TITLE

IP6K gene identification in plant genomes by tag searching

AUTHOR(S)
Fassetti, Fabio; Leone, Ofelia; Palopoli, Luigi; Rombo, Simona E.; Saiardi, Adolfo
PUB. DATE
January 2011
SOURCE
BMC Proceedings;2011 Supplement 2, Vol. 5 Issue Suppl 2, p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
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.
ACCESSION #
60440531

 

Related Articles

  • Comparative mapping of DNA sequences in rye ( Secale cereale L.) in relation to the rice genome. Hackauf, B.; Rudd, S.; Voort, J.; Miedaner, T.; Wehling, P. // Theoretical & Applied Genetics;Jan2009, Vol. 118 Issue 2, p371 

    The rice genome has proven a valuable resource for comparative approaches to address individual genomic regions in Triticeae species at the molecular level. To exploit this resource for rye genetics and breeding, an inventory was made of EST-derived markers with known genomic positions in rye,...

  • Rice genome: A recipe for revolution? Cyranoski, David // Nature;4/24/2003, Vol. 422 Issue 6934, p796 

    Focuses on genome sequencing of agriculturally important species of rice. Identification of each rice gene and assigning of functions to them; Significance of DNA microarrays in gene functioning; Use of microarrays to screen for alleles.

  • A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks. Zhen Gao; Ruizhe Zhao; Jianhua Ruan // BMC Genomics;2013, Vol. 14 Issue Suppl 1, p1 

    Background: Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple method for cis-regulatory network discovery which aims to avoid some of the common problems of previous approaches. Results: Using promoter sequences and gene expression...

  • Opinion: The Human Genome Diversity Project: past, present and future. Cavalli-Sforza, L. Luca // Nature Reviews Genetics;Apr2005, Vol. 6 Issue 4, p333 

    The Human Genome Project, in accomplishing its goal of sequencing one human genome, heralded a new era of research, a component of which is the systematic study of human genetic variation. Despite delays, the Human Genome Diversity Project has started to make progress in understanding the...

  • A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528. Studholme, David J.; Ibanez, Selena Gimenez; MacLean, Daniel; Dangl, Jeffery L.; Chang, Jeff H.; Rathjen, John P. // BMC Genomics;2009, Vol. 10, p395 

    Background: Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector'...

  • Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Temnykh, S.; Park, William D.; Ayres, Nicola; Cartinhour, Sam; Hauck, N.; Lipovich, L.; Cho, Y. G.; Ishii, T.; McCouch, S. R. // Theoretical & Applied Genetics;Mar2000, Vol. 100 Issue 5, p697 

    In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence repeats (SSRs) were extracted from several...

  • Detecting disease rare alleles using single SNPs in families and haplotyping in unrelated subjects from the Genetic Analysis Workshop 17 data. Kraja, Aldi T.; Czajkowski, Jacek; Feitosa, Mary F.; Borecki, Ingrid B.; Province, Michael A. // BMC Proceedings;2011 Supplement 9, Vol. 5 Issue Suppl 9, p1 

    We present an evaluation of discovery power for two association tests that work well with common alleles but are applied to the Genetic Analysis Workshop 17 simulations with rare causative single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] < 1%). The methods used were...

  • Detection of identity by descent using next-generation whole genome sequencing data.  // BMC Bioinformatics;2012, Vol. 13 Issue 1, p121 

    The article presents a study focusing on Identity by descent (IBD). It states that IBD has played an important role in the discovery of genetic loci underlying human diseases. It further discusses the DNA sequencing which enables the comprehensive analysis of genomes. It also mentions that IBD...

  • Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals. Reneker, Jeff; Chi-Ren Shyu // BMC Bioinformatics;2005, Vol. 6, p111 

    Background: Searching for small tandem/disperse repetitive DNA sequences streamlines many biomedical research processes. For instance, whole genomic array analysis in yeast has revealed 22 PHO-regulated genes. The promoter regions of all but one of them contain at least one of the two core Pho4p...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics