Genome-Wide Identification of Na+/H+ Antiporter (NHX) Genes in Sugar Beet (Beta vulgaris L.) and Their Regulated Expression under Salt Stress

Wu, Guo-Qiang; Wang, Jinlong; Li, Shanjia

doi:10.3390/genes10050401

Cited by 62 publications

(67 citation statements)

References 77 publications

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“…The phylogenetic analysis indicated that GbNHX has paralogous or orthologous groups with other Gossypium species members. The NHX genes in P. trichocarpa [69], S. bicolor [67], and B. vulgaris [86] showed three phylogenetic clusters based on their location in the cell; we found the same results for cotton NHX transporters. An amiloride binding site (L/F)FF(I/L)(Y/F)LLPPI, a typical feature of NHX transporters in plants [87,88], is present in the N-terminal of these proteins; the presence of amiloride even in a micro amount in the Na + /H + exchangers inhibits the transport of Na+ transport [89].…”

Section: Discussionsupporting

confidence: 79%

Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum

Akram

Song

Liang

et al. 2020

Genes

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Cotton is an important economic crop affected by different abiotic stresses at different developmental stages. Salinity limits the growth and productivity of crops worldwide. Na+/H+ antiporters play a key role during the plant development and in its tolerance to salt stress. The aim of the present study was a genome-wide characterization and expression pattern analysis under the salinity stress of the sodium-proton antiporter (NHX) of Gossypium barbadense in comparison with Gossypium hirsutum. In G. barbadense, 25 NHX genes were identified on the basis of the Na+_H+ exchanger domain. All except one of the G. barbadense NHX transporters have an Amiloride motif that is a known inhibitor of Na+ ions in plants. A phylogenetic analysis inferred three classes of GbNHX genes—viz., Vac (GbNHX1, 2 and 4), Endo (GbNHX6), and PM (GbNHX7). A high number of the stress-related cis-acting elements observed in promoters show their role in tolerance against abiotic stresses. The Ka/Ks values show that the majority of GbNHX genes are subjected to strong purifying selection under the course of evolution. To study the functional divergence of G. barbadense NHX transporters, the real-time gene expression was analyzed under salt stress in the root, stem, and leaf tissues. In G. barbadense, the expression was higher in the stem, while in G. hirsutum the leaf and root showed a high expression. Moreover, our results revealed that NHX2 homologues in both species have a high expression under salinity stress at higher time intervals, followed by NHX7. The protein-protein prediction study revealed that GbNHX7 is involved in the CBL-CIPK protein interaction pathway. Our study also provided valuable information explaining the molecular mechanism of Na+ transport for the further functional study of Gossypium NHX genes.

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Section: Discussionsupporting

confidence: 79%

Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum

Akram

Song

Liang

et al. 2020

Genes

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“…Both GhNHX1A/1D and GhNHX4A/4D are structurally significantly different from the other NHX family members, which is consistent with the results of the phylogenetic analysis, confirming that the GhNHX family members form two subgroups. The vacuolar-type members of different species have between 13 and 14 exons, whereas the endosomal-type NHX genes have 18–22 exons [ 44 , 46 , 52 , 53 , 54 ]. The results of the current study are consistent with these published findings, implying that the important functions of this family were conserved during evolution.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of the Gossypium hirsutum NHX Genes Reveals That the Endosomal-Type GhNHX4A Is Critical for the Salt Tolerance of Cotton

