Sequence and expression analysis of the thioredoxin protein gene family in rice

Thioredoxin (Trx) proteins play important biological functions in cells by changing redox via thioldisulfied exchange. This system is especially widespread in plants. Through database search, we identified 30 potential Trx protein-encoding genes (OsTrx) in rice (Oryza sativa L.). An analysis of the complete set of OsTrx proteins is presented here, including chromosomal location, conserved motifs, domain duplication, and phylogenetic relationships. Our findings suggest that the expansion of the Trx gene family in rice, in large part, occurred due to gene duplication. A comprehensive expression profile of Trx genes family was investigated by analyzing the signal data of this family extracted from the whole genome microarray analysis of Minghui 63 and Zhenshan 97, two indica parents, and their hybrid Shanyou 63, using 27 different tissues representing the entire life cycle of rice. Results revealed specific expression of some members at germination transition as well as the 3-leaf stage during the vegetative growth phase of rice. OsTrx genes were also found to be differentially up- or down-regulated in rice seedlings subjected to treatments of phytohormones and light/dark conditions. The expression levels of the OsTrx genes in the different tissues and under different treatments were also checked by RT-PCR analysis. The identification of OsTrx genes showing differential expression in specific tissues among different genotypes or in response to different environmental cues could provide a new avenue for functional analyses in rice.     

Genomewide comparative phylogenetic and molecular evolutionary analysis of tubby-like protein family in Arabidopsis, rice, and poplar

Tubby-like proteins, which are characterized by a highly conserved tubby domain, play an important role in the maintenance and function of neuronal cells during postdifferentiation and development in mammals. In additional to the tubby domain, most tubby-like proteins in plants also possess an F-box domain. Plants also appear to harbor a large number of TLP genes. To gain insight into how TLP genes evolved in plants, we conducted a comparative phylogenetic and molecular evolutionary analysis of the tubby-like protein gene family in Arabidopsis, rice, and poplar. Genomewide screening identified 11 TLP genes in Arabidopsis, 14 in rice, and 11 in poplar. Phylogenetic trees, domain organizations, and intron/exon structures classified this family into three subfamilies and indicated that species-specific expansion contributed to the evolution of this family in plants. We determined that in rice and poplar, the tubby-like protein family had expanded mainly through segmental duplication events. Tissue-specific expression analysis indicated that functional diversification of the duplicated TLP genes was a major feature of long-term evolution. Our results also demonstrated that the tubby and F-box domains had co-evolved during the evolution of proteins containing both domains.     

Genome-wide identification and characterisation of F-box family in maize

F-box-containing proteins, as the key components of the protein degradation machinery, are widely distributed in higher plants and are considered as one of the largest known families of regulatory proteins. The F-box protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, systematic analysis of the F-box family in maize (Zea mays) has not been reported yet. In this paper, we identified and characterised the maize F-box genes in a genome-wide scale, including phylogenetic analysis, chromosome distribution, gene structure, promoter analysis and gene expression profiles. A total of 359 F-box genes were identified and divided into 15 subgroups by phylogenetic analysis. The F-box domain was relatively conserved, whereas additional motifs outside the F-box domain may indicate the functional diversification of maize F-box genes. These genes were unevenly distributed in ten maize chromosomes, suggesting that they expanded in the maize genome because of tandem and segmental duplication events. The expression profiles suggested that the maize F-box genes had temporal and spatial expression patterns. Putative cis-acting regulatory DNA elements involved in abiotic stresses were observed in maize F-box gene promoters. The gene expression profiles under abiotic stresses also suggested that some genes participated in stress responsive pathways. Furthermore, ten genes were chosen for quantitative real-time PCR analysis under drought stress and the results were consistent with the microarray data. This study has produced a comparative genomics analysis of the maize ZmFBX gene family that can be used in further studies to uncover their roles in maize growth and development.     

