Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)

Pradhan, Seema; Kant, Chandra; Verma, Subodh; Bhatia, Sabhyata

doi:10.1371/journal.pone.0180469

Cited by 29 publications

(18 citation statements)

References 70 publications

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“…Cysteine-cysteine-cysteine-histidine (CCCH) zinc-finger proteins usually possess one to seven copies of CCCH motifs, which are newly defined as C-X 4–17 -C-X 4–6 -C-X 3 -H [ 5 , 6 , 7 ]. CCCH genes are widely distributed in organisms from bacteria to eukaryotes [ 5 , 8 ], and members of this gene family in various plants have also been predicted in silico [ 5 , 6 , 7 , 9 , 10 , 11 , 12 ]. For instance, 68 CCCH-type zinc-finger protein genes divided into 11 subfamilies have been identified in the Arabidopsis thaliana genome [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

BcMF30a and BcMF30c, Two Novel Non-Tandem CCCH Zinc-Finger Proteins, Function in Pollen Development and Pollen Germination in Brassica campestris ssp. chinensis

Xiong

Liu

et al. 2020

IJMS

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Chinese cabbage (Brassica campestris) is an economically important leaf vegetable crop worldwide. Mounting studies have shown that cysteine-cysteine-cysteine-histidine (CCCH) zinc-finger protein genes are involved in various plant growth and development processes. However, research on the involvement of these genes in male reproductive development is still in its infancy. Here, we identified 11 male fertility-related CCCH genes in Chinese cabbage. Among them, a pair of paralogs encoding novel non-tandem CCCH zinc-finger proteins, Brassica campestris Male Fertility 30a (BcMF30a) and BcMF30c, were further characterized. They were highly expressed in pollen during microgametogenesis and continued to express in germinated pollen. Further analyses demonstrated that both BcMF30a and BcMF30c may play a dual role as transcription factors and RNA-binding proteins in plant cells. Functional analysis showed that partial bcmf30a bcmf30c pollen grains were aborted due to the degradation of pollen inclusion at the microgametogenesis phase, and the germination rate of viable pollen was also greatly reduced, indicating that BcMF30a and BcMF30c are required for both pollen development and pollen germination. This research provided insights into the function of CCCH proteins in regulating male reproductive development and laid a theoretical basis for hybrid breeding of Chinese cabbage.

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Section: Introductionmentioning

confidence: 99%

BcMF30a and BcMF30c, Two Novel Non-Tandem CCCH Zinc-Finger Proteins, Function in Pollen Development and Pollen Germination in Brassica campestris ssp. chinensis

Xiong

Liu

et al. 2020

IJMS

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“…A number of studies indicated that C3H genes were involved in various development stage and different stress response. For example, previous studies revealed that CarC3H26 and 51 had higher expression during early stages of chickpea seed development (Pradhan et al, 2017). In rice, OsC3H33, OsC3H37 and OsC3H50 were induced by salt stress (Muhamman, Waqas & Asia, 2010).…”

Section: Excellent Candidates For Salt-tolerance Improvementmentioning

confidence: 98%

“…The C3H members play important roles in plant response to the environment. A number of researchers have elucidated the association of C3Hs with diverse plant growth regulatory processes via genome-wide analysis in Arabidopsis and rice (Wang et al, 2008), poplar (Chai et al, 2012), maize (Peng et al, 2012), switchgrass (Yuan et al, 2015), alfalfa (Zhang et al, 2013), citrus (Liu et al, 2014), tomato (Xu, 2014), grape vine (Wang, Zhong & Cheng, 2014), chickpea (Pradhan et al, 2017), banana (Mazumdar et al, 2017) and cabbage (Rameneni et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia

