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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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Alignment of the ACD from the MEME results for the GmHsp20 with Hsp20 from Pfam. The HMM obtained via MEME analysis for putative GmHsp20s (A); HMM logo from Pfam representing the Hsp20 domain(PF00011). (B). The asterisks indicate matches between HMMs.
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Figure 1: Alignment of the ACD from the MEME results for the GmHsp20 with Hsp20 from Pfam. The HMM obtained via MEME analysis for putative GmHsp20s (A); HMM logo from Pfam representing the Hsp20 domain(PF00011). (B). The asterisks indicate matches between HMMs.

Mentions: Hidden Markov model (HMM) analysis and name search resulted in the identification of 73 and 74 gene models from the Superfamily 1.75 and Phytozome v8.0 Soybean databases, respectively. After removing overlapping hits, 76 putative GmHsp20 were retrieved. PROSITE and MEME scans of these sequences confirmed the presence of an ACD in 74 of the 76 gene models. However, these ACD were identified in the C-terminal region of only 62 of the putative GmHsp20 gene models (Figure 1 and Additional file 1: Figure S1).


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)

Alignment of the ACD from the MEME results for the GmHsp20 with Hsp20 from Pfam. The HMM obtained via MEME analysis for putative GmHsp20s (A); HMM logo from Pfam representing the Hsp20 domain(PF00011). (B). The asterisks indicate matches between HMMs.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Alignment of the ACD from the MEME results for the GmHsp20 with Hsp20 from Pfam. The HMM obtained via MEME analysis for putative GmHsp20s (A); HMM logo from Pfam representing the Hsp20 domain(PF00011). (B). The asterisks indicate matches between HMMs.
Mentions: Hidden Markov model (HMM) analysis and name search resulted in the identification of 73 and 74 gene models from the Superfamily 1.75 and Phytozome v8.0 Soybean databases, respectively. After removing overlapping hits, 76 putative GmHsp20 were retrieved. PROSITE and MEME scans of these sequences confirmed the presence of an ACD in 74 of the 76 gene models. However, these ACD were identified in the C-terminal region of only 62 of the putative GmHsp20 gene models (Figure 1 and Additional file 1: Figure S1).

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