Transcriptome-Wide Identification of CCCH-Type Zinc Finger Proteins Family in Pinus massoniana and RR-TZF Proteins in Stress Response

Wang, Dengbao; Yao, Sheng; Agassin, Romaric Hippolyte; Zhang, Mengyang; Lou, Xuan; Huang, Zichen; Zhang, Jinfeng; Ji, Kongshu

doi:10.3390/genes13091639

Cited by 5 publications

(3 citation statements)

References 36 publications

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“…The primer sequences used for vector construction are provided in Table S1. The empty pGBKT7 vector was used as a negative control, and PmC3H20 which was validated previously [46] was used as a positive control. Subsequently, these fusion vectors were transformed into yeast strain AH109 (YC1010, Weidi Biotechnology, Shanghai, China) according to the operational approach.…”

Section: Transcriptional-activation Activity Assaymentioning

confidence: 99%

Identification and Expression Patterns of WOX Transcription Factors under Abiotic Stresses in Pinus massoniana

Wang,

Qiu,

et al. 2024

IJMS

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WUSCHEL-related homeobox (WOX) transcription factors (TFs) play a crucial role in regulating plant development and responding to various abiotic stresses. However, the members and functions of WOX proteins in Pinus massoniana remain unclear. In this study, a total of 11 WOX genes were identified, and bioinformatics methods were used for preliminary identification and analysis. The phylogenetic tree revealed that most PmWOXs were distributed in ancient and WUS clades, with only one member found in the intermediate clade. We selected four highly conserved WOX genes within plants for further expression analysis. These genes exhibited expressions across almost all tissues, while PmWOX2, PmWOX3, and PmWOX4 showed high expression levels in the callus, suggesting their potential involvement in specific functions during callus development. Expression patterns under different abiotic stresses indicated that PmWOXs could participate in resisting multiple stresses in P. massoniana. The identification and preliminary analysis of PmWOXs lay the foundation for further research on analyzing the resistance molecular mechanism of P. massoniana to abiotic stresses.

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Section: Transcriptional-activation Activity Assaymentioning

confidence: 99%

Identification and Expression Patterns of WOX Transcription Factors under Abiotic Stresses in Pinus massoniana

Wang,

Qiu,

et al. 2024

IJMS

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“…TZF proteins only contain two tandem C3H-type zinc finger motifs, whereas non-TZF proteins have one or more than two C3H-type zinc finger motifs [ 10 ]. In plants, the TZFs with C3H motifs also are called RR-TZFs [ 11 ]. Recent studies have shown that C3H proteins are involved in plant development and their stress response [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato (Solanum tuberosum L.)

Deng,

Yang,

Liu

et al. 2023

IJMS

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Transcription factors containing a CCCH structure (C3H) play important roles in plant growth and development, and their stress response, but research on the C3H gene family in potato has not been reported yet. In this study, we used bioinformatics to identify 50 C3H genes in potato and named them StC3H-1 to StC3H-50 according to their location on chromosomes, and we analyzed their physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, collinearity relationship, and cis-regulatory element. The gene expression pattern analysis showed that many StC3H genes are involved in potato growth and development, and their response to diverse environmental stresses. Furthermore, RT-qPCR data showed that the expression of many StC3H genes was induced by high temperatures, indicating that StC3H genes may play important roles in potato response to heat stress. In addition, Some StC3H genes were predominantly expressed in the stolon and developing tubers, suggesting that these StC3H genes may be involved in the regulation of tuber development. Together, these results provide new information on StC3H genes and will be helpful for further revealing the function of StC3H genes in the heat stress response and tuber development in potato.

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“…In recent years, transcriptome sequencing has been widely recognized as an effective method for the identification of plant transcription factor families under specific conditions for species such as S. integra, whose genome data have not yet been published. For example, transcriptome-wide identification and expression analysis of the MYB, ERKY, and CCCH families of Pinus massoniana under abiotic stress, such as phosphorus deficiency [22][23][24], the WRKY family of Eucalyptus globulus under cold acclimation [25], and the R2R3-MYB family of barley under boron stress [26] have been completed. Full-length transcriptome sequencing (also known as third-generation sequencing, or NGS) technology based on the PacBio platform has been developed in recent years to provide longer read lengths and higher accuracy [27] than next-generation sequencing (NGS) technology.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress

Yue

Huang

et al. 2023

IJMS

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The NAC (NAM-ATAF1/2-CUC) transcription factor family is one of the largest plant-specific transcription factor families, playing an important role in plant growth and development and abiotic stress response. As a short-rotation woody plant, Salix integra (S. integra) has high lead (Pb) phytoremediation potential. To understand the role of NAC in S. integra Pb tolerance, 53 SiNAC transcripts were identified using third-generation and next-generation transcriptomic data from S. integra exposed to Pb stress, and a phylogenetic analysis revealed 11 subfamilies. A sequence alignment showed that multiple subfamilies represented by TIP and ATAF had a gene that produced more than one transcript under Pb stress, and different transcripts had different responses to Pb. By analyzing the expression profiles of SiNACs at 9 Pb stress time points, 41 of 53 SiNACs were found to be significantly responsive to Pb. Short time-series expression miner (STEM) analysis revealed that 41 SiNACs had two significant Pb positive response patterns (early and late), both containing 10 SiNACs. The SiNACs with the most significant Pb response were mainly from the ATAF and NAP subfamilies. Therefore, 4 and 3 SiNACs from the ATAF and NAP subfamilies, respectively, were selected as candidate Pb-responsive SiNACs for further structural and functional analysis. The RT-qPCR results of 7 transcripts also confirmed the different Pb response patterns of the ATAF and NAP subfamilies. SiNAC004 and SiNAC120, which were randomly selected from two subfamilies, were confirmed to be nuclear localization proteins by subcellular localization experiments. Functional prediction analysis of the associated transcripts of seven candidate SiNACs showed that the target pathways of ATAF subfamily SiNACs were “sulfur metabolism” and “glutathione metabolism”, and the target pathways of NAP subfamily SiNACs were “ribosome” and “phenylpropanoid biosynthesis”. This study not only identified two NAC subfamilies with different Pb response patterns but also identified Pb-responsive SiNACs that could provide a basis for subsequent gene function verification.

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Transcriptome-Wide Identification of CCCH-Type Zinc Finger Proteins Family in Pinus massoniana and RR-TZF Proteins in Stress Response

Cited by 5 publications

References 36 publications

Identification and Expression Patterns of WOX Transcription Factors under Abiotic Stresses in Pinus massoniana

Identification and Expression Patterns of WOX Transcription Factors under Abiotic Stresses in Pinus massoniana

Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato (Solanum tuberosum L.)

Transcriptome-Wide Identification and Response Pattern Analysis of the Salix integra NAC Transcription Factor in Response to Pb Stress

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