共查询到20条相似文献,搜索用时 15 毫秒
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Background
In plant organelles, specific messenger RNAs (mRNAs) are subjected to conversion editing, a process that often converts the first or second nucleotide of a codon and hence the encoded amino acid. No systematic patterns in converted sites were found on mRNAs, and the converted sites rarely encoded residues located at the active sites of proteins. The role and origin of RNA editing in plant organelles remain to be elucidated.Results
Here we study the relationship between amino acid residues encoded by edited codons and the structural characteristics of these residues within proteins, e.g., in protein-protein interfaces, elements of secondary structure, or protein structural cores. We find that the residues encoded by edited codons are significantly biased toward involvement in helices and protein structural cores. RNA editing can convert codons for hydrophilic to hydrophobic amino acids. Hence, only the edited form of an mRNA can be translated into a polypeptide with helix-preferring and core-forming residues at the appropriate positions, which is often required for a protein to form a functional three-dimensional (3D) structure.Conclusion
We have performed a novel analysis of the location of residues affected by RNA editing in proteins in plant organelles. This study documents that RNA editing sites are often found in positions important for 3D structure formation. Without RNA editing, protein folding will not occur properly, thus affecting gene expression. We suggest that RNA editing may have conferring evolutionary advantage by acting as a mechanism to reduce susceptibility to DNA damage by allowing the increase in GC content in DNA while maintaining RNA codons essential to encode residues required for protein folding and activity. 相似文献8.
OsPPR6, a pentatricopeptide repeat protein involved in editing and splicing chloroplast RNA,is required for chloroplast biogenesis in rice 总被引:3,自引:0,他引:3
Jianpeng Tang Wenwei Zhang Kai Wen Gaoming Chen Juan Sun Yunlu Tian Weijie Tang Jun Yu Hongzhou An Tingting Wu Fei Kong William Terzaghi Chunming Wang Jianmin Wan 《Plant molecular biology》2017,95(4-5):345-357
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Alicja A. Babst-Kostecka Christian Parisod Cécile Godé Pierre Vollenweider Maxime Pauwels 《Plant and Soil》2014,383(1-2):245-256
Background and aims
Pseudometallophytes are model organisms for adaptation and population differentiation because they persist in contrasting edaphic conditions of metalliferous and non-metalliferous habitats. We examine patterns of genetic divergence and local adaptation of Biscutella laevigata to assess historical and evolutionary processes shaping its genetic structure.Methods
We sampled all known populations of B. laevigata in Poland and analyzed respective soil metal concentrations. For genotyping we used nine nuclear microsatellite loci. Population genetic pools were identified (Bayesian clustering) and we estimated genetic parameters and demographic divergence between metallicolous and non-metallicolous populations (ABC-approach).Results
Populations clustered into two groups which corresponded to their edaphic origin and diverged 1,200 generations ago. We detected a significant decrease in genetic diversity and evidence for a recent bottleneck in metallicolous populations. Genetic structure was unrelated to site distribution but is rather influenced by environmental conditions (i.e. soil metal concentration).Conclusions
The intriguing disjunctive distribution of B. laevigata in Poland results from a fragmentation of the species range during the Holocene, rather than recent long-distance-dispersal events. The genetic structure of populations, however, continues to be modified by microevolutionary processes at anthropogenic sites. These clear divergence patterns promote B. laevigata as a model species for plant adaptation to polluted environments. 相似文献10.
Stapleton M Carlson J Brokstein P Yu C Champe M George R Guarin H Kronmiller B Pacleb J Park S Wan K Rubin GM Celniker SE 《Genome biology》2002,3(12):research0080.1-808
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Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans 总被引:1,自引:0,他引:1
Background
Genome variability can have a profound influence on the virulence of pathogenic microbes. The availability of genome sequences for two strains of the AIDS-associated fungal pathogen Cryptococcus neoformans presented an opportunity to use comparative genome hybridization (CGH) to examine genome variability between strains of different mating type, molecular subtype, and ploidy.Results
Initially, CGH was used to compare the approximately 100 kilobase MAT a and MATα mating-type regions in serotype A and D strains to establish the relationship between the Log2 ratios of hybridization signals and sequence identity. Subsequently, we compared the genomes of the environmental isolate NIH433 (MAT a) and the clinical isolate NIH12 (MATα) with a tiling array of the genome of the laboratory strain JEC21 derived from these strains. In this case, CGH identified putative recombination sites and the origins of specific segments of the JEC21 genome. Similarly, CGH analysis revealed marked variability in the genomes of strains representing the VNI, VNII, and VNB molecular subtypes of the A serotype, including disomy for chromosome 13 in two strains. Additionally, CGH identified differences in chromosome content between three strains with the hybrid AD serotype and revealed that chromosome 1 from the serotype A genome is preferentially retained in all three strains.Conclusion
The genomes of serotypes A, D, and AD strains exhibit extensive variation that spans the range from small differences (such as regions of divergence, deletion, or amplification) to the unexpected disomy for chromosome 13 in haploid strains and preferential retention of specific chromosomes in naturally occurring diploids. 相似文献13.
