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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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Hidden Markov model logos obtained using MEME/TOMTOM based on predicted soybean Hsp20 promoter sequences. The motifs obtained via MEME analysis were plotted according to their position within the consensus sequences, and their locations are presented as graphs using HMM. The events are classified by p-value and aligned with motifs available at DB. The motif e-value is an estimate of the expected number of motifs with the same size and occurrence that would be present in a set of similarly sized random sequences. The heights of the symbols at each motif position indicate sequence conservation. The sequences were manually highlighted to indicate the perfect recognized HSE consensus (red box; nGAAnnTTCnnGAAn or nTTCnnGAAnnTTCn) and the imperfect HSE module (yellow box). Three motifs are found, with the elements being represented by the perfect HSE in alignments 1 (Matches to Query: 1) and 3 (Matches to Query: 3) in the figure. Only the upstream sequences of gene models with a predicted 5′UTR were analyzed.
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Figure 2: Hidden Markov model logos obtained using MEME/TOMTOM based on predicted soybean Hsp20 promoter sequences. The motifs obtained via MEME analysis were plotted according to their position within the consensus sequences, and their locations are presented as graphs using HMM. The events are classified by p-value and aligned with motifs available at DB. The motif e-value is an estimate of the expected number of motifs with the same size and occurrence that would be present in a set of similarly sized random sequences. The heights of the symbols at each motif position indicate sequence conservation. The sequences were manually highlighted to indicate the perfect recognized HSE consensus (red box; nGAAnnTTCnnGAAn or nTTCnnGAAnnTTCn) and the imperfect HSE module (yellow box). Three motifs are found, with the elements being represented by the perfect HSE in alignments 1 (Matches to Query: 1) and 3 (Matches to Query: 3) in the figure. Only the upstream sequences of gene models with a predicted 5′UTR were analyzed.

Mentions: Using the set of 65 GmHsp20 candidates, we searched for those candidates that had been detected in previous general gene expression experiments (see Methods). This search resulted in a total of 51 likely candidates (Additional file 2: Table S1). All 51 GmHsp20 candidates showed at least one repetition of the putative HSE in the 500bp, or 1,500 bp its applied, promoter region (Figure 2; Additional file 1: Figure S3 through S5, and Additional file 2: Table S2). Thus, all of these potential candidates were considered in silico-predicted GmHsp20 genes.


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)

Hidden Markov model logos obtained using MEME/TOMTOM based on predicted soybean Hsp20 promoter sequences. The motifs obtained via MEME analysis were plotted according to their position within the consensus sequences, and their locations are presented as graphs using HMM. The events are classified by p-value and aligned with motifs available at DB. The motif e-value is an estimate of the expected number of motifs with the same size and occurrence that would be present in a set of similarly sized random sequences. The heights of the symbols at each motif position indicate sequence conservation. The sequences were manually highlighted to indicate the perfect recognized HSE consensus (red box; nGAAnnTTCnnGAAn or nTTCnnGAAnnTTCn) and the imperfect HSE module (yellow box). Three motifs are found, with the elements being represented by the perfect HSE in alignments 1 (Matches to Query: 1) and 3 (Matches to Query: 3) in the figure. Only the upstream sequences of gene models with a predicted 5′UTR were analyzed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Hidden Markov model logos obtained using MEME/TOMTOM based on predicted soybean Hsp20 promoter sequences. The motifs obtained via MEME analysis were plotted according to their position within the consensus sequences, and their locations are presented as graphs using HMM. The events are classified by p-value and aligned with motifs available at DB. The motif e-value is an estimate of the expected number of motifs with the same size and occurrence that would be present in a set of similarly sized random sequences. The heights of the symbols at each motif position indicate sequence conservation. The sequences were manually highlighted to indicate the perfect recognized HSE consensus (red box; nGAAnnTTCnnGAAn or nTTCnnGAAnnTTCn) and the imperfect HSE module (yellow box). Three motifs are found, with the elements being represented by the perfect HSE in alignments 1 (Matches to Query: 1) and 3 (Matches to Query: 3) in the figure. Only the upstream sequences of gene models with a predicted 5′UTR were analyzed.
Mentions: Using the set of 65 GmHsp20 candidates, we searched for those candidates that had been detected in previous general gene expression experiments (see Methods). This search resulted in a total of 51 likely candidates (Additional file 2: Table S1). All 51 GmHsp20 candidates showed at least one repetition of the putative HSE in the 500bp, or 1,500 bp its applied, promoter region (Figure 2; Additional file 1: Figure S3 through S5, and Additional file 2: Table S2). Thus, all of these potential candidates were considered in silico-predicted GmHsp20 genes.

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