Research Article
Whole Genome-wide Identification of Homologous Candidate Genes in Legume Related to the Regulation of Circadian clock 
,
Fang Wei1,2, ,
Mengdie Cai1,2 ,
Jie Zhang1,2 ,
Zhenpeng Liu1 ,
Xuanjun Fang1,2,3,4 
2 Cuixi Academy of Biotechnology, Zhuji, 311800,China
3 Hainan Institute of Tropical Agricultural Resources, Sanya, 572025,China
4 College of Life Sciences and Technology, Guangxi University, Nanning, 530005,China
Author Correspondence author
Plant Gene and Trait, 2017, Vol. 8, No. 4 doi: 10.5376/pgt.2017.08.0004
Received: 01 Mar., 2017 Accepted: 21 Mar., 2017 Published: 31 Mar., 2017
Li Z.F., Wei F., Cai M.D., Zhang J., Liu Z.P., and Fang X.J., 2017, Whole Genome-wide Identification of Homologous Candidate Genes in Legume Related to the Regulation of Circadian clock, 8(4): 31-55 (doi: 10.5376/pgt.2017.08.0004)
Background
In most higher plants, the biological clock mechanism involved in almost all of the regulation of plant metabolism, growth and development process, and obviously controlled their many physiological and biochemical reactions (Li et al., 2015; Covington et al., 2008). Plant leaf movement, stomatal closure, hypocotyl extension, especially the florescence which was regulated by photoperiod were controlled by the plant's internal biological clock, which could coordinate a variety of physiological activities, so that the body's growth and development, including a variety of physiological activities could be carried out at the appropriate time (Harmer et al., 2000; Mcclung et al., 2001).
In the past, the research on the biological clock control network was mainly focused on the model plant Arabidopsis thaliana, and the related studies in other plants were relatively rare. Arabidopsis thaliana had been identified a number of biological clock regulation related genes, and been revealed a number of biological clock regulation mechanism of physiological pathways. Most of the biological clock control network related genes encoded transcription factors, and some encoded kinase and phosphatase (Dunlap, 2004; Edery, 2005; Toh, 2001). Most of them were related to the light signal pathway of plants.
In this research, Medicago truncatula and Lotus japonicas were the model plant in legumes, and Glycine max was the important economic crop. These three species had completed the whole genome sequencing which could provide complete genomic data for our analysis. In the model plant, Arabidopsis thaliana, we found the regulation factor of the biological clock of Arabidopsis thaliana by the main gene ontology, and according to the relevant literature to supplement and support. What's more, the obtained regulation factors from Medicago truncatula, Lotus japonicas and Glycine max Linn. Merr were compared and analyzed by bioinformatics on the complete genomic level.
1 Results and Analysis
1.1 Identification of candidate genes of ELF3/ELF4 in legume
ELF3 were not found the relevant conservative functional domains in the CDD, Prosite, Pfam-A class database. However, we could see from the Pfam-B class database and multi series connection, there were four more conservative structure domains in ELF3. And ELF4 had a DUF conservative domain (Figure 1).
|
Figure 1 ELF3/ELF4 protein sequences alignment, conservation domain analysis of protein, molecular evolutionary tree and the distance between four species Note: A: ELF3 protein sequences alignment; B: Conservation domain analysis of ELF4 protein; C: ELF4 protein sequences alignment; D: Molecular evolutionary tree of ELF3/ELF4 proteins; E: The distance of ELF3/ELF4 protein between four species |
.png)
In Medicago truncatula, ELF3 was found no orthologous candidate genes, and ELF4 had one orthologous gene, the similarity was 27.0%. In Lotus japonicas, ELF3 had two orthologous candidate gene segments, and ELF4 had one orthologous gene segment. In Glycine max Linn. Merr, ELF3 had six orthologous candidate gene, the sequence similarity was generally higher than the ELF3 orthologous candidate genes in Medicago truncatula and Lotus japonicas. In addition, ELF3a, ELF3b and ELF3c, the similaritie of these three candidate gene was more than 30%, which had a high quality of PUT support (Table 1).
