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Visse-Mansiaux M, Shumbe L, Brostaux Y, Ballmer T, Smit I, Dupuis B, Vanderschuren H. Identification of potato varieties suitable for cold storage and reconditioning: A safer alternative to anti-sprouting chemicals for potato sprouting control. Food Res Int 2024; 184:114249. [PMID: 38609227 DOI: 10.1016/j.foodres.2024.114249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/14/2024]
Abstract
Low temperature storage as an alternative to anti-sprouting chemicals in potato storage may induce reducing sugars (RS) accumulation (i.e. glucose and fructose) in potato tubers. This phenomenon is called "cold induced sweetening" (CIS) and occurs in certain varieties. CIS leads to a decrease in the organoleptic qualities and darkening of processed potato and the accumulation of toxic molecules such as acrylamide. To identify potato varieties suitable for storage at low temperatures, we screened six commercial processing varieties: Lady Claire (LC), Verdi, Kiebitz (KB), Pirol, Agria and Markies for their CIS characteristics and sprout-forming potential after storage at 4 °C and 8 °C. Our findings reveal that 4 °C storage allows for efficient sprout reduction in all six tested varieties for up to 4.5 months of storage. Three CIS-resistant varieties, namely Verdi, Lady Claire and Kiebitz, were identified as able to be stored for up to four months at 4 °C with limited increase in glucose content. Conversely, Pirol, Agria and Markies showed an increase in glucose content with a decrease in storage temperature and can be considered as CIS-susceptible varieties. After processing into crisps, the CIS-susceptible varieties displayed poor crisp color quality (brown to black color crisps) after storage for two months at 4 °C compared to the storage at 8 °C, whereas the CIS-resistant varieties had good crisp color quality (pale yellow color crisps) after storage at both 4 and 8 °C. Interestingly, the trends of total RS and/or glucose content in the CIS-resistant and in the CIS-susceptible varieties were correlated with the trends in Vacuolar Invertase (VInv) gene expression for most varieties, as well as with the trends in acrylamide content after processing. In addition, reconditioning of Markies variety after storage at 4 °C by gradually increasing the temperature to 15 °C resulted in a significant decrease of VInv transcript levels (reduction of 80 %), acrylamide content (reduction of 75 %) and glucose content when compared to a storage at 4 °C without reconditioning. Those results demonstrate that the reconditioning technique is a key factor for a sustainable potato storage and for improving the quality of processed potatoes.
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Affiliation(s)
- Margot Visse-Mansiaux
- Agroscope, Swiss Confederation's Center for Agricultural Research, Plant-Production Systems, Cultivation Techniques and Varieties in Arable Farming, Route de Duillier 50, 1260 Nyon, Switzerland; Plant Genetics Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Leonard Shumbe
- Plant Genetics Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Yves Brostaux
- Applied Statistics, Computer Science and Modeling Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Theodor Ballmer
- Agroscope, Swiss Confederation's Center for Agricultural Research, Plant-Production Systems, Cultivation Techniques and Varieties in Arable Farming, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Inga Smit
- Max Rubner-Institut (MRI), Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Cereals, Detmold, Germany.
| | - Brice Dupuis
- Agroscope, Swiss Confederation's Center for Agricultural Research, Plant-Production Systems, Cultivation Techniques and Varieties in Arable Farming, Route de Duillier 50, 1260 Nyon, Switzerland.
| | - Hervé Vanderschuren
- Plant Genetics Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; Tropical Crop Improvement Laboratory, Biosystems Department, KU Leuven, 3001 Heverlee, Belgium.
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Steinacher C, Rieder D, Turner JE, Solanky N, Nishio SY, Usami SI, Hausott B, Schrott-Fischer A, Dudas J. Validation of RNA Extraction Methods and Suitable Reference Genes for Gene Expression Studies in Developing Fetal Human Inner Ear Tissue. Int J Mol Sci 2024; 25:2907. [PMID: 38474154 DOI: 10.3390/ijms25052907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive gene expression investigation requires high-quality RNA extraction, in sufficient amounts for real-time quantitative polymerase chain reaction and next-generation sequencing. In this work, we compared different RNA extraction methods and evaluated different reference genes for gene expression studies in the fetal human inner ear. We compared the RNA extracted from formalin-fixed paraffin-embedded tissue with fresh tissue stored at -80 °C in RNAlater solution and validated the expression stability of 12 reference genes (from gestational week 11 to 19). The RNA from fresh tissue in RNAlater resulted in higher amounts and a better quality of RNA than that from the paraffin-embedded tissue. The reference gene evaluation exhibited four stably expressed reference genes (B2M, HPRT1, GAPDH and GUSB). The selected reference genes were then used to examine the effect on the expression outcome of target genes (OTOF and TECTA), which are known to be regulated during inner ear development. The selected reference genes displayed no differences in the expression profile of OTOF and TECTA, which was confirmed by immunostaining. The results underline the importance of the choice of the RNA extraction method and reference genes used in gene expression studies.
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Affiliation(s)
- Claudia Steinacher
- Department of Otorhinolaryngology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Jasmin E Turner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 4EP, UK
| | - Nita Solanky
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto 3-1-1 Asahi, Nagano 390-8621, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto 3-1-1 Asahi, Nagano 390-8621, Japan
| | - Barbara Hausott
- Institute of Neuroanatomy, Medical University Innsbruck, 6020 Innsbruck, Austria
| | | | - Jozsef Dudas
- Department of Otorhinolaryngology, Medical University Innsbruck, 6020 Innsbruck, Austria
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Jaiswal S, Paul K, Raman KV, Tyagi S, Saakre M, Tilgam J, Bhattacharjee S, Vijayan J, Mondal KK, Sreevathsa R, Pattanayak D. Amelioration of cold-induced sweetening in potato by RNAi mediated silencing of StUGPase encoding UDP-glucose pyrophosphorylase. FRONTIERS IN PLANT SCIENCE 2023; 14:1133029. [PMID: 36875591 PMCID: PMC9981964 DOI: 10.3389/fpls.2023.1133029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Cold-induced sweetening (CIS) is an unwanted physiological phenomenon in which reducing sugars (RS) get accumulated in potato (Solanum tuberosum) upon cold storage. High RS content makes potato commercially unsuitable for processing due to the unacceptable brown color in processed products like chips, fries, etc., and the production of a potential carcinogen, acrylamide. UDP-glucose pyrophosphorylase (UGPase) catalyzes the synthesis of UDP-glucose towards the synthesis of sucrose and is also involved in the regulation of CIS in potato. The objective of the present work was RNAi-mediated downregulation of the StUGPase expression level in potato for the development of CIS tolerant potato. Hairpin RNA (hpRNA) gene construct was developed by placing UGPase cDNA fragment in sense and antisense orientation intervened by GBSS intron. Internodal stem explants (cv. Kufri Chipsona-4) were transformed with hpRNA gene construct, and 22 transgenic lines were obtained by PCR screening of putative transformants. Four transgenic lines showed the highest level of RS content reduction following 30 days of cold storage, with reductions in sucrose and RS (glucose & fructose) levels of up to 46% and 57.5%, respectively. Cold stored transgenic potato of these four lines produced acceptable chip colour upon processing. The selected transgenic lines carried two to five copies of the transgene. Northern hybridization revealed an accumulation of siRNA with a concomitant decrease in the StUGPase transcript level in these selected transgenic lines. The present work demonstrates the efficacy of StUGPase silencing in controlling CIS in potato, and the strategy can be employed for the development of CIS tolerant potato varieties.
