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16 pages, 2041 KiB

Open AccessArticle

The Drought-Mediated Soybean GmNAC085 Functions as a Positive Regulator of Plant Response to Salinity

by Xuan Lan Thi Hoang, Nguyen Nguyen Chuong, Tran Thi Khanh Hoa, Hieu Doan, Pham Hoang Phuong Van, Le Dang Minh Trang, Pham Ngoc Thai Huyen, Dung Tien Le, Lam-Son Phan Tran and Nguyen Phuong Thao

Int. J. Mol. Sci. 2021, 22(16), 8986; https://doi.org/10.3390/ijms22168986 - 20 Aug 2021

Cited by 10 | Viewed by 3540

Abstract

Abiotic stress factors, such as drought and salinity, are known to negatively affect plant growth and development. To cope with these adverse conditions, plants have utilized certain defense mechanisms involved in various aspects, including morphological, biochemical and molecular alterations. Particularly, a great deal [...] Read more.

Abiotic stress factors, such as drought and salinity, are known to negatively affect plant growth and development. To cope with these adverse conditions, plants have utilized certain defense mechanisms involved in various aspects, including morphological, biochemical and molecular alterations. Particularly, a great deal of evidence for the biological importance of the plant-specific NAM, ATAF1/2, CUC2 (NAC) transcription factors (TFs) in plant adaptation to abiotic stress conditions has been reported. A previous in planta study conducted by our research group demonstrated that soybean (Glycine max) GmNAC085 mediated drought resistance in transgenic Arabidopsis plants. In this study, further characterization of GmNAC085 function in association with salt stress was performed. The findings revealed that under this condition, transgenic soybean plants overexpressing GmNAC085 displayed better germination rates than wild-type plants. In addition, biochemical and transcriptional analyses showed that the transgenic plants acquired a better defense system against salinity-induced oxidative stress, with higher activities of antioxidant enzymes responsible for scavenging hydrogen peroxide or superoxide radicals. Higher transcript levels of several key stress-responsive genes involved in the proline biosynthetic pathway, sodium ion transporter and accumulation of dehydrins were also observed, indicating better osmoprotection and more efficient ion regulation capacity in the transgenic lines. Taken together, these findings and our previous report indicate that GmNAC085 may play a role as a positive regulator in plant adaptation to drought and salinity conditions. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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15 pages, 4034 KiB

Open AccessArticle

Genome-Wide Association Study in Rice Revealed a Novel Gene in Determining Plant Height and Stem Development, by Encoding a WRKY Transcription Factor

by Xiaoshuang Wei, Hailian Zhou, Deying Xie, Jianguo Li, Mingchong Yang, Tianli Chang, Dongxin Wang, Lihua Hu, Guosheng Xie, Jihong Wang and Lingqiang Wang

Int. J. Mol. Sci. 2021, 22(15), 8192; https://doi.org/10.3390/ijms22158192 - 30 Jul 2021

Cited by 19 | Viewed by 3567

Abstract

Semi-dwarfism is a main agronomic trait in crop breeding. In this study, we performed genome-wide association study (GWAS) and identified a new quantitative trait nucleotide (QTN) for rice shoot length. The peak QTN (C/T) was located in the first coding region of a [...] Read more.

Semi-dwarfism is a main agronomic trait in crop breeding. In this study, we performed genome-wide association study (GWAS) and identified a new quantitative trait nucleotide (QTN) for rice shoot length. The peak QTN (C/T) was located in the first coding region of a group III WRKY transcription factor OsWRKY21 (LOC_Os01g60640). Interestingly, further haplotype analysis showed that C/T difference only existed in the indica group but not in the japonica group, resulting in significant differences in plant height among the different indica rice varieties. OsWRKY21 was expressed in embryo, radicle, shoots, leaves, and stems. Most notably, overexpressing OsWRKY21 resulted in the semi-dwarf phenotype, early heading date and short internodes compared to the wild type, while the knockout mutant plants by CRISPR/Cas9 technology yielded the opposite. The overexpressing lines exhibited the decreased length of the cells near sclerenchyma epidermis, accompanied with the lower levels of indole-3-acetic acid (IAA) and gibberellin 3 (GA₃), but increased levels of the abscisic acid (ABA) and salicylic acid (SA) in the internodes at heading stage. Moreover, the semi-dwarf phenotype could be fully rescued by exogenous GA₃ application at seedling stage. The RNA-seq and qRT-PCR analysis confirmed the differential expression levels of genes in development and the stress responses in rice, including GA metabolism (GA20ox2, GA2ox6, and YABY1) and cell wall biosynthesis (CesA4, 7, and 9) and regulation (MYB103L). These data suggest the essential role of OsWRKY21 in regulation of internode elongation and plant height in rice. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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24 pages, 13618 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profiling of the WOX Gene Family in Citrus sinensis and Functional Analysis of a CsWUS Member