|
Table 1 The ortholog candidate genes of LF3/ELF4 in three species of Legumes Note: F: the whole candidate gene was covered by PUT sequence, or at both ends were covered by PUT sequence and the 80% of whole gene was covered by PUT sequence; N: the gene could not find a line with the suitable PUT sequence; E: one part or several parts of the gene were covered by the suitable PUT sequence, but had not reached the standard of F |
.png)
1.2 Identification of candidate genes of CCR2 in legume
CCR2 had two orthologous candidate genes in Medicago truncatula, and the similarity of CCR2 at around 70%, and the full length of the MtCCR2a was covered with a PUT sequence. CCR2 also had two orthologous genes in Lotus japonicas, the full length of the two genes was covered with a PUT sequence, and the similarities were 64% and 66.8%, respectively. CCR2 had four direct homologous genes in Glycine max, and the similarity is between 50% and 70%, the full length of the three genes was covered with a PUT sequence (Table 2; Figure 2).
|
Table 2 The ortholog candidate genes of CCR2 in three species of Legume Note: F: The whole candidate genes was covered by PUT sequence, or at both ends were covered by PUT sequence and the 80% of whole gene was covered by PUT sequence; E: one part or several parts of the gene were covered by the suitable PUT sequence, but had not reached the standard of F |
.png)
|
Figure 2 CRR2 amino acid sequences alignment, conservation domain analysis of protein, molecular evolutionary tree and evolutionary distance Note: A: Conservation domain analysis of CRR2 protein; B: CRR2 amino acid sequences alignment; C: Molecular evolutionary tree of CRR2 proteins; D: The evolutionary distance of CRR2 protein between four species |
.png)
1.3 Identification of orthologous candidate genes of CRB in legume
CRB had one orthologous candidate genes in Lotus japonicus, two orthologous candidate genes in Glycine max, these 3 genes were full length expression in their own body, and CRB had high conservation in Arabidaaopsis, Lotus japonicus, and Glycine max, the similarity was above 80% (Table 3; Figure 3).
|
Table 3 The orthologous candidate genes of CRB in three species of legume Note: F: The whole candidate genes were covered by PUT sequence, or at both ends were covered by PUT sequence and the 80% of whole gene was covered by PUT sequence |
.png)
|
Figure 3 Molecular evolutionary tree and evolutionary distance of CRB proteins and the distance of CRB protein between four species Note: A: Molecular evolutionary tree of CRB proteins; B: The evolutionary distance of CRB protein between four species |
.png)
1.4 Identification of orthologous candidate genes of LWD1/LWD2 in legume
LWD2, LWD1 protein had a WD40 conservative domain in the middle near the C-terminal. LWD2 was not found orthologous candidate genes in the three species of the legume species, which may had been lost in the long term evolution of the legume species. The conservation of LWD1 in Arabidopsis thaliana and three species of legume was very high, the similarity of MtLWD1, LjLWD1, GmLWD1a, GmLWD1b and LWD1 was 90.6%, 91.2%, 92.4%, 92.1%, and in addition to MtLWD1, the gene was full length expressed in Lotus japonicus and Glycine max (Table 4; Figure 4).
|
Table 4 The ortholog candidate genes of LWD1/LWD2 in three species of Legume. Note: F: the whole candidate gene was covered by PUT sequence, or both ends were covered by PUT sequence and the 80% of whole gene was covered by PUT sequence; E: one part or several parts of the gene were covered by the suitable PUT sequence, but had not reached the standard of F |
.png)
|
Figure 4 LWD1/LWD2 amino acid sequences alignment, conservation domain analysis of protein, molecular evolutionary tree and the evolutionary distance Note: A: Conservation domain analysis of LWD1/LWD2 protein; B: LWD1/LWD2 amino acid sequences alignment; C: Molecular evolutionary tree of LWD1/LWD2 proteins; D: The evolutionary distance of LWD1/LWD2 between four species |
.png)
1.5 Identification of orthologous candidate genes of FIO1 in legume
FIO1 was not found the orthologous genes in Medicago truncatula, and found one orthologous candidate gene fragment in Lotus japonicas, but the gene fragment did not have the EST expression data in Lotus japonicas, which might be a pseudogene. Based on this, we hypothesized that the FIO1 gene might have degenerated in the long term evolution of the Medicago. However, there were two orthologous candidate genes in Glycine max, which both were full length, one had EST expression, and the other was full length expression. It showed that FIO1 also exercised the normal function in the Glycine max, and from the similarity and EST expression data of view, the possibility of GmFIO1b exercised the function of biological clock was relatively large (Table 5; Figure 5).
