scholarly journals Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12221
Author(s):  
Junchang Li ◽  
Yumei Jiang ◽  
Jing Zhang ◽  
Yongjing Ni ◽  
Zhixin Jiao ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Protein Structures ◽  
Promoter Regions ◽  
Production Studies ◽  
Homoeologous Genes ◽  
Duplication Events ◽  
Wheat Development ◽  
Exogenous Iaa

Tillering ability is a key agronomy trait for wheat (Triticum aestivum L.) production. Studies on a dwarf monoculm wheat mutant (dmc) showed that ARF11 played an important role in tillering of wheat. In this study, a total of 67 ARF family members were identified and clustered to two main classes with four subgroups based on their protein structures. The promoter regions of T. aestivum ARF (TaARF) genes contain a large number of cis-acting elements closely related to plant growth and development, and hormone response. The segmental duplication events occurred commonly and played a major role in the expansion of TaARFs. The gene collinearity degrees of the ARFs between wheat and other grasses, rice and maize, were significantly high. The evolution distances among TaARFs determine their expression profiles, such as homoeologous genes have similar expression profiles, like TaARF4-3A-1, TaARF4-3A-2 and their homoeologous genes. The expression profiles of TaARFs in various tissues or organs indicated TaARF3, TaARF4, TaARF9 and TaARF22 and their homoeologous genes played basic roles during wheat development. TaARF4, TaARF9, TaARF12, TaARF15, TaARF17, TaARF21, TaARF25 and their homoeologous genes probably played basic roles in tiller development. qRT-PCR analyses of 20 representative TaARF genes revealed that the abnormal expressions of TaARF11 and TaARF14 were major causes constraining the tillering of dmc. Indole-3-acetic acid (IAA) contents in dmc were significantly less than that in Guomai 301 at key tillering stages. Exogenous IAA application significantly promoted wheat tillering, and affected the transcriptions of TaARFs. These data suggested that TaARFs as well as IAA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of ARFs in wheat.

scholarly journals Cloning and functional characterization of the human fractalkine receptor promoter regions

2002 ◽  
Vol 368 (3) ◽  
pp. 753-760 ◽  
Author(s):  
Alexandre GARIN ◽  
Philippe PELLET ◽  
Philippe DETERRE ◽  
Patrice DEBRÉ ◽  
Christophe COMBADIÈRE
Keyword(s):  
Functional Characterization ◽  
Cell Types ◽  
Promoter Regions ◽  
Exon 2 ◽  
Reading Frame ◽  
Fractalkine Receptor ◽  
A Cell ◽  
Exon 4 ◽  
Coronary Events

We have previously shown that reduced expression of the fractalkine receptor, CX3CR1, is correlated with rapid HIV disease progression and with reduced susceptibility to acute coronary events. In order to elucidate the mechanisms underlying transcriptional regulation of CX3CR1 expression, we structurally and functionally characterized the CX3CR1 gene. It consists of four exons and three introns spanning over 18kb. Three transcripts are produced by splicing the three untranslated exons with exon 4, which contains the complete open reading frame. The transcript predominantly found in leucocytes corresponds to the splicing of exon 2 with exon 4. Transcripts corresponding to splicing of exons 1 and 4 are less abundant in leucocytes and splicing of exons 3 and 4 are rare longer transcripts. A constitutive promoter activity was found in the regions extending upstream from untranslated exons 1 and 2. Interestingly, exons 1 and 2 enhanced the activity of their respective promoters in a cell-specific manner. These data show that the CX3CR1 gene is controlled by three distinct promoter regions, which are regulated by their respective untranslated exons and that lead to the transcription of three mature messengers. This highly complex regulation may allow versatile and precise expression of CX3CR1 in various cell types.

