Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.

Abstract Background Plant homeodomain (PHD) finger proteins are widely present in all eukaryotes and play important roles in chromatin remodeling and transcriptional regulation. The PHD finger can specifically bind a number of histone modifications as an “epigenome reader”, and mediate the activation or repression of underlying genes. Many PHD finger genes have been characterized in animals, but only few studies were conducted on plant PHD finger genes to this day. Brassica rapa (AA, 2n = 20) is an economically important vegetal, oilseed and fodder crop, and also a good model crop for functional and evolutionary studies of important gene families among Brassica species due to its close relationship to Arabidopsis thaliana. Results We identified a total of 145 putative PHD finger proteins containing 233 PHD domains from the current version of B. rapa genome database. Gene ontology analysis showed that 67.7% of them were predicted to be located in nucleus, and 91.3% were predicted to be involved in protein binding activity. Phylogenetic, gene structure, and additional domain analyses clustered them into different groups and subgroups, reflecting their diverse functional roles during plant growth and development. Chromosomal location analysis showed that they were unevenly distributed on the 10 B. rapa chromosomes. Expression analysis from RNA-Seq data showed that 55.7% of them were constitutively expressed in all the tested tissues or organs with relatively higher expression levels reflecting their important housekeeping roles in plant growth and development, while several other members were identified as preferentially expressed in specific tissues or organs. Expression analysis of a subset of 18 B. rapa PHD finger genes under drought and salt stresses showed that all these tested members were responsive to the two abiotic stress treatments. Conclusions Our results reveal that the PHD finger genes play diverse roles in plant growth and development, and can serve as a source of candidate genes for genetic engineering and improvement of Brassica crops against abiotic stresses. This study provides valuable information and lays the foundation for further functional determination of PHD finger genes across the Brassica species.

Download Full-text

Genome-wide investigation of Hydroxycinnamoyl CoA: Shikimate Hydroxycinnamoyl Transferase (HCT) gene family in Carthamus tinctorius L.

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha49312489 ◽

2021 ◽

Vol 49 (3) ◽

pp. 12489

Author(s):

Sun FAN ◽

Naveed AHMAD ◽

Jin LIBO ◽

Zhang XINYUE ◽

Ma XINTONG ◽

...

Keyword(s):

Abiotic Stress ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Growth And Development ◽

Carthamus Tinctorius ◽

Plant Growth And Development ◽

Monolignol Biosynthesis ◽

Genome Wide ◽

Wide Range

Hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) is mainly associated with monolignol biosynthesis, a central precursor to producing guaiacyl and syringyl lignins in plants. However, the explicit regulatory mechanism of HCT-mediated monolignol biosynthesis in plants still remained unclear. Here, the genome-wide analysis of the HCT gene family in Carthamus tinctorius as a target for understanding growth, development, and stress-responsive mechanisms was investigated. A total of 82 CtHCT genes were identified and characterized. Most of the CtHCTs proteins demonstrated the presence of two common conserved domains, including HXXXD and DFGWG. In addition, the conserved structure of protein motifs, PPI network, cis-regulatory units, and gene structure analysis demonstrated several genetic determinants reflecting the wide range of functional diversity of CtHCT-encoding genes. The observed expression analysis of CtHCT genes in different flowering stages under normal conditions partially highlighted their putative roles in plant growth and development pathways. Moreover, CtHCT genes appeared to be associated with abiotic stress responses as validated by the expression profiling in various flowering phases under light irradiation and MeJA treatment. Altogether, these findings provide new insights into identifying crucial molecular targets associated with plant growth and development and present practical information for understanding abiotic stress-responsive mechanisms in plants.

Download Full-text

Genome-wide Identification and Expression Pattern Analysis of Zinc-finger Homeodomain Transcription Factors in Tomato under Abiotic Stress

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04245-17 ◽

2018 ◽

Vol 143 (1) ◽

pp. 14-22 ◽

Cited By ~ 3

Author(s):

Jingkang Hu ◽

Yingmei Gao ◽

Tingting Zhao ◽

Jingfu Li ◽

Meini Yao ◽

...

Keyword(s):