Liu

Kan

et al. 2020

PeerJ

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Transcription factors regulate gene expression in response to various external and internal cues by activating or suppressing downstream genes. Significant progress has been made in identifying and characterizing the Cysteine3Histidine (C3H) gene family in several dicots and monocots. They are characterized by their signature motif of three cysteine and one histidine residues, and reportedly play important roles in regulation of plant growth, developmental processes and environmental responses. In this study, we performed genome-wide and deep analysis of putative C3H genes, and a total of 117 PbeC3H members, were identified in P. betulaefolia and classified into 12 groups. Results were supported by the gene structural characteristics and phylogenetic analysis. These genes were unevenly distributed on 17 chromosomes. The gene structures of the C3H genes were relatively complex but conserved in each group. The C3H genes experienced a WGD event that occurred in the ancestor genome of P. betulaefolia and apple before their divergence based on the synonymous substitutions (Ks) values. There were 35 and 37 pairs of paralogous genes in the P. betulaefolia and apple genome, respectively, and 87 pairs of orthologous genes between P. betulaefolia and apple were identified. Except for one orthologous pairs PbeC3H66 and MD05G1311700 which had undergone positive selection, the other C3H genes had undergone purifying selection. Expression profiles showed that high salinity stress could influence the expression level of C3H genes in P. betulaefolia. Four members were responsive to salt stress in roots, nine were responsive to salt stress in leaves and eight showed inhibited expression in leaves. Results suggested important roles of PbeC3H genes in response to salt stress and will be useful for better understanding the complex functions of the C3H genes, and will provide excellent candidates for salt-tolerance improvement.

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“…However, recent evidence suggests that CCCH (C3H) as a novel type Znf transcription factors regulate gene expression by binding on targets genes mRNA [7][8][9]. To verify its characteristics, based on the genome-data, the comprehensive analysis of C3H Znf family was performed in dicotyledonous Arabidopsis thaliana [9], Medicago truncatula [10], Populus trichocarpa [11], Clementine mandarin [12], Vitis vinifera [13], Cicer arietinum [14], monocotyledonous Musa acuminata [15], Zea mays [16], and Oryza sativa [9] , showed that C3H Znf family widely involved in biotic and abiotic pathways. Besides, C3H Znf members have various functions.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide investigation of CCCH zinc finger family in longan (Dimocarpus longan Lour): characteristic identification and expression profiles in longan somatic embryo

Su¹,

Jiang²,

Huang³

et al. 2020

Preprint

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Background: CCCH Zinc finger ( Znf ) transcription factors ( TF ), as a novel type Znf genes, regulate genes expression by binding on their mRNA and play important roles in plant abiotic stress, growth and development. However, no overall genome-wide analysis or expression profiling of CCCH ( C3H ) gene family in Dimocarpous longan , especially during the early stages of somatic embryo in longan has been studied. Longan is a tropical/subtropical fruit tree of great economic importance in Southeast Asia,and longan embryogenesis is the main factor affecting fruit quality and yield. Results: In this study, a comprehensive analysis of longan C3H （ DlC3H ）gene family was carried out. 49 DlC3H genes were identified from longan genome database,which divided into 3 clades. Besides, genes characteristics, phylogenetic tree, gene structure, motif composition were comprehensively analyzed. The analysis of alternative splicing events (AS) suggested that AS events of DlC3H genes were related to longan non-embryonic and embryonic callus transformation. Promoter analysis indicted that most of DlC3H genes included cis -elements associated with hormones and stress response. Quantitative real-time PCR analysis indicated that 26 DlC3Hs ,which possess MeJA and ABA responsive cis -elements, showed different expression patterns and may involved into ABA and MeJA signaling pathway. The expression profiles of 17 DlC3Hs were performed in four stages of longan, the results showed that only DlC3H01/07/14/16/38 was consistent with the data in the transcriptome. DlC3H 07/14/16/36/49 were highly expressed in EC and only DlC3H 04/38 was in GE , suggesting that they have different functions in embryonic development. Finally, sRNAs were verified involved into regulating 6 DlC3Hs . Conclusion: This study provides the first systematic analysis of CCCH protein in longan somatic embryo. Particularly, CCCH genes may be involved in hormone and stress respond, and somatic embryogenesis. Our results presented here may provide a insight into the characteristics and functions of this family in somatic embryogenesis.

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Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)

Cited by 29 publications

References 70 publications

BcMF30a and BcMF30c, Two Novel Non-Tandem CCCH Zinc-Finger Proteins, Function in Pollen Development and Pollen Germination in Brassica campestris ssp. chinensis

BcMF30a and BcMF30c, Two Novel Non-Tandem CCCH Zinc-Finger Proteins, Function in Pollen Development and Pollen Germination in Brassica campestris ssp. chinensis

Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia

Genome-wide investigation of CCCH zinc finger family in longan (Dimocarpus longan Lour): characteristic identification and expression profiles in longan somatic embryo

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