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Analysis of root proteome unravels differential molecular responses during compatible and incompatible interaction between chickpea (Cicer arietinum L.) and Fusarium oxysporum f. sp. ciceri Race1 (Foc1).

Chatterjee M, Gupta S, Bhar A, Chakraborti D, Basu D, Das S - BMC Genomics (2014)

Bottom Line: The fungus invades the plant via roots, colonizes the xylem vessels and prevents the upward translocation of water and nutrients, finally resulting in wilting of the entire plant.Network analyses of identified proteins revealed intra and inter relationship of these proteins with their neighbors as well as their association with different defense signaling pathways. qRT-PCR analyses were performed to correlate the mRNA and protein levels of some proteins of representative classes.Thus, functional characterization of identified PR proteins (PR1, BGL2, TLP), Trypsin protease inhibitor, ABA responsive protein, cysteine protease, protein disulphide isomerase, ripening related protein and albumins are expected to serve as important molecular components for biotechnological application and development of sustainable resistance against Foc1.

View Article: PubMed Central - PubMed

Affiliation: Authors Address: Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata 700054, West Bengal, India. sampa@jcbose.ac.in.

ABSTRACT

Background: Vascular wilt caused by Fusarium oxysporum f. sp. ciceri Race 1 (Foc1) is a serious disease of chickpea (Cicer arietinum L.) accounting for approximately 10-15% annual crop loss. The fungus invades the plant via roots, colonizes the xylem vessels and prevents the upward translocation of water and nutrients, finally resulting in wilting of the entire plant. Although comparative transcriptomic profiling have highlighted some important signaling molecules, but proteomic studies involving chickpea-Foc1 are limited. The present study focuses on comparative root proteomics of susceptible (JG62) and resistant (WR315) chickpea genotypes infected with Foc1, to understand the mechanistic basis of susceptibility and/or resistance.

Results: The differential and unique proteins of both genotypes were identified at 48 h, 72 h, and 96 h post Foc1 inoculation. 2D PAGE analyses followed by MALDI-TOF MS and MS/MS identified 100 differentially (>1.5 fold<, p<0.05) or uniquely expressed proteins. These proteins were further categorized into 10 functional classes and grouped into GO (gene ontology) categories. Network analyses of identified proteins revealed intra and inter relationship of these proteins with their neighbors as well as their association with different defense signaling pathways. qRT-PCR analyses were performed to correlate the mRNA and protein levels of some proteins of representative classes.

Conclusions: The differential and unique proteins identified indicate their involvement in early defense signaling of the host. Comparative analyses of expression profiles of obtained proteins suggest that albeit some common components participate in early defense signaling in both susceptible and resistant genotypes, but their roles and regulation differ in case of compatible and/or incompatible interactions. Thus, functional characterization of identified PR proteins (PR1, BGL2, TLP), Trypsin protease inhibitor, ABA responsive protein, cysteine protease, protein disulphide isomerase, ripening related protein and albumins are expected to serve as important molecular components for biotechnological application and development of sustainable resistance against Foc1.

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Comparison of mRNA and protein expression levels of eleven representative genes. Quantitative real time PCR was performed using gene specific primers (Additional file 2). The log10 transformed fold change values (infected/control) of protein spot intensities and mRNA expression level were plotted at different time intervals (48 h, 72 h and 96 h) after infection with Foc1 for both chickpea genotypes. JG62 represented by grey color bars and WR315 represented by black color bars. The proteins selected are SOD (superoxide dismutase), PMIP (Pasma membrane intrinsic protein), ICDH (Isocitrate dehydrogenase), FLP (Fructokinase like protein), TIM (Triose phosphate isomerase), GNBP (Guanine nucleotide binding protein), PDI (Protein disulfide isomerase), EF1 (Elongation factor1), BGL2 (Glucan-endo-1, 3-beta-glucosidase), TLP (Thaumatin like protein), PR1 (Pathogenesis related protein1).
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Fig5: Comparison of mRNA and protein expression levels of eleven representative genes. Quantitative real time PCR was performed using gene specific primers (Additional file 2). The log10 transformed fold change values (infected/control) of protein spot intensities and mRNA expression level were plotted at different time intervals (48 h, 72 h and 96 h) after infection with Foc1 for both chickpea genotypes. JG62 represented by grey color bars and WR315 represented by black color bars. The proteins selected are SOD (superoxide dismutase), PMIP (Pasma membrane intrinsic protein), ICDH (Isocitrate dehydrogenase), FLP (Fructokinase like protein), TIM (Triose phosphate isomerase), GNBP (Guanine nucleotide binding protein), PDI (Protein disulfide isomerase), EF1 (Elongation factor1), BGL2 (Glucan-endo-1, 3-beta-glucosidase), TLP (Thaumatin like protein), PR1 (Pathogenesis related protein1).

