or accessory subunits? In this issue of the Biochemical Journal, Angerer et al. have provided new evidence to suggest that the supernumerary subunits are important for enzyme stability. This commentary aims to put this suggestion into context.     

Symbiont genes in host genomes: fragments with a future?

While lateral transfer is the rule in the evolutionary history of bacterial and archaeal genes, events of transfer from prokaryotes to eukaryotes are rare. Germline-transmitted animal symbionts, such as Wolbachia pipientis, are well placed to participate in such transfers. In a recent issue of Science, Dunning Hotopp et al. identified instances of transfer of Wolbachia DNA to host genomes. It is unknown whether these transfers represent innovation in animal evolution.     

How many genes in a genome?

Despite the current good level of annotation, the Drosophila genome still holds surprises. A recent study has added perhaps 2,000 genes to the predicted total, and raises a number of questions about how genome annotation data should be stored and presented.     

Do we need many genes for phylogenetic inference?

Fifty-six nuclear protein coding genes from Taxonomically Broad EST Database and other databases were selected for phylogenomic-based examination of alternative phylogenetic hypotheses concerning intergroup relationship between multicellular animals (Metazoa) and other representatives of Opisthokonta. The results of this work support sister group relationship between Metazoa and Choanoflagellata. Both of these groups form the taxon Holozoa along with the monophyletic Ichthyosporea or Mesomycetozoea (a group that includes Amoebidium parasiticum, Sphaeroforma arctica, and Capsaspora owczarzaki). These phylogenetic hypotheses receive high statistical support both when utilizing whole alignment and when only 5000 randomly selected alignment positions are used. The presented results suggest subdivision of Fungi into Eumycota and lower fungi, Chytridiomycota. The latter form a monophyletic group that comprises Chytridiales+Spizellomycetales+Blastocladiales (Batrachochytrium, Spizellomyces, Allomyces, Blastocladiella), contrary to the earlier reports based on the analysis of 18S rRNA and a limited set of protein coding genes. The phylogenetic distribution of genes coding for a ubiquitin-fused ribosomal protein S30 implies at least three independent cases of gene fusion: in the ancestors of Holozoa, in heterotrophic Heterokonta (Oomycetes and Blastocystis) and in the ancestors of Cryptophyta and Glaucophyta. Ubiquitin-like sequences fused with ribosomal protein S30 outside of Holozoa are not FUBI orthologs. Two independent events of FUBI replacement by the ubiquitin sequence were detected in the lineage of C. owczarzaki and in the monophyletic group of nematode worms Tylenchomorpha+Cephalobidae. Bursaphelenchus xylophilus (Aphelenchoidoidea) retains a state typical of the rest of the Metazoa. The data emphasize the fact that the reliability of phylogenetic reconstructions depends on the number of analyzed genes to a lesser extent than on our ability to recognize reconstruction artifacts.     

Pollen grains: Why so many?

My objective is the examination of selective forces that affect pollen number. Relationships among other floral traits of animalpollinated plants, including pollen size, stigma area and depth, and the pollen-bearing area of the pollinator may affect pollen number and also provide a model to examine how change in one trait may elicit change in other traits. The model provides a conceptual framework for appreciating intra- and inter-specific differences in these traits. An equivalent model is presented for wind-pollinated plants. For these plants the distance between putative mates may be the most important factor affecting pollen number. I briefly consider how many pollen grains must reach a stigma to assure fruit set. I use pollen-ovule ratios (P/Os) to examine how breeding system, sexual system, pollen vector, and dispersal unit influence pollen grain number. I also compare the P/Os of plants with primary and secondary pollen presentation and those that provide only pollen as a reward with those that provide nectar as part or all of the reward. There is a substantial decrease in P/O from xenogamy to facultative xenogamy to autogamy. Relative to homoecious species the P/Os of species with most other sexual systems are higher. This suggests that there is a cost associated with changes in sexual system. The P/Os of wind-pollinated plants are substantially higher than those of animal-pollinated plants, and the available data suggest there is little difference in the pollination efficiency of the various animal vectors. The P/Os of plants whose pollen is dispersed in tetrads, polyads, or pollinia are substantially lower than those of species whose pollen is dispersed as monads. There was no difference in the P/Os of plants with primary and secondary pollen presentation. The P/Os of plants that provide only pollen as a reward were higher than those that provide nectar as a reward. All of these conclusions merit additional testing as they are based on samples that are relatively small and/or systematically biased.     

