Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

A Rapid and Simplified Method to Isolate Specific Regulators Based on Biotin-Avidin Binding Affinities in Crops

Transcription factors (TFs) are indispensable components of transcriptional regulatory pathways involved in crop growth and development. Herein, we developed a new method for the identification of upstream TFs specific to genes in crops based on the binding affinities of biotin and avidin. First, we constructed and verified the new biotin and avidin system (BAS) by a coprecipitation assay. Subsequently, the feasibility of DNA-based BAS (DBAS) was further proved by in vivo and in vitro assays. Furthermore, we cloned the promoter of rice OsNRT1.1B and the possible regulators were screened and identified. Additionally, partial candidates were validated by the electrophoresis mobility shift assay (EMSA), yeast one-hybrid, and luciferase activity assays. Remarkably, the results showed that the candidates PIP3 and PIP19 both responded to nitrate immediately and overexpression of PIP3 caused retard growth, which indicates that the candidates are functional and the new DBAS method is useful to isolate regulators in crops.

Comprehensive Genomic Analysis of Trihelix Family in Tea Plant (Camellia sinensis) and Their Putative Roles in Osmotic Stress

In plants, Trihelix transcription factors are responsible for regulating growth, development, and reaction to various abiotic stresses. However, their functions in tea plants are not yet fully understood. This study identified a total of 40 complete Trihelix genes in the tea plant genome, which are classified into five clades: GT-1 (5 genes), GT-2 (8 genes), GTγ (2 genes), SH4 (7 genes), and SIP1 (18 genes). The same subfamily exhibits similar gene structures and functional domains. Chromosomal mapping analysis revealed that chromosome 2 has the most significant number of trihelix family members. Promoter analysis identified cis-acting elements in C. sinensis trihelix (CsTH), indicating their potential to respond to various phytohormones and stresses. The expression analysis of eight representative CsTH genes from four subfamilies showed that all CsTHs were expressed in more tissues, and three CsTHs were significantly induced under ABA, NaCl, and drought stress. This suggests that CsTHs plays an essential role in tea plant growth, development, and response to osmotic stress. Furthermore, yeast strains have preliminarily proven that CsTH28, CsTH36, and CsTH39 can confer salt and drought tolerance. Our study provides insights into the phylogenetic relationships and functions of the trihelix transcription factors in tea plants. It also presents new candidate genes for stress-tolerance breeding.

Genome-Wide Identification of the Trihelix Transcription Factor Family and Functional Analysis of the Drought Stress-Responsive Genes in Melilotus albus

The trihelix gene family is a plant-specific family of transcription factors that play an important role in many metabolic pathways, including plant growth and development and stress responses. Drought stress is a major factor limiting the distribution and yield of Melilotus albus. However, the distribution of this gene family in M. albus and its biological functions in response to drought stress have not been reported. To investigate the responses of functional genes to drought stress in M. albus, in this study, a total of 34 MaGTs were identified and characterized, of which 32 MaGT proteins were predicted to be nuclear-localized. Based on conserved motif and phylogenetic analyses, the MaGTs could be divided into five subgroups (GT-1, GT-2, SH4, GT-γ, SIP1). Seven potential candidate genes for drought tolerance were screened and identified via qRT-PCR based on a transcriptome data analysis of drought stress in M. albus. The results indicated that MaGT17 was not only significantly upregulated in the roots after 24 h of drought stress, but also showed a significant induction in the shoots. This finding further confirms that MaGT17 is capable of responding to drought stress in M. albus. Taken together, these results will offer essential insights for understanding the underlying molecular mechanisms of the trihelix proteins and useful data for further research on the growth, development and stress responses of trihelix proteins in M. albus.

In-silico analysis of heat shock transcription factor (OsHSF) gene family in rice (Oryza sativa L.)

BACKGROUND

One of the most important cash crops worldwide is rice (Oryza sativa L.). Under varying climatic conditions, however, its yield is negatively affected. In order to create rice varieties that are resilient to abiotic stress, it is essential to explore the factors that control rice growth, development, and are source of resistance. HSFs (heat shock transcription factors) control a variety of plant biological processes and responses to environmental stress. The in-silico analysis offers a platform for thorough genome-wide identification of OsHSF genes in the rice genome.