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Affiliation(s)
- Sandeep Jaiswal
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Post Graduate (PG) School, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Krishnayan Paul
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Post Graduate (PG) School, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K. Venkat Raman
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Saurabh Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Manjesh Saakre
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Post Graduate (PG) School, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jyotsana Tilgam
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Post Graduate (PG) School, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sougata Bhattacharjee
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Post Graduate (PG) School, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Joshitha Vijayan
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Kalyan Kumar Mondal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Abstract
Small RNAs (sRNAs) are key regulators of transcriptomes and proteomes of organisms through their sequence-specific interaction with complementary RNA targets. sRNAs can be classified according to their origin and mode of action into different classes such as: microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). The abundance and specific spatio-temporal expression of many sRNAs, especially miRNAs, is relevant for their biological function. Northern blotting is a widely used technique to study sRNAs because it is quantitative, relatively inexpensive, and readily available for most laboratories. This chapter describes the protocols for radioactive and non-radioactive sRNA Northern blot analysis, which includes RNA extraction, polyacrylamide gel electrophoresis, membrane transfer, hybridisation and detection of sRNA using oligonucleotide probes. The protocol is described to prepare most of the reagents needed in the lab, but also timesaving commercial reagent alternatives are included. Suggestions and nuances obtained from experience are included as Notes.
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Affiliation(s)
- Claudia Martinho
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
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Simon I, Persky Z, Avital A, Harat H, Schroeder A, Shoseyov O. Foliar Application of dsRNA Targeting Endogenous Potato ( Solanum tuberosum) Isoamylase Genes ISA1, ISA2, and ISA3 Confers Transgenic Phenotype. Int J Mol Sci 2022; 24:ijms24010190. [PMID: 36613634 PMCID: PMC9820567 DOI: 10.3390/ijms24010190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/11/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Isoamylase (ISA) is a debranching enzyme found in many plants, which hydrolyzes (1-6)-α-D glucosidic linkages in starch, amylopectin, and β-dextrins, and is thought to be responsible for starch granule formation (ISA1 and ISA2) and degradation (ISA3). Lipid-modified PEI (lmPEI) was synthesized as a carrier for long double-stranded RNA (dsRNA, 250-bp), which targets the three isoamylase isoforms. The particles were applied to the plant via the foliar spray and were differentially effective in suppressing the expressions of ISA1 and ISA2 in the potato leaves, and ISA3 in the tubers. Plant growth was not significantly impaired, and starch levels in the tubers were not affected as well. Interestingly, the treated plants had significantly smaller starch granule sizes as well as increased sucrose content, which led to an early sprouting phenotype. We confirm the proposal of previous research that an increased number of small starch granules could be responsible for an accelerated turnover of glucan chains and, thus, the rapid synthesis of sucrose, and we propose a new relationship between ISA3 and the starch granule size. The implications of this study are in achieving a transgenic phenotype for endogenous plant genes using a systemic, novel delivery system, and foliar applications of dsRNA for agriculture.
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Affiliation(s)
- Ido Simon
- Robert H. Smith Faculty of Agriculture Food and Environment, Hebrew University, Rehovot 76100, Israel
| | - Zohar Persky
- Robert H. Smith Faculty of Agriculture Food and Environment, Hebrew University, Rehovot 76100, Israel
| | - Aviram Avital
- Department of Chemical Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Hila Harat
- Robert H. Smith Faculty of Agriculture Food and Environment, Hebrew University, Rehovot 76100, Israel
| | - Avi Schroeder
- Department of Chemical Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Oded Shoseyov
- Robert H. Smith Faculty of Agriculture Food and Environment, Hebrew University, Rehovot 76100, Israel
- Correspondence:
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Isayenka I, Beaudoin N. The Streptomyces scabiei Pathogenicity Factor Thaxtomin A Induces the Production of Phenolic Compounds in Potato Tubers. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11233216. [PMID: 36501257 PMCID: PMC9737112 DOI: 10.3390/plants11233216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 05/27/2023]
Abstract
The phytotoxin thaxtomin A (TA) is the key pathogenicity factor synthesized by the bacteria Streptomyces scabiei, the main causal agent of common scab of potato (Solanum tuberosum L.). TA treatment of potato tuber flesh produces a brown color that was attributed to necrosis. The intensity of TA-induced browning was generally thought to correlate with potato sensitivity to the disease. In this study, we found that TA-induced browning was much more intense in the potato tuber flesh of the common scab moderately resistant variety Russet Burbank (RB) than that observed in tubers of the disease-susceptible variety Yukon Gold (YG). However, there was no significant difference in the level of TA-induced cell death detected in both varieties, suggesting that tubers response to TA does not correlate with the level of sensitivity to common scab. TA-treated potato tuber tissues accumulated significantly higher levels of phenolic compounds than untreated controls, with a higher phenol content detected in RB TA-treated tissues than in those of YG. Browning was associated with a significant induction of the expression of genes of the phenylpropanoid pathway in RB tubers, indicating that TA activated this metabolic pathway. These results suggest that tuber flesh browning induced by TA is due to the accumulation of phenolic compounds. These phenolics may play a role in the protection of potato tubers against S. scabiei.
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Zhai Y, Davenport B, Schuetz K, Pappu HR. An on-site adaptable test for rapid and sensitive detection of Potato mop-top virus, a soil-borne virus of potato (Solanum tuberosum). PLoS One 2022; 17:e0270918. [PMID: 35914219 PMCID: PMC9343021 DOI: 10.1371/journal.pone.0270918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Potato mop-top virus (PMTV) is considered an emerging threat to potato production in the United States. PMTV is transmitted by a soil-borne protist, Spongospora subterranean. Rapid, accurate, and sensitive detection of PMTV in leaves and tubers is an essential component in PMTV management program. A rapid test that can be adapted to in-field, on-site testing with minimal sample manipulation could help in ensuring the sanitary status of the produce in situations such as certification programs and shipping point inspections. Toward that goal, a rapid and highly sensitive recombinase polymerase amplification (RPA)-based test was developed for PMTV detection in potato tubers. The test combines the convenience of RPA assay with a simple sample extraction procedure, making it amenable to rapid on-site diagnosis of PMTV. Furthermore, the assay was duplexed with a plant internal control to monitor sample extraction and RPA reaction performance. The method described could detect as little as 10 fg of PMTV RNA transcript in various potato tissues, the diagnostic limit of detection (LOQ) similar to that of traditional molecular methods.