Genome-Wide Identification of the F-box Gene Family and Expression Analysis under Drought and Salt Stress in Barley

The F-box protein-encoding gene family plays an essential role in plant stress resistance. In present study, 126 non-redundant F-box genes were identified in barley (Hordeum vulgare L., Hv). The corresponding proteins contained 165– 887 amino acid residues and all were amphiphilic, except 5 proteins. Phylogenetic analysis of F-box protein sequences in barley and stress-related F-box protein sequences in wheat and Arabidopsis thaliana (At) was used to classify barley F-box genes are divided into 9 subfamilies (A–I). A structure-based sequence alignment demonstrated that F-box proteins were highly conserved with a total of 10 conserved motifs. In total, 124 F-box genes were unevenly distributed on 7 chromosomes; another 2 genes have not been anchored yet. The gene structure analysis revealed high variability in the number of exons and introns in F-box genes. Comprehensive analysis of expression profiles and phylogenetic tree analysis, a total of 12 F-box genes that may be related to stress tolerance in barley were screened. Of the 12 detected F-box genes, 8 and 10 were upregulated after drought and salt stress treatments, respectively, using quantitative real-time polymerase chain reaction (qRT-PCR). This study is the first systematic analysis conducted on the F-box gene family in barley, which is of great importance for clarifying this family’s bioinformatic characteristics and elucidating its function in barley stress resistance. These results will serve as a theoretical reference for subsequent research on molecular regulation mechanisms, genetic breeding, and improvement.     

cDNA cloning and expression analysis of a novel human F-box domain containing gene†

F-box proteins are a large family of eukaryotic proteins that are characterized by an approximately 40 amino acid motif. Some F-box proteins are critical for the controlled degradation of cellular regulatory proteins. Here we report that a novel member of F-box proteins, FBXO35 gene, was cloned and identified during the large-scale sequencing analysis from a human fetal brain cDNA library. FBXO35 gene shares amino acid similarity with several putative mouse genes not only in F-box domain but also in the rest of the sequence, which indicates that FBXO35 might also contain some other unknown conserved domain. RT-PCR analysis indicated that FBXO35 gene had a ubiquitously low expression pattern in most human adult tissues. According to bioinformatics analysis, the FBXO35 gene was found located in chromosome 3p21.     

Analyses of phylogeny, evolution, conserved sequences and genome-wide expression of the ICK/KRP family of plant CDK inhibitors

Background and Aims

The cell cycle is controlled by cyclin-dependent kinases (CDKs), and CDK inhibitors are major regulators of their activities. The ICK/KRP family of CDK inhibitors has been reported in several plants, with seven members in arabidopsis; however, the phylogenetic relationship among members in different species is unknown. Also, there is a need to understand how these genes and proteins are regulated. Furthermore, little information is available on the functional differences among ICK/KRP family members.

Methods

We searched publicly available databases and identified over 120 unique ICK/KRP protein sequences from more than 60 plant species. Phylogenetic analysis was performed using 101 full-length sequences from 40 species and intron–exon organization of ICK/KRP genes in model species. Conserved sequences and motifs were analysed using ICK/KRP protein sequences from arabidopsis (Arabidopsis thaliana), rice (Orysa sativa) and poplar (Populus trichocarpa). In addition, gene expression was examined using microarray data from arabidopsis, rice and poplar, and further analysed by RT-PCR for arabidopsis.

Key Results and Conclusions

Phylogenetic analysis showed that plant ICK/KRP proteins can be grouped into three major classes. Whereas the C-class contains sequences from dicotyledons, monocotyledons and gymnosperms, the A- and B-classes contain only sequences from dicotyledons or monocotyledons, respectively, suggesting that the A- and B-classes might have evolved from the C-class. This classification is also supported by exon–intron organization. Genes in the A- and B- classes have four exons, whereas genes in the C-class have only three exons. Analysis of sequences from arabidopsis, rice and poplar identified conserved sequence motifs, some of which had not been described previously, and putative functional sites. The presence of conserved motifs in different family members is consistent with the classification. In addition, gene expression analysis showed preferential expression of ICK/KRP genes in certain tissues. A model has been proposed for the evolution of this gene family in plants.     

水稻Trihelix转录因子家族全基因组分析及功能预测

Trihelix转录因子家族在植物生长发育以及响应逆境胁迫等方面发挥着重要作用,但目前基于水稻全基因组水平鉴定和分析该基因家族的研究尚未见相关报道。本文利用生物信息学方法在水稻基因组数据库中鉴定到Trihelix家族成员31个,序列聚类和功能结构域分析发现该家族均含有高度保守的、特征性的Trihelix结构域;根据亲缘关系远近和结构域特点,将其分为5个亚家族(Ⅰ~Ⅴ)。通过与拟南芥、二穗短炳草和高粱中Trihelix家族的聚类分析发现,这4个物种中Trihelix家族的分类相一致,但每个物种均含有不同亚家族的成员,表明该基因家族的分化早于物种的分化。基于MEME程序分析水稻Trihelix转录因子家族的保守基序与聚类分析结果具有较高的一致性。染色体区段复制分析表明,部分Trihelix家族成员在水稻以及水稻与其他物种之间存在种内和种间的染色体区段复制;生物芯片数据分析发现,Trihelix基因家族在水稻不同组织中、以及对6种不同植物激素的响应呈现多样化的表达谱。采用RiceFREND在线数据库分析发现,水稻Trihelix转录因子家族的20个成员与其他蛋白存在互作关系。本研究结果初步明确了水稻Trihelix转录因子家族的进化特点、染色体分布、染色体区段复制关系、组织表达、激素应答,以及该家族蛋白与其他蛋白质的互作情况,为进一步揭示Trihelix转录因子家族的分子进化规律和生物学功能奠定了基础。     

KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis>)

KT/HAK/KUP potassium transporter protein-encoding genes constitute a large family in the plant kingdom. The KT/HAK/KUP family is important for various physiological processes of plant life. In this study, we identified 27 potential KT/HAK/KUP family genes in rice (Oryza sativa) by database searching. Analysis of these KT/HAK/KUP family members identified three conserved motifs with unknown functions, and 11-15 trans-membrane segments, most of which are conserved. A total of 144 putative cis-elements were found in the 2 kb upstream region of these genes, of which a Ca2+-responsive cis-element, two light-responsive cis-elements, and a circadian-regulated cis-element were identified in the majority of the members, suggesting regulation of these genes by these signals. A comprehensive expression analysis of these genes was performed using data from microarrays hybridized with RNA samples of 27 tissues covering the entire life cycle from three rice genotypes, Minghui 63, Zhenshan 97, and Shanyou 63. We identified preferential expression of two OsHAK genes in stamen at 1 day before flowering compared with all the other tissues. OsHAK genes were also found to be differentially upregulated or downregulated in rice seedlings subjected to treatments with three hormones. These results would be very useful for elucidating the roles of these genes in growth, development, and stress response of the rice plant.     

水稻SBP基因家族的生物信息学分析(英文)

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SBP)转录因子家族是植物特有的一类转录因子。本文确定了20水稻基因组上编码的SBP基因。通过分类,染色体定位,保守区确定,亲缘关系,以及水稻SBP家族中的重复基因及该家族成员形成蛋白二聚体的可能性进行分析,其次利用了Affymetrix水稻基因组芯片数据,对所有这些基因的表达谱进行了分析。结果表明,水稻SBP基因在花和种子的发育过程中可能发挥重要作用,而其对环境胁迫却不敏感。这对进一步研究SBP的功能提供了有价值的线索和思路。     

拟南芥、水稻和杨树JMJC家族全基因组分析

采用HMMER与BLAST相结合的方法确定拟南芥,水稻和杨树三种模式植物全基因组JMJC蛋白基因个数分别为21,20,24,并对其染色体定位,基因结构,保守功能域进行了系统分析,在系统进化分析基础上,将JMJC家族分为11个亚家族,内含子外显子结构分析与MPSS表达模式分析结果也进一步支持了进化关系研究.本研究有助于揭示植物JMJC基因家族的进化历史,为后续JMJ基因家族的功能提供线索,为进一步研究植物JMJC基因家族提供理论基础。     

拟南芥和水稻SET结构域基因家族全基因组鉴定、分类和表达

ET(Su(var), Enhancer of zeste (E(z)), and Trithorax)结构域基因家族是一组含有保守SET结构域的蛋白的统称, 它们参与蛋白甲基化, 影响染色体结构, 并且调控基因表达, 在植物发育中起着重要的作用。分析拟南芥和水稻中SET结构域基因家族进化关系, 对研究这一基因家族中各成员的功能有着重要的意义。我们系统地鉴定了47个拟南芥(Arabidopsis thaliana)和43个水稻(Orysa sativa japonica cultivar Nipponbare)的SET结构域基因, 染色体定位和基因复制分析表明SET结构域基因扩增是由片段复制和反转录引起的, 根据这些结构域差异和系统发育分析把拟南芥和水稻的SET结构域基因划分成5个亚家族。通过分析SET结构域基因家族在拟南芥和水稻各个发育阶段的表达谱, 发现SET结构域基因绝大部分至少在一个组织中表达; 大部分在花和花粉中高表达; 一些SET结构域基因在某些组织中有特异的表达模式, 表明与组织发育有密切的关系。在拟南芥和水稻中分别找到了4个差异表达基因。拟南芥4个差异基因都在花粉管高表达, 水稻4个差异基因有3个在雄性花蕊中高表达, 另一个在幼穗中高表达。