RESUMO
To gain insight into the biogenesis of photosystem II (PSII) and to identify auxiliary factors required for this process, we characterized the mutant hcf173 of Arabidopsis thaliana. The mutant shows a high chlorophyll fluorescence phenotype (hcf) and is severely affected in the accumulation of PSII subunits. In vivo labeling experiments revealed a drastically decreased synthesis of the reaction center protein D1. Polysome association experiments suggest that this is primarily caused by reduced translation initiation of the corresponding psbA mRNA. Comparison of mRNA steady state levels indicated that the psbA mRNA is significantly reduced in hcf173. Furthermore, the determination of the psbA mRNA half-life revealed an impaired RNA stability. The HCF173 gene was identified by map-based cloning, and its identity was confirmed by complementation of the hcf phenotype. HCF173 encodes a protein with weak similarities to the superfamily of the short-chain dehydrogenases/reductases. The protein HCF173 is localized in the chloroplast, where it is mainly associated with the membrane system and is part of a higher molecular weight complex. Affinity chromatography of an HCF173 fusion protein uncovered the psbA mRNA as a component of this complex.
Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/fisiologia , Núcleo Celular/fisiologia , Fatores de Iniciação em Eucariotos/metabolismo , Biossíntese de Proteínas , RNA Mensageiro/genética , RNA de Plantas/genética , Sequência de Aminoácidos , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Proteínas de Arabidopsis/isolamento & purificação , Proteínas de Arabidopsis/metabolismo , Sequência de Bases , Cromatografia de Afinidade , Sequência Conservada , DNA Complementar/genética , DNA de Plantas/genética , Dactinomicina/farmacologia , Fatores de Iniciação em Eucariotos/genética , Immunoblotting , Dados de Sequência Molecular , Mutagênese , Complexo de Proteína do Fotossistema II/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Transcrição Gênica/efeitos dos fármacosRESUMO
We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests. We build upon the tree alignment algorithm for ordered trees given by Jiang et. al (1995) and extend it to calculate local forest alignments, which is essential for finding local similar regions in RNA secondary structures. The time complexity of our algorithm is O(|F(1)| |F(2) deg(F(1)) deg(F(2)) (deg(F(1)) + deg(F(2))) where |F(i)| is the number of nodes in forest F(i) and deg (F(i)) is the degree of F(i). We provide carefully engineered dynamic programming implementations using dense, two-dimensional tables which considerably reduces the space requirement. We suggest a new representation of RNA secondary structures as forests that allow reasonable scoring of edit operations on RNA secondary structures. The comparison of RNA secondary structures is facilitated by a new visualization technique for RNA secondary structure alignments. Finally, we show how potential regulatory motifs can be discovered solely by their structural preservation, and independent of their sequence conservation and position.
