scholarly journals Comprehensive genome wide identification and expression analysis of MTP gene family in tomato (Solanum lycopersicum) under multiple heavy metal stress

2021 ◽  
Author(s):  
Ahmed H. El- Sappah ◽  
Ahmed S. Elrys ◽  
El-Sayed M. Desoky ◽  
Xia Zhao ◽  
Wang Bingwen ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Gene Family ◽  
Solanum Lycopersicum ◽  
Expression Analysis ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Genome Wide

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 the HMA Gene Family and Expression Analysis under Cd Stress in Barley

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1849
Author(s):  
Chiran Zhang ◽  
Qianhui Yang ◽  
Xiaoqin Zhang ◽  
Xian Zhang ◽  
Tongyuan Yu ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Analysis ◽  
Stress Resistance ◽  
Agricultural Development ◽  
Structural Characteristics ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Cd Stress

In recent years, cadmium (Cd) pollution in soil has increased with increasing industrial activities, which has restricted crop growth and agricultural development. The heavy metal ATPase (HMA) gene family contributes to heavy metal stress resistance in plants. In this study, 21 HMA genes (HvHMAs) were identified in barley (Hordeumvulgare L., Hv) using bioinformatics methods. Based on phylogenetic analysis and domain distribution, barley HMA genes were divided into five groups (A–E), and complete analyses were performed in terms of physicochemical properties, structural characteristics, conserved domains, and chromosome localization. The expression pattern analysis showed that most HvHMA genes were expressed in barley and exhibited tissue specificity. According to the fragments per kilobase of exon per million fragments values in shoots from seedlings at the 10 cm shoot stage (LEA) and phylogenetic analysis, five HvHMA genes were selected for expression analysis under Cd stress. Among the five HvHMA genes, three (HvHMA1, HvHMA3, and HvHMA4) were upregulated and two (HvHMA2 and HvHMA6) were downregulated following Cd treatments. This study serves as a foundation for clarifying the functions of HvHMA proteins in the heavy metal stress resistance of barley.

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 Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Ahmed H. El-Sappah ◽  
Rania G. Elbaiomy ◽  
Ahmed S. Elrys ◽  
Yu Wang ◽  
Yumin Zhu ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Gene Ontology ◽  
Gene Family ◽  
Medicago Truncatula ◽  
Metal Ion ◽  
Metal Tolerance ◽  
Functional Characterization ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Gene Similarity

Metal tolerance proteins (MTPs) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and mineral acquisition. However, the molecular behaviors and biological functions of this family in Medicago truncatula are scarcely known. A total of 12 potential MTP candidate genes in the M. truncatula genome were successfully identified and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, docking analysis, gene ontology, and previous gene expression. M. truncatula MTPs (MtMTPs) were further classified into three major cation diffusion facilitator (CDFs) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The structural analysis of MtMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. Cis-acting element analysis suggested that various abiotic stresses and phytohormones could induce the most MtMTP gene transcripts. Among all MTPs, PF16916 is the specific domain, whereas GLY, ILE, LEU, MET, ALA, SER, THR, VAL, ASN, and PHE amino acids were predicted to be the binding residues in the ligand-binding site of all these proteins. RNA-seq and gene ontology analysis revealed the significant role of MTP genes in the growth and development of M. truncatula. MtMTP genes displayed differential responses in plant leaves, stems, and roots under five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). Ten, seven, and nine MtMTPs responded to at least one metal ion treatment in the leaves, stems, and roots, respectively. Additionally, MtMTP1.1, MtMTP1.2, and MtMTP4 exhibited the highest expression responses in most heavy metal treatments. Our results presented a standpoint on the evolution of MTPs in M. truncatula. Overall, our study provides a novel insight into the evolution of the MTP gene family in M. truncatula and paves the way for additional functional characterization of this gene family.

scholarly journals Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance

2020 ◽  
Vol 21 (6) ◽  
pp. 2209 ◽  
Author(s):  
Yuanyuan Wan ◽  
Zhen Wang ◽  
Jichun Xia ◽  
Shulin Shen ◽  
Mingwei Guan ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Brassica Species ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Plant Tolerance ◽  
Genome Wide Analysis ◽  
Genome Wide

Phosphorus transporter (PHT) genes encode H2PO4−/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1–PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.

scholarly journals Genome-Wide Identification of Metal Tolerance Genes in Potato (Solanum Tuberosum): Response to Two Heavy Metal Stress

2021 ◽  
Author(s):  
Dandan Li ◽  
Guandi He ◽  
Weijun Tian ◽  
Yun Huang ◽  
Lulu Meng ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Heavy Metal ◽  
Solanum Tuberosum ◽  
Gene Family ◽  
Transmembrane Domain ◽  
Metal Tolerance ◽  
Cadmium Stress ◽  
Heavy Metal Stress ◽  
Metal Stress ◽  
Zinc Stress

Abstract Metal tolerance proteins play an important role in the transport and tolerance of divalent heavy metals in plant species. Potatoes are an important food crop whose yields can be deeply affected by heavy metals. However, there is a lack of information concerning the members and function of the MTP gene family in Solanum tuberosum. In this study, we identified and screened 11 MTP genes in potatoes which we named as StMTP1 to StMTP11 based on their positions on the chromosomes. Phylogenetic analysis divided these 11 MTP genes into three subfamilies; Mn-MTP, Zn-MTP and Zn/Fe-MTP. HXXXD and DXXXD conserved motifs were found on or around the transmembrane domain II and transmembrane domain V of these proteins. The highly conserved histidine and aspartic acid residues may be related to the transport of metal ions. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the expression levels of StMTP9 and StMTP10 in leaf tissues increased by around 24-fold following cadmium stress for 24 hours. We hypothesize that StMTP9 and StMTP10 respond to cadmium stress. StMTP11 showed the highest level of expression in stem tissues after 6 hours of zinc stress at more than 13 times the level of expression in controls indicating that StMTP11 is more sensitive to zinc stress. In summary, our results further the current understanding of the molecular mechanisms regulated by members of the MTP gene family in plant responses to heavy metal stress.

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