|
Table 5 The ortholog candidate genes of LHY in three species of legume Note: F: the whole candidate gene was covered by PUT sequence, or both ends were covered by PUT sequence and the 80% of whole gene was covered by PUT sequence; N: the gene could not find a line with the suitable PUT sequence; E: one part or several parts of the gene were covered by the suitable PUT sequence, but had not reached the standard of F |
.png)
|
Figure 5 Conservation domain analysis and amino acid sequences alignment of FIO1 protein Note: A: Conservation domain analysis of protein; B: Amino acid sequences alignment |
.png)
1.6 Identification of orthologous candidate genes of LUX in legume
LUX had one orthologous gene each in Medicago truncatula and Lotus japonicas, with the EST expression data, the similarity of them was 45.7% and 42.3%. LUX had two direct homologous genes in Glycine max, in which GmLUX2 had the full length PUT sequence support (Table 6).
|
Table 6 The ortholog candidates genes of LUX in three species of legume. Note: F: the whole candidate gene was covered by PUT sequence, or both ends were covered by PUT sequence and the 80% of whole gene was covered by PUT sequence; E: one part or several parts of the gene were covered by the suitable PUT sequence, but had not reached the standard of F |
.png)
From the evolutionary distance of the molecular evolutionary tree (Figure 6), we could get that the period of GmLUX1 and GmLUX2 separation was later.
|
Figure 6 LUX amino acid sequences alignment, conservation domain analysis of protein, molecular evolutionary tree and the evolutionary distance Note: A: LUX amino acid sequences alignment; B: Molecular evolutionary tree of LUX proteins; C: The distance of LUX between four species |
.png)
1.7 Identification of orthologous candidate genes of ZIK4 in Legume
ZIK4 had 3 orthologous candidate genes in Medicago truncatula, and similarity between each of them and ZIK4 was more than 50%, and all had EST expression data. ZIK4 had 2 orthologous candidate gene in Lotus japonicas, and similarity between each of them and ZIK4 was also more than 50%, and also had EST expression data.
ZIK4 had 5 orthologous candidate genes in Glycine max, and the similarity between GmZIK4a and ZIK4 was also more than 60% and had EST expression data while that between GmZIK4c and ZIK4 was below 50%, and the whole gene sequences of GmZIK4c and GmZIK4b were covered by PUT sequence. In the 5 Glycine max orthologs, from the results of molecular evolutionary tree constructed according to ZIK4, all 3 species of legume had their corresponding paralogous genes of ZIK4. They are LjZIK4b, MtZIK4c and GmZIK4e, respectively. Their presence indicated that ZIK4 had differentiated and another homologous gene of ZIK4 had got has been lost in Arabidopsis thaliana before the separation of Leguminosae and Cruciferae (Table 7; Figure 7).
