FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing.

BACKGROUND: RNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs and the corresponding coding DNA sequences. Software tools successful for the search of genes in other organisms not always are able to correctly perform this task in plants organellar genomes. Moreover, the available software tools predicting RNA editing events utilise algorithms that do not account for events which may generate a novel start codon. RESULTS: We present FEDRO, a Java software tool implementing a novel strategy to generate candidate Open Reading Frames (ORFs) resulting from Cytidine to Uridine (c→u) editing substitutions which occur in the mitochondrial genome (mtDNA) of a given input plant. The goal is to predict putative proteins of plants mitochondria that have not been yet annotated. In order to validate the generated ORFs, a screening is performed by checking for sequence similarity or presence in active transcripts of the same or similar organisms. We illustrate the functionalities of our framework on a model organism. CONCLUSIONS: The proposed tool may be used also on other organisms and genomes. FEDRO is publicly available at http://math.unipa.it/rombo/FEDRO .

IP6K gene identification in plant genomes by tag searching.

BACKGROUND: Plants have played a special role in inositol polyphosphate (IP) research since in plant seeds was discovered the first IP, the fully phosphorylated inositol ring of phytic acid (IP6). It is now known that phytic acid is further metabolized by the IP6 Kinases (IP6Ks) to generate IP containing pyro-phosphate moiety. The IP6K are evolutionary conserved enzymes identified in several mammalian, fungi and amoebae species. Although IP6K has not yet been identified in plant chromosomes, there are many clues suggesting its presences in vegetal cells. RESULTS: In this paper we propose a new approach to search for the plant IP6K gene, that lead to the identification in plant genome of a nucleotide sequence corresponding to a specific tag of the IP6K family. Such a tag has been found in all IP6K genes identified up to now, as well as in all genes belonging to the Inositol Polyphosphate Kinases superfamily (IPK). The tag sequence corresponds to the inositol-binding site of the enzyme, and it can be considered as characterizing all IPK genes. To this aim we applied a technique based on motif discovery. We exploited DLSME, a software recently proposed, which allows for the motif structure to be only partially specified by the user. First we applied the new method on mitochondrial DNA (mtDNA) of plants, where such a gene could have been nested, possibly encrypted and hidden by virtue of the editing and/or trans-splicing processes. Then we looked for the gene in nuclear genome of two model plants, Arabidopsis thaliana and Oryza sativa. CONCLUSIONS: The analysis we conducted in plant mitochondria provided the negative, though we argue relevant, result that IP6K does not actually occur in vegetable mtDNA. Very interestingly, the tag search in nuclear genomes lead us to identify a promising sequence in chromosome 5 of Oryza sativa. Further analyses are in course to confirm that this sequence actually corresponds to IP6K mammalian gene.

A human derived SSADH coding variant is replacing the ancestral allele shared with primates.

BACKGROUND: A growing number of reports describe markers with high frequencies of the ancestral alleles in Africa, contrasting with high frequencies and possibly fixation of derived variants out of Africa. Such a pattern can be explained by either neutral or non-neutral processes. AIM: The study examined worldwide frequencies of two non-synonymous variants in NAD(+)-dependent succinic semialdehyde dehydrogenase (SSADH), in a search for possible signatures of natural selection favouring the derived alleles. SUBJECTS AND METHODS: The typing of 1574 subjects were compiled, representing 60 populations from all continents. SSADH haplotype frequencies were correlated across 52 populations to those of 260 single nucleotide polymorphism (SNP) markers deposited in the CEPH database and of markers reported to be under positive Darwinian selection. RESULTS: In the world population, the c.538C variant is proceeding to replace the ancestral c.538T, shared with primates. The overall population differentiation is within the normal range. A significant correlation was also found between the frequencies of the derived alleles in SSADH and Microcephalin (MCPH1), which showed concerted changes worldwide and, at least in Asian populations, also on a restricted geographical scale. CONCLUSION: The analysis of robust correlations based on a large panel of populations is potentially able to identify clusters of genomic regions or genes showing co-evolution of the frequencies of derived alleles.