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Genome-wide analysis of the Hsp20 gene family in soybean: comprehensive sequence, genomic organization and expression profile analysis under abiotic and biotic stresses.

Lopes-Caitar VS, de Carvalho MC, Darben LM, Kuwahara MK, Nepomuceno AL, Dias WP, Abdelnoor RV, Marcelino-Guimarães FC - BMC Genomics (2013)

Bottom Line: The Hsp20 genes are associated with stress caused by HS and other abiotic factors, but have recently been found to be associated with the response to biotic stresses.The obtained expression profiles revealed that the majority of the 51 GmHsp20 candidates are induced under HT, but other members of this family could also be involved in normal cellular functions, unrelated to HT.Some of the GmHsp20 genes might be specialized to respond to nematode stress, and the predicted promoter structure of these genes seems to have a particular conserved pattern related to their biological function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Brazilian Agricultural Research Corporation's - EMBRAPA Soybean, Londrina, Brazil. francismar.marcelino@embrapa.br.

ABSTRACT

Background: The Hsp20 genes are associated with stress caused by HS and other abiotic factors, but have recently been found to be associated with the response to biotic stresses. These genes represent the most abundant class among the HSPs in plants, but little is known about this gene family in soybean. Because of their apparent multifunctionality, these proteins are promising targets for developing crop varieties that are better adapted to biotic and abiotic stresses. Thus, in the present study an in silico identification of GmHsp20 gene family members was performed, and the genes were characterized and subjected to in vivo expression analysis under biotic and abiotic stresses.

Results: A search of the available soybean genome databases revealed 51 gene models as potential GmHsp20 candidates. The 51 GmHsp20 genes were distributed across a total of 15 subfamilies where a specific predicted secondary structure was identified. Based on in vivo analysis, only 47 soybean Hsp20 genes were responsive to heat shock stress. Among the GmHsp20 genes that were potentials HSR, five were also cold-induced, and another five, in addition to one GmAcd gene, were responsive to Meloidogyne javanica infection. Furthermore, one predicted GmHsp20 was shown to be responsive only to nematode infection; no expression change was detected under other stress conditions. Some of the biotic stress-responsive GmHsp20 genes exhibited a divergent expression pattern between resistant and susceptible soybean genotypes under M. javanica infection. The putative regulatory elements presenting some conservation level in the GmHsp20 promoters included HSE, W-box, CAAT box, and TA-rich elements. Some of these putative elements showed a unique occurrence pattern among genes responsive to nematode infection.

Conclusions: The evolution of Hsp20 family in soybean genome has most likely involved a total of 23 gene duplications. The obtained expression profiles revealed that the majority of the 51 GmHsp20 candidates are induced under HT, but other members of this family could also be involved in normal cellular functions, unrelated to HT. Some of the GmHsp20 genes might be specialized to respond to nematode stress, and the predicted promoter structure of these genes seems to have a particular conserved pattern related to their biological function.

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Illustration of the elements of the structural models of the GmHsp20 gene promoter region. The Cold Stress and Nematode Stress Models were identified using Frameworker/Genomatix. This program was employed to search for the main common elements between genes and the highest frequencies of their positions. In the Cold Stress Model (A), the identified HSEs positioned with a negative orientation have p-values of 0.0381311. The model for the AHBP, GTBX, VTBP (TATAbox vertebrate) and PTBT (TATAbox plant) elements has a p-value 1.67 e-04. The model with a W-box shows a p-value of 5.02 e-01. Another model identified a CAAT box with a p-value of 0.167564. In the Nematode Stress Model (B), the identified HSE position has a p-value of 9.37 e-01. The model with the ABRE, MYBS, MYCL and HEAT cis-elements presented a p-value of 9.57 e-04. Another model, without stabilization of the mandatory elements, included the L1BX, AHBP, GTBX, VTBP and HEAT elements with a p-value of 4.789 e-06. All of the models found for each specific stress were concatenated to form a single representative model.
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Figure 9: Illustration of the elements of the structural models of the GmHsp20 gene promoter region. The Cold Stress and Nematode Stress Models were identified using Frameworker/Genomatix. This program was employed to search for the main common elements between genes and the highest frequencies of their positions. In the Cold Stress Model (A), the identified HSEs positioned with a negative orientation have p-values of 0.0381311. The model for the AHBP, GTBX, VTBP (TATAbox vertebrate) and PTBT (TATAbox plant) elements has a p-value 1.67 e-04. The model with a W-box shows a p-value of 5.02 e-01. Another model identified a CAAT box with a p-value of 0.167564. In the Nematode Stress Model (B), the identified HSE position has a p-value of 9.37 e-01. The model with the ABRE, MYBS, MYCL and HEAT cis-elements presented a p-value of 9.57 e-04. Another model, without stabilization of the mandatory elements, included the L1BX, AHBP, GTBX, VTBP and HEAT elements with a p-value of 4.789 e-06. All of the models found for each specific stress were concatenated to form a single representative model.

Mentions: The results of the in silico analysis and in vivo expression profiling of the GmHsp20 candidates under biotic and abiotic stress conditions were used to determine a putative transcription factor binding site (TFBS) combinatorial models for their promoters. Comparative analysis of the promoters of the five GmHsp20 genes responsive to cold stress (GmHsp16.4C, GmHsp18.2A, GmHsp18.0B, GmHsp27.3 and GmHsp22.0) resulted in five putative operational models containing the mandatory HEAT element. Other putative common elements were L1BX, AHBP, GTBX, VTBP, MYBS, MYCL, MYBL and ABRE (Figure 9).