How do alterations in plant mitochondrial genomes disrupt pollen development?

Cytoplasmic male sterility arises when mitochondrial activities are disrupted that are essential for pollen development. Rearrangements in the mitochondrial genome that create novel open reading frames are strongly correlated with CMS phenotypes in a number of systems. The morphological aberrations which indicate CMS-associated degeneration are frequently restricted to the male sporogenous tissue and a limited number of vegetative tissues. In several cases, this tissue specificity may result from interactions between the mitochondrial genome and nuclear genes that regulate mitochondrial gene expression. A molecular mechanism by which CMS might be caused has not been conclusively demonstrated for any system. Several hypotheses for general mechanisms by which mitochondrial dysfunction might disrupt pollen development are discussed, based on similarities between the novel CMS-associated genes from a number of systems.     

Autism: many genes, common pathways?

Autism is a heterogeneous neurodevelopmental syndrome with a complex genetic etiology. It is still not clear whether autism comprises a vast collection of different disorders akin to intellectual disability or a few disorders sharing common aberrant pathways. Unifying principles among cases of autism are likely to be at the level of brain circuitry in addition to molecular pathways.     

Lessons from sequenced genomes. Overlapping genes in Methanococcus jannaschii?

This paper describes our finding on overlapping genes in Methanococcus jannaschii genome. We found that one of the open reading frames (ORFs) within the M. jannaschii genome contains the nucleotide sequence of tRNA(Ser), which raises a serious question of the correctness of the initiation codon assignment for that ORF. We suggest that there are two other possible AUG initiation codons downstream from the TTG triplet, which was initially considered as a translation start site. Only one of the AUG triplets is preceded by the Shine-Dalgarno sequence that seems to be required for binding the ribosome and initiation of translation.     

Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?

Replication generates bacterial chromosomes with strands that differ in the number of genes and base composition. It has been suggested that in bacteria such as Bacillus subtilis, PolC is responsible for the synthesis of the leading strand and DnaE for the lagging strand, whereas in many other bacteria DnaE is responsible for the synthesis of both strands. Here, I show that the possession of PolC correlates with leading strands that contain an average of 78% of genes compared with 58% for genomes that do not contain PolC. This suggests that asymmetrical replication forks could have a major role in defining and constraining the structure of the bacterial chromosome. The presence of PolC is not correlated with compositional strand bias, suggesting that the two biases result from different types of structural asymmetry.     

Why are proteins O-glycosylated?

The O-linked oligosaccharides of glycoproteins are usually clustered within heavily glycosylated regions of the peptide chain. Steric interactions between carbohydrate and peptide within these clusters induce the peptide core to adopt a stiff and extended conformation and this conformational effect appears to represent a major function of O-glycosylation.     

The evolution of Pyrosequencing® for microbiology: From genes to genomes

Leptospirosis is caused by Leptospira, gram negative spirochaetes whose microbiologic identification is difficult due to their low rate of growth and metabolic activity. In Colombia leptospirosis diagnosis is achieved by serological techniques without unified criteria for what positive titers are. In this study we compared polymerase chain reaction (PCR) with microbiological culture and dark field microscopy for the diagnosis of leptospirosis. Microbiological and molecular techniques were performed on 83 samples of urine taken from bovines in the savannahs surrounding Bogotá in Colombia, with presumptive diagnosis of leptospirosis. 117 samples of urine taken from healthy bovines were used as negative controls. 83 samples were MAT positive with titers ≥ 1:50; 81 with titers ≥ 1:100; and 66 with titers ≥ 1:200. 36% of the total samples (73/200) were Leptospira positives by microbiological culture, 32% (63/200) by dark field microscopy and 37% (74/200) by PCR. Amplicons obtained by PCR were 482 base pair long which are Leptospira specific. An amplicon of 262 base pairs typical of pathogenic Leptospira was observed in 71 out of the 74 PCR positive samples. The remaining 3 samples showed a 240 base pair amplicon which is typical of saprophytic Leptospira. PCR as a Leptospira diagnosis technique was 100% sensitive and 99% specific in comparison to microbiological culture. Kappa value of 0.99 indicated an excellent concordance between these techniques. Sensitivity and specificity reported for MAT when compared to microbiological culture was 0.95 and 0.89 with a ≥ 1:50 cut off. PCR was a reliable method for the rapid and precise diagnosis of leptospirosis when compared to traditional techniques in our study. The research presented here will be helpful to improve diagnosis and control of leptospirosis in Colombia and other endemic countries.