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 Functional Characterization of an Amaranth Natterin-4-Like-1 Gene in Arabidopsis thaliana

2022 ◽  
Vol 5 ◽  
Author(s):  
Gabriela Cabrales-Orona ◽  
Norma Martínez-Gallardo ◽  
John Paul Délano-Frier
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Functional Characterization ◽  
Water Deficit Stress ◽  
Photosynthetic Parameters ◽  
Grain Amaranth ◽  
Amaranthus Hypochondriacus ◽  
Defensive Function ◽  
Fungal Plant Pathogens

The functional characterization of an Amaranthus hypochondriacus Natterin-4-Like-1 gene (AhN4L-1) coding for an unknown function protein characterized by the presence of an aerolysin-like pore-forming domain in addition to two amaranthin-like agglutinin domains is herewith described. Natterin and nattering-like proteins have been amply described in the animal kingdom. However, the role of nattering-like proteins in plants is practically unknown. The results described in this study, obtained from gene expression data in grain amaranth and from AhN4L-1-overexpressing Arabidopsis thaliana plants indicated that this gene was strongly induced by several biotic and abiotic conditions in grain amaranth, whereas data obtained from the overexpressing Arabidopsis plants further supported the defensive function of this gene, mostly against bacterial and fungal plant pathogens. GUS and GFP AhN4L-1 localization in roots tips, leaf stomata, stamens and pistils also suggested a defensive function in these organs, although its participation in flowering processes, such as self-incompatibility and abscission, is also possible. However, contrary to expectations, the overexpression of this gene negatively affected the vegetative and reproductive growth of the transgenic plants, which also showed no increased tolerance to salinity and water-deficit stress. The latter despite the maintenance of significantly higher chlorophyll levels and photosynthetic parameters under intense salinity stress. These results are discussed in the context of the physiological roles known to be played by related lectins and AB proteins in plants.

Cloning and functional characterization of a superfamily of microbial inwardly rectifying potassium channels

2006 ◽  
Vol 26 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Si Sun ◽  
Jo Han Gan ◽  
Jennifer J. Paynter ◽  
Stephen J. Tucker
Keyword(s):  
Functional Properties ◽  
Functional Characterization ◽  
Unicellular Eukaryote ◽  
Channel Blockers ◽  
E Coli ◽  
Inwardly Rectifying Potassium Channels ◽  
Genes Encoding ◽  
Functionally Diverse ◽  
Inwardly Rectifying

Our understanding of the mammalian inwardly rectifying family of K+ channels (Kir family) has recently been advanced by X-ray crystal structures of two homologous prokaryotic orthologs (KirBac1.1 and KirBac3.1). However, the functional properties of these KirBac channels are still poorly understood. To address this problem, we cloned and characterized genes encoding KirBac orthologs from a wide variety of different prokaryotes and a simple unicellular eukaryote. The functional properties of these KirBacs were then examined by growth complementation in a K+ uptake-deficient strain of Escherichia coli (TK2420). Whereas some KirBac genes exhibited robust growth complementation, others either did not complement or showed temperature-dependent complementation including KirBac1.1 and KirBac3.1. In some cases, KirBac expression was also toxic to the growth of E. coli. The KirBac family exhibited a range of sensitivity to the K+ channel blockers Ba2+ and Cs+ as well as differences in their ability to grow on very low-K+ media, thus demonstrating major differences in their permeation properties. These results reveal the existence of a functionally diverse superfamily of microbial KirBac genes and present an excellent resource for the structural and functional analysis of this class of K+ channels. Furthermore, the complementation assay used in this study provides a simple and robust method for the functional characterization of a range of prokaryotic K+ channels that are difficult to study by traditional methods.

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 Two Members of a Network of Putative Na+/H+ Antiporters Are Involved in Salt and pH Tolerance of the Freshwater Cyanobacterium Synechococcus elongatus

2008 ◽  
Vol 190 (19) ◽  
pp. 6318-6329 ◽  
Author(s):  
Maria Billini ◽  
Kostas Stamatakis ◽  
Vicky Sophianopoulou
Keyword(s):  
Functional Characterization ◽  
Synechococcus Elongatus ◽  
Amino Acid Sequences ◽  
High Salt ◽  
Alkaline Ph ◽  
Ph Tolerance ◽  
Low Salt ◽  
Genes Encoding ◽  
Pcc 7942

ABSTRACT Synechococcus elongatus strain PCC 7942 is an alkaliphilic cyanobacterium that tolerates a relatively high salt concentration as a freshwater microorganism. Its genome sequence revealed seven genes, nha1 to nha7 (syn_pcc79420811, syn_pcc79421264, syn_pcc7942359, syn_pcc79420546, syn_pcc79420307, syn_pcc79422394, and syn_pcc79422186), and the deduced amino acid sequences encoded by these genes are similar to those of Na+/H+ antiporters. The present work focused on molecular and functional characterization of these nha genes encoding Na+/H+ antiporters. Our results show that of the nha genes expressed in Escherichia coli, only nha3 complemented the deficient Na+/H+ antiporter activity of the Na+-sensitive TO114 recipient strain. Moreover, two of the cyanobacterial strains with separate disruptions in the nha genes (Δnha1, Δnha2, Δnha3, Δnha4, Δnha5, and Δnha7) had a phenotype different from that of the wild type. In particular, ΔnhA3 cells showed a high-salt- and alkaline-pH-sensitive phenotype, while Δnha2 cells showed low salt and alkaline pH sensitivity. Finally, the transcriptional profile of the nha1 to nha7 genes, monitored using the real-time PCR technique, revealed that the nha6 gene is upregulated and the nha1 gene is downregulated under certain environmental conditions.

Functional characterization of the three genes encoding 1-deoxy-D-xylulose 5-phosphate synthase in maize

2011 ◽  
Vol 62 (6) ◽  
pp. 2023-2038 ◽  
Author(s):  
E. Cordoba ◽  
H. Porta ◽  
A. Arroyo ◽  
C. San Roman ◽  
L. Medina ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Genes Encoding ◽  
Phosphate Synthase

scholarly journals Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Yong Zou ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Gene Structure ◽  
Abiotic Stresses ◽  
Growth And Development ◽  
Expression Profiles ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Evolutionary Features ◽  
Erf Family

Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

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