Mentions: To correlate the protein levels with mRNA levels eleven representative genes corresponding to MS/MS identified proteins were selected and their transcript accumulation versus protein abundance analyzed (FigureĀ 5). The genes of corresponding proteins selected for transcript accumulation were pathogenesis related protein 1(PR1) (sp 145), thaumatin like protein (TLP) (sp 83), glucan-endo-1,3-beta-glucosidase EC 3.2.1.39 (BGL) (sp239), elongation factor 1 (EF1) (sp 275), protein disulfide isomerase (PDI) (sp 102), guanine nucleotide binding protein (GNBP) (sp 233), triose phosphate isomerase EC 5.3.1.1 (TIM) (sp 109), fructokinase like protein (FLP) (sp54), isocitrate dehydrogenase EC 1.1.1.42 (ICDH) (sp 165), plasma membrane intrinsic protein (PMIP) (sp19) and superoxide dismutase EC 1.15.1.1 (SOD) (sp 103). In general the abundance of mRNA differed from that of protein levels suggesting that the fold increment and/or decrement in mRNA accumulation do not correlate with the protein fold changes. Except for PR1, TLP and ICDH, the other eight proteins and their corresponding transcripts showed a similar qualitative trend in their accumulation patterns. However, the profiles did not provide quantitative similarity. PR, TLP and ICDH showed dissimilar patterns suggesting that mRNA and protein levels often exhibit different profiles. Transcript to protein production involves several regulatory factors which are spatially and temporally regulated due to which there are seldom profile matches between mRNA and protein levels. Moreover this disparity between mRNA and protein level might be due to posttranscriptional or posttranslational modifications, complexities of protein expression or presence of multigene families [39]. Similar results were reported in proteomic analysis of strawberry during Colletotrichum fragariae infection [99].Figure 5


Analysis of root proteome unravels differential molecular responses during compatible and incompatible interaction between chickpea (Cicer arietinum L.) and Fusarium oxysporum f. sp. ciceri Race1 (Foc1).

Chatterjee M, Gupta S, Bhar A, Chakraborti D, Basu D, Das S - BMC Genomics (2014)

Comparison of mRNA and protein expression levels of eleven representative genes. Quantitative real time PCR was performed using gene specific primers (Additional file 2). The log10 transformed fold change values (infected/control) of protein spot intensities and mRNA expression level were plotted at different time intervals (48 h, 72 h and 96 h) after infection with Foc1 for both chickpea genotypes. JG62 represented by grey color bars and WR315 represented by black color bars. The proteins selected are SOD (superoxide dismutase), PMIP (Pasma membrane intrinsic protein), ICDH (Isocitrate dehydrogenase), FLP (Fructokinase like protein), TIM (Triose phosphate isomerase), GNBP (Guanine nucleotide binding protein), PDI (Protein disulfide isomerase), EF1 (Elongation factor1), BGL2 (Glucan-endo-1, 3-beta-glucosidase), TLP (Thaumatin like protein), PR1 (Pathogenesis related protein1).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC4237293&req=5