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Affiliation(s)
- Ying Zhai
- Department of Plant Pathology, Washington State University, Pullman, WA, United States of America
| | | | | | - Hanu R. Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States of America
- * E-mail:
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Kumar R, Kaundal P, Tiwari RK, Siddappa S, Kumari H, Lal MK, Naga KC, Sharma S, Sagar V, Kumar M. Establishment of a one-step reverse transcription recombinase polymerase amplification assay for the detection of potato virus S. J Virol Methods 2022; 307:114568. [PMID: 35718004 DOI: 10.1016/j.jviromet.2022.114568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/05/2022] [Accepted: 06/13/2022] [Indexed: 10/18/2022]
Abstract
Potato virus S (PVS) is a noteworthy threat to the propagation of healthy seed potatoes. Accurate and speedy detection is critical for effective PVS management. In the present study, an isothermal-based one-step reverse transcription-recombinase polymerase amplification (RT-RPA) approach was developed to detect PVS infection in potato leaves and tubers. A primer set based on the coat protein gene successfully amplified a 158 bp product out of three primer sets examined. The amplification reaction took less than 30 min to complete with no account of cross-reactivity with major potato viruses. Additionally, amplification of RT-RPA products was performed on the heating system and/or water bath at 38-42 °C. The results of sensitivity analysis revealed that one-step RT-RPA has shown 100 times higher sensitivity than routine RT-PCR for the detection of PVS in infected leaves. Furthermore, ten times higher sensitivity of RT-RPA was observed in infected tubers. The methodology was simplified further by the use of template RNA extracted using a cellular disc paper-based extraction method that detected the PVS more effectively than purified total RNA. PVS was detected in 175 samples (leaves and tubers each) of several potato varieties using this innovative technique. To our acquaintance, this is the first report of one-step RT-RPA using a basic RNA extract derived through cellular disc paper that is significantly sensitive and precise for PVS detection in potatoes. The advantages of one-step RT-RPA in terms of proficiency, robustness, and the availability of a highly pure RNA template make it an attractive choice for seed accreditation, resistance breeding, and field inspections.
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Affiliation(s)
- Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla 171 001, H.P., India.
| | - Priyanka Kaundal
- ICAR-Central Potato Research Institute, Shimla 171 001, H.P., India
| | | | | | - Hema Kumari
- ICAR-Central Potato Research Institute, Shimla 171 001, H.P., India
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla 171 001, H.P., India
| | | | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla 171 001, H.P., India
| | - Vinay Sagar
- ICAR-Central Potato Research Institute, Shimla 171 001, H.P., India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Regional Station, Modipuram 250110, Uttar Pradesh, India
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Kumar GNM, Kannangara CG, Knowles NR. Nucleases are upregulated in potato tubers afflicted with zebra chip disease. PLANTA 2022; 255:54. [PMID: 35103848 DOI: 10.1007/s00425-022-03832-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
The defense response of potato tubers afflicted with zebra chip disease involves oxidatively mediated upregulation of nucleases that likely modulate localized programmed cell death to restrict the phloem-mobile, CLso bacterial pathogen to the vasculature. Zebra chip (ZC) is a bacterial disease of potato (Solanum tuberosum L.) caused by Candidatus Liberibacter solanacearum (CLso). Tubers from infected plants develop characteristic brown discoloration of the vasculature, a result of localized programmed cell death (PCD). We examined the potential contribution of nucleases in the response of tubers to CLso infection. Specific activities of the major isozymes of dsDNase, ssDNase, and RNase were substantially upregulated in tubers from CLso-infected plants, despite their significantly lower soluble protein content. However, ZC disease had no effect on nuclease isozyme profiles. Activities of the predominant nuclease isoforms from healthy and CLso-infected tubers had similar pH optima, thermotolerance, and responses to metallic co-factors. Nuclease activities were heat stable to 60 °C and resistant to precipitation with 70% (v/v) isopropanol, which constitute effective techniques for partial purification. DNase and RNase isozyme activities were highest at pH 7.2-8.5 and 6.8-7.2, respectively, and profiles were similar for tubers from CLso-infected and non-infected plants. RNase activities were mostly insensitive to inhibition by EDTA, except at pH 8.5 and above. DNase activities were inhibited by EDTA but less sensitive to inhibition at high pH than the RNases. The EDTA-mediated inhibition of DNase (ds/ss) activities was restored with ZnSO4, but not Ca+2 or Mg+2. By contrast, ZnSO4 inhibited the activities of RNases. DTT and CuSO4 inhibited the activities of all three nucleases. These results suggest that activation of tuber nucleases is dependent on the oxidation of sulfhydryl groups to disulfide and/or oxidation of Zn to Zn+2. In light of previous published results that established extensive CLso-induced upregulation of oxidative stress metabolism in tubers, we propose a model to show how increased nuclease activity could result from a glutathione-mediated oxidation of nuclease sulfhydryl groups in diseased tubers. DNases and RNases are likely an integral part of the hypersensitive response and may modulate PCD to isolate the pathogen to the vascular tissues of tubers.
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Affiliation(s)
- G N Mohan Kumar
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA.
| | - C G Kannangara
- Department of Crop and Soils, Washington State University, Pullman, WA, 99163, USA
- , 335/4A, 2nd Cross Street, Kotte Road, Nugegoda, Sri Lanka
| | - N Richard Knowles
- Department of Horticulture, Washington State University, Pullman, WA, 99163, USA
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Leelawijitkul S, Kongsil P, Kittipadakul P, Juntawong P. Correlation Between Relative Gene Expression Patterns of Two Flowering locus T ( MeFT1 and MeFT2) in Cassava Leaf and Flowering Traits Under Different Flowering Induction Conditions. Pak J Biol Sci 2022; 25:369-379. [PMID: 35638506 DOI: 10.3923/pjbs.2022.369.379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
<b>Background and Objective:</b> <i>Flowering locus T</i> (<i>FT</i>) genes are involved in the flower induction mechanism in plants as florigen signals. The objective of this study was to study the relationship between the expression of <i>Flowering locus T</i> genes (<i>MeFTs</i>) in cassava and flowering traits under the different flowering induction conditions. <b>Materials and Methods:</b> The experimental design for flowering induction was RCBD for 4 replications. There were 5 treatment factors which were control, red light set from 5 pm to 7 am, 0.5 mM 6-benzyladenine (BA) with 2 mM silver thio-sulfate (STS), paclobutrazol for 6 g/plant and potassium chlorate (KCIO<sub>3</sub>) for 250 g/plant. The number of plants with flower bunches and the average number of bunches per plant in two cassava varieties were collected each month from 5-9 months after planting (MAP). The leaf samples were collected from HB80 and R9 varieties at 5-7 MAP for RNA extraction to study <i>MeFT1</i> and <i>MeFT2</i> expression. <b>Results:</b> The results show that <i>MeFT1</i> expression level positively correlated with flowering traits in the same month, while <i>MeFT2</i> expression level positively correlated with flowering traits in the following months. <b>Conclusion:</b> Therefore, expression of <i>MeFT2</i> can be used for the prediction of cassava flowering in the following month which will assist the breeder for the crossing management.
