Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones

Yer, Esra Nurten; Baloğlu, Mehmet Cengiz; Ayan, Sezgin

doi:10.1016/j.gene.2018.08.049

Cited by 39 publications

(31 citation statements)

References 93 publications

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“…They were mainly found in the inner parts of the cell, membranes, and organelles. When other studies in the literature were examined, it was found that Hsp families were mostly located in intracellular parts in eucalyptus (Çelik Altunoğlu, 2016) and poplar (Zhang et al, 2015;Yer et al, 2016;Yer et al, 2018). The results for watermelon Hsp proteins have parallels with the results of these studies.…”

Section: Discussionmentioning

confidence: 63%

“…It has also been observed that the most recent divergence time for LEA genes was between watermelon and poplar (Çelik Altunoğlu, 2017). In addition, the earliest divergence of Hsp genes in the poplar genome was determined with the rice genome, as for many watermelon Hsp genes (Yer et al, 2018). These results may help achieve better understanding of the evolutionary relationship between these organisms and the watermelon based on the Hsp genes.…”

Section: Discussionmentioning

confidence: 91%

“…In the literature, similar gene numbers have been observed in other organisms when compared to the Hsp genes detected in the watermelon genome. In a study conducted by our research group, it was determined that 60 sHsp, 145 Hsp40, 49 Hsp60, 34 Hsp70, 12 Hsp90, and 90 Hsp100 genes were identified in the poplar genome (Yer et al, 2016;Yer et al, 2018). Members of the Hsp70 family are the most thoroughly studied group of stress proteins up to the present.…”

Section: Discussionmentioning

confidence: 99%

“…In rice, it was detected that some sHsp transcripts started to increase in a short time as 5 min under 41 °C heat stress (Guan et al, 2004). When considering the expressions of genes orthologous to ClaHsp genes in poplar, the PtHsp70-09 gene with the number of Potri.003G006300.1, which was orthologous to ClaHsp70-07, and PtHsp90-12 gene with the number of Potri.017G146600.1, which was orthologous to ClaHsp90-04, displayed an increase pattern after salt stress application in various poplar clones (Yer et al, 2018). In addition, considering RNA sequence data by Tang et al, with the number of Potri.004G224400.1 and PtHsp70-20 with the number of Potri.009G079700.1, which were orthologous of ClaHsp70-07, were induced under drought stress conditions in the leaf tissues of poplar (Populus trichocarpa) (Tang et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Complete genomic data of organisms are useful for determining important gene families using bioinformatics methods. Hsps have been characterized in many plant species, including Arabidopsis (Swindell et al, 2007), wheat (Muthusamy et al, 2017), sunflower , rice (Singh et al, 2010;Jiang et al, 2014;Wang et al, 2014), tomato (Zai et al, 2017), poplar (Yer et al, 2016;Yer et al, 2018), and eucalyptus (Altunoğlu, 2016). The complete genome sequence of watermelon was published by Guo et al in 2013; however, to our knowledge, Hsp family members have not yet been defined in the watermelon genome.…”

mentioning

confidence: 99%

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Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses

Altunoğlu¹,

Keleş²,

Can³

et al. 2019

Turk J Biol

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Heat shock protein (Hsp) gene family members in the watermelon genome were identified and characterized by bioinformatics analysis. In addition, expression profiles of genes under combined drought and heat stress conditions were experimentally analyzed. In the watermelon genome, 39 genes belonging to the sHsp family, 101 genes belonging to the Hsp40 family, 23 genes belonging to the Hsp60 family, 12 genes belonging to the Hsp70 family, 6 genes belonging to the Hsp90 family, and 102 genes belonging to the Hsp100 family were found. It was also observed that the proteins in the same cluster in the phylogenetic trees had similar motif patterns. When the estimated 3-dimensional structures of the Hsp proteins were examined, it was determined that the α-helical structure was dominant in almost all families. The most orthologous relationship appeared to be between watermelon, soybean, and poplar in the ClaHsp gene families. For tissue-specific gene expression analysis under combined stress conditions, expression analysis of one representative Hsp gene each from root, stem, leaf, and shoot tissues was performed by real-time PCR. A significant increase was detected usually at 30 min in almost all tissues. This study provides extensive information for watermelon Hsps, and can enhance our knowledge about the relationships between Hsp genes and combined stresses.

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Section: Discussionmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses

Altunoğlu¹,

Keleş²,

Can³

et al. 2019

Turk J Biol

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In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

et al. 2022

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Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.

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Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust

et al. 2021

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Heat-shock proteins (HSPs), which are encoded by conserved gene families in plants, are crucial for development and responses to diverse stresses. However, the wheat (Triticum aestivum L.) HSPs have not been systematically classified, especially those involved in protecting plants from disease. Here, we classified 119 DnaJ (Hsp40) proteins (TaDnaJs; encoded by 313 genes) and 41 Hsp70 proteins (TaHsp70s; encoded by 95 genes) into six and four groups, respectively, via a phylogenetic analysis. An examination of protein sequence alignment revealed diversity in the TaDnaJ structural organization, but a highly conserved J-domain, which was usually characterized by an HPD motif followed by DRD or DED motifs. The expression profiles of HSP-encoding homologous genes varied in response to Blumeria graminis f. sp. tritici (Bgt) and Puccinia striiformis f. sp. tritici (Pst) stress. A quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated a lack of similarity in the expression of DnaJ70b, Hsp70-30b, and Hsp90-4b in Bgt-infected resistant and susceptible wheat. Furthermore, a direct interaction between DnaJ70 and TaHsp70-30 was not detected in a yeast two-hybrid (Y2H) assay, but screening cDNA library and Y2H evidence supported that TaHsp70-30 not only interacts directly with heat-shock transcription factor (HSF) A9-like protein but also interacts with TaHsp90-4 by HSP organizing protein. This study revealed the structure and expression profiles of the HSP-encoding genes in wheat, which may be useful for future functional elucidation of wheat HSPs responses to fungal infections.

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Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones

Cited by 39 publications

References 93 publications

Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses

Identification of watermelon heat shock protein members and tissue-specific gene expression analysis under combined drought and heat stresses

In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

Identification and expression analysis of heat‐shock proteins in wheat infected with powdery mildew and stripe rust

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