by Faiza Shafique Khan, Ren-Fang Zeng, Zhi-Meng Gan, Jin-Zhi Zhang and Chun-Gen Hu

Int. J. Mol. Sci. 2021, 22(9), 4919; https://doi.org/10.3390/ijms22094919 - 6 May 2021

Cited by 28 | Viewed by 5020

Abstract

WUSCHEL-related homeobox (WOX) transcription factors (TFs) are well known for their role in plant development but are rarely studied in citrus. In this study, we identified 11 putative genes from the sweet orange genome and divided the citrus WOX genes [...] Read more.

WUSCHEL-related homeobox (WOX) transcription factors (TFs) are well known for their role in plant development but are rarely studied in citrus. In this study, we identified 11 putative genes from the sweet orange genome and divided the citrus WOX genes into three clades (modern/WUSCHEL(WUS), intermediate, and ancient). Subsequently, we performed syntenic relationship, intron-exon organization, motif composition, and cis-element analysis. Co-expression analysis based on RNA-seq and tissue-specific expression patterns revealed that CsWOX gene expression has multiple intrinsic functions. CsWUS homolog of AtWUS functions as a transcriptional activator and binds to specific DNA. Overexpression of CsWUS in tobacco revealed dramatic phenotypic changes, including malformed leaves and reduced gynoecia with no seed development. Silencing of CsWUS in lemon using the virus-induced gene silencing (VIGS) system implied the involvement of CsWUS in cells of the plant stem. In addition, CsWUS was found to interact with CsCYCD3, an ortholog in Arabidopsis (AtCYCD3,1). Yeast one-hybrid screening and dual luciferase activity revealed that two TFs (CsRAP2.12 and CsHB22) bind to the promoter of CsWUS and regulate its expression. Altogether, these results extend our knowledge of the WOX gene family along with CsWUS function and provide valuable findings for future study on development regulation and comprehensive data of WOX members in citrus. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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15 pages, 4277 KiB

Open AccessArticle

Genome-Wide Identification, Classification and Expression Analysis of the MYB Transcription Factor Family in Petunia

by Guanqun Chen, Weizhi He, Xiangxin Guo and Junsong Pan

Int. J. Mol. Sci. 2021, 22(9), 4838; https://doi.org/10.3390/ijms22094838 - 3 May 2021

Cited by 26 | Viewed by 4184

Abstract

A lot of researches have been focused on the evolution and function of MYB transcription factors (TFs). For revealing the formation of petunia flower color diversity, MYB gene family in petunia was identified and analyzed. In this study, a total of 155 MYB [...] Read more.

A lot of researches have been focused on the evolution and function of MYB transcription factors (TFs). For revealing the formation of petunia flower color diversity, MYB gene family in petunia was identified and analyzed. In this study, a total of 155 MYB genes, including 40 1R-MYBs, 106 R2R3-MYBs, 7 R1R2R3-MYBs and 2 4R-MYBs, have been identified in the Petunia axillaris genome. Most R2R3 genes contain three exons and two introns, whereas the number of PaMYB introns varies from 0 to 12. The R2R3-MYB members could be divided into 28 subgroups. Analysis of gene structure and protein motifs revealed that members within the same subgroup presented similar exon/intron and motif organization, further supporting the results of phylogenetic analysis. Genes in subgroup 10, 11 and 21 were mainly expressed in petal, not in vegetative tissues. Genes in subgroup 9, 19, 25 and 27 expressed in all tissues, but the expression patterns of each gene were different. According to the promoter analysis, five R2R3-MYB and two MYB-related genes contained MBSI cis-element, which was involved in flavonoid biosynthetic regulation. PaMYB100/DPL has been reported to positively regulate to pigmentation. However, although PaMYB82, PaMYB68 and Pa1RMYB36 contained MBSI cis-element, their function in flavonoid biosynthesis has not been revealed. Consistent with existing knowledge, PaMYBs in subgroup 11 had similar function to AtMYBs in subgroup 6, genes in which played an important role in anthocyanin biosynthesis. In addition, PaMYB1 and PaMYB40 belonged to P9 (S7) and were potentially involved in regulation of flavonoid synthesis in petunia vegetative organs. This work provides a comprehensive understanding of the MYB gene family in petunia and lays a significant foundation for future studies on the function and evolution of MYB genes in petunia. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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15 pages, 4566 KiB