|
Table 7 The orthologous candidate genes of ZIK4 in three species of Legume Note: F: the whole candidate gene was covered by PUT sequence, or both ends were covered by PUT sequence and 80% of the whole gene sequences were covered by PUT sequence; E: a certain part or several parts of the gene were covered by suitable PUT sequence, but had not reached the standard of F |
.png)
|
Figure 7 ZIK4 amino acid sequences alignment, protein conserved domain analysis, molecular evolutionary tree and the evolutionary distance Note: A: Protein conserved domain analysis of ZIK4; B: ZIK4 amino acid sequences alignment; C: Molecular evolutionary tree of ZIK4 protein; D: The evolutionary distance of ZIK4 among four species |
.png)
The evolutionary history of ZIK4 in Cruciferae and Leguminosae may be as follows: Before the separation of Cruciferae and Leguminosae, ZIK4 was replicated into ZIK4A and ZIK4B, and after the separation ZIK4B was lost in Arabidopsis thaliana, while ZIK4A and ZIK4B were preserved in Leguminosae, and before the separation of Medicago and Glycine, ZIK4A was replicated into ZIK4A1 and ZIK4A2, Later on, Medicago and Glycine were separated, and ZIK4A2 was lost in Lotus japonicus, but ZIK4A1 was preserved as LjZIK4a, ZIK4A1 and ZIK4A2 were both preserved in Medicago truncatula as MtZIK4a and MtZIK4b, respectively. In Glycine max, ZIK4A1 and ZIK4A2 were replicated again, ZIK4A1 into GmZIK4b, GmZIK4c and ZIK4A2, into GmZIK4a and GmZIK4d. While after the differentiation of Cruciferae and Leguminosae, ZIK4B was replicated at least once and later some genes got lost. Therefore, only single copies were preserved in 3 species of Leguminosae, namely MtZIK4c, LjZIK4b and GmZIK4e, respectively.
1.8 Identification of orthologous candidate genes of LIP1 in Legume
LIP1 had one orthologous candidate gene in Medicago truncatula. Its similarity with LIP1 was 57.3% and had EST expression data. LIP1 had only one orthologous candidate gene fragment in Lotus japonicas, also with EST expression data. LIP1 had two orthologous candidate genes in Glycine max, both of which had PUT sequence of full length. The similarity between GmLIP1b and LIP1 was as high as 75.5% (Table 8; Figure 8).
|
Table 8 The orthologous candidate genes of LHY in three species of Legume Note: F: the whole candidate gene was covered by PUT sequence, or both ends were covered by PUT sequence and 80% of the whole gene sequences were covered by PUT sequence; E: a certain part or several parts of the gene were covered by suitable PUT sequence, but had not reached the standard of F |
.png)
|
Figure 8 LIP1 amino acid sequences alignment, conservation domain analysis of protein, molecular evolutionary tree and the evolutionary distance Note: A: Conservation domain analysis of LIP1 protein; B: LIP1 protein sequences alignment; C: Molecular evolution tree of LIP1 proteins; D: The distance of LIP1 protein between four species |
.png)
1.9 Identification of orthologous candidate genes of SFR6 in Legume
SFR6 gene in Medicago truncatula and Lotus japonicus each had an orthologous candidate gene. Among them, MtSFR6 was full length, and the similarity to SFR6 was 31.7%, but there was no EST expression data. While the LjSFR6 was partial sequence, there was no EST expression data.
SFR6 gene in Glycine max had 3 orthologous candidate genes, and all of them were full length and had EST expression data, the similarity among GmSFR6a, GmSFR6c and SFR6 was high. But from the view of the analogy of the amino acid, GmSFR6b in the C side had a deletion of large segment sequences. We speculated that GmSFR6b may have lost its basic function in the biological clock and there was a trend of becoming a fake gene. And GmSFR6c was also had sequence deletion in the C side, which may occur a certain degree of functional changes (Table 9).
|
Table 9 The orthologous candidate genes of SFR6 in three species of Legume Note: N: the gene could not find a line with the suitable PUT sequence; E: one part or several parts of the gene were covered by the suitable PUT sequence, but had not reached the standard of F |
.png)
From view of the molecular phylogenetic tree constructed by SFR6, MtSFR6 was in the outermost layer, which suggested that MtSFR6 was SFR6 paralogous gene, and there was no SFR6 paralogous gene in 3 orthologous candidate genes of Glycine max (Figure 9).
|
Figure 9 SFR6 amino acid sequences alignment, molecular evolutionary tree and the evolutionary distanceNote: A: SFR6 amino acid sequences alignment; B: Molecular evolutionary tree of SFR6 proteins; C: The evolutionary distance of SFR6 protein between four species |
.png)
There was no relevant conserved functional domain of SFR6 in CDD, but from the view of the analogy of the amino acid, the C terminal sequence of SFR6 had more conservative in the 2 species of arabidopsis and leguminosae (Figure 9).
