Arabidopsis thaliana ICE 2 gene: Phylogeny, structural evolution and functional diversification from ICE1

Kurbidaeva, Amina; Ежова, Т. А.; Novokreshchenova, Maria

doi:10.1016/j.plantsci.2014.08.011

Cited by 53 publications

(47 citation statements)

References 53 publications

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“…The closely clustered CgbHLHs and AtbHLHs in the same subfamily/group may have similar functions. In group 1, AtbHLH29 (FIT), AtbHLH33 (ICE2), AtbHLH116 (ICE1), AtbHLH93 (NFL), AtbHLH61, and AtbHLH21 (AMS) have been shown to be involved in Fe deficiency, cold tolerance and flower development [32,[53][54][55], suggesting that there are similar functions for the CgbHLHs of this group. In the other groups, many AtbHLH genes such as AtbHLH70 (MYC70) and AtbHLH45 (MUTE) in group 2, AtbHLH10, AtbHLH89 and AtbHLH91 in group 3, AtbHLH38, AtbHLH39, AtbHLH100 and AtbHLH101 in group 4, etc.…”

Section: Discussionmentioning

confidence: 99%

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

et al. 2020

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Background: Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown. Results: In this study, we identified a total of 128 CgbHLHs from pummelo (Citrus grandis) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency. Conclusions: In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

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Section: Discussionmentioning

confidence: 99%

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

et al. 2020

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“…These results implied bHLH027 plays essential roles in abiotic stresses in papaya. In addition, the transcript of CpbHLH062 was also increased under cold treatment, its orthologue is AtbHLH033/ICE2, which involving the cold response and the ABA pathway [42,50], implying the CpbHLH062 may involved the cold stress. bHLH053 was downregulated under salt, drought and ABA stresses.…”

Section: Go Annotation Of Cpbhlh Proteinsmentioning

confidence: 96%

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in papaya (Carica papaya L.)

Yang¹,

Kuang²,

Zhou³

et al. 2019

Preprint

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Background : As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya ( Carica papaya L. ) has been reported previously. Results: In this study, a total of 73 CpbHLH genes were found in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis, with one orphans. Almost all of the CpbHLH in the same subfamily shared similar gene structures and protein motifs according to an analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLH genes varied from 1 to 11 with an average of 5. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis -element analysis revealed that most of the CpbHLH genes contained cis -elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that Cp bHLH mainly functions in protein dimerization activity and DNA-binding, and most Cp bHLH proteins were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some predicted CpbHLH genes that might be responsible for abiotic stress responses in papaya. Conclusions : A total of 73 bHLH transcription factors were identified from papaya, and their gene structures, conserved domains, sequence features, phylogenetic relationship, promoter cis -element, GO annotation and gene expression profiles responsible for abiotic stress were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of Cp bHLHs. Keywords : papaya, genome-wide analysis, bHLH transcription factors, abiotic stress

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“…(NFL), AtbHLH61, and AtbHLH21 (AMS) have been shown to be involved in Fe deficiency, cold tolerance and flower development [32,[53][54][55], suggesting that there are similar functions for the CgbHLHs of this group. In the other groups, many AtbHLH genes such as AtbHLH70 (MYC70) and Based on these previous studies, the potential functions of most CgbHLH genes could be predicted.…”

Section: Candidate Cgbhlh Members In Response To Fe Deficiencymentioning

confidence: 99%

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

Zhang

Qiu

Hui

et al. 2020

Preprint

View full text Add to dashboard Cite

Background Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown. Results In this study, we identified a total of 128 CgbHLHs from pummelo ( Citrus grandis ) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency. Conclusions In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

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Arabidopsis thaliana ICE 2 gene: Phylogeny, structural evolution and functional diversification from ICE1

Cited by 53 publications

References 53 publications

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in papaya (Carica papaya L.)

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

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