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Qingpo Liu

Publications and source records attributed to Qingpo Liu.

10 recordsLinked to original sources
PubMed2007

Molecular phylogeny, evolution, and functional divergence of the LSD1-like gene family: inference from the rice genome.

The identification of LSD1-like genes in parasite, green algae, moss, pine, and monocot and dicot species allowed us to trace the phylogenetic history of this gene family. Computational analysis showed that the diversification of members of this family could be dated back to the early stage of plant evolution. The evolution of plant LSD1-like genes was possibly shaped by two duplication events. These proteins, which contain three copies of the LSD1 zinc finger (zf-LSD1) domain within their entire polypeptides and play crucial roles in modulating disease defense and cell death, resulted from the second duplication. A gain of zf-LSD1 domain model was reasonable for explaining the origination of three-zf-LSD1 domain-containing proteins. The zf-LSD1 domain phylogeny showed that the middle (M) and C-terminal (C) domains originated from a common ancestor; the N-terminal (N) domain might be more ancient than the former two. The divergence of the N, M, and C domains was well before the monocot-dicot split. Coevolution analysis revealed that four intramolecular domain pairs, including the N domain and the interregion between the M and the C domains (INTER2), the M and C domain, the N- and C-terminus, and the M domain and C-terminus, possibly coevolved during the evolution of three-zf-LSD1 domain-containing proteins. The three zf-LSD1 domains are evolutionary conserved. Thus, the differences at the N- and C-terminus would be crucial for functional specificity of LSD1 genes. Strong functional constraints should work on the zf-LSD1 domains, whereas reduced functional constraint was found in the INTER2 region. Functional divergence analysis showed that three-zf-LSD1 domain-containing proteins were significantly functionally divergent from those proteins containing only one zf-LSD1 domain, a result demonstrating that shifted evolutionary rates between the two clusters were significantly different from each other.

Amino Acid Sequence↗
PubMed2006

Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans.

The main factors shaping codon usage bias in the Deinococcus radiodurans genome were reported. Correspondence analysis (COA) was carried out to analyze synonymous codon usage bias. The results showed that the main trend was strongly correlated with gene expression level assessed by the "Codon Adaptation Index" (CAI) values, a result that was confirmed by the distribution of genes along the first axis. The results of correlation analysis, variance analysis and neutrality plot indicated that gene nucleotide composition was clearly contributed to codon bias. CDS length was also key factor in dictating codon usage variation. A general tendency of more biased codon usage of genes with longer CDS length to higher expression level was found. Further, the hydrophobicity of each protein also played a role in shaping codon usage in this organism, which could be confirmed by the significant correlation between the positions of genes placed on the first axis and the hydrophobicity values (r=-0.100, P<0.01). In summary, gene expression level played a crucial role, nucleotide mutational bias, CDS length and the hydrophobicity of each protein just in a minor way in shaping the codon usage pattern of D. radiodurans. Notably, 19 codons firstly defined as "optimal codons" may provide useful clues for molecular genetic engineering and evolutionary studying.

Codon↗
PubMed2005

Computational identification and systematic analysis of the ACR gene family in Oryza sativa.

Based on sequence similarity search and domain detection, nine ACT domain repeat protein-coding genes (the "ACR" genes) in rice were identified, which were mainly distributed on the chromosomes 2, 3, 4, and 8. An InterPro database search indicated that four copies of the ACT domain linearly occupied the entire polypeptide. The first three ACT domains were linked by two different sequences. However, the fourth ACT domain was extremely close to ACT3. Gene structure comparisons showed large differences in exon numbers, from three to eight, among members of the rice ACR gene family. In addition, it appeared that gene duplication might be operative when the compositions of exons and introns were analyzed. Phylogenetic analysis divided the ACR gene family into five distinct groups, and this division was generally according to the expression patterns of the ACR genes. The Arabidopsis and rice ACR proteins were clustered across together, suggesting that these ACR genes might originate from an ancient common ancestor. Notably, the identification of orthologues and paralogues would be useful for rice gene functional annotation.

Chromosome Mapping↗
PubMed2005

Comparative study of rice and Arabidopsis actin-depolymerizing factors gene families.

Actin-depolymerizing factors (ADF) is one of the small actin-binding proteins that regulate actin dynamics in cells. Analysis of the complete rice and Arabidopsis protein sequences revealed 12 ADF proteins, respectively. A further study on the similarities and differences between ADF throughout rice and Arabidopsis genome was carried out at the level of genomic organization and protein structure. The strict conservation of essential structural features suggested that the mode of action and physiological function of these proteins, as well as the expression pattern of their coding genes, might be very similar. The ADF proteins were divided into four groups based on the phylogenetic relationships of the amino acid sequences, and was comparable with previous studies.