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Kumar R, Kaundal P, Tiwari RK, Siddappa S, Kumari H, Chandra Naga K, Sharma S, Kumar M. Rapid and sensitive detection of potato virus X by one-step reverse transcription-recombinase polymerase amplification method in potato leaves and dormant tubers. Mol Cell Probes 2021; 58:101743. [PMID: 34051280 DOI: 10.1016/j.mcp.2021.101743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Potato virus X (PVX), is a serious threat to global potato production. A simple and rapid detection method is imperative for PVX diagnosis and early management. In this study, an isothermal one-step reverse transcription-recombinase polymerase amplification (RT-RPA) method was optimized for the quick and convenient detection of PVX in potato leaves and tubers. Our results revealed that this one-step RT-RPA method was highly efficient than the conventional reverse transcription-polymerase chain reaction (RT-PCR). The amplification reaction was free from cross-reactivity with other common potato viruses and completed within 30 min. Moreover, this RT-RPA assay did not require a thermocycler based specific temperature phase amplification and can be easily performed using a simple heating block or water bath at a temperature range of 39-42 °C. The sensitivity assay demonstrated that the developed one-step RT-RPA method was 100 times more sensitive than a routine one-step RT-PCR. Initially, the purified total RNA as the template isolated from infected leaves of potato was used for the detection of PVX. One-step RT-RPA was later performed using cellular disc paper-based simple RNA extract as a template that could detect the virus more efficiently than purified total RNA. The performance of the one-step RT-RPA assay was further evaluated using 500 field samples of leaves and tubers representing different cultivars and geographical regions. To our knowledge, this is the first report of rapid, sensitive, and reliable detection of PVX infection by one-step RT-RPA using cellular disc paper-based simple RNA extract from leaves and dormant tubers of potato. It is superior to the common RT-PCR assay in terms of its versatility, quickness, and independence of highly purified RNA template and can be adopted as a substitute to RT-PCR as an effective technique for seed potato certification, quarantine, breeding, and field surveys.
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Affiliation(s)
- Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, 171 001, H. P, India.
| | - Priyanka Kaundal
- ICAR-Central Potato Research Institute, Shimla, 171 001, H. P, India.
| | | | | | - Hema Kumari
- ICAR-Central Potato Research Institute, Shimla, 171 001, H. P, India.
| | | | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, 171 001, H. P, India.
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Regional Station, Modipuram, 250110, Uttar Pradesh, India.
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Šola I, Vujčić Bok V, Pinterić M, Auer S, Ludwig-Müller J, Rusak G. Improving the phytochemical profile and bioactivity of Chinese cabbage sprouts by interspecific transfer of metabolites. Food Res Int 2020; 137:109726. [DOI: 10.1016/j.foodres.2020.109726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/04/2020] [Accepted: 09/14/2020] [Indexed: 12/23/2022]
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13
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Kumar P, Garrido E, Zhao K, Zheng Y, Alseekh S, Vargas-Ortiz E, Fernie AR, Fei Z, Poveda K, Jander G. Tecia solanivora infestation increases tuber starch accumulation in Pastusa Suprema potatoes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1083-1096. [PMID: 29888549 DOI: 10.1111/jipb.12675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
In response to infestation with larvae of the Guatemalan tuber moth (Tecia solanivora), some Solanum tuberosum (potato) varieties exhibit an overcompensation response, whereby the total dry mass of uninfested tubers is increased. Here, we describe early responses, within the first few days, of T. solanivora feeding, in the Colombian potato variety Pastusa Suprema. Non-targeted metabolite profiling showed significant secondary metabolism changes in T. solanivora-infested tubers, but not in uninfested systemic tubers. In contrast, changes in primary metabolism were greater in uninfested systemic tubers than in the infested tubers, with a notable 80% decline in systemic tuber sucrose levels within 1 d of T. solanivora infestation. This suggested either decreased sucrose transport from the leaves or increased sink strength, i.e., more rapid sucrose to starch conversion in the tubers. Increased sucrose synthesis was indicated by higher rubisco activase and lower starch synthase gene expression in the leaves of infested plants. Elevated sink strength was demonstrated by 45% more total starch deposition in systemic tubers of T. solanivora-infested plants compared to uninfested control plants. Thus, rather than investing in increased defense of uninfested tubers, Pastusa Suprema promotes deposition of photoassimilates in the form of starch as a response to T. solanivora infestation.
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Affiliation(s)
- Pavan Kumar
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853, USA
| | - Etzel Garrido
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | - Kun Zhao
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853, USA
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Erandi Vargas-Ortiz
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853, USA
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853, USA
| | - Katja Poveda
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | - Georg Jander
- Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853, USA
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14
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Beyene G, Solomon FR, Chauhan RD, Gaitán‐Solis E, Narayanan N, Gehan J, Siritunga D, Stevens RL, Jifon J, Van Eck J, Linsler E, Gehan M, Ilyas M, Fregene M, Sayre RT, Anderson P, Taylor NJ, Cahoon EB. Provitamin A biofortification of cassava enhances shelf life but reduces dry matter content of storage roots due to altered carbon partitioning into starch. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1186-1200. [PMID: 29193665 PMCID: PMC5978869 DOI: 10.1111/pbi.12862] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 05/21/2023]
Abstract
Storage roots of cassava (Manihot esculenta Crantz), a major subsistence crop of sub-Saharan Africa, are calorie rich but deficient in essential micronutrients, including provitamin A β-carotene. In this study, β-carotene concentrations in cassava storage roots were enhanced by co-expression of transgenes for deoxy-d-xylulose-5-phosphate synthase (DXS) and bacterial phytoene synthase (crtB), mediated by the patatin-type 1 promoter. Storage roots harvested from field-grown plants accumulated carotenoids to ≤50 μg/g DW, 15- to 20-fold increases relative to roots from nontransgenic plants. Approximately 85%-90% of these carotenoids accumulated as all-trans-β-carotene, the most nutritionally efficacious carotenoid. β-Carotene-accumulating storage roots displayed delayed onset of postharvest physiological deterioration, a major constraint limiting utilization of cassava products. Large metabolite changes were detected in β-carotene-enhanced storage roots. Most significantly, an inverse correlation was observed between β-carotene and dry matter content, with reductions of 50%-60% of dry matter content in the highest carotenoid-accumulating storage roots of different cultivars. Further analysis confirmed a concomitant reduction in starch content and increased levels of total fatty acids, triacylglycerols, soluble sugars and abscisic acid. Potato engineered to co-express DXS and crtB displayed a similar correlation between β-carotene accumulation, reduced dry matter and starch content and elevated oil and soluble sugars in tubers. Transcriptome analyses revealed a reduced expression of genes involved in starch biosynthesis including ADP-glucose pyrophosphorylase genes in transgenic, carotene-accumulating cassava roots relative to nontransgenic roots. These findings highlight unintended metabolic consequences of provitamin A biofortification of starch-rich organs and point to strategies for redirecting metabolic flux to restore starch production.