SFR6 in the evolutionary history of Leguminosae and Arabidopsis thaliana may be as follows: the original gene SFR6A happened a replication before the separation of Cruciferae and Leguminosae. In the evolutionary process of legume, SFR6A1 and SFR6A2 were differentiated in Glycine and Medicago, SFR6A1 was lost in Medicago, and reserved the SFR6A2, which was MtSFR6. SFR6A2 was lost in Glycine. SFR6A1 was copied in the whole genome duplication event after the separation of Glycine and Medicago, replication for GmSFR6a and GmSFR6c, and GmSFR6a may be due to some kind of mechanism occurred another duplication, copied as GmSFR6a and GmSFR6b, and due to the absence of biological clock function, GmSFR6b not confronted the pressure of natural selection, therefore, GmSFR6b had a deletion mutation and degraded into pseudogenes. Besides, SFR6A2 was lost some gene segments and retained SFR6A1 in Arabidopsis thaliana.
1.10 Identification of orthologous candidate genes of ARR3/ARR4 in Legume
ARR4 was not found any orthologous candidate genes in the three species of Legume. ARR3 had one orthologous candidate gene each in Medicago truncatula and Lotus japonicas, the similarity of which was 48.8% and 51.3%, and the full length of genes were covered by the PUT sequence, it meant that there were most likely to be expressed and to be exercised the corresponding function of biological clock (Table 10; Figure 10).
|
Table 10 The orthologous candidate genes of ARR3 in three species of Legume Note: N: the gene could not find a line with the suitable PUT sequence; E: one part or several parts of the gene were covered by the suitable PUT sequence, but had not reached the standard of F |
.png)
|
Figure 10 ARR3 amino acid sequences alignment, conservation domain analysis of protein, molecular evolutionary tree and the evolutionary distance Note: A: Conservation domain analysis of ARR3 protein; B: ARR3 amino acid sequences alignment; C: Molecular evolutionary tree of ARR3 proteins; D: The evolutionary distance of ARR3 protein between four species |
.png)
Near the N side, ARR3 had a conserved domain named REC associated with phosphorylation, which included phosphorylation sites, dimer.
1.11 Identification of orthologous candidate genes of TEJ in Legume
TEJ had one orthologous candidate gene in Medicago truncatula, with a part of the expression data, had two orthologous candidate genes in Lotus japonicas, the LjTEJ1 was full-length and the LjTEJ2 was part of full length, had one orthologous candidate gene in Glycine max. The similarity between these orthologous candidate gene and TEJ genes in Arabidopsis was more than 50% (Table 11; Figure 11).
|
Table 11 The orthologous candidate genes of TEJ in three species of Legume Note: E: one part or several parts of the gene were covered by the suitable PUT sequence, but had not reached the standard of F |
.png)
|
Figure 11 TEJ amino acid sequences alignment, conservation domain analysis of protein, molecular evolutionary tree and the evolutionary distance Note: A: Conservation domain analysis of TEJ protein; B: TEJ protein sequences alignment; C: Molecular evolutionary tree of TEJ proteins; D: The evolutionary distance of TEJ protein between four species |
.png)
2 Discussion
We had identified 34 candidate genes related to the biological clock of Glycine max, 16 candidate genes related to the biological clock of lotus, 12 candidate genes related to the biological clock of Medicago truncatula. We constructed 11 molecular phylogenetic trees based on the candidate genes of the identified genes, and analyzed the function of these genes in combination with functional domain and multi sequence alignment. The analysis showed that the biological clock regulation pathway occurred in different degrees of differentiation in Arabidopsis and three species of Legume, especially in some key components, such as the core component of biological clock control and key genes of controlling florescence. By Arabidopsis thaliana as reference, the differentiation degree of the biological clock regulates network related genes in Lotus japonicus and Medicago truncatula was greater than Glycine max, which might be due to the genome of Lotus japonicus and Medicago truncatula far less than Glycine max.