Transcription factors–DNA interactions in rice: identification and verification

2019 ◽  
Vol 21 (3) ◽  
pp. 946-956 ◽  
Author(s):  
Zijie Shen ◽  
Yuan Lin ◽  
Quan Zou
Keyword(s):  
Transcription Factors ◽  
Functional Characterization ◽  
Rice Genome ◽  
Research Strategies ◽  
Promoter Regions ◽  
Rice Varieties ◽  
Rice Genome Sequence ◽  
Advantages And Disadvantages ◽  
Genomics Research

Abstract The completion of the rice genome sequence paved the way for rice functional genomics research. Additionally, the functional characterization of transcription factors is currently a popular and crucial objective among researchers. Transcription factors are one of the groups of proteins that bind to either enhancer or promoter regions of genes to regulate expression. On the basis of several typical examples of transcription factor analyses, we herein summarize selected research strategies and methods and introduce their advantages and disadvantages. This review may provide some theoretical and technical guidelines for future investigations of transcription factors, which may be helpful to develop new rice varieties with ideal traits.

Expression Profiles Analysis and Functional Characterization of MicroRNA-660 in Skeletal Muscle Differentiation

2017 ◽  
Vol 118 (8) ◽  
pp. 2387-2394 ◽  
Author(s):  
Binglin Yue ◽  
Jiyao Wu ◽  
Yanhuan Wang ◽  
Chunlei Zhang ◽  
Xingtang Fang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Muscle Differentiation ◽  
Skeletal Muscle Differentiation

scholarly journals Leaping into the Unknown World of Sporisorium scitamineum Candidate Effectors

2020 ◽  
Vol 6 (4) ◽  
pp. 339
Author(s):  
Natália Sousa Teixeira-Silva ◽  
Patrícia Dayane Carvalho Schaker ◽  
Hugo Vianna Silva Rody ◽  
Thiago Maia ◽  
Christopher M. Garner ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Subcellular Location ◽  
Sporisorium Scitamineum ◽  
Effector Genes ◽  
Molecular Events ◽  
Phosphatase 2A ◽  
Set Up

Sporisorium scitamineum is a biotrophic fungus causing sugarcane smut disease. In this study, we set up a pipeline and used genomic and dual transcriptomic data previously obtained by our group to identify candidate effectors of S. scitamineum and their expression profiles in infected smut-resistant and susceptible sugarcane plants. The expression profile of different genes after infection in contrasting sugarcane genotypes assessed by RT-qPCR depended on the plant genotypes and disease progression. Three candidate effector genes expressed earlier only in resistant plants, four expressed in both genotypes, and three later in susceptible plants. Ten genes were cloned and transiently expressed in N. benthamiana leaves to determine their subcellular location, while four localized in more than one compartment. Two candidates, g3890 having a nucleoplasmic and mitochondrial location and g5159 targeting the plant cell wall, were selected to obtain their possible corresponding host targets using co-immunoprecipitation (CoIP) experiments and mass spectrometry. Various potential interactors were identified, including subunits of the protein phosphatase 2A and an endochitinase. We investigated the presence of orthologs in sugarcane and using transcriptome data present their expression profiles. Orthologs of sugarcane shared around 70% similarity. Identifying a set of putative fungal effectors and their plant targets provides a valuable resource for functional characterization of the molecular events leading to smut resistance in sugarcane plants and uncovers further opportunities for investigation.

scholarly journals Functional characterization of 3D protein structures informed by human genetic diversity

2019 ◽  
Vol 116 (18) ◽  
pp. 8960-8965 ◽  
Author(s):  
Michael Hicks ◽  
Istvan Bartha ◽  
Julia di Iulio ◽  
J. Craig Venter ◽  
Amalio Telenti
Keyword(s):  
Large Scale ◽  
Functional Characterization ◽  
Protein Structures ◽  
Large Scale Data ◽  
Allosteric Sites ◽  
Missense Variation ◽  
Binding Pockets ◽  
Definition Of ◽  
Scale Data

Sequence variation data of the human proteome can be used to analyze 3D protein structures to derive functional insights. We used genetic variant data from nearly 140,000 individuals to analyze 3D positional conservation in 4,715 proteins and 3,951 homology models using 860,292 missense and 465,886 synonymous variants. Sixty percent of protein structures harbor at least one intolerant 3D site as defined by significant depletion of observed over expected missense variation. Structural intolerance data correlated with deep mutational scanning functional readouts for PPARG, MAPK1/ERK2, UBE2I, SUMO1, PTEN, CALM1, CALM2, and TPK1 and with shallow mutagenesis data for 1,026 proteins. The 3D structural intolerance analysis revealed different features for ligand binding pockets and orthosteric and allosteric sites. Large-scale data on human genetic variation support a definition of functional 3D sites proteome-wide.

scholarly journals Key wheat GRF genes constraining wheat tillering of mutant dmc

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11235
Author(s):  
Jing Zhang ◽  
Junchang Li ◽  
Yongjing Ni ◽  
Yumei Jiang ◽  
Zhixin Jiao ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Acetic Acid ◽  
Indole Acetic Acid ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Tissue Expression ◽  
Wild Type ◽  
Gene Structures ◽  
Wheat Mutant

Tillering is a key agronomy trait for wheat (Triticum aestivum L.) production. Previously, we have reported a dwarf-monoculm wheat mutant (dmc) obtained from cultivar Guomai 301 (wild type, WT), and found growth regulating factors (GRFs) playing important roles in regulating wheat tillering. This study is to systematically investigate the roles of all the wheat GRFs (T. aestivum GRFs, TaGRFs) in regulating tillering, and screen out the key regulators. A total of 30 TaGRFs were identified and their physicochemical properties, gene structures, conserved domains, phylogenetic relationships and tissue expression profiles were analyzed. The expression levels of all the TaGRFs were significantly lower in dmc than those in WT at early tillering stage, and the abnormal expressions of TaGRF2-7(A, B, D), TaGRF5-7D, TaGRF10-6(A, B, D) and TaGRF11-2A were major causes constraining the tillering of dmc. The transcriptions of TaGRFs were significantly affected by exogenous indole acetic acid (IAA) and gibberellin acid (GA3) applications, which suggested that TaGRFs as well as IAA, GA signaling were involved in controlling wheat tillering. This study provided valuable clues for functional characterization of GRF genes in wheat.

GENOME-WIDE IDENTIFICATION AND COMPUTATIONAL CHARACTERIZATION OF THE NUCLEAR FACTOR-YC SUB-UNITS IN GRAIN AMARANTH (Amaranthus hypochondriacus)

2021 ◽  
Vol 66 (3) ◽  
pp. 161-169
Author(s):  
Huyen Tran Thi Thanh ◽  
Hong La Viet ◽  
Quynh Le Thi Ngoc ◽  
Thuy Pham Chau ◽  
Quyen Ha Thi ◽  
...  
Keyword(s):  
Growth And Development ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Chemical Properties ◽  
Nuclear Factor ◽  
Grain Amaranth ◽  
Amaranthus Hypochondriacus ◽  
Grand Average ◽  
Genes Encoding

Nuclear factor-Y (NF-Y) has been known as one of the plant-specific transcription factors that play key roles in numerous biological processes during the growth and development of plant species. In this study, a comprehensive analysis of NF-YC sub-units in grain amaranth (Amaranthus hypochondriacus) was carried out based on the bioinformatics approaches. Firstly, a total of five members of the NF-YC sub-units was reported in the grain amaranth. Its structural analyses revealed that the NF-YC sub-units were variable in physic-chemical properties, like protein sizes, molecular masses, isoelectric point, instability index, and grand average of hydropathy. Of our interest, the expression profiles of genes encoding NF-YC sub-units in various tissues\organs during the growth and development of grain amaranth. We found that three genes, including AhNF-YC01, AhNF-YC04, and AhNF-YC05 were highly expressed in leaf, root, floral, immature seed, and stem tissues. Interestingly, AhNF-YC05 was exclusively expressed in leaf and stem tissues. Taken together, our study could provide a solid understanding for further functional characterization of genes encoding NF-YC sub-units in grain amaranth.

scholarly journals Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jing Wen ◽  
Peng-Feng Li ◽  
Feng Ran ◽  
Peng-Cheng Guo ◽  
Jia-Tian Zhu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Small Scale ◽  
Preferential Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Duplication Events ◽  
Small Scale Duplication