RESULTS

In this study, 25 randomly dispersed HSF genes with significant DNA binding domains (DBD) were found in the rice genome. According to a gene structural analysis, all members of the OsHSF family share Gly-66, Phe-67, Lys-69, Trp-75, Glu-76, Phe-77, Ala-78, Phe-82, Ile-93, and Arg-96. Rice HSF family genes are widely distributed in the vegetative organs, first in the roots and then in the leaf and stem; in contrast, in reproductive tissues, the embryo and lemma exhibit the highest levels of gene expression. According to chromosomal localization, tandem duplication and repetition may have aided in the development of novel genes in the rice genome. OsHSFs have a significant role in the regulation of gene expression, regulation in primary metabolism and tolerance to environmental stress, according to gene networking analyses.

CONCLUSION

Six genes viz; Os01g39020, Os01g53220, Os03g25080, Os01g54550, Os02g13800 and Os10g28340 were annotated as promising genes. This study provides novel insights for functional studies on the OsHSFs in rice breeding programs. With the ultimate goal of enhancing crops, the data collected in this survey will be valuable for performing genomic research to pinpoint the specific function of the HSF gene during stress responses.

Genome-wide characterization, evolutionary analysis, and expression pattern analysis of the trihelix transcription factor family and gene expression analysis under MeJA treatment in Panax ginseng

Panax ginseng is a well-known medicinal plant with several pharmacological uses in China. The trihelix family transcription factors, also known as GT factors, can be involved in the regulation of growth and developmental processes in plants. There have been no in-depth reports or systematic studies about the trihelix transcription factor in ginseng. In this study, the structure, chromosomal localization, gene duplication, phylogeny, functional differentiation, expression patterns and coexpression interactions of trihelix transcripts were analysed using bioinformatics methods based on the ginseng transcriptome database. Thirty-two trihelix transcription factor genes were identified in ginseng, and these genes were alternatively spliced to obtain 218 transcripts. These transcripts were unevenly distributed on different chromosomes of ginseng, and phylogenetic analysis classified the PgGT transcripts into five subgroups. Gene Ontology (GO) analysis classified PgGT transcripts into eight functional subclasses, indicating that they are functionally diverse. The expression pattern analysis of 218 PgGT transcripts revealed that their expression was tissue-specific and spatiotemporally-specific in 14 different tissues of 4-year-old ginseng, 4 different ages of ginseng roots, and 42 farmers' cultivars of 4-year-old ginseng roots. Despite the differences in the expression patterns of these transcripts, coexpression network analysis revealed that these transcripts could be expressed synergistically in ginseng. In addition, two randomly selected PgGT transcripts in each of the five different subfamilies were subjected to methyl jasmonate treatment at different times, and PgGT was able to respond to the regulation of methy1 jasmonate. These results provide a theoretical basis and gene resources for an in-depth study of the function of trihelix genes in other plants.

Genome-Wide Identification and Expression Profiling Analysis of the Trihelix Gene Family and response of PgGT1 under Abiotic Stresses in Platycodon grandiflorus

The trihelix gene family plays an important role in plant growth and abiotic stress responses. Through the analysis of genomic and transcriptome data, 35 trihelix family members were identified for the first time in Platycodon grandiflorus; they were classified into five subfamilies: GT-1, GT-2, SH4, GTγ, and SIP1. The gene structure, conserved motifs and evolutionary relationships were analyzed. Prediction of physicochemical properties of the 35 trihelix proteins founded, the number of amino acid molecules is between 93 and 960, theoretical isoelectric point is between 4.24 and 9.94, molecular weight is between 9829.77 and 107435.38, 4 proteins among them were stable, and all GRAVY is negative. The full-length cDNA sequence of the PgGT1 gene of the GT-1 subfamily was cloned by PCR. It is a 1165 bp ORF encoding a 387 amino acid protein, with a molecular weight of 43.54 kDa. The predicted subcellular localization of the protein in the nucleus was experimentally verified. After being treated with NaCl, PEG6000, MeJA, ABA, IAA, SA, and ethephon, the expression of PgGT1 gene showed an up-regulated trend except for the roots treated with NaCl and ABA. This study laid a bioinformatics foundation for the research of trihelix gene family and the cultivation of excellent germplasm of P. grandiflorus.