Actin Depolymerizing Factors↗
PubMed2005

Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species.

A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm species Oryza sativa, Zea mays, Triticum aestivum and Arabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes in O. sativa, Z. mays, and T. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.

Arabidopsis↗
PubMed2005

Comparative analysis of base biases around the stop codons in six eukaryotes.

Using full-length cDNA sequences, a comparative analysis of sequence patterns around the stop codons in six eukaryotes was performed. Here, it was showed that the codon immediately before and after the stop codons (defined as -1 codon and +1 codon, respectively) were much more biased than other examined positions, especially at the second position of -1 codons and the first position of +1 codons which were rich in As/Us and purines, respectively, for most species. The author speculated that strongly biased sequence pattern from position -2 to +4 might act as an extended translation termination signal. Translation termination was catalyzed by release factors that recognized the stop codons. The multiple amino acid sequence alignment of eukaryotic release factor 1 (eRF1) of 20 species showed that there were 16 residue sites that were strictly conserved, especially the invariant amino acids Ile70 and Lys71. Accordingly, it could be inferred that those candidate amino acids might involve in the recognition process. Moreover, the possible stop signal recognition hypothesis was also discussed herein.

Amino Acid Sequence↗
PubMed2004

Synonymous codon usage and gene function are strongly related in Oryza sativa.

The relationship between codon usage and gene function was investigated while considering a dataset of 2106 nuclear genes of Oryza sativa. The results of standard chi(2) test and F-statistic showed that for every 59 synonymous codons, a strongly significant association with gene functional categories existed in rice, indicating that codon usage was generally coordinated with gene function whether it was at the level of individual amino acids or at the level of nucleotides. However, it could not be directly said that the use of every codons differed significantly between any two functional categories. Notably, there existed large difference both in selection for biased codons or selection intensity among functional categories. Therefore, we identified at least two classes of genes: one group of genes, mainly belonging to the "METABOLISM" category, was tended to use G- and/or C-ending codons while the other was more biased to choose codons ending with A and/or U. The latter group contained genes of various functions, especially those genes classified into the "Nuclear Structure" category. These observations will be more important for molecular genetic engineering and genome functional annotation.

Chromosome Mapping↗
PubMed2004

Computational identification and sequence analysis of stop codon readthrough genes in Oryza sativa.

Using an approach based on the Readthrough Candidate Extraction System (RCES), we extracted 111 candidates from 9620 gene sequences of rice. The results of homology search and sequence analysis demonstrated that these candidates included actual readthrough genes that would be important for further investigating the mechanism of translation termination regulated by readthrough event, and could also give some useful clues for functional genome annotation. Between the candidates and non-candidates of gene sequences in rice, there exist significant base biases at the positions surrounding the stop codons. These positions, especially both -1 and +4, are referred to as part of an extended stop signal. In candidates, G at position -1, and G or C at position +4 are much more favored than that in non-candidates. Both stop sequence patterns, GUAGC and GUGAG, might drive high readthrough efficiency in rice. Secondary structure analysis revealed that the -1 and +1 amino acids around the first stop codon of candidates have a strong bias toward arginine, particularly the +1 position (20.7%), which indicated that the amino acids at the readthrough region being frequently located in the hydrophilic region of beta-turn might be a determinant for efficient translation termination or not.

Base Sequence↗
PubMed2004

Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa.

In this paper, the main factors shaping codon usage in the mitochondrion genome of rice were reported. Correspondence analysis, a commonly used multivariate statistical approach, was carried out to analyze synonymous codon usage bias. The results showed that the main trend was strongly correlated with the gene expression level assessed by the 'Codon Adaptation Index' value, a result that was confirmed by the distribution of genes along the first axis. From the results that there were two significant correlations between axis 1 coordinates and the GC, GC3s content at silent sites of each sequence, and clearly significant correlations between the 'Effective Number of Codons' values and GC, GC3s content, we inferred that codon usage bias was affected by gene nucleotide composition also. In addition, the hydrophobicity of each protein also played some roles in shaping codon usage in this organelle, which could be confirmed by the significant correlation between the positions of genes placed on the first axis and the hydrophobicity value of each protein. In summary, natural selection played a crucial role, nucleotide mutational bias and amino acid composition only in a minor way, in shaping codon usage in the mitochondrion genome of rice. Notably, 21 codons defined firstly as 'optimal codons' might provide some more useful information for gene engineering and/or evolution studying.

Journal Article↗