Open AccessArticle

Tartary Buckwheat (Fagopyrum tataricum) NAC Transcription Factors FtNAC16 Negatively Regulates of Pod Cracking and Salinity Tolerant in Arabidopsis

by Jing Wang, ZhaoTang Ma, Bo Tang, HaoYu Yu, ZiZhong Tang, TongLiang Bu, Qi Wu and Hui Chen

Int. J. Mol. Sci. 2021, 22(6), 3197; https://doi.org/10.3390/ijms22063197 - 21 Mar 2021

Cited by 13 | Viewed by 2999

Abstract

The thick and hard fruit shell of Fagopyrum tataricum (F. tataricum) represents a processing bottleneck. At the same time, soil salinization is one of the main problems faced by modern agricultural production. Bioinformatic analysis indicated that the F. tataricum transcription factor [...] Read more.

The thick and hard fruit shell of Fagopyrum tataricum (F. tataricum) represents a processing bottleneck. At the same time, soil salinization is one of the main problems faced by modern agricultural production. Bioinformatic analysis indicated that the F. tataricum transcription factor FtNAC16 could regulate the hull cracking of F. tataricum, and the function of this transcription factor was verified by genetic transformation of Arabidopsis thaliana (A. thaliana). Phenotypic observations of the wild-type (WT), OE-FtNAC16, nst1/3 and nst1/3-FtNAC16 plant lines confirmed that FtNAC16 negatively regulated pod cracking by downregulating lignin synthesis. Under salt stress, several physiological indicators (POD, GSH, Pro and MDA) were measured, A. thaliana leaves were stained with NBT (Nitroblue Tetrazolium) and DAB (3,3’-diaminobenzidine), and all genes encoding enzymes in the lignin synthesis pathway were analyzed. These experiments confirmed that FtNAC16 increased plant sensitivity by reducing the lignin content or changing the proportions of the lignin monomer. The results of this study may help to elucidate the possible association between changes in lignin monomer synthesis and salt stress and may also contribute to fully understanding the effects of FtNAC16 on plant growth and development, particularly regarding fruit pod cracking and environmental adaptability. In future studies, it may be useful to obtain suitable cracking varieties and salt-tolerant crops through molecular breeding. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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18 pages, 4958 KiB

Open AccessArticle

Potato NAC Transcription Factor StNAC053 Enhances Salt and Drought Tolerance in Transgenic Arabidopsis

by Qi Wang, Cun Guo, Zhiyuan Li, Jinhao Sun, Zhichao Deng, Lichao Wen, Xiaoxu Li and Yongfeng Guo

Int. J. Mol. Sci. 2021, 22(5), 2568; https://doi.org/10.3390/ijms22052568 - 4 Mar 2021

Cited by 43 | Viewed by 3856

Abstract

The NAC (NAM, ATAF1/2, and CUC2) transcription factors comprise one of the largest transcription factor families in plants and play important roles in stress responses. However, little is known about the functions of potato NAC family members. Here we report the cloning of [...] Read more.

The NAC (NAM, ATAF1/2, and CUC2) transcription factors comprise one of the largest transcription factor families in plants and play important roles in stress responses. However, little is known about the functions of potato NAC family members. Here we report the cloning of a potato NAC transcription factor gene StNAC053, which was significantly upregulated after salt, drought, and abscisic acid treatments. Furthermore, the StNAC053-GFP fusion protein was found to be located in the nucleus and had a C-terminal transactivation domain, implying that StNAC053 may function as a transcriptional activator in potato. Notably, Arabidopsis plants overexpressing StNAC053 displayed lower seed germination rates compared to wild-type under exogenous ABA treatment. In addition, the StNAC053 overexpression Arabidopsis lines displayed significantly increased tolerance to salt and drought stress treatments. Moreover, the StNAC053-OE lines were found to have higher activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) under multiple stress treatments. Interestingly, the expression levels of several stress-related genes including COR15A,DREB1A, ERD11, RAB18, ERF5, and KAT2, were significantly upregulated in these StNAC053-overexpressing lines. Taken together, overexpression of the stress-inducible StNAC053 gene could enhance the tolerances to both salt and drought stress treatments in Arabidopsis, likely by upregulating stress-related genes. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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14 pages, 3899 KiB

