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Qingzhong Xue

Publications and source records attributed to Qingzhong Xue.

11 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↗
PubMed2005

Tri-nucleotide repeats and their association with genes in rice genome.

Tri-nucleotide repeats (TNRs) are extremely abundant in rice genome, of which CCG/CGG repeats have an advantage over other repeats, with approximate half of all the TNRs in the genome. Our results show that rice genome has relatively abundant TNRs with high GC content, and containing only purines or pyrimidines under the same GC content. The AAT/ATT repeats that occur predominantly in intergenic and intronic regions have a considerably higher average length than that of other repeats. The highest frequency of TNRs occurs in 5'-UTR regions, followed by in coding and 5'-flanking regions. Purines-rich TNRs prefer to the coding regions, but pyrimidines-rich TNRs exhibit a stronger bias to upstream regions, suggesting that they might be considered as the regulatory elements in gene expression. As if TNRs located predominantly near the start of coding regions do not significantly influence on the protein function.

5' Untranslated Regions↗
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

The serine carboxypeptidase like gene family of rice (Oryza sativa L. ssp. japonica).

Serine carboxypeptidases (SCPs) comprise a large family of protein hydrolyzing enzymes and have roles ranging from protein turnover and C-terminal processing to wound responses and xenobiotic metabolism. The proteins can be classified into three groups, namely carboxypeptidase I, II and III, based on their coding protein sequences and the fact that each family is characterized by a central catalytic domain of unique topology designated as the "alpha/beta hydrolase fold". The available SCP protein sequences have been utilized as datasets to build a HMM (hidden Markov model) profile, which is used to search the rice (Oryza sativa L. ssp. japonica) proteome. A total of 71 SCP and serine carboxypeptidase-like (SCPL) protein-coding genes exist in rice. The intron-exon structure, chromosome localization, expression and characteristics of encoded protein sequences of the 71 putative genes are reviewed.

Amino Acid Sequence↗
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↗
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↗
PubMed2003

[Response of indica rice in two genic male-sterile lines to temperature and photoperiod].

Investigations on the fertility conversion of two photoperiod- and temperature sensitive genic male-sterile lines Zheda 247S and Peiai 64s under natural conditions in Hangzhou showed that there was a little impact of photoperiod on their fertility expression, while temperature was the main factor. Among daily mean temperature, daily maximum temperature and daily minimum temperature, the last one had the most significant correlation with the fertility. The temperature sensitive stage of Zheda 247S and Peiai 64S was 318 and 621 days before heading, the critical temperature of their fertility conversion was 25.28 and 25.66 degrees C, and the critical date was September 19th and September 25th, respectively. Compared to Peiai 64S, Zheda 247S had a more evident fertility conversion, its sterility was more complete and its self-setting percentage was higher at fertile stage, and the duration of the fertile stage was longer. Zheda 247S could be reproduced in Hangzhou.

Oryza↗
PubMed2002

[cDNA cloning and sequence analysis of genome segment S7 of rice black-streaked dwarf virus].

Genome segments 7 of zhejiang and Hebei isolates of rice black-streaked dwarf virus (RBSDV) were amplified and sequenced. Segment 7 of Zhejiang isolate was consisted of 2193 nts (EMBL accession no. AJ297427) in length and that of Hebei isolate was 2190 nts (AJ297428). Both segments contained two non-overlapping open reading frames (ORFs), which encoded two polypeptides with molecular weights of 41 kD and 36 kD. These two segments shared 99% nucleotide identity, 100% and 94.4% amino acid identities of ORF1 and ORF2, shared 93.5% and 93.8% identities at nucleotide level, 98.1% (ORF1) and 96.5%/97.8% (ORF2) at amino acid level with S7 of Japanese RBSDV, and shared 85.1% and 85.3% identities at nucleotide level, 92.3% (ORF1), 85.5%/86.8% (ORF2) at amino acid level with S6 of Italian MRDV.

Amino Acid Sequence↗