Genome-wide Classification, Identification and Expression Profile of the C3HC4-type RING Finger Gene Family in Poplar (Populus trichocarpa)

Liu, Quangang; Yang, Jingli; Wang, Zhanchao; Xu, Xuemei; Mao, Xuliang; Li, Dandan; Hu, Xiaoqing; Jin, Dongchun; Li, Chenghao

doi:10.1007/s11105-015-0870-1

Cited by 13 publications

(11 citation statements)

References 56 publications

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“…Therefore, homologous genes may show differences in gene function and signal transduction. These results were similar to those of a previous analysis of the C3HC4-type RING finger gene family in Populus [ 65 ].…”

Section: Discussionsupporting

confidence: 91%

Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa)

et al. 2015

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BackgroundC2H2 zinc-finger (C2H2-ZF) proteins are a large gene family in plants that participate in various aspects of normal plant growth and development, as well as in biotic and abiotic stress responses. To date, no overall analysis incorporating evolutionary history and expression profiling of the C2H2-ZF gene family in model tree species poplar (Populus trichocarpa) has been reported.Principal FindingsHere, we identified 109 full-length C2H2-ZF genes in P. trichocarpa, and classified them into four groups, based on phylogenetic analysis. The 109 C2H2-ZF genes were distributed unequally on 19 P. trichocarpa linkage groups (LGs), with 39 segmental duplication events, indicating that segmental duplication has been important in the expansion of the C2H2-ZF gene family. Promoter cis-element analysis indicated that most of the C2H2-ZF genes contain phytohormone or abiotic stress-related cis-elements. The expression patterns of C2H2-ZF genes, based on heatmap analysis, suggested that C2H2-ZF genes are involved in tissue and organ development, especially root and floral development. Expression analysis based on quantitative real-time reverse transcription polymerase chain reaction indicated that C2H2-ZF genes are significantly involved in drought, heat and salt response, possibly via different mechanisms.ConclusionsThis study provides a thorough overview of the P. trichocarpa C2H2-ZF gene family and presents a new perspective on the evolution of this gene family. In particular, some C2H2-ZF genes may be involved in environmental stress tolerance regulation. PtrZFP2, 19 and 95 showed high expression levels in leaves and/or roots under environmental stresses. Additionally, this study provided a solid foundation for studying the biological roles of C2H2-ZF genes in Populus growth and development. These results form the basis for further investigation of the roles of these candidate genes and for future genetic engineering and gene functional studies in Populus.

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Section: Discussionsupporting

confidence: 91%

Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa)

et al. 2015

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“…A total of 425 RING-finger proteins were identified in whole rice (Oryza sativa) proteome and are divided into four types: RNIG-H2 (281), RING-HC (119), RING-v (23), and RING-C2 (2) [15]. Eighty percent of rice RING-finger proteins have been shown to possess E3 ligase activity [16,17]. At the same time, 731 RING-finger domains in 715 predicted proteins were divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47),RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5), and RING-G (1) [18].…”

Section: Introductionmentioning

confidence: 99%

Research Progress on Plant RING-Finger Proteins

Sun

Ahmed

et al. 2019

Genes

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E3 ubiquitin ligases are the most expanded components of the ubiquitin proteasome system (UPS). They mediate the recognition of substrates and later transfer the ubiquitin (Ub) of the system. Really Interesting New Gene (RING) finger proteins characterized by the RING domain, which contains 40–60 residues, are thought to be E3 ubiquitin ligase. RING-finger proteins play significant roles in plant growth, stress resistance, and signal transduction. In this study, we mainly describe the structural characteristics, classifications, and subcellular localizations of RING-finger proteins, as well the physiological processes of RING-finger proteins in plant growth and development. We also summarize the functions of plant RING-finger proteins in plant stress resistance. Finally, further research on plant RING-finger proteins is suggested, thereby establishing a strong foundation for the future study of plant RING-finger proteins.

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“…A previous study reported 91 RING-HC genes in P. trichocarpa [71]. In this study, we have identified 540 RING genes in P. trichocarpa, which were classified into three types, namely RING-H2 (288), RING-HC (183) and RING-v (69).…”

Section: Discussionmentioning

confidence: 89%

Identification of RING-H2 Gene Candidates Related to Wood Formation in Poplar

Tong

Shen

Cao

et al. 2019

Forests

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RING-H2 genes, the most abundant RING-type genes encoding putative ubiquitin ligase E3, are involved in diverse biological processes. Whether RING-H2 genes are related to wood formation remains to be identified in trees. In this study, we identified 288 RING-H2 genes in Populus trichocarpa, and found that the segmental and tandem duplication events contributed to RING-H2 gene expansion. Microarray dataset (from Affymetrix poplar genome arrays) showed that 64 of the 249 RING-H2 genes were highly or preferentially expressed in stem xylem. According to the AspWood RNAseq dataset, the transcription levels of genes PtrRHH21, 33, 48, 69, 88, 93, 94, 121, 141, 166, 175, 192, 208, 214, 250 and 257 were significantly increased in the xylem ranging from the expanding xylem to the lignifying xylem, suggesting their association with wood formation. Promoter analyses revealed that most of the preferentially xylem-expressed RING-H2 genes possessed SNBE, TERE, M46RE, AC and SMRE cis-elements, which are involved in secondary cell wall biosynthesis and programmed cell death. Based on the promoter GUS-based analysis result, PtrRHH94 was indicated to be associated with wood formation in transgenic P. trichocarpa. Taken together, dozens of Populus RING-H2 gene candidates associated with wood formation have been identified based on multiple gene expression analyses.

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Genome-wide Classification, Identification and Expression Profile of the C3HC4-type RING Finger Gene Family in Poplar (Populus trichocarpa)

Cited by 13 publications

References 56 publications

Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa)

Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa)

Research Progress on Plant RING-Finger Proteins

Identification of RING-H2 Gene Candidates Related to Wood Formation in Poplar

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