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Affiliation(s)
- Getu Beyene
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Felix R. Solomon
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Center for Plant Science InnovationDepartment of BiochemistryE318 Beadle CenterUniversity of Nebraska‐LincolnLincolnNEUSA
| | | | | | | | | | - Dimuth Siritunga
- Department of BiologyUniversity of Puerto RicoMayaguezPuerto Rico
| | | | - John Jifon
- Department of Horticultural SciencesTexas A&M AgriLife Research and Extension CenterWeslacoTXUSA
| | | | | | - Malia Gehan
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Muhammad Ilyas
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of ArizonaTucsonAZUSA
| | - Martin Fregene
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
African Development BankAbidjan 01Côte d'Ivoire
| | - Richard T. Sayre
- New Mexico ConsortiumLos Alamos National LaboratoryLos AlamosNMUSA
| | | | | | - Edgar B. Cahoon
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Center for Plant Science InnovationDepartment of BiochemistryE318 Beadle CenterUniversity of Nebraska‐LincolnLincolnNEUSA
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15
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Neilson J, Lagüe M, Thomson S, Aurousseau F, Murphy AM, Bizimungu B, Deveaux V, Bègue Y, Jacobs JME, Tai HH. Gene expression profiles predictive of cold-induced sweetening in potato. Funct Integr Genomics 2017; 17:459-476. [PMID: 28236275 DOI: 10.1007/s10142-017-0549-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/18/2017] [Accepted: 01/30/2017] [Indexed: 10/24/2022]
Abstract
Cold storage (2-4 °C) used in potato production to suppress diseases and sprouting during storage can result in cold-induced sweetening (CIS), where reducing sugars accumulate in tuber tissue leading to undesirable browning, production of bitter flavors, and increased levels of acrylamide with frying. Potato exhibits genetic and environmental variation in resistance to CIS. The current study profiles gene expression in post-harvest tubers before cold storage using transcriptome sequencing and identifies genes whose expression is predictive for CIS. A distance matrix for potato clones based on glucose levels after cold storage was constructed and compared to distance matrices constructed using RNA-seq gene expression data. Congruence between glucose and gene expression distance matrices was tested for each gene. Correlation between glucose and gene expression was also tested. Seventy-three genes were found that had significant p values in the congruence and correlation tests. Twelve genes from the list of 73 genes also had a high correlation between glucose and gene expression as measured by Nanostring nCounter. The gene annotations indicated functions in protein degradation, nematode resistance, auxin transport, and gibberellin response. These 12 genes were used to build models for prediction of CIS using multiple linear regression. Nine linear models were constructed that used different combinations of the 12 genes. An F-box protein, cellulose synthase, and a putative Lax auxin transporter gene were most frequently used. The findings of this study demonstrate the utility of gene expression profiles in predictive diagnostics for severity of CIS.
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Affiliation(s)
- Jonathan Neilson
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada.
| | - M Lagüe
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - S Thomson
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - F Aurousseau
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - A M Murphy
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - B Bizimungu
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
| | - V Deveaux
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - Y Bègue
- Station de Recherche du Comite Nord, Sipre-Responsable Scientifique Creation Varietale, 18 La Chaussée, 76110, Bretteville du Grand Caux, France
| | - J M E Jacobs
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch, New Zealand
| | - H H Tai
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, 850 Lincoln Rd., Fredericton, N. B, E3B 4Z7, Canada
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16
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Sandoval Pineda JF, Ochoa Corona F, Torres Rojas E. Evaluación de diferentes métodos de extracción de ARN a partir del hongo nativo Xylaria sp. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2017. [DOI: 10.15446/rev.colomb.biote.v19n1.57114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La extracción de ARN de calidad constituye el primer paso para el análisis de la expresión génica. Sin embargo, su obtención no es sencilla debido a la susceptibilidad de esta molécula a la presencia de contaminantes como ARNasas, proteínas y polisacáridos. Adicionalmente, debido a la diversa composición de la pared celular de los hongos se requiere optimizar los procesos de extracción de ARN para organismos específicos. Este estudio evalúo el uso de diferentes metodologías de homogeneización de tejido (nitrógeno líquido y liofilización) y extracción de ARN (Trizol, CTAB y RNeasy mini kit) a partir del hongo nativo ascomiceto Xylaria sp. Se determinó la pureza, concentración e integridad del ARN obtenido por medio de espectrofotometría y electroforesis. Adicionalmente, se diseñaron cebadores de referencia para el gen β-Tubulina a partir del alineamiento de secuencias de este gen obtenidas de diferentes ascomicetes. Estos cebadores fueron utilizados para evaluar si el ARN extraído es amplificable mediante RT-PCR. Se determinó que la homogeneización de tejido por medio de liofilización generó mayores rendimientos de extracción independientemente del protocolo de extracción utilizado; sin embargo, éstos alteraron la integridad del ARN. Se obtuvo un ARN con mayor pureza con el protocolo CTABy un mayor rendimiento con el RNeasy mini kit. Los resultados indican que el ARN extraído, independientemente de la metodología de homogeneización y extracción utilizada, es amplificable mediante RT-PCR. No obstante, se recomienda homogeneizar el tejido con nitrógeno líquido y extraer con RNeasy mini kit por la brevedad del protocolo de extracción y calidad obtenida.