Ren

Zhou

et al. 2020

IJMS

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Soil salinization, which is primarily due to excessive Na+ levels, is a major abiotic stress adversely affecting plant growth and development. The Na+/H+ antiporter (NHX) is a transmembrane protein mediating the transport of Na+ or K+ and H+ across the membrane to modulate the ionic balance of plants in response to salt stress. Research regarding NHXs has mainly focused on the vacuolar-type NHX family members. However, the biological functions of the endosomal-type NHXs remain relatively uncharacterized. In this study, 22 NHX family members were identified in Gossypium hirsutum. A phylogenetic analysis divided the GhNHX genes into two categories, with 18 and 4 in the vacuolar and endosomal groups, respectively. The chromosomal distribution of the NHX genes revealed the significant impact of genome-wide duplication during the polyploidization process on the number of GhNHX genes. Analyses of gene structures and conserved motifs indicated that GhNHX genes in the same phylogenetic cluster are conserved. Additionally, the salt-induced expression patterns confirmed that the expression levels of most of the GhNHX genes are affected by salinity. Specifically, in the endosomal group, GhNHX4A expression was substantially up-regulated by salt stress. A yeast functional complementation test proved that GhNHX4A can partially restore the salt tolerance of the salt-sensitive yeast mutant AXT3. Silencing GhNHX4A expression decreased the resistance of cotton to salt stress because of an increase in the accumulation of Na+ in stems and a decrease in the accumulation of K+ in roots. The results of this study may provide the basis for an in-depth characterization of the regulatory functions of NHX genes related to cotton salt tolerance, especially the endosomal-type GhNHX4A. Furthermore, the presented data may be useful for selecting appropriate candidate genes for the breeding of new salt-tolerant cotton varieties.

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“…The hidden Markov model profile of the Sugar_tr (PF00083) was downloaded from the Pfam website 3 . Then, all these candidate PTL protein sequences were separately obtained by HMMER 3.2.1 with default parameters (Finn et al, 2011) and BlastP homology search with E-value cutoff e −5 (Kong et al, 2017;Wu et al, 2019). Only the longest splice variant of each gene locus was adopted in this study.…”

Section: Identification and Phylogenetic Tree Construction Of Plt Genesmentioning

confidence: 99%

Micro-Evolution Analysis Reveals Diverged Patterns of Polyol Transporters in Seven Gramineae Crops

et al. 2020

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Polyol transporters (PLTs), also called polyol/monosaccharide transporters, is of significance in determining plant development and sugar transportation. However, the diverged evolutionary patterns of the PLT gene family in Gramineae crops are still unclear. Here a micro-evolution analysis was performed among the seven Gramineae representative crops using whole-genome sequences, i.e., Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Oryza rufipogon (Or), Oryza sativa (Os), Sorghum bicolor (Sb), Setaria italica (Si), and Zea mays (Zm), leading to the identification of 12, 11, 12, 15, 20, 24, and 20 PLT genes, respectively. In this study, all PLT genes were divided into nine orthogroups (OGs). However, the number of PLT genes and the distribution of PLT OGs were not the same in these seven Gramineae species, and different OGs were also subject to different purification selection pressures. These results indicated that the PLT OGs of the PLT gene family have been expanded or lost unevenly in all tested species. Then, our results of gene duplication events confirmed that gene duplication events promoted the expansion of the PLT gene family in some Gramineous plants, namely, Bd, Or, Os, Si, Sb, and Zm, but the degree of gene family expansion, the type of PLT gene duplication, and the differentiation time of duplicate gene pairs varied greatly among these species. In addition, the sequence alignment and the internal repeat analysis of all PLTs protein sequences implied that the PLT protein sequences may originate from an internal repeat duplication of an ancestral six transmembrane helical units. Besides that, the protein motifs result highlighted that the PLT protein sequences were highly conserved, whereas the functional differentiation of the PLT genes was characterized by different gene structures, upstream elements, as well as co-expression analysis. The gene expression analysis of rice and maize showed that the PLT genes have a wide range of expression patterns, suggesting diverse biological functions. Taken together, our finding provided a perspective on the evolution differences and the functional characterizations of PLT genes in Gramineae representative crops.

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Genome-Wide Identification of Na+/H+ Antiporter (NHX) Genes in Sugar Beet (Beta vulgaris L.) and Their Regulated Expression under Salt Stress

Cited by 62 publications

References 77 publications

Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum

Genome-Wide Characterization and Expression Analysis of NHX Gene Family under Salinity Stress in Gossypium barbadense and Its Comparison with Gossypium hirsutum

Genome-Wide Identification of the Gossypium hirsutum NHX Genes Reveals That the Endosomal-Type GhNHX4A Is Critical for the Salt Tolerance of Cotton

Micro-Evolution Analysis Reveals Diverged Patterns of Polyol Transporters in Seven Gramineae Crops

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