Identification of HQT gene family and their potential function in CGA synthesis and abiotic stresses tolerance in vegetable sweet potato

Hydroxycinnamate-CoA quinate hydroxycinnamoyl transferase (HQT) enzyme affect plant secondary metabolism and are crucial for growth and development. To date, limited research on the genome-wide analysis of HQT family genes and their regulatory roles in chlorogenic acid (CGA) accumulation in leafy vegetable sweet potato is available. Here, a total of 58 HQT family genes in the sweet potato genome (named IbHQT) were identified and analyzed. We studied the chromosomal distribution, phylogenetic relationship, motifs distribution, collinearity, and cis-acting element analysis of HQT family genes. This study used two sweet potato varieties, high CGA content Fushu 7-6-14-7 (HC), and low CGA content Fushu 7-6 (LC). Based on the phylogenetic analysis, clade A was unique among the identified four clades as it contained HQT genes from various species. The chromosomal location and collinearity analysis revealed that tandem gene duplication may promote the IbHQT gene expansion and expression. The expression patterns and profile analysis showed changes in gene expression levels at different developmental stages and under cold, drought, and salt stress conditions. The expression analysis verified by qRT-PCR revealed that IbHQT genes were highly expressed in the HC variety leaves than in the LC variety. Furthermore, cloning and gene function analysis unveiled that IbHQT family genes are involved in the biosynthesis and accumulation of CGA in sweet-potato. This study expands our understanding of the regulatory role of HQT genes in sweet-potato and lays a foundation for further functional characterization and genetic breeding by engineering targeted HQT candidate genes in various sweet-potato varieties and other species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01299-4.

Genome-wide analysis of the 6B-INTERACTING PROTEIN1 gene family with functional characterization of MdSIP1-2 in Malus domestica

Trihelix transcription factors consist of five subfamilies, including GT-1, GT-2, SH4, GTγ, and SIP1, which play important roles in the responses to biotic and abiotic stresses, however, seldom is known about the role of the SIP1 genes in apples. In this study, 12 MdSIP1 genes were first identified in apples by genome-wide analysis, and contained conserved MYB/SANT-like domains. Expression patterns analyses showed that the MdSIP1 genes had different tissue expression patterns, and different transcription levels in response to abiotic stresses, indicating that MdSIP1s may play multiple roles under various abiotic stresses. Among them, the MdSIP1-2 gene was cloned and ectopic transformed into Arabidopsis, and its biology function was identified. The subcellular localization showed that MdSIP1-2 protein was specifically localized in the nucleus, and that overexpression of MdSIP1-2 promoted the development of lateral roots, increased abscisic acid (ABA) sensitivity, and improved salt and drought tolerance. These findings suggested that MdSIP1-2 plays an important role in root development, ABA synthesis, and salt and drought stress tolerance. In conclusion, these results lay a solid foundation for determining the role of MdSIP1 in the growth and development and abiotic stress tolerance of apples.

GT Transcription Factors of Rosa rugosa Thunb. Involved in Salt Stress Response

Rosa rugosa was a famous aromatic plant while poor salt tolerance of commercial cultivars has hindered its culture in saline-alkali soil. In many plants, the roles of GT (or trihelix) genes in salt stresses responses have been emerging. In the wild R. rugosa, a total of 37 GTs (RrGTs) were grouped into GT-1, GT-2, GTγ, SH4, and SIP1 lineages. SIP1 lineage expanded by transposition. The motifs involved in the binding of GT cis-elements were conserved. Four RrGTs (RrGT11/14/16/18) significantly differentially expressed in roots or leaves under salt stress. The responsive patterns within 8 h NaCl treatment indicated that RrGTγ-4 (RrGT18) and RrGT-1 (RrGT16) were significantly induced by salt in roots of R. rugosa. Subcellular localizations of RrSIP1 (RrGT11) and RrGTγ-4 were on chloroplasts while RrGT-1 and RrSIP2 (RrGT14) located on cell nucleus. Regulation of ion transport could be the most important role of RrSIPs and RrGTγ-4. And RrGT-1 could be a halophytic gene with higher transcription abundance than glycophytic GT-1. These results provide key clue for further investigations of roles of RrGTs in salt stress response and would be helpful in the understanding the salt tolerance regulation mechanism of R. rugosa.

Identification and analysis of differentially expressed trihelix genes in maize (Zea mays) under abiotic stresses

Background

Trihelix transcription factors play important roles in triggering plant growth and imparting tolerance against biotic and abiotic stresses. However, a systematical analysis of the trihelix transcription factor family under heat and drought stresses in maize has not been reported.

Methods

PlantTFDB and TBtools were employed to identify the trihelix domain-containing genes in the maize genome. The heat-regulated transcriptome data for maize were obtained from NCBI to screen differentially expressed ZmTHs genes through statistical analysis. The basic protein sequences, chromosomal localization, and subcellular localization were analyzed using Maize GDB, Expasy, SOMPA, TBtools, and Plant-mPLoc. The conserved motifs, evolutionary relationships, and cis-elements, were analyzed by MEME, MEGA7.0 and PlantCARE software, respectively. The tissue expression patterns of ZmTHs and their expression profiles under heat and drought stress were detected using quantitative real-time PCR (qRT-PCR).