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17
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Potato tuber herbivory increases resistance to aboveground lepidopteran herbivores. Oecologia 2016; 182:177-87. [PMID: 27147449 DOI: 10.1007/s00442-016-3633-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/05/2016] [Indexed: 10/25/2022]
Abstract
Plants mediate interactions between aboveground and belowground herbivores. Although effects of root herbivory on foliar herbivores have been documented in several plant species, interactions between tuber-feeding herbivores and foliar herbivores are rarely investigated. We report that localized tuber damage by Tecia solanivora (Guatemalan tuber moth) larvae reduced aboveground Spodoptera exigua (beet armyworm) and Spodoptera frugiperda (fall armyworm) performance on Solanum tuberosum (potato). Conversely, S. exigua leaf damage had no noticeable effect on belowground T. solanivora performance. Tuber infestation by T. solanivora induced systemic plant defenses and elevated resistance to aboveground herbivores. Lipoxygenase 3 (Lox3), which contributes to the synthesis of plant defense signaling molecules, had higher transcript abundance in T. solanivora-infested leaves and tubers than in equivalent control samples. Foliar expression of the hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase (HQT) and 3-hydroxy-3-methylglutaryl CoA reductase I (HMGR1) genes, which are involved in chlorogenic acid and steroidal glycoalkaloid biosynthesis, respectively, also increased in response to tuber herbivory. Leaf metabolite profiling demonstrated the accumulation of unknown metabolites as well as the known potato defense compounds chlorogenic acid, α-solanine, and α-chaconine. When added to insect diet at concentrations similar to those found in potato leaves, chlorogenic acid, α-solanine, and α-chaconine all reduced S. exigua larval growth. Thus, despite the fact that tubers are a metabolic sink tissue, T. solanivora feeding elicits a systemic signal that induces aboveground resistance against S. exigua and S. frugiperda by increasing foliar abundance of defensive metabolites.
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18
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Kumar GNM, Knowles LO, Knowles NR. Zebra chip disease decreases tuber (Solanum tuberosum L.) protein content by attenuating protease inhibitor levels and increasing protease activities. PLANTA 2015; 242:1153-1166. [PMID: 26092706 DOI: 10.1007/s00425-015-2346-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/03/2015] [Indexed: 06/04/2023]
Abstract
Zebra chip disease of potato decreases protease inhibitor levels resulting in enhanced serine-type protease activity, decreased protein content and altered protein profiles of fully mature tubers. Zebra-chip (ZC), caused by Candidatus Liberibacter solanacearum (CLso), is a relatively new disease of potato that negatively affects growth, yield, propagation potential, and fresh and process qualities of tubers. Diseased plants produce tubers with characteristic brown discoloration of vascular tissue accompanied by elevated levels of free amino acids and reducing sugars. Here we demonstrate that ZC disease induces selective protein catabolism in tubers through modulating protease inhibitor levels. Soluble protein content of tubers from CLso-infected plants was 33% lower than from non-infected plants and electrophoretic analyses revealed substantial reductions in major tuber proteins. Patatin (~40 kDa) and ser-, asp- (22 kDa) and cys-type (85 kDa) protease inhibitors were either absent or greatly reduced in ZC-afflicted tubers. In contrast to healthy (non-infected) tubers, the proteolytic activity in CLso infected tubers was high and the ability of extracts from infected tubers to inhibit trypsin (ser-type) and papain (cys-type) proteases greatly attenuated. Moreover, extracts from CLso-infected tubers rapidly catabolized proteins purified from healthy tubers (40 kDa patatin, 22 kDa protease inhibitors, 85 kDa potato multicystatin) when subjected to proteolysis individually. In contrast, crude extracts from non-infected tubers effectively inhibited the proteolytic activity from ZC-afflicted tubers. These results suggest that the altered protein profile of ZC afflicted tubers is largely due to loss of ser- and cys-type protease inhibitors. Further analysis revealed a novel PMSF-sensitive (ser) protease (ca. 80-120 kDa) in CLso infected tubers. PMSF abolished the proteolytic activities responsible for degrading patatin, the 22 kDa protease inhibitor(s) and potato multicystatin by CLso infected tubers. The disease-induced loss of patatin and protease inhibitors therefore appears to be modulated by ser-type protease(s). The selective catabolism of proteins in ZC-afflicted tubers undoubtedly affects downstream aspects of carbohydrate and amino acid metabolism, which is ultimately reflected by the accumulation of reducing sugars, free amino acids and reduced sprouting capacity.
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Affiliation(s)
- G N Mohan Kumar
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture, Washington State University, P.O. Box 646414, Pullman, WA, 99164-6414, USA.
| | - Lisa O Knowles
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture, Washington State University, P.O. Box 646414, Pullman, WA, 99164-6414, USA
| | - N Richard Knowles
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture, Washington State University, P.O. Box 646414, Pullman, WA, 99164-6414, USA.
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19
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García-Baldenegro CV, Vargas-Arispuro I, Islas-Osuna M, Rivera-Domínguez M, Aispuro-Hernández E, Martínez-Téllez MÁ. Total RNA quality of lyophilized and cryopreserved dormant grapevine buds. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2015.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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20
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Piłsyk S, Natorff R, Gawińska-Urbanowicz H, Kruszewska JS. Fusarium sambucinum astA gene expressed during potato infection is a functional orthologue of Aspergillus nidulans astA. Fungal Biol 2015; 119:509-17. [PMID: 25986548 DOI: 10.1016/j.funbio.2015.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 02/02/2023]
Abstract
Sulfate assimilation plays a vital role in prototrophic organisms. Orthologues of the alternative sulfate transporter (AstA) gene from Aspergillus nidulans were identified in the fungal plant pathogens Fusarium sambucinum and Fusarium graminearum. By physiological and biochemical analyses, the AstA orthologues were determined to be able to uptake sulfate from the environment. Similarly to astA in A. nidulans, the FsastA gene was found to be regulated by sulfur metabolite repression (SMR) in a sulfur-dependent manner. In contrast, the FgastA transcript was undetectable, however, when the FgastA gene was expressed heterologously in A. nidulans, the translated FgAstA protein acted as a sulfate transporter. Interestingly, F. sambucinum astA expression was remarkably augmented in infected potato tubers, despite the presence abundant sulfate and was found not to be correlated with plant resistance.