Abstract Background NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we report the global characterization of NPF in the important oil crop Brassica napus, including that for phylogeny, gene/protein structures, duplications, and expression patterns. Results A total of 199 B. napus (BnaNPFs) NPF-coding genes were identified. Phylogenetic analyses categorized these genes into 11 subfamilies, including three new ones. Sequence feature analysis revealed that members of each subfamily contain conserved gene and protein structures. Many hormone−/abiotic stress-responsive cis-acting elements and transcription factor binding sites were identified in BnaNPF promoter regions. Chromosome distribution analysis indicated that BnaNPFs within a subfamily tend to cluster on one chromosome. Syntenic relationship analysis showed that allotetraploid creation by its ancestors (Brassica rapa and Brassica oleracea) (57.89%) and small-scale duplication events (39.85%) contributed to rapid BnaNPF expansion in B. napus. A genome-wide spatiotemporal expression survey showed that NPF genes of each Arabidopsis and B. napus subfamily have preferential expression patterns across developmental stages, most of them are expressed in a few organs. RNA-seq analysis showed that many BnaNPFs (32.66%) have wide exogenous hormone-inductive profiles, suggesting important hormone-mediated patterns in diverse bioprocesses. Homologs in a clade or branch within a given subfamily have conserved organ/spatiotemporal and hormone-inductive profiles, indicating functional conservation during evolution. qRT-PCR-based comparative expression analysis of the 12 BnaNPFs in the NPF2–1 subfamily between high- and low-glucosinolate (GLS) content B. napus varieties revealed that homologs of AtNPF2.9 (BnaNPF2.12, BnaNPF2.13, and BnaNPF2.14), AtNPF2.10 (BnaNPF2.19 and BnaNPF2.20), and AtNPF2.11 (BnaNPF2.26 and BnaNPF2.28) might be involved in GLS transport. qRT-PCR further confirmed the hormone-responsive expression profiles of these putative GLS transporter genes. Conclusion We identified 199 B. napus BnaNPFs; these were divided into 11 subfamilies. Allopolyploidy and small-scale duplication events contributed to the immense expansion of BnaNPFs in B. napus. The BnaNPFs had preferential expression patterns in different tissues/organs and wide hormone-induced expression profiles. Four BnaNPFs in the NPF2–1 subfamily may be involved in GLS transport. Our results provide an abundant gene resource for further functional analysis of BnaNPFs.

scholarly journals Systematic Analysis of the bZIP Family in Tobacco and Functional Characterization of NtbZIP62 Involvement in Salt Stress

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 148
Author(s):  
Zhiyuan Li ◽  
Jiangtao Chao ◽  
Xiaoxu Li ◽  
Gongbo Li ◽  
Dean Song ◽  
...  
Keyword(s):  
Salt Stress ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Segmental Duplications ◽  
Basic Leucine Zipper ◽  
Systematic Analysis ◽  
Duplication Events ◽  
Tobacco Genome ◽  
Gene Structures

The basic leucine zipper (bZIP) transcription factors play important regulatory roles, influencing plant growth and responses to environmental stresses. In the present study, 132 bZIP genes identified in the tobacco genome were classified into 11 groups with Arabidopsis and tomato bZIP members, based on the results of a phylogenetic analysis. An examination of gene structures and conserved motifs revealed relatively conserved exon/intron structures and motif organization within each group. The results of an investigation of whole-genome duplication events indicated that segmental duplications were crucial for the expansion of the bZIP gene family in tobacco. Expression profiles confirmed that the NtbZIP genes are differentially expressed in various tissues, and several genes are responsive to diverse stresses. Notably, NtbZIP62, which was identified as an AtbZIP37/ABF3 homolog, was highly expressed in response to salinity. Subcellular localization analyses proved that NtbZIP62 is a nuclear protein. Furthermore, the overexpression of NtbZIP62 in tobacco significantly enhanced the salt stress tolerance of the transgenic plants. The results of this study may be relevant for future functional analyses of the bZIP genes in tobacco.

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