Fig5: Comparison of mRNA and protein expression levels of eleven representative genes. Quantitative real time PCR was performed using gene specific primers (Additional file 2). The log10 transformed fold change values (infected/control) of protein spot intensities and mRNA expression level were plotted at different time intervals (48 h, 72 h and 96 h) after infection with Foc1 for both chickpea genotypes. JG62 represented by grey color bars and WR315 represented by black color bars. The proteins selected are SOD (superoxide dismutase), PMIP (Pasma membrane intrinsic protein), ICDH (Isocitrate dehydrogenase), FLP (Fructokinase like protein), TIM (Triose phosphate isomerase), GNBP (Guanine nucleotide binding protein), PDI (Protein disulfide isomerase), EF1 (Elongation factor1), BGL2 (Glucan-endo-1, 3-beta-glucosidase), TLP (Thaumatin like protein), PR1 (Pathogenesis related protein1).
Mentions: To correlate the protein levels with mRNA levels eleven representative genes corresponding to MS/MS identified proteins were selected and their transcript accumulation versus protein abundance analyzed (FigureĀ 5). The genes of corresponding proteins selected for transcript accumulation were pathogenesis related protein 1(PR1) (sp 145), thaumatin like protein (TLP) (sp 83), glucan-endo-1,3-beta-glucosidase EC 3.2.1.39 (BGL) (sp239), elongation factor 1 (EF1) (sp 275), protein disulfide isomerase (PDI) (sp 102), guanine nucleotide binding protein (GNBP) (sp 233), triose phosphate isomerase EC 5.3.1.1 (TIM) (sp 109), fructokinase like protein (FLP) (sp54), isocitrate dehydrogenase EC 1.1.1.42 (ICDH) (sp 165), plasma membrane intrinsic protein (PMIP) (sp19) and superoxide dismutase EC 1.15.1.1 (SOD) (sp 103). In general the abundance of mRNA differed from that of protein levels suggesting that the fold increment and/or decrement in mRNA accumulation do not correlate with the protein fold changes. Except for PR1, TLP and ICDH, the other eight proteins and their corresponding transcripts showed a similar qualitative trend in their accumulation patterns. However, the profiles did not provide quantitative similarity. PR, TLP and ICDH showed dissimilar patterns suggesting that mRNA and protein levels often exhibit different profiles. Transcript to protein production involves several regulatory factors which are spatially and temporally regulated due to which there are seldom profile matches between mRNA and protein levels. Moreover this disparity between mRNA and protein level might be due to posttranscriptional or posttranslational modifications, complexities of protein expression or presence of multigene families [39]. Similar results were reported in proteomic analysis of strawberry during Colletotrichum fragariae infection [99].Figure 5

Bottom Line: The fungus invades the plant via roots, colonizes the xylem vessels and prevents the upward translocation of water and nutrients, finally resulting in wilting of the entire plant.Network analyses of identified proteins revealed intra and inter relationship of these proteins with their neighbors as well as their association with different defense signaling pathways. qRT-PCR analyses were performed to correlate the mRNA and protein levels of some proteins of representative classes.Thus, functional characterization of identified PR proteins (PR1, BGL2, TLP), Trypsin protease inhibitor, ABA responsive protein, cysteine protease, protein disulphide isomerase, ripening related protein and albumins are expected to serve as important molecular components for biotechnological application and development of sustainable resistance against Foc1.

View Article: PubMed Central - PubMed

Affiliation: Authors Address: Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata 700054, West Bengal, India. sampa@jcbose.ac.in.

ABSTRACT

Background: Vascular wilt caused by Fusarium oxysporum f. sp. ciceri Race 1 (Foc1) is a serious disease of chickpea (Cicer arietinum L.) accounting for approximately 10-15% annual crop loss. The fungus invades the plant via roots, colonizes the xylem vessels and prevents the upward translocation of water and nutrients, finally resulting in wilting of the entire plant. Although comparative transcriptomic profiling have highlighted some important signaling molecules, but proteomic studies involving chickpea-Foc1 are limited. The present study focuses on comparative root proteomics of susceptible (JG62) and resistant (WR315) chickpea genotypes infected with Foc1, to understand the mechanistic basis of susceptibility and/or resistance.

Results: The differential and unique proteins of both genotypes were identified at 48 h, 72 h, and 96 h post Foc1 inoculation. 2D PAGE analyses followed by MALDI-TOF MS and MS/MS identified 100 differentially (>1.5 fold<, p<0.05) or uniquely expressed proteins. These proteins were further categorized into 10 functional classes and grouped into GO (gene ontology) categories. Network analyses of identified proteins revealed intra and inter relationship of these proteins with their neighbors as well as their association with different defense signaling pathways. qRT-PCR analyses were performed to correlate the mRNA and protein levels of some proteins of representative classes.

Conclusions: The differential and unique proteins identified indicate their involvement in early defense signaling of the host. Comparative analyses of expression profiles of obtained proteins suggest that albeit some common components participate in early defense signaling in both susceptible and resistant genotypes, but their roles and regulation differ in case of compatible and/or incompatible interactions. Thus, functional characterization of identified PR proteins (PR1, BGL2, TLP), Trypsin protease inhibitor, ABA responsive protein, cysteine protease, protein disulphide isomerase, ripening related protein and albumins are expected to serve as important molecular components for biotechnological application and development of sustainable resistance against Foc1.

Show MeSH
Related in: MedlinePlus