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Affiliation(s)
- Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A str., 02-106 Warsaw, Poland.
| | - Renata Natorff
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A str., 02-106 Warsaw, Poland
| | | | - Joanna S Kruszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A str., 02-106 Warsaw, Poland
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21
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Huang T, Joshi V, Jander G. The catabolic enzyme methionine gamma-lyase limits methionine accumulation in potato tubers. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:883-93. [PMID: 24738868 DOI: 10.1111/pbi.12191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 03/07/2014] [Accepted: 03/17/2014] [Indexed: 05/07/2023]
Abstract
Increasing methionine in potato tubers is desirable, both to increase the availability of this limiting essential amino acid and to enhance the aroma of baked and fried potatoes. Previous attempts to elevate potato methionine content using transgenic approaches have focused on increasing methionine biosynthesis. Higher isoleucine accumulation in these transgenic tubers suggested that the potatoes compensate for increased methionine biosynthesis with enhanced catabolism via methionine gamma-lyase (MGL), thereby producing 2-ketybutyrate for isoleucine biosynthesis. In the current study, we show that potato StMGL1 encodes a functional MGL in potato tubers. In planta silencing of StMGL1 results in an increased methionine to isoleucine ratio in the free amino acid profile of potato tubers and, in some transgenic lines, elevated accumulation of free methionine. In both wild-type and transgenic tubers, the ratio of methionine to isoleucine is negatively correlated with the level of StMGL1 transcript. A three-dimensional distribution of free amino acids in potato tubers is also described.
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Affiliation(s)
- Tengfang Huang
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
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22
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Schreiber L, Nader-Nieto AC, Schönhals EM, Walkemeier B, Gebhardt C. SNPs in genes functional in starch-sugar interconversion associate with natural variation of tuber starch and sugar content of potato (Solanum tuberosum L.). G3 (BETHESDA, MD.) 2014; 4:1797-811. [PMID: 25081979 PMCID: PMC4199688 DOI: 10.1534/g3.114.012377] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/17/2014] [Indexed: 01/17/2023]
Abstract
Starch accumulation and breakdown are vital processes in plant storage organs such as seeds, roots, and tubers. In tubers of potato (Solanum tuberosum L.) a small fraction of starch is converted into the reducing sugars glucose and fructose. Reducing sugars accumulate in response to cold temperatures. Even small quantities of reducing sugars affect negatively the quality of processed products such as chips and French fries. Tuber starch and sugar content are inversely correlated complex traits that are controlled by multiple genetic and environmental factors. Based on in silico annotation of the potato genome sequence, 123 loci are involved in starch-sugar interconversion, approximately half of which have been previously cloned and characterized. By means of candidate gene association mapping, we identified single-nucleotide polymorphisms (SNPs) in eight genes known to have key functions in starch-sugar interconversion, which were diagnostic for increased tuber starch and/or decreased sugar content and vice versa. Most positive or negative effects of SNPs on tuber-reducing sugar content were reproducible in two different collections of potato cultivars. The diagnostic SNP markers are useful for breeding applications. An allele of the plastidic starch phosphorylase PHO1a associated with increased tuber starch content was cloned as full-length cDNA and characterized. The PHO1a-HA allele has several amino acid changes, one of which is unique among all known starch/glycogen phosphorylases. This mutation might cause reduced enzyme activity due to impaired formation of the active dimers, thereby limiting starch breakdown.
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Affiliation(s)
- Lena Schreiber
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| | - Anna Camila Nader-Nieto
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| | - Elske Maria Schönhals
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| | - Birgit Walkemeier
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
| | - Christiane Gebhardt
- Max Planck Institute for Plant Breeding Research, Department of Plant Breeding and Genetics, 50829 Cologne, Germany
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23
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Zommick DH, Knowles LO, Pavek MJ, Knowles NR. In-season heat stress compromises postharvest quality and low-temperature sweetening resistance in potato (Solanum tuberosum L.). PLANTA 2014; 239:1243-1263. [PMID: 24615233 DOI: 10.1007/s00425-014-2048-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/18/2014] [Indexed: 06/03/2023]
Abstract
The effects of soil temperature during tuber development on physiological processes affecting retention of postharvest quality in low-temperature sweetening (LTS) resistant and susceptible potato cultivars were investigated. 'Premier Russet' (LTS resistant), AO02183-2 (LTS resistant) and 'Ranger Russet' (LTS susceptible) tubers were grown at 16 (ambient), 23 and 29 °C during bulking (111-164 DAP) and maturation (151-180 DAP). Bulking at 29 °C virtually eliminated yield despite vigorous vine growth. Tuber specific gravity decreased as soil temperature increased during bulking, but was not affected by temperature during maturation. Bulking at 23 °C and maturation at 29 °C induced higher reducing sugar levels in the proximal (basal) ends of tubers, resulting in non-uniform fry color at harvest, and abolished the LTS-resistant phenotype of 'Premier Russet' tubers. AO02183-2 tubers were more tolerant of heat for retention of LTS resistance. Higher bulking and maturation temperatures also accelerated LTS and loss of process quality of 'Ranger Russet' tubers, consistent with increased invertase and lower invertase inhibitor activities. During LTS, tuber respiration fell rapidly to a minimum as temperature decreased from 9 to 4 °C, followed by an increase to a maximum as tubers acclimated to 4 °C; respiration then declined over the remaining storage period. The magnitude of this cold-induced acclimation response correlated directly with the extent of buildup in sugars over the 24-day LTS period and thus reflected the effects of in-season heat stress on propensity of tubers to sweeten and lose process quality at 4 °C. While morphologically indistinguishable from control tubers, tubers grown at elevated temperature had different basal metabolic (respiration) rates at harvest and during cold acclimation, reduced dormancy during storage, greater increases in sucrose and reducing sugars and associated loss of process quality during LTS, and reduced ability to improve process quality through reconditioning. Breeding for retention of postharvest quality and LTS resistance should consider strategies for incorporating more robust tolerance to in-season heat stress.
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Affiliation(s)
- Daniel H Zommick
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture, Washington State University, P.O. Box 646414, Pullman, WA, 99164-6414, USA
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24
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Salvato F, Havelund JF, Chen M, Rao RSP, Rogowska-Wrzesinska A, Jensen ON, Gang DR, Thelen JJ, Møller IM. The potato tuber mitochondrial proteome. PLANT PHYSIOLOGY 2014; 164:637-53. [PMID: 24351685 PMCID: PMC3912095 DOI: 10.1104/pp.113.229054] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 12/16/2013] [Indexed: 05/17/2023]
Abstract
Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins were resolved by one-dimensional gel electrophoresis, and tryptic peptides were extracted from gel slices and analyzed by liquid chromatography-tandem mass spectrometry using an Orbitrap XL. Using four different search programs, a total of 1,060 nonredundant proteins were identified in a quantitative manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome (possibly as high as 85%). The dynamic range of protein expression spanned 1,800-fold and included nearly all components of the electron transport chain, tricarboxylic acid cycle, and protein import apparatus. Additionally, we identified 71 pentatricopeptide repeat proteins, 29 membrane carriers/transporters, a number of new proteins involved in coenzyme biosynthesis and iron metabolism, the pyruvate dehydrogenase kinase, and a type 2C protein phosphatase that may catalyze the dephosphorylation of the pyruvate dehydrogenase complex. Systematic analysis of prominent posttranslational modifications revealed that more than 50% of the identified proteins harbor at least one modification. The most prominently observed class of posttranslational modifications was oxidative modifications. This study reveals approximately 500 new or previously unconfirmed plant mitochondrial proteins and outlines a facile strategy for unbiased, near-comprehensive identification of mitochondrial proteins and their modified forms.
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Affiliation(s)
| | - Jesper F. Havelund
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - Mingjie Chen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - R. Shyama Prasad Rao
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - Ole N. Jensen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - David R. Gang
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
| | - Jay J. Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211 (F.S., M.C., R.S.P.R., J.J.T.)
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, DK-4200 Slagelse, Denmark (J.F.H., I.M.M.)
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark (J.F.H., A.R.-W., O.N.J.); and
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 (D.R.G.)
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Zommick DH, Kumar GNM, Knowles LO, Knowles NR. Translucent tissue defect in potato (Solanum tuberosum L.) tubers is associated with oxidative stress accompanying an accelerated aging phenotype. PLANTA 2013; 238:1125-1145. [PMID: 24037414 DOI: 10.1007/s00425-013-1951-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/20/2013] [Indexed: 06/02/2023]
Abstract
Translucent tissue defect (TTD) is an undesirable postharvest disorder of potato tubers characterized by the development of random pockets of semi-transparent tissue containing high concentrations of reducing sugars. Translucent areas turn dark during frying due to the Maillard reaction. The newly released cultivar, Premier Russet, is highly resistant to low temperature sweetening, but susceptible to TTD. Symptoms appeared as early as 170 days after harvest and worsened with time in storage (4-9 °C, 95 % RH). In addition to higher concentrations of glucose, fructose and sucrose, TTD resulted in lower dry matter, higher specific activities of starch phosphorylase and glc-6-phosphate dehydrogenase, higher protease activity, loss of protein, and increased concentrations of free amino acids (esp. asparagine and glutamine). The mechanism of TTD is unknown; however, the disorder has similarities with the irreversible senescent sweetening that occurs in tubers during long-term storage, where much of the decline in quality is a consequence of progressive increases in oxidative stress with advancing age. The respiration rate of non-TTD 'Premier Russet' tubers was inherently higher (ca. 40 %) than that of 'Russet Burbank' tubers (a non-TTD cultivar). Moreover, translucent tissue from 'Premier Russet' tubers had a 1.9-fold higher respiration rate than the average of non-translucent tissue and tissue from non-TTD tubers. Peroxidation of membrane lipids during TTD development resulted in increased levels of malondialdehyde and likely contributed to a measurable increase in membrane permeability. Superoxide dismutase and catalase activities and the ratio of oxidized to total glutathione were substantially higher in translucent tissue. TTD tubers also contained twofold less ascorbate than non-TTD tubers. TTD appears to be a consequence of oxidative stress associated with accelerated aging of 'Premier Russet' tubers.
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Affiliation(s)
- Daniel H Zommick
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture, Washington State University, P.O. Box 646414, Pullman, WA, 99164-6414, USA
| | - G N Mohan Kumar
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture, Washington State University, P.O. Box 646414, Pullman, WA, 99164-6414, USA
| | - Lisa O Knowles
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture, Washington State University, P.O. Box 646414, Pullman, WA, 99164-6414, USA
| | - N Richard Knowles
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture, Washington State University, P.O. Box 646414, Pullman, WA, 99164-6414, USA.
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Bowrin V, Rouse-Miller J, Sutton F, Sirju-Charran G. Formamide-based RNA isolation at above zero temperatures from high starch cassava tubers. PHYTOCHEMICAL ANALYSIS : PCA 2013; 24:93-96. [PMID: 22826189 DOI: 10.1002/pca.2390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 06/22/2012] [Accepted: 06/27/2012] [Indexed: 06/01/2023]
Abstract
INTRODUCTION Cassava (Manihot esculenta) tubers are a main source of carbohydrate for a large percentage of people in the tropics. However, obtaining RNA from such high starch tubers proves problematic because gelation occurs during standard isolation procedures. In preliminary studies, formamide was used to homogenise tubers at room temperature and no gelation was observed. OBJECTIVES To develop a simple, reproducible formamide-based procedure for RNA isolation from high starch tissues without the initial use of liquid nitrogen or lyophilisation. A second objective was to determine the impact of storage of formamide homogenates at 4°C on RNA integrity. METHODOLOGY Tubers were homogenised in 100% formamide at room temperature and stored for 1, 4 or 7 days at 4°C. Homogenates were centrifuged at 14000 × g for 10 min and RNA recovered from the supernatants by isopropanol precipitation followed by dissolution in guanidinium buffer. Protein was removed by standard phenol-chloroform-isoamyl alcohol extraction and RNA recovered by isopropanol precipitation. For immediate RNA isolation, formamide homogenates can be processed without incubation at 4°C. RESULTS In formamide homogenates a non-gelatinous white pellet was observed which was identified as starch by Lugol's staining. Intact RNA was observed by agarose gel electrophoresis. The RNA was successfully used in downstream RT-PCR reactions. CONCLUSION Formamide maintained the integrity of the RNA during tissue processing at 25 ± 2°C and storage at 4°C. This room temperature formamide-based RNA isolation procedure met the criteria of simplicity, low-cost, reproducibility and addressed gelation problems associated with high starch tissues.
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Affiliation(s)
- Valerie Bowrin
- Department of Life Sciences, The University of The West Indies, St Augustine, Trinidad and Tobago.
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Das A, Roy A, Hess D, Das S. Characterization of a Highly Potent Insecticidal Lectin from <i>Colocasia esculenta</i> Tuber and Cloning of Its Coding Sequence. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.42a053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lopez-Gomollon S, Mohorianu I, Szittya G, Moulton V, Dalmay T. Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions. PLANTA 2012; 236:1875-87. [PMID: 22922939 DOI: 10.1007/s00425-012-1734-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/27/2012] [Indexed: 05/03/2023]
Abstract
MicroRNAs negatively regulate the accumulation of mRNAs therefore when they are expressed in the same cells their expression profiles show an inverse correlation. We previously described one positively correlated miRNA/target pair, but it is not known how widespread this phenomenon is. Here, we investigated the correlation between the expression profiles of differentially expressed miRNAs and their targets during tomato fruit development using deep sequencing, Northern blot and RT-qPCR. We found an equal number of positively and negatively correlated miRNA/target pairs indicating that positive correlation is more frequent than previously thought. We also found that the correlation between microRNA and target expression profiles can vary between mRNAs belonging to the same gene family and even for the same target mRNