RESUMEN
Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence.
Asunto(s)
Antígenos de Plantas/genética , Productos Agrícolas/genética , ADN Bacteriano/genética , Proteínas de Plantas/genética , Homología de Secuencia de Aminoácido , Secuencia de Aminoácidos , Biología Computacional , Bases de Datos de Proteínas , Datos de Secuencia Molecular , Plantas Modificadas Genéticamente , Alineación de SecuenciaRESUMEN
We report the results of sequence analysis and chromosomal distribution of all distinguishable long terminal repeat (LTR) retrotransposons (Cer elements) in the Caenorhabditis elegans genome. Included in this analysis are all readily recognizable full-length and fragmented elements, as well as solo LTRs. Our results indicate that there are 19 families of Cer elements, some of which display significant subfamily structure. Cer elements can be clustered based on their tRNA primer binding sites (PBSs). These clusters are in concordance with our reverse transcriptase- and LTR-based phylogenies. Although we find that most Cer elements are located in the gene depauperate chromosome ends, some elements are located in or near putative genes and may contribute to gene structure and function. The results of RT-PCR analyses are consistent with this prediction.
Asunto(s)
Caenorhabditis elegans/genética , Evolución Molecular , Genoma , Retroelementos/genética , Animales , Cromosomas/genética , Genes de Helminto/genética , Familia de Multigenes/genética , ARN/genética , Procesamiento Postranscripcional del ARN/genética , ARN Mensajero/genética , ARN de Transferencia/genética , Retroelementos/fisiología , Secuencias Repetidas Terminales/genética , Secuencias Repetidas Terminales/fisiología , Transcripción GenéticaRESUMEN
Most species of the genus Salsola (Chenopodiaceae) that have been examined exhibit C(4) photosynthesis in leaves. Four Salsola species from Central Asia were investigated in this study to determine the structural and functional relationships in photosynthesis of cotyledons compared to leaves, using anatomical (Kranz versus non-Kranz anatomy, chloroplast ultrastructure) and biochemical (activities of photosynthetic enzymes of the C(3) and C(4) pathways, (14)C labeling of primary photosynthesis products and (13)C/(12)C carbon isotope fractionation) criteria. The species included S. paulsenii from section Salsola, S. richteri from section Coccosalsola, S. laricina from section Caroxylon, and S. gemmascens from section Malpigipila. The results show that all four species have a C(4) type of photosynthesis in leaves with a Salsoloid type Kranz anatomy, whereas both C(3) and C(4) types of photosynthesis were found in cotyledons. S. paulsenii and S. richteri have NADP- (NADP-ME) C(4) type biochemistry with Salsoloid Kranz anatomy in both leaves and cotyledons. In S. laricina, both cotyledons and leaves have NAD-malic enzyme (NAD-ME) C(4) type photosynthesis; however, while the leaves have Salsoloid type Kranz anatomy, cotyledons have Atriplicoid type Kranz anatomy. In S. gemmascens, cotyledons exhibit C(3) type photosynthesis, while leaves perform NAD-ME type photosynthesis. Since the four species studied belong to different Salsola sections, this suggests that differences in photosynthetic types of leaves and cotyledons may be used as a basis or studies of the origin and evolution of C(4) photosynthesis in the family Chenopodiaceae.