Open AccessArticle

Genome-Wide Characterization, Evolution, and Expression Profile Analysis of GATA Transcription Factors in Brachypodium distachyon

by Weiye Peng, Wei Li, Na Song, Zejun Tang, Jing Liu, Yunsheng Wang, Sujun Pan, Liangying Dai and Bing Wang

Int. J. Mol. Sci. 2021, 22(4), 2026; https://doi.org/10.3390/ijms22042026 - 18 Feb 2021

Cited by 28 | Viewed by 3461

Abstract

The GATA proteins, functioning as transcription factors (TFs), are involved in multiple plant physiological and biochemical processes. In this study, 28 GATA TFs of Brachypodium distachyon (BdGATA) were systematically characterized via whole-genome analysis. BdGATA genes unevenly distribute on five chromosomes of B. distachyon [...] Read more.

The GATA proteins, functioning as transcription factors (TFs), are involved in multiple plant physiological and biochemical processes. In this study, 28 GATA TFs of Brachypodium distachyon (BdGATA) were systematically characterized via whole-genome analysis. BdGATA genes unevenly distribute on five chromosomes of B. distachyon and undergo purifying selection during the evolution process. The putative cis-acting regulatory elements and gene interaction network of BdGATA were found to be associated with hormones and defense responses. Noticeably, the expression profiles measured by quantitative real-time PCR indicated that BdGATA genes were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatment, and 10 of them responded to invasion of the fungal pathogen Magnaporthe oryzae, which causes rice blast disease. Genome-wide characterization, evolution, and expression profile analysis of BdGATA genes can open new avenues for uncovering the functions of the GATA genes family in plants and further improve the knowledge of cellular signaling in plant defense. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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17 pages, 4895 KiB

Open AccessArticle

Transcriptome Analysis of the Fruit of Two Strawberry Cultivars “Sunnyberry” and “Kingsberry” That Show Different Susceptibility to Botrytis cinerea after Harvest

by Kyuweon Lee, Jeong Gu Lee, Kyeonglim Min, Jeong Hee Choi, Sooyeon Lim and Eun Jin Lee

Int. J. Mol. Sci. 2021, 22(4), 1518; https://doi.org/10.3390/ijms22041518 - 3 Feb 2021

Cited by 12 | Viewed by 4159

Abstract

Gray mold (Botrytis cinerea) is a fungal plant pathogen causing postharvest decay in strawberry fruit. Here, we conducted a comparative transcriptome analysis to identify differences in gene expression between the immature-green (IG) and mature-red (MR) stages of the “Sunnyberry” (gray mold-resistant) [...] Read more.

Gray mold (Botrytis cinerea) is a fungal plant pathogen causing postharvest decay in strawberry fruit. Here, we conducted a comparative transcriptome analysis to identify differences in gene expression between the immature-green (IG) and mature-red (MR) stages of the “Sunnyberry” (gray mold-resistant) and “Kingsberry” (gray mold susceptible) strawberry cultivars. Most of the genes involved in lignin and alkane-type wax biosynthesis were relatively upregulated in “Sunnyberry”. However, pathogenesis-related proteins encoding R- and antioxidant-related genes were comparatively upregulated in “Kingsberry”. Analysis of gene expression and physiological traits in the presence and absence of B. cinerea inoculation revealed that the defense response patterns significantly differed between IG and MR rather than the cultivars. “Kingsberry” showed higher antioxidant induction at IG and upregulated hemicellulose-strengthening and R genes at MR. Hence, “Sunnyberry” and “Kingsberry” differed mainly in terms of the expression levels of the genes forming cuticle, wax, and lignin and controlling the defense responses. These discrepancies might explain the relative difference between these strawberry cultivars in terms of their postharvest responses to B. cinerea. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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15 pages, 2672 KiB