Results

A total of 44 trihelix family members were discovered, and members were distributed over 10 chromosomes in the maize genome. A total of 11 genes were identified that were regulated by heat stress; these were unevenly distributed on chromosomes 1, 2, 4, 5, and 10. ZmTHs encoded a total of 16 proteins, all of which were located in the nucleus; however, ZmTH04.1 was also distributed in the chloroplast. The protein length varied from 206 to 725 amino acids; the molecular weight ranged from 22.63 to 76.40 kD; and the theoretical isoelectric point (pI) ranged from 5.24 to 11.2. The protein's secondary structures were mainly found to be random coils and α-helices, with fewer instances of elongation chains and β-rotations. Phylogenetic relationship analysis showed that these can be divided into five sub-groups. The conserved domain of ZmTHs was GT1 or MyB_DNA-Bind_4. The protein and gene structure of ZmTHs differed greatly among the subfamilies, while the structures within the subfamilies were similar. The promoter of ZmTHs contained abundant tissue-specific expression cis-acting elements and abiotic stress response elements. qRT-PCR analysis showed that ZmTHs expression levels were significantly different in different tissues. Furthermore, the expression of ZmTH08 was dramatically up-regulated by heat stress, while the expression of ZmTH03, ZmTH04, ZmTH05, ZmTH06, ZmTH07, ZmTH09, ZmTH10, and ZmTH11 were down-regulated by heat stress. Upon PEG-simulated drought stress, ZmTH06 was significantly up-regulated, while ZmTH01 and ZmTH07 were down-regulated.

Conclusions

We performed a genome-wide, systematic identification and analysis of differentially expressed trihelix genes under heat and drought stresses in maize.

Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

BACKGROUND

Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum.

RESULTS

Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum.

CONCLUSIONS

In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.

Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

Background

The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in several dicots and monocots, this gene family is yet to be studied in Chenopodium quinoa (quinoa).

Results

In this study, 47 C. quinoa trihelix (CqTH) genes were in the quinoa genome. Phylogenetic analysis of the CqTH and trihelix genes from Arabidopsis thaliana and Beta vulgaris revealed that the genes were clustered into five subfamilies: SIP1, GTγ, GT1, GT2, and SH4. Additionally, synteny analysis revealed that the CqTH genes were located on 17 chromosomes, with the exception of chromosomes 8 and 11, and 23 pairs of segmental duplication genes were detected. Furthermore, expression patterns of 10 CqTH genes in different plant tissues and at different developmental stages under abiotic stress and phytohormone treatment were examined. Among the 10 genes, CqTH02, CqTH25, CqTH18, CqTH19, CqTH25, CqTH31, and CqTH36, were highly expressed in unripe achenes 21 d after flowering and in mature achenes compared with other plant tissues. Notably, the 10 CqTH genes were upregulated in UV-treated leaves, whereas CqTH36 was consistently upregulated in the leaves under all abiotic stress conditions.

Conclusions

The findings of this study suggest that gene duplication could be a major driver of trihelix gene evolution in quinoa. These findings could serve as a basis for future studies on the roles of CqTH transcription factors and present potential genetic markers for breeding stress-resistant and high-yielding quinoa varieties.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08726-y.

Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L

BACKGROUND

The basic leucine zipper (bZIP) transcription factor (TF) is one of the largest families of transcription factors (TFs). It is widely distributed and highly conserved in animals, plants, and microorganisms. Previous studies have shown that the bZIP TF family is involved in plant growth, development, and stress responses. The bZIP family has been studied in many plants; however, there is little research on the bZIP gene family in tobacco.

RESULTS

In this study, 77 bZIPs were identified in tobacco and named NtbZIP01 through to NtbZIP77. These 77 genes were then divided into eleven subfamilies according to their homology with Arabidopsis thaliana. NtbZIPs were unevenly distributed across twenty-two tobacco chromosomes, and we found sixteen pairs of segmental duplication. We further studied the collinearity between these genes and related genes of six other species. Quantitative real-time polymerase chain reaction analysis identified that expression patterns of bZIPs differed, including in different organs and under various abiotic stresses. NtbZIP49 might be important in the development of flowers and fruits; NtbZIP18 might be an important regulator in abiotic stress.

CONCLUSIONS

In this study, the structures and functions of the bZIP family in tobacco were systematically explored. Many bZIPs may play vital roles in the regulation of organ development, growth, and responses to abiotic stresses. This research has great significance for the functional characterisation of the tobacco bZIP family and our understanding of the bZIP family in higher plants.