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Hector Sanchez-Villeda Steven Schroeder Sherry Flint-Garcia Katherine E Guill Masanori Yamasaki Michael D McMullen 《BMC bioinformatics》2008,9(1):154
Background
With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor.Results
We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected.Conclusion
We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism.16.
Yoon Joo Young Yeom Jeonghun Lee Heebum Kim Kyutae Na Seungjin Park Kunsoo Paek Eunok Lee Cheolju 《BMC bioinformatics》2011,12(1):1-12
Background
Continuing research into the global multiple sequence alignment problem has resulted in more sophisticated and principled alignment methods. Unfortunately these new algorithms often require large amounts of time and memory to run, making it nearly impossible to run these algorithms on large datasets. As a solution, we present two general methods, Crumble and Prune, for breaking a phylogenetic alignment problem into smaller, more tractable sub-problems. We call Crumble and Prune meta-alignment methods because they use existing alignment algorithms and can be used with many current alignment programs. Crumble breaks long alignment problems into shorter sub-problems. Prune divides the phylogenetic tree into a collection of smaller trees to reduce the number of sequences in each alignment problem. These methods are orthogonal: they can be applied together to provide better scaling in terms of sequence length and in sequence depth. Both methods partition the problem such that many of the sub-problems can be solved independently. The results are then combined to form a solution to the full alignment problem.Results
Crumble and Prune each provide a significant performance improvement with little loss of accuracy. In some cases, a gain in accuracy was observed. Crumble and Prune were tested on real and simulated data. Furthermore, we have implemented a system called Job-tree that allows hierarchical sub-problems to be solved in parallel on a compute cluster, significantly shortening the run-time.Conclusions
These methods enabled us to solve gigabase alignment problems. These methods could enable a new generation of biologically realistic alignment algorithms to be applied to real world, large scale alignment problems. 相似文献17.
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Mats Ensterö Örjan Åkerborg Daniel Lundin Bei Wang Terrence S Furey Marie Öhman Jens Lagergren 《BMC bioinformatics》2010,11(1):6
Background
Several bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of genes that are hyper-edited in their non-coding intronic regions, especially in alu retrotransposable elements, but very few substrates that are site-selectively edited in coding regions. Known RNA edited substrates suggest, however, that site selective A-to-I editing is particularly important for normal brain development in mammals. 相似文献19.
Weiliang Shi Grace Wahba Rafael A Irizarry Hector Corrada Bravo Stephen J Wright 《BMC bioinformatics》2012,13(1):1-10
Background
The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research. We present a novel method called MergeAlign which constructs consensus MSAs from multiple independent MSAs and assigns an alignment precision score to each column.Results
Using conventional benchmark tests we demonstrate that on average MergeAlign MSAs are more accurate than MSAs generated using any single matrix of sequence substitution. We show that MergeAlign column scores are related to alignment precision and hence provide an ab initio method of estimating alignment precision in the absence of curated reference MSAs. Using two novel and independent alignment performance tests that utilise a large set of orthologous gene families we demonstrate that increasing MSA performance leads to an increase in the performance of downstream phylogenetic analyses.Conclusion
Using multiple tests of alignment performance we demonstrate that this novel method has broad general application in biological research. 相似文献20.
Okechukwu S Ogah Gail D Adegbite Rufus O Akinyemi Julius O Adesina Albert A Alabi Oscar I Udofia Roseline F Ogundipe Julius KL Osinfade 《BMC research notes》2008,1(1):1-10