Sugarcane Serine Peptidase Inhibitors, Serine Peptidases, and Clp Protease System Subunits Associated with Sugarcane Borer (Diatraea saccharalis) Herbivory and Wounding
Abstract
:1. Introduction
2. Results
2.1. Macroarray Hybridization
2.2. Validation of D. saccharalis-Inducible Genes
2.2.1. Sugarcane Bowman-Birk Inhibitor (SacBBI) Genes
2.2.2. Sugarcane Maize-peptidase-inhibitor-like (SacMPI-like) and Chymotrypsin Inhibitor 1B-like (SacCI1B-like) Genes
2.2.3. Serine Peptidases and Clp Protease System Subunits
2.3. Validation of D. saccharalis-Repressed Genes
3. Discussion
4. Materials and Methods
4.1. Plant Material and Insects
4.1.1. Phase 1—Sugarcane and D. saccharalis Experiments Used for Macroarray Hibridization
4.1.2. Phase 2—qPCR Monitoring of Selected ESTs Identified through Macroarray
4.2. Macroarray Construction
4.3. Macroarray Normalization
4.4. Probe Preparation
4.5. Macroarray Analysis
4.6. Expression Analysis by Real-Time Quantitative PCR
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Sugarcane Clone Identification a | E-Value | Identity (%) | BLAST Hit b | Description c |
---|---|---|---|---|
SacBBI1 GI: 34966865 GB: CA113558.1 | 2 × 10−24 | 73/87 (84%) | GI:195610004 | Bowman–Birk type wound-induced proteinase inhibitor WIP1 precursor [Zea mays] |
SacBBI2 GI: 35951517 GB: CA261007.1 | 1 × 10−40 | 85/98 (87%) | GI:115434342 | Bowman–Birk type proteinase inhibitor Oryza sativa Japonica Group |
SacBBI3 GI: 35965021 GB: CA266304.1 | 5 × 10−43 | 74/88 (84%) | GI:195610814 | Bowman–Birk type bran trypsin inhibitor precursor [Zea mays] |
SacBBI4 GI: 35984624 GB: CA272687.1 | 2 × 10−39 | 85/98 (87%) | GI:115434342 | Bowman–Birk type proteinase inhibitor Oryza sativa Japonica Group |
SacMPI-like1 GI: 34922345 GB: CA070500.1 | 4 × 10−26 | 51/60 (85%) | GI:214015177 | Maize proteinase inhibitor [Zea mays subsp. parviglumis] |
SacMPI-like2 GI: 35258606 GB: CA212876.1 | 6 × 10−33 | 59/66 (89%) | GI:75994161 | Maize protease inhibitor [Zea mays subsp. parviglumis] |
SacMPIlike3 GI: 36014330 GB:CA282462.1 | 1 × 10−31 | 58/70 (83%) | GI:214015219 | Maize proteinase inhibitor [Zea mays subsp. parviglumis] |
SacMPI-like4 GI: 36037506 GB: CA288211.1 | 9 × 10−29 | 55/65 (85%) | GI:214015093 | Maize proteinase inhibitor [Zea mays subsp. parviglumis] |
SacMPI-like5 GI: 36065043 GB:CA297188.1 | 2 × 10−28 | 56/65 (85%) | GI:214015177 | Maize proteinase inhibitor [Zea mays subsp. parviglumis] |
SacCI-1B-like GI: 35010896 GB: CA129230.1 | 0.067 | 17/26 (65%) | GI:226507138 | Subtilisin-chymotrypsin inhibitor CI-1B [Zea mays] |
SacClp-like1 CA136349.1 | 2 × 10−77 | 94/94 (100%) | GI:242061800 | Clp amino terminal domain; Sorghum bicolor |
SacChy-like GI: 35946811 GB: CA258670.1 | 1 × 10−153 | 215/221 (97%) | GI:242077536 | PDZ domain of trypsin-like serine proteases |
SacCPD-like1 GI: 36002999 GB: CA278685.1 | No significant similarity found |
Sugarcane Clone Identification a | E-Value | Identity (%) | BLAST Hit b | Description c |
---|---|---|---|---|
SacClp-like2 GI: 34940929 GB: CA087622.1 | 1 × 10−137 | 192/198 (97%) | GI:195612324 | ATP-dependent Clp protease proteolytic subunit 2 [Zea mays] |
SacClp-like3 GI: 34966311 GB: CA113004.1 | 4 × 10−143 | 208/224 (93%) | GI:413935895 | Putative chaperone clp family protein [Zea mays] |
SacClp-like4 GI: 35005555 GB: CA126553.1 | 5 × 10−62 | 131/150 (87%) | GI:347602486 | ATP-dependent Clp protease ATP-binding subunit ClpC homolog 1, Oryza sativa Japonica Group |
SacClp-like5 GI: 35081269 GB: CA164148.1 | 7 × 10−108 | 180/189 (95%) | GI:475585607 | ATP-dependent Clp protease ATP-binding subunit clpA-like CD4A protein, chloroplastic [Aegilops tauschii] |