Abiotic Stress ◽

Plant Growth ◽

Zinc Finger ◽

Stress Responses ◽

Growth And Development ◽

Phylogenetic Analyses ◽

Plant Responses ◽

Plant Growth And Development ◽

Significant Information ◽

Functional Studies

Members of the zinc-finger homeodomain (ZF-HD) family play a key role in the control of plant growth and development, which are involved in plant responses to stress. Although many functional studies of this gene family have been performed in different plants, the features of this family in tomato (Solanum lycopersicum) remain unknown. In this study, we identified 22 ZF-HD genes in the tomato genome and classified them into seven groups located on six chromosomes. Expression of 15 ZF-HD genes in tomato was studied in different tissues to identify their putative functions in many aspects of plant growth and development. Based on previous phylogenetic analyses in arabidopsis (Arabidopsis thaliana), our results showed that some tomato SL-ZH (S. lycopersicum zinc-finger homeodomain) genes cluster into the same neighbor-joining (NJ) branch as arabidopsis, indicating that these genes may share similar structures and functions in these plants. Gene expression analysis demonstrated that the tomato ZF-HD gene may be involved in abiotic stress responses, the SL-ZH13 gene in cold stress and the SL-ZH15 gene in drought stress; almost all tomato ZF-HD genes were responsive to salt stress, except for SL-ZH7, -ZH8, and -ZH22. However, the structures and functions of unknown groups require further research. In conclusion, this study identified tomato ZF-HD genes and analyzed their gene structures, subfamily distribution, and expression characteristics. These experiments combined with previous research findings reveal significant information and insight for future studies on the agronomic features and stress resistance in tomato.

Download Full-text

Signaling Peptides Regulating Abiotic Stress Responses in Plants

Frontiers in Plant Science ◽

10.3389/fpls.2021.704490 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jin Sun Kim ◽

Byeong Wook Jeon ◽

Jungmook Kim

Keyword(s):

Abiotic Stress ◽

Plant Growth ◽

Signaling Pathways ◽

Stress Responses ◽

Growth And Development ◽

Control Plant ◽

Phosphate Deficiency ◽

Plant Responses ◽

Plant Growth And Development ◽

Signaling Peptides

As sessile organisms, plants are exposed to constantly changing environments that are often stressful for their growth and development. To cope with these stresses, plants have evolved complex and sophisticated stress-responsive signaling pathways regulating the expression of transcription factors and biosynthesis of osmolytes that confer tolerance to plants. Signaling peptides acting like phytohormones control various aspects of plant growth and development via cell-cell communication networks. These peptides are typically recognized by membrane-embedded receptor-like kinases, inducing activation of cellular signaling to control plant growth and development. Recent studies have revealed that several signaling peptides play important roles in plant responses to abiotic stress. In this mini review, we provide recent findings on the roles and signaling pathways of peptides that are involved in coordinating plant responses to abiotic stresses, such as dehydration, high salinity, reactive oxygen species, and heat. We also discuss recent developments in signaling peptides that play a role in plant adaptation responses to nutrient deficiency stress, focusing on nitrogen and phosphate deficiency responses.

Download Full-text

Functions of PPR Proteins in Plant Growth and Development

International Journal of Molecular Sciences ◽

10.3390/ijms222011274 ◽

2021 ◽

Vol 22 (20) ◽

pp. 11274

Author(s):

Xiulan Li ◽

Mengdi Sun ◽

Shijuan Liu ◽

Qian Teng ◽

Shihui Li ◽

...

Keyword(s):

Plant Growth ◽

Stress Responses ◽

Rna Processing ◽

Growth And Development ◽

Molecular Mechanisms ◽

Rna Binding ◽

Plant Mitochondria ◽

Research Progress ◽

Plant Growth And Development ◽

Ppr Proteins

Pentatricopeptide repeat (PPR) proteins form a large protein family in land plants, with hundreds of different members in angiosperms. In the last decade, a number of studies have shown that PPR proteins are sequence-specific RNA-binding proteins involved in multiple aspects of plant organellar RNA processing, and perform numerous functions in plants throughout their life cycle. Recently, computational and structural studies have provided new insights into the working mechanisms of PPR proteins in RNA recognition and cytidine deamination. In this review, we summarized the research progress on the functions of PPR proteins in plant growth and development, with a particular focus on their effects on cytoplasmic male sterility, stress responses, and seed development. We also documented the molecular mechanisms of PPR proteins in mediating RNA processing in plant mitochondria and chloroplasts.

Download Full-text

Genome-Wide Identification and Comparative Analysis of ARF Family Genes in Three Apiaceae Species

Frontiers in Genetics ◽

10.3389/fgene.2020.590535 ◽

2021 ◽

Vol 11 ◽

Author(s):

Qiaoying Pei ◽

Nan Li ◽

Qihang Yang ◽

Tong Wu ◽

Shuyan Feng ◽

...

Keyword(s):

Plant Growth ◽

Gene Family ◽

Growth And Development ◽

Expression Patterns ◽

Gene Families ◽

Plant Growth And Development ◽

Response Factors ◽

Auxin Response Factors ◽

Functional Analyses ◽

Significant Positive Selection

The family Apiaceae includes many important vegetables and medicinal plants. Auxin response factors (ARFs) play critical roles in regulating plant growth and development. Here, we performed a comprehensive analysis of the ARF gene family in three Apiaceae species, celery, coriander, and carrot, and compared the results with the ARF gene family of lettuce, Arabidopsis, and grape. We identified 156 ARF genes in all six species and 89 genes in the three Apiaceae species, including 28, 34, and 27 in celery, coriander, and carrot, respectively. The paralogous gene number in coriander was far greater than that in carrot and celery. Our analysis revealed that ARF genes of the three Apiaceae species in 34 branches of the phylogenetic tree underwent significant positive selection. Additionally, our findings indicated that whole-genome duplication played an important role in ARF gene family expansion. Coriander contained a greater number of ARF genes than celery and carrot because of more gene duplications and less gene losses. We also analyzed the expression of ARF genes in three tissues by RNA-seq and verified the results by quantitative real-time PCR. Furthermore, we found that several paralogous genes exhibited divergent expression patterns. Overall, this study provides a valuable resource for exploring how ARF family genes regulate plant growth and development in other plants. Since this is the first report of the ARF gene family in Apiaceae, our results will serve as a guide for comparative and functional analyses of ARF and other gene families in Apiaceae.