Genome-wide analysis of the Hsp20 gene family in soybean: comprehensive sequence, genomic organization and expression profile analysis under abiotic and biotic stresses.

Lopes-Caitar VS, de Carvalho MC, Darben LM, Kuwahara MK, Nepomuceno AL, Dias WP, Abdelnoor RV, Marcelino-Guimarães FC - BMC Genomics (2013)

Illustration of the elements of the structural models of the GmHsp20 gene promoter region. The Cold Stress and Nematode Stress Models were identified using Frameworker/Genomatix. This program was employed to search for the main common elements between genes and the highest frequencies of their positions. In the Cold Stress Model (A), the identified HSEs positioned with a negative orientation have p-values of 0.0381311. The model for the AHBP, GTBX, VTBP (TATAbox vertebrate) and PTBT (TATAbox plant) elements has a p-value 1.67 e-04. The model with a W-box shows a p-value of 5.02 e-01. Another model identified a CAAT box with a p-value of 0.167564. In the Nematode Stress Model (B), the identified HSE position has a p-value of 9.37 e-01. The model with the ABRE, MYBS, MYCL and HEAT cis-elements presented a p-value of 9.57 e-04. Another model, without stabilization of the mandatory elements, included the L1BX, AHBP, GTBX, VTBP and HEAT elements with a p-value of 4.789 e-06. All of the models found for each specific stress were concatenated to form a single representative model.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852298&req=5

Figure 9: Illustration of the elements of the structural models of the GmHsp20 gene promoter region. The Cold Stress and Nematode Stress Models were identified using Frameworker/Genomatix. This program was employed to search for the main common elements between genes and the highest frequencies of their positions. In the Cold Stress Model (A), the identified HSEs positioned with a negative orientation have p-values of 0.0381311. The model for the AHBP, GTBX, VTBP (TATAbox vertebrate) and PTBT (TATAbox plant) elements has a p-value 1.67 e-04. The model with a W-box shows a p-value of 5.02 e-01. Another model identified a CAAT box with a p-value of 0.167564. In the Nematode Stress Model (B), the identified HSE position has a p-value of 9.37 e-01. The model with the ABRE, MYBS, MYCL and HEAT cis-elements presented a p-value of 9.57 e-04. Another model, without stabilization of the mandatory elements, included the L1BX, AHBP, GTBX, VTBP and HEAT elements with a p-value of 4.789 e-06. All of the models found for each specific stress were concatenated to form a single representative model.
Mentions: The results of the in silico analysis and in vivo expression profiling of the GmHsp20 candidates under biotic and abiotic stress conditions were used to determine a putative transcription factor binding site (TFBS) combinatorial models for their promoters. Comparative analysis of the promoters of the five GmHsp20 genes responsive to cold stress (GmHsp16.4C, GmHsp18.2A, GmHsp18.0B, GmHsp27.3 and GmHsp22.0) resulted in five putative operational models containing the mandatory HEAT element. Other putative common elements were L1BX, AHBP, GTBX, VTBP, MYBS, MYCL, MYBL and ABRE (Figure 9).

Bottom Line: The Hsp20 genes are associated with stress caused by HS and other abiotic factors, but have recently been found to be associated with the response to biotic stresses.The obtained expression profiles revealed that the majority of the 51 GmHsp20 candidates are induced under HT, but other members of this family could also be involved in normal cellular functions, unrelated to HT.Some of the GmHsp20 genes might be specialized to respond to nematode stress, and the predicted promoter structure of these genes seems to have a particular conserved pattern related to their biological function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Brazilian Agricultural Research Corporation's - EMBRAPA Soybean, Londrina, Brazil. francismar.marcelino@embrapa.br.

ABSTRACT

Background: The Hsp20 genes are associated with stress caused by HS and other abiotic factors, but have recently been found to be associated with the response to biotic stresses. These genes represent the most abundant class among the HSPs in plants, but little is known about this gene family in soybean. Because of their apparent multifunctionality, these proteins are promising targets for developing crop varieties that are better adapted to biotic and abiotic stresses. Thus, in the present study an in silico identification of GmHsp20 gene family members was performed, and the genes were characterized and subjected to in vivo expression analysis under biotic and abiotic stresses.

Results: A search of the available soybean genome databases revealed 51 gene models as potential GmHsp20 candidates. The 51 GmHsp20 genes were distributed across a total of 15 subfamilies where a specific predicted secondary structure was identified. Based on in vivo analysis, only 47 soybean Hsp20 genes were responsive to heat shock stress. Among the GmHsp20 genes that were potentials HSR, five were also cold-induced, and another five, in addition to one GmAcd gene, were responsive to Meloidogyne javanica infection. Furthermore, one predicted GmHsp20 was shown to be responsive only to nematode infection; no expression change was detected under other stress conditions. Some of the biotic stress-responsive GmHsp20 genes exhibited a divergent expression pattern between resistant and susceptible soybean genotypes under M. javanica infection. The putative regulatory elements presenting some conservation level in the GmHsp20 promoters included HSE, W-box, CAAT box, and TA-rich elements. Some of these putative elements showed a unique occurrence pattern among genes responsive to nematode infection.

Conclusions: The evolution of Hsp20 family in soybean genome has most likely involved a total of 23 gene duplications. The obtained expression profiles revealed that the majority of the 51 GmHsp20 candidates are induced under HT, but other members of this family could also be involved in normal cellular functions, unrelated to HT. Some of the GmHsp20 genes might be specialized to respond to nematode stress, and the predicted promoter structure of these genes seems to have a particular conserved pattern related to their biological function.

Show MeSH
Related in: MedlinePlus