Open AccessArticle

Auxin-Induced SaARF4 Downregulates SaACO4 to Inhibit Lateral Root Formation in Sedum alfredii Hance

by Dong Xu, Zhuchou Lu, Guirong Qiao, Wenmin Qiu, Longhua Wu, Xiaojiao Han and Renying Zhuo

Int. J. Mol. Sci. 2021, 22(3), 1297; https://doi.org/10.3390/ijms22031297 - 28 Jan 2021

Cited by 4 | Viewed by 2569

Abstract

Lateral root (LR) formation promotes plant resistance, whereas high-level ethylene induced by abiotic stress will inhibit LR emergence. Considering that local auxin accumulation is a precondition for LR generation, auxin-induced genes inhibiting ethylene synthesis may thus be important for LR development. Here, we [...] Read more.

Lateral root (LR) formation promotes plant resistance, whereas high-level ethylene induced by abiotic stress will inhibit LR emergence. Considering that local auxin accumulation is a precondition for LR generation, auxin-induced genes inhibiting ethylene synthesis may thus be important for LR development. Here, we found that auxin response factor 4 (SaARF4) in Sedum alfredii Hance could be induced by auxin. The overexpression of SaARF4 decreased the LR number and reduced the vessel diameters. Meanwhile, the auxin distribution mode was altered in the root tips and PIN expression was also decreased in the overexpressed lines compared with the wild-type (WT) plants. The overexpression of SaARF4 could reduce ethylene synthesis, and thus, the repression of ethylene production decreased the LR number of WT and reduced PIN expression in the roots. Furthermore, the quantitative real-time PCR, chromatin immunoprecipitation sequencing, yeast one-hybrid, and dual-luciferase assay results showed that SaARF4 could bind the promoter of 1-aminocyclopropane-1-carboxylate oxidase 4 (SaACO4), associated with ethylene biosynthesis, and could downregulate its expression. Therefore, we concluded that SaARF4 induced by auxin can inhibit ethylene biosynthesis by repressing SaACO4 expression, and this process may affect auxin transport to delay LR development. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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19 pages, 2492 KiB

Open AccessArticle

Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L.

by Abirami Rajavel, Selina Klees, Johanna-Sophie Schlüter, Hendrik Bertram, Kun Lu, Armin Otto Schmitt and Mehmet Gültas

Int. J. Mol. Sci. 2021, 22(3), 1033; https://doi.org/10.3390/ijms22031033 - 21 Jan 2021

Cited by 10 | Viewed by 3356

Abstract

Transcription factors (TFs) and their complex interplay are essential for directing specific genetic programs, such as responses to environmental stresses, tissue development, or cell differentiation by regulating gene expression. Knowledge regarding TF–TF cooperations could be promising in gaining insight into the developmental switches [...] Read more.

Transcription factors (TFs) and their complex interplay are essential for directing specific genetic programs, such as responses to environmental stresses, tissue development, or cell differentiation by regulating gene expression. Knowledge regarding TF–TF cooperations could be promising in gaining insight into the developmental switches between the cultivars of Brassica napus L., namely Zhongshuang11 (ZS11), a double-low accession with high-oil- content, and Zhongyou821 (ZY821), a double-high accession with low-oil-content. In this regard, we analysed a time series RNA-seq data set of seed tissue from both of the cultivars by mainly focusing on the monotonically expressed genes (MEGs). The consideration of the MEGs enables the capturing of multi-stage progression processes that are orchestrated by the cooperative TFs and, thus, facilitates the understanding of the molecular mechanisms determining seed oil content. Our findings show that TF families, such as NAC, MYB, DOF, GATA, and HD-ZIP are highly involved in the seed developmental process. Particularly, their preferential partner choices as well as changes in their gene expression profiles seem to be strongly associated with the differentiation of the oil content between the two cultivars. These findings are essential in enhancing our understanding of the genetic programs in both cultivars and developing novel hypotheses for further experimental studies. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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13 pages, 2493 KiB

Open AccessArticle

Quantitative Proteomics Reveals that GmENO2 Proteins Are Involved in Response to Phosphate Starvation in the Leaves of Glycine max L.

by Ling Cheng, Wanling Min, Man Li, Lili Zhou, Chuan-Chih Hsu, Xuelian Yang, Xue Jiang, Zhijie Ruan, Yongjia Zhong, Zhi-Yong Wang and Wenfei Wang

Int. J. Mol. Sci. 2021, 22(2), 920; https://doi.org/10.3390/ijms22020920 - 18 Jan 2021

Cited by 11 | Viewed by 2920

Abstract

Soybean (Glycine max L.) is a major crop providing important source for protein and oil for human life. Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt to phosphate (Pi) [...] Read more.

Soybean (Glycine max L.) is a major crop providing important source for protein and oil for human life. Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt to phosphate (Pi) limitation condition. However, the underlying molecular mechanisms responsible for LP stress response remain largely unknown. Here, we performed a label-free quantification (LFQ) analysis of soybean leaves grown under low and high phosphate conditions. We identified 267 induced and 440 reduced differential proteins from phosphate-starved leaves. Almost a quarter of the LP decreased proteins are involved in translation processes, while the LP increased proteins are accumulated in chlorophyll biosynthetic and carbon metabolic processes. Among these induced proteins, an enolase protein, GmENO2a was found to be mostly induced protein. On the transcriptional level, GmENO2a and GmENO2b, but not GmENO2c or GmENO2d, were dramatically induced by phosphate starvation. Among 14 enolase genes, only GmENO2a and GmENO2b genes contain the P1BS motif in their promoter regions. Furthermore, GmENO2b was specifically induced in the GmPHR31 overexpressing soybean plants. Our findings provide molecular insights into how soybean plants tune basic carbon metabolic pathway to adapt to Pi deprivation through the ENO2 enzymes. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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15 pages, 1308 KiB

Open AccessArticle

In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data

by Selina Klees, Thomas Martin Lange, Hendrik Bertram, Abirami Rajavel, Johanna-Sophie Schlüter, Kun Lu, Armin Otto Schmitt and Mehmet Gültas

Int. J. Mol. Sci. 2021, 22(2), 789; https://doi.org/10.3390/ijms22020789 - 14 Jan 2021

Cited by 11 | Viewed by 4405

Abstract

Regulatory SNPs (rSNPs) are a special class of SNPs which have a high potential to affect the phenotype due to their impact on DNA-binding of transcription factors (TFs). Thus, the knowledge about such rSNPs and TFs could provide essential information regarding different genetic [...] Read more.

Regulatory SNPs (rSNPs) are a special class of SNPs which have a high potential to affect the phenotype due to their impact on DNA-binding of transcription factors (TFs). Thus, the knowledge about such rSNPs and TFs could provide essential information regarding different genetic programs, such as tissue development or environmental stress responses. In this study, we use a multi-omics approach by combining genomics, transcriptomics, and proteomics data of two different Brassica napus L. cultivars, namely Zhongshuang11 (ZS11) and Zhongyou821 (ZY821), with high and low oil content, respectively, to monitor the regulatory interplay between rSNPs, TFs and their corresponding genes in the tissues flower, leaf, stem, and root. By predicting the effect of rSNPs on TF-binding and by measuring their association with the cultivars, we identified a total of 41,117 rSNPs, of which 1141 are significantly associated with oil content. We revealed several enriched members of the TF families DOF, MYB, NAC, or TCP, which are important for directing transcriptional programs regulating differential expression of genes within the tissues. In this work, we provide the first genome-wide collection of rSNPs for B. napus and their impact on the regulation of gene expression in vegetative and floral tissues, which will be highly valuable for future studies on rSNPs and gene regulation. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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24 pages, 8099 KiB

Open AccessArticle

Arabidopsis bZIP18 and bZIP52 Accumulate in Nuclei Following Heat Stress where They Regulate the Expression of a Similar Set of Genes

by Anna J. Wiese, Lenka Steinbachová, Ljudmilla Timofejeva, Vojtěch Čermák, Božena Klodová, Ranjani S. Ganji, Mariana Limones-Mendez, Pavel Bokvaj, Said Hafidh, David Potěšil and David Honys

Int. J. Mol. Sci. 2021, 22(2), 530; https://doi.org/10.3390/ijms22020530 - 7 Jan 2021

Cited by 19 | Viewed by 5328

Abstract

Heat stress (HS) is a major abiotic stress that negatively impacts crop yields across the globe. Plants respond to elevated temperatures by changing gene expression, mediated by transcription factors (TFs) functioning to enhance HS tolerance. The involvement of Group I bZIP TFs in [...] Read more.

Heat stress (HS) is a major abiotic stress that negatively impacts crop yields across the globe. Plants respond to elevated temperatures by changing gene expression, mediated by transcription factors (TFs) functioning to enhance HS tolerance. The involvement of Group I bZIP TFs in the heat stress response (HSR) is not known. In this study, bZIP18 and bZIP52 were investigated for their possible role in the HSR. Localization experiments revealed their nuclear accumulation following heat stress, which was found to be triggered by dephosphorylation. Both TFs were found to possess two motifs containing serine residues that are candidates for phosphorylation. These motifs are recognized by 14–3–3 proteins, and bZIP18 and bZIP52 were found to bind 14–3–3 ε, the interaction of which sequesters them to the cytoplasm. Mutation of both residues abolished 14–3–3 ε interaction and led to a strict nuclear localization for both TFs. RNA-seq analysis revealed coordinated downregulation of several metabolic pathways including energy metabolism and translation, and upregulation of numerous lncRNAs in particular. These results support the idea that bZIP18 and bZIP52 are sequestered to the cytoplasm under control conditions, and that heat stress leads to their re-localization to nuclei, where they jointly regulate gene expression. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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20 pages, 5273 KiB

Open AccessArticle

Protein Levels of Several Arabidopsis Auxin Response Factors Are Regulated by Multiple Factors and ABA Promotes ARF6 Protein Ubiquitination

by Keke Li, Sheng Wang, Hong Wu and Hong Wang

Int. J. Mol. Sci. 2020, 21(24), 9437; https://doi.org/10.3390/ijms21249437 - 11 Dec 2020

Cited by 23 | Viewed by 4166

Abstract

The auxin response factor (ARF) transcription factors are a key component in auxin signaling and play diverse functions in plant growth, development, and stress response. ARFs are regulated at the transcript level and posttranslationally by protein modifications. However, relatively little is known regarding [...] Read more.

The auxin response factor (ARF) transcription factors are a key component in auxin signaling and play diverse functions in plant growth, development, and stress response. ARFs are regulated at the transcript level and posttranslationally by protein modifications. However, relatively little is known regarding the control of ARF protein levels. We expressed five different ARFs with an HA (hemagglutinin) tag and observed that their protein levels under the same promoter varied considerably. Interestingly, their protein levels were affected by several hormonal and environmental conditions, but not by the auxin treatment. ABA (abscisic acid) as well as 4 °C and salt treatments decreased the levels of HA-ARF5, HA-ARF6, and HA-ARF10, but not that of HA-ARF19, while 37 °C treatment increased the levels of the four HA-ARFs, suggesting that the ARF protein levels are regulated by multiple factors. Furthermore, MG132 inhibited the reduction of HA-ARF6 level by ABA and 4 °C treatments, suggesting that these treatments decrease HA-ARF6 level through 26S proteasome-mediated protein degradation. It was also found that ABA treatment drastically increased HA-ARF6 ubiquitination, without strongly affecting the ubiquitination profile of the total proteins. Together, these results reveal another layer of control on ARFs, which could serve to integrate multiple hormonal and environmental signals into the ARF-regulated gene expression. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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18 pages, 3318 KiB

Open AccessArticle

Identification and Characterization of PLATZ Transcription Factors in Wheat

by Yuxin Fu, Mengping Cheng, Maolian Li, Xiaojiang Guo, Yongrui Wu and Jirui Wang

Int. J. Mol. Sci. 2020, 21(23), 8934; https://doi.org/10.3390/ijms21238934 - 25 Nov 2020

Cited by 27 | Viewed by 3479

Abstract

The PLATZ (plant AT-rich protein and zinc-binding protein) transcription factor family is a class of plant-specific zinc-dependent DNA-binding proteins. PLATZ has essential roles in seed endosperm development, as well as promoting cell proliferation duration in the earlier stages of the crops. In the [...] Read more.

The PLATZ (plant AT-rich protein and zinc-binding protein) transcription factor family is a class of plant-specific zinc-dependent DNA-binding proteins. PLATZ has essential roles in seed endosperm development, as well as promoting cell proliferation duration in the earlier stages of the crops. In the present study, 62 TaPLATZ genes were identified from the wheat genome, and they were unequally distributed on 15 chromosomes. According to the phylogenetic analysis, 62 TaPLATZ genes were classified into six groups, including two groups that were unique in wheat. Members in the same groups shared similar exon-intron structures. The polyploidization, together with genome duplication of wheat, plays a crucial role in the expansion of the TaPLATZs family. Transcriptome data indicated a distinct divergence expression pattern of TaPLATZ genes that could be clustered into four modules. The TaPLATZs in Module b possessed a seed-specific expression pattern and displayed obvious high expression in the earlier development stage of seeds. Subcellular localization data of TaPLATZs suggesting that they likely perform a function as a conventional transcription factor. This study provides insight into understanding the structure divergence, evolutionary features, expression profiles, and potential function of PLATZ in wheat. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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18 pages, 3582 KiB

Open AccessArticle

Identification of Phytochrome-Interacting Factor Family Members and Functional Analysis of MdPIF4 in Malus domestica

by Peng-Fei Zheng, Xun Wang, Yu-Ying Yang, Chun-Xiang You, Zhen-Lu Zhang and Yu-Jin Hao

Int. J. Mol. Sci. 2020, 21(19), 7350; https://doi.org/10.3390/ijms21197350 - 5 Oct 2020

Cited by 28 | Viewed by 3089

Abstract

Phytochrome-interacting factors (PIFs), members of the basic helix-loop-helix transcription factor family that have been extensively investigated in Arabidopsis thaliana, play essential roles in plant growth and development. However, PIF members have not been systematically investigated in apples, a worldwide perennial woody crop [...] Read more.

Phytochrome-interacting factors (PIFs), members of the basic helix-loop-helix transcription factor family that have been extensively investigated in Arabidopsis thaliana, play essential roles in plant growth and development. However, PIF members have not been systematically investigated in apples, a worldwide perennial woody crop of economic importance. Here, seven PIF genes were identified from the Malus × domestica reference genome. Chromosomal locations, gene structures, and phylogenetic relationships of these members were analyzed. Analysis of cis-acting elements in promoter regions of MdPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Subsequently, subcellular localization and transcriptional activity analysis revealed that MdPIFs were typical nuclear transcription factors with transcriptional activation ability. Expression analysis demonstrated that MdPIF genes had different gene expression patterns for various abiotic factors. Moreover, overexpressed MdPIF4 reduced the sensitivity of apple calluses to abscisic acid (ABA). Our work lays foundations for further investigation of PIF functions in plant growth and development in apples. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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19 pages, 1766 KiB

Open AccessReview

MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development

by Ruixue Xiao, Chong Zhang, Xiaorui Guo, Hui Li and Hai Lu

Int. J. Mol. Sci. 2021, 22(7), 3560; https://doi.org/10.3390/ijms22073560 - 30 Mar 2021

Cited by 106 | Viewed by 7351

Abstract

The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing [...] Read more.

The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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20 pages, 2342 KiB

Open AccessReview

NAC Transcription Factors as Positive or Negative Regulators during Ongoing Battle between Pathogens and Our Food Crops

by Zhiyuan Bian, Huanhuan Gao and Chongying Wang

Int. J. Mol. Sci. 2021, 22(1), 81; https://doi.org/10.3390/ijms22010081 - 23 Dec 2020

Cited by 63 | Viewed by 6478

Abstract

The NAC (NAM, ATAF1/2, and CUC2) family of proteins is one of the largest plant-specific transcription factor (TF) families and its members play varied roles in plant growth, development, and stress responses. In recent years, NAC TFs have been demonstrated to participate in [...] Read more.

The NAC (NAM, ATAF1/2, and CUC2) family of proteins is one of the largest plant-specific transcription factor (TF) families and its members play varied roles in plant growth, development, and stress responses. In recent years, NAC TFs have been demonstrated to participate in crop-pathogen interactions, as positive or negative regulators of the downstream defense-related genes. NAC TFs link signaling pathways between plant hormones, including salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA), or other signals, such as reactive oxygen species (ROS), to regulate the resistance against pathogens. Remarkably, NAC TFs can also contribute to hypersensitive response and stomatal immunity or can be hijacked as virulence targets of pathogen effectors. Here, we review recent progress in understanding the structure, biological functions and signaling networks of NAC TFs in response to pathogens in several main food crops, such as rice, wheat, barley, and tomato, and explore the directions needed to further elucidate the function and mechanisms of these key signaling molecules. Full article

(This article belongs to the Special Issue Functions of Transcription Factors in Plant Growth, Performance and Responses to Environmental Stresses)

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