scholarly journals The Hsp70 Gene family in Solanum Lycopersicum; Genome-wide Identification and Expression Analysis Under Heavy Metals Stresses

2021 ◽  
Author(s):  
Ahmed El Sappah ◽  
Manzar Abbas ◽  
Ahmed S. Elrys ◽  
Vivek Yadav ◽  
Hamza H. El-Sappah ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Gene Ontology ◽  
Gene Family ◽  
Candidate Genes ◽  
Solanum Lycopersicum ◽  
Expression Analysis ◽  
Hsp70 Gene ◽  
Rna Seq ◽  
Genome Wide

Abstract The Heat shock protein-70 (Hsp70) gene family is one of the protective mechanisms; however, it has not been widely studied in tomatoes. Therefore, the current study provides the first report genome-wide analysis of the Hsp70 gene family in tomato (Solanum lycopersicum L.) under five heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+) stresses. We identified 23 candidate genes of the Hsp70 gene family based on the PF00012 domain through bioinformatics studies, including gene structure, distribution, synteny, phylogenetic tree, protein-protein interactions, gene ontology, and previous RNA-seq data analysis followed by qRT-PCR analysis. Based on the phylogenetic analysis, the 23 candidate genes were classified into five subfamilies where the same subfamily contains similar SlHsp70 proteins. Many pairs of SlHsp70 gene duplications have appeared, consisting of tandem and segment duplication. In addition, analysis of previous RNA-seq besides the gene ontology gave us significant evidence about the vital roles of these genes during tomato development and growth. The SlHsp7s showed different responses, which were varied depend on different plant tissues and types of heavy metal. Some of the SlHsp70s were up-regulated after heavy metal exposure, such as Cd2+/SlHsp70-23 and Mn2+/ SlHsp70-8. Still, down-regulated others such as Fe2+/ SlHsp70-18. Finally, our gene expression analysis revealed the significant roles of the Hsp70s, especially, SlHsp70- 3, SlHsp70-8, SlHsp70-12, SlHsp70-19, and SlHsp70-23, with the different heavy metals treatments.

scholarly journals The Hsp70 Gene Family in Boleophthalmus pectinirostris: Genome-Wide Identification and Expression Analysis under High Ammonia Stress

Animals ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 36
Author(s):  
Zhaochao Deng ◽  
Shanxiao Sun ◽  
Tianxiang Gao ◽  
Zhiqiang Han
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Expression Patterns ◽  
Large Body ◽  
Hypoxic Condition ◽  
Hsp70 Gene ◽  
High Concentration ◽  
Genome Wide ◽  
Boleophthalmus Pectinirostris ◽  
Shock Proteins

Heat shock proteins 70 have triggered a remarkable large body of research in various fishes; however, no genome-wide identification and expression analysis has been performed on the Hsp70 gene family of Boleophthalmus pectinirostris. In this study, we identified 20 Hsp70 genes within the genome of B. pectinirostris and provided insights into their response to high environmental ammonia (HEA) stress. Positive selection on stress response genes and expansion of hspa1a and hspa1a-like genes might be related to terrestrial adaptations in this species. The expression patterns of the Hsp70 gene family in the gill and liver of B. pectinirostris under HEA stress were studied by examining transcriptome data. The results showed that most Hsp70 genes were downregulated after high concentration ammonia exposure. The downregulation may be related to the hypoxic condition of the tissues.

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein (MTP) Gene Family in Medicago Truncatula Under a Broad Range of Heavy Metals Stress

2021 ◽  
Author(s):  
Ahmed H. El Sappah ◽  
Rania G. Elbaiomy ◽  
Jia Li ◽  
Kuan Yan ◽  
Yu Wang ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Gene Ontology ◽  
Metal Tolerance ◽  
Protein Structures ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Rna Seq ◽  
Expression Levels ◽  
Gene Similarity

Abstract Metal tolerance proteins (MTP) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and minerals acquisition. However, the molecular behaviors and biological functions of this family in M. truncatula are scarcely known. We identified 12 potential MTP candidate genes and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, protein structures, gene ontology, and previous RNA-seq data. MtMTPs were classified into three major cation diffusion facilitator (CDFs) groups; Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. Structural analysis of SlMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. RNA-seq and gene ontology analysis revealed a significant role of MTP genes during M. truncatula growth and development.MTP genes showed tissue-specific and variable expression levels under the stress of the following five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). Expression levels of Fe2+/MtMTP11 and Mn2+/MtMTP4 were upregulated, while Mn2+/MtMTP5 was downregulated. In conclusion, MtMTP1.1, MtMTP1.2, and MtMTP4 play a key role under heat and heavy metal stress in M. truncatula.

scholarly journals Genome-Wide Identification of MATE Gene Family in Potato (Solanum tuberosum L.) and Expression Analysis in Heavy Metal Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Yun Huang ◽  
Guandi He ◽  
Weijun Tian ◽  
Dandan Li ◽  
Lulu Meng ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Gene Family ◽  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Solanum Tuberosum L ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Expression Levels ◽  
Genome Wide ◽  
A Genome

A genome-wide identification and expression analysis of multidrug and toxic compound extrusion (MATE) gene family in potato was carried out to explore the response of MATE proteins to heavy meta stress. In this study, we identified 64 MATE genes from potato genome, which are located on 12 chromosomes, and are divided into I–IV subfamilies based on phylogenetic analysis. According to their order of appearance on the chromosomes, they were named from StMATE1–64. Subcellular location prediction showed that 98% of them are located on the plasma membrane as transporters. Synteny analysis showed that five pairs of collinearity gene pairs belonged to members of subfamily I and subfamily II had two pairs indicating that the duplication is of great significance to the evolution of genes in subfamilies I and II. Gene exon–intron structures and motif composition are more similar in the same subfamily. Every StMATE gene contained at least one cis-acting element associated with regulation of hormone transport. The relative expression levels of eight StMATE genes were significantly upregulated under Cu2+ stress compared with the non-stress condition (0 h). After Cd2+ stress for 24 h, the expression levels of StMATE33 in leaf tissue were significantly increased, indicating its crucial role in the process of Cd2+ stress. Additionally, StMATE18/60/40/33/5 were significantly induced by Cu2+ stress, while StMATE59 (II) was significantly induced by Ni2+ stress. Our study initially explores the biological functions of StMATE genes in the regulation of heavy metal stress, further providing a theoretical basis for studying the subsequent molecular mechanisms in detail.

scholarly journals Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cuili Pan ◽  
Zhaoxiong Lei ◽  
Shuzhe Wang ◽  
Xingping Wang ◽  
Dawei Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Adipocyte Differentiation ◽  
Bos Taurus ◽  
Adipogenic Differentiation ◽  
Critical Role ◽  
Bos Indicus ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

scholarly journals Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 23
Author(s):  
Antt Htet Wai ◽  
Muhammad Waseem ◽  
A B M Mahbub Morshed Khan ◽  
Ujjal Kumar Nath ◽  
Do Jin Lee ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Abiotic Stress Tolerance ◽  
Dependent Manner ◽  
Solanum Lycopersicum L ◽  
Genome Wide ◽  
Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

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