From the evolutionary point of view, the function of orthologous genes from different species were all from the same ancestral gene differentiation, in general the function of them was most close, in absence of experimental data to support the case, the candidate gene by homologous gene identification was inferred the most similar genes with related genes function of Arabidopsis. Compared with the traditional methods of molecular biology, bioinformatics was more convenient, more purposeful, could be analyzed in whole gene level, and the conclusion was also more comprehensive, could have a certain reference value for the research in the experimental stage of the biological clock regulation network of Legume.
3 Materials and Methods
3.1 Source and obtain of genome data
The acquisition and analysis of raw data on Medicago truncatula, Lotus japonicus and Glycine max was mainly online. The genome database and the corresponding web sites of 4 species were listed in the Table 12.
|
Table 12 The Name and Website of the Databank of four species |
.png)
3.2 Using GO to obtain the network related genes of Arabidopsis thaliana circadian clock control
We searched biological clock, clock circadian, rhythm circadian and other keywords on Gene Ontology, got the Go term (Table 13), and then entered the TAIR database, acquired sequences of biological clock related genes and other related information.
|
Table 13 GO item and number of plant biological clock |
.png)
3.3 Identification of orthologous gene
The amino acid sequences of the related genes in Arabidopsis thaliana were used to carry out Blastp or tBlastn on the respective genomic databases of 3 species of legumes, selected the sequences which score was above 100 and E value was below -30 as the candidate sequence. The highest similarity sequences of be compared sequences would be carried out reverse Blastp in NCBI in Arabidopsis protein database to determine whether it was orthologous gene. If not, it was indicated that the species had no orthologous gene; if it was, then with the sequence as the standard, we further identified other orthologous genes.
3.4 Analysis of the functional domain of conservative structure
We analyzed the conservative domain of the target sequence by comprehensive utilization of CDD (Conserved Domain Search) (Marchler-Bauer et al., 2007; Marchler-Bauer et al., 2005) on the NCBI.
3.5 Multiple sequence alignments, phylogenetic tree construction and evolutionary analysis
Using ClustalX program, we carried out the amino acid sequence alignment of the orthologous candidate genes of these four species, and adopted the default parameters. The phylogenetic tree was constructed with the NJ method of MEGA4 software, and the evolutionary distance was calculated from 1000 times. At the same time, according to the phylogenetic trees, we could roughly calculate the evolutionary history of a gene between Legumes and Cruciferae.
3.6 Acquisition and analysis of expression data
The PUT sequence of PlantGDB was a high quality EST sequence (Tang et al., 2008), which was clustered, dislodged the redundant and partially stitched for the full length of cDNA. Nucleotide sequence of orthologous candidate genes was conducted BLASTN with PUT sequence, if the similarity with matching on PUT sequence was greater than 95% ,the base length was longer than 200 bp, the E value was less than 1E-30, we thought that the PUT could prove the matching of orthologous candidate gene really expression. We divided EST evidence into 3 categories: F, E, N, F meant that the entire candidate gene was covered by PUT sequence, or the both ends sequence and the 80 percent of the entire gene sequence were covered by PUT sequence. N meant that the gene could not find the matching PUT sequence; E indicated that some part of the gene or a few parts was in line with the requirements of the PUT sequence coverage, but not reached the F standard.
3.7 Re annotation of gene
When identified the homologous candidate gene of the three species of Legume, because of the incomplete or annotation errors genomic information, the No full-length ORF gene was appeared, and we would reannotate the the sequence of the genomic region corresponding to the ORF gene in GenScan, to obtain the full-length ORF gene. And the ORF sequence obtained would be carried out re-blast alignment with the genomic sequences of corresponding species PlantGDB to confirm whether it corresponded to the original genomic region, at the same time, amino acid sequence of ORF sequence translation would be carried out reverse Blastp in NCBI in Arabidopsis protein database to determine whether it was orthologous gene.
Authors’ contributions
Li Zongfei was the executor of this experiment, and was responsible for the experimental design, implementation, data analysis and draft writing; Wei Fang and Liu Zhenpeng were participated in the data analysis, the formation and amendment of the draft; Cai Mengdie and Zhang Jie were responsible for manuscript proofreading; Fang Xuanjun determined the research project conception, guided writing and revising paper. All authors have read and approved the final manuscript.