Download Full-text

Rice SUT and SWEET Transporters

International Journal of Molecular Sciences ◽

10.3390/ijms222011198 ◽

2021 ◽

Vol 22 (20) ◽

pp. 11198

Author(s):

Zhi Hu ◽

Zhenjia Tang ◽

Yanming Zhang ◽

Liping Niu ◽

Fang Yang ◽

...

Keyword(s):

Plant Growth ◽

Stress Responses ◽

Growth And Development ◽

Gene Knockout ◽

Family Members ◽

Sugar Transporter ◽

Biotic And Abiotic Stress ◽

Plant Growth And Development ◽

Sugar Transporters ◽

Regulation Mechanisms

Sugar transporters play important or even indispensable roles in sugar translocation among adjacent cells in the plant. They are mainly composed of sucrose–proton symporter SUT family members and SWEET family members. In rice, 5 and 21 members are identified in these transporter families, and some of their physiological functions have been characterized on the basis of gene knockout or knockdown strategies. Existing evidence shows that most SUT members play indispensable roles, while many SWEET members are seemingly not so critical in plant growth and development regarding whether their mutants display an aberrant phenotype or not. Generally, the expressions of SUT and SWEET genes focus on the leaf, stem, and grain that represent the source, transport, and sink organs where carbohydrate production, allocation, and storage take place. Rice SUT and SWEET also play roles in both biotic and abiotic stress responses in addition to plant growth and development. At present, these sugar transporter gene regulation mechanisms are largely unclear. In this review, we compare the expressional profiles of these sugar transporter genes on the basis of chip data and elaborate their research advances. Some suggestions concerning future investigation are also proposed.

Download Full-text

Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽

10.7717/peerj.7950 ◽

2019 ◽

Vol 7 ◽

pp. e7950 ◽

Cited By ~ 2

Author(s):

Yongbin Wang ◽

Lei Ling ◽

Zhenfeng Jiang ◽

Weiwei Tan ◽

Zhaojun Liu ◽

...

Keyword(s):

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Growth And Development ◽

Genomic Data ◽

Evolutionary Analysis ◽

Rna Seq ◽

Plant Growth And Development ◽

Genome Wide ◽

Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

Download Full-text

Cloning and expression analysis of ZmABI3 gene in Zea mays

Turkish Journal of Biochemistry ◽

10.1515/tjb-2016-0303 ◽

2017 ◽

Vol 42 (3) ◽

Cited By ~ 1

Author(s):

Qiaoyun Weng ◽

Jinhui Song ◽

Hailian Ma ◽

Jincheng Yuan ◽

Yanmin Zhao ◽

...

Keyword(s):

Zea Mays ◽

Transcription Factor ◽

Plant Growth ◽

Plant Species ◽

Expression Analysis ◽

Growth And Development ◽

Cloning And Expression ◽

Plant Growth And Development ◽

New Gene ◽

B3 Domain

AbstractObjectiveABI3 is a B3 domain transcription factor existed in various plant species. Studies showed that ABI3 play important role in plant growth and development.MethodsTheResultsOne gene contained B3 domain was isolated from maize, designated asConclusionA new gene contained a B3 domain was cloned and named as

Download Full-text

Understanding and exploiting autophagy signaling in plants

Essays in Biochemistry ◽

10.1042/ebc20170034 ◽

2017 ◽

Vol 61 (6) ◽

pp. 675-685 ◽

Cited By ~ 14

Author(s):

Henri Batoko ◽

Yasin Dagdas ◽

Frantisek Baluska ◽

Agnieszka Sirko

Keyword(s):

Abiotic Stress ◽

Plant Growth ◽

Growth And Development ◽

Molecular Mechanisms ◽

Regulatory Mechanisms ◽

Catabolic Pathway ◽

Plant Growth And Development ◽

The Core ◽

Important Pathway ◽

Sessile Organisms

Autophagy is an essential catabolic pathway and is activated by various endogenous and exogenous stimuli. In particular, autophagy is required to allow sessile organisms such as plants to cope with biotic or abiotic stress conditions. It is thought that these various environmental signaling pathways are somehow integrated with autophagy signaling. However, the molecular mechanisms of plant autophagy signaling are not well understood, leaving a big gap of knowledge as a barrier to being able to manipulate this important pathway to improve plant growth and development. In this review, we discuss possible regulatory mechanisms at the core of plant autophagy signaling.

Download Full-text