SacCPD-like2 GI: 34966324 GB: CA113017.1 | 4 × 10−127 | 177/198 (89%) | GI:195637388 | Serine carboxypeptidase K10B2.2 precursor [Zea mays] |
SacCPD-like3 GI: 35050806 GB: CA149102.1 | 7 × 10−58 | 94/105 (90%) | GI:226507958 | Serine carboxypeptidase K10B2.2 precursor [Zea mays] |
SacSub-like1 GI: 34948297 GB: CA094990.1 | 2 × 10−136 | 199/221 (90%) | GI:414880317 | TPA: putative subtilase family protein [Zea mays] |
SacSub-like2 GI: 34967468 GB: CA114161.1 | 2 × 10−42 | 80/100 (80%) | GI:42407651 | Putative subtilisin-like proteinase [Oryza sativa Japonica Group] |
SacSub-like3 GI: 34967945 GB: CA114638.1 | 6 × 10−76 | 124/158 (78%) | GI:475577050 | Subtilisin-like protease [Aegilops tauschii] |
Role | Arabidopsis Subunit | Accession | Sugarcane EST Homologue | Expression Profile * |
---|---|---|---|---|
Clp AAA+ chaperones | ClpC1 | AT5G50920 | CA119085.1 | - |
CA124181.1 | - | |||
CA126553.1 (SacClp-like4) | −1.9 ± 0.07 | |||
CA132637.1 | - | |||
CA164148.1 (SacClp-like5) | −1.9 ± 0.06 | |||
ClpC2 | AT3G48870 | CA113004.1 (SacClp-like3) | −6.4 ± 0.03 | |
ClpD | AT5G51070 | CA119462.1 | - | |
CA136349.1 (SacClp-like1) | 27,11 ± 10,31 | |||
CA145821.1 | - | |||
CA194919.1 | - | |||
CA212375.1 | - | |||
serine-type ClpP | ClpP1 | ATCG00670 | CA119497.1 | - |
ClpP3 | AT1G66670 | CA119729.1 | - | |
ClpP4 | AT5G45390 | CA107353.1 | - | |
ClpP5 | AT1G02560 | CA074329.1 | - | |
CA183086.1 | - | |||
ClpP6 | AT1G11750 | CA282400.1 | - | |
ClpP7 | AT5G23140 | - | - | |
ClpP-related ClpR | ClpR1 | AT1G49970 | CA108609.1 | - |
CA108695.1 | - | |||
ClpR2 | AT1G12410 | CA087622.1 (SacClp-like2) | −2.1 ± 0.14 | |
ClpR3 | AT1G09130 | Not found | ||
ClpR4 | AT4G17040 | CA113615.1 | - |
Sugarcane Clone Name | GenBank Accession Number | Relative mRNA Level | p Value |
---|---|---|---|
SacClp-like2 | CA087622.1 | ‒2.1 ± 0.14 | p < 0.005 |
SacClp-like3 | CA113004.1 | ‒6.4 ± 0.03 | p < 0.005 |
SacClp-like4 | CA126553.1 | ‒1.9 ± 0.07 | p < 0.005 |
SacClp-like5 | CA164148.1 | ‒1.9 ± 0.06 | p < 0.005 |
SacCPD-like2 | CA113017.1 | ‒2.1 ± 0.07 | p < 0.005 |
SacCPD-like3 | CA149102.1 | ‒44.2 ± 0.008 | p < 0.005 |
SacSub-like1 | CA094990.1 | ‒4.4 ± 0.04 | p < 0.005 |
SacSub-like2 | CA114161.1 | ‒2.7 ± 0.08 | p < 0.005 |
SacSub-like3 | CA114638.1 | ‒1.6 ± 0.06 | p < 0.005 |
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Medeiros, A.H.; Mingossi, F.B.; Dias, R.O.; Franco, F.P.; Vicentini, R.; Mello, M.O.; Moura, D.S.; Silva-Filho, M.C. Sugarcane Serine Peptidase Inhibitors, Serine Peptidases, and Clp Protease System Subunits Associated with Sugarcane Borer (Diatraea saccharalis) Herbivory and Wounding. Int. J. Mol. Sci. 2016, 17, 1444. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17091444
Medeiros AH, Mingossi FB, Dias RO, Franco FP, Vicentini R, Mello MO, Moura DS, Silva-Filho MC. Sugarcane Serine Peptidase Inhibitors, Serine Peptidases, and Clp Protease System Subunits Associated with Sugarcane Borer (Diatraea saccharalis) Herbivory and Wounding. International Journal of Molecular Sciences. 2016; 17(9):1444. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17091444
Chicago/Turabian StyleMedeiros, Ane H., Fabiana B. Mingossi, Renata O. Dias, Flávia P. Franco, Renato Vicentini, Marcia O. Mello, Daniel S. Moura, and Marcio C. Silva-Filho. 2016. "Sugarcane Serine Peptidase Inhibitors, Serine Peptidases, and Clp Protease System Subunits Associated with Sugarcane Borer (Diatraea saccharalis) Herbivory and Wounding" International Journal of Molecular Sciences 17, no. 9: 1444. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17091444