Acknowledgement
This research was sponsored by the Open Invention Fund of Life Science and Biotechnology (No 20161201) of Cuixi Academy of Biotechnology. Authors would thank Ms Jia Xuan for critical review and edit English manuscript.
Barak S., Tobin E.M., Andronis C., Sugano S., and Green R.M., 2000, All in good time: the Arabidopsis circadian clock, Trends in Plant Science, 5(12): 517-522
https://doi.org/10.1016/S1360-1385(00)01785-4
Covington M.F., Maloof J.N., Straume M., Kay S.A., and Harmer S.L., 2008, Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development, Genome Biology, 9(9): R130
https://doi.org/10.1186/gb-2008-9-8-r130
Devlin P.F., and Kay S.A., 2001, Circadian photoperception, Annual Review of Physiology, 63(1): 677-694
https://doi.org/10.1146/annurev.physiol.63.1.677
Doyle M.R., Davis S.J., Bastow R.M., Mcwatter H.G., Kozma-Bognár L., Nagy F., Millar A.J., and Amasino R.M., 2002, The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana, Nature, 419(6920): 74-77
https://doi.org/10.1038/nature00954
Dunlap J.C., 2004, Kinases and circadian clocks: per goes it alone, Developmental Cell, 6(2): 160-161
https://doi.org/10.1016/S1534-5807(04)00030-9
Edery I., 2005, Role of posttranscriptional regulation in circadian clocks: Lessons from Drosophila, Chronobiology International, 16(4): 377-414
https://doi.org/10.3109/07420529908998716
Fujiwara S., Wang L., Han L., Suh S., Salome P.A., McClung C.R., and Somers D.E., 2008, Post-translational regulation of the arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins, Journal of Biological Chemistry, 283(34): 23073-23083
https://doi.org/10.1074/jbc.M803471200
Harmer S.L., Hogenesch J.B., Straume M., Chang H., Han B., Zhu T., Wang X., Kreps J.A., and Kay S.A., 2000, Orchestrated transcription of key pathways in Arabidopsis by the circadian clock, Science, 290(5499): 2110-2113
https://doi.org/10.1126/science.290.5499.2110
Harmon F., Imaizumi T., and Gray W.M., 2008, CUL1 regulates TOC1 protein stability in the Arabidopsis circadian clock, The Plant Journal, 55(4): 568-579
https://doi.org/10.1111/j.1365-313X.2008.03527.x
Johnson C.H., 2001, Endogenous time keepers in photosynthetic organisms, Annual Review of Physiology, 63(1): 695-728
https://doi.org/10.1146/annurev.physiol.63.1.695
Kevei E., Gyula P., Fehér B., Tóth R., Viczián A., Kircher S., Rea D., Dorjgotov D., Schäfer E., Millar A.J., Kozma-Bognár L., Nagy F., 2007, Arabidopsis thaliana circadian clock is regulated by the small GTPase LIP1, Current Biology, 17(17): 1456-1464
https://doi.org/10.1016/j.cub.2007.07.018
Kim J., Kim Y., Yeom M., Kim J.H., and Nam H.G., 2008, FIONA1 is essential for regulating period length in the Arabidopsis circadian clock, Plant Cell, 20(2):307-319
https://doi.org/10.1105/tpc.107.055715
Kojima S., Takahashi Y., Kobayashi Y., Monna L., Sasaki T., Araki T., and Yano M., 2002, Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions, Plant Cell Physiol, 43(10): 1096-1105
https://doi.org/10.1093/pcp/pcf156
Li Z.F., Zhang J., Liu Z.P., and Fang X.J., 2015, Gene Regulation Network of Biological Clock in Plant, Fenzi Zhiwu Yuzhong (online) (Molecular Plant Breeding), 13(1): 1001-1008
Li Z.F., Zhuo W., Liu Z.P., and Fang X.J., 2015, Effects of Gene Regulation of Circadian Clock on Plant Growth and Development, Douke Jiyinzuxue Yu Yichuanxue (online) (Legume Genomics and Genetics), 6(1): 1-4
Marchler-Bauer A., Anderson J.B., Cherukuri P.F., DeWeese-Scott C., Geer L.Y., Gwadz M., He S.Q., Hurwitz D.I., Jackson J.D., Ke Z.X., Lanczycki C.J., Liebert C.A., Liu C.L., Lu F., Marchler G.H., Mullokandov M., Shoemaker B.A., Simonyan V., Song J.S., Thiessen P.A., Yamashita R.A., Yin J.J., Zhang D.C., and Bryant S.H., 2005, CDD: a conserved domain database for protein classification, Nucleic Acids Research, 33(S1): 192-196
Marchler-Bauer A., Anderson J.B., Derbyshire M.K., DeWeese-Scott C., Gonzales N.R., Gwadz M., Hao L., He S.Q., Hurwitz D.I., Jackson J.D., Ke Z.X., Krylov D., Lanczycki C.J., Liebert C.A., Liu C.L., Lu F., Lu S.N., Marchler G.H., Mullokandov M., Song J.S., Thanki N., Yamashita R.A., Yin J.J., Zhang D.C., and Bryant S.H., 2007, CDD: a conserved domain database for interactive domain family analysis, Nucleic Acids Research, 35(1): 237-240
https://doi.org/10.1093/nar/gkl951
Mas P., 2005, Circadian clock signaling in Arabidopsis thaliana: from gene expression to physiology and development, International Journal of Developmental Biology, 49(5-6): 491-500
https://doi.org/10.1387/ijdb.041968pm
Mcclung C.R., 2001, Circadian rhythms in plants, Annual Review of Plant Biology, 52(52): 139-162
https://doi.org/10.1146/annurev.arplant.52.1.139
Mizuno T., 2004, Plant response regulators implicated in signal transduction and circadian rhythm，Current Opinion in Plant Biology, 7(5): 499-505
https://doi.org/10.1016/j.pbi.2004.07.015
Mizuno T., 2004, Plant response regulators implicated in signal transduction and circadian rhythm, Current Opinion in Plant Biology, 7(9): 499-505
https://doi.org/10.1016/j.pbi.2004.07.015
Onai K., and Ishiura M., 2005, PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock, Genes to Cells Devoted to Molecular & Cellular Mechanisms, 10(10): 963-972
https://doi.org/10.1111/j.1365-2443.2005.00892.x
Schning J.C., Streitner C., Page D.R., Hennig S., Uchida K., Wolf E., Furuya M., and Staiger D., 2007, Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation, Plant Journal, 52(6): 1119-1130
https://doi.org/10.1111/j.1365-313X.2007.03302.x
Strayer C.A., Oyama T., Schultz T.F., Raman R., Somers D.E., Más P., Panda S., Kreps J.A.， and Kay S.A., 2000, Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog, Science, 289(5480): 768-771
https://doi.org/10.1126/science.289.5480.768
Streitner C., Danisman S., Wehrle F., Scning J.C., Alfano J.R., and Staiger D., 2008, The small glycine-rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana, Plant Journal for Cell & Molecular Biology, 56(2): 239-250
https://doi.org/10.1111/j.1365-313X.2008.03591.x
Tang W.Q., 2008, Bioinformatics analysis of plant light signal transduction pathway, Thesis for M.S., Fujian Agriculture and Forestry University, Supervisor: Wu W.R., pp. 28-31
Toh K.L., Jones C.R., He Y., Eide E.J., Hinz W.A., Virshup D.M., Ptacek L.J., and Fu Y.H., 2001, An hPER2 phosphorylation site mutation in familial advanced sleep phase syndrome, Science, 291(5506): 1040-1043
. PDF(683KB)
. FPDF
. HTML
. Online fPDF
Associated material
. Readers' comments
Other articles by authors
. Zongfei Li
. Fang Wei
. Mengdie Cai
. Jie Zhang
. Zhenpeng Liu
. Xuanjun Fang
Related articles
. Biological clock
. Legume
. Lotus Japonicus
. Medicago truncatula
. Homologous candidate genes
. Whole genome-wide identification
Tools
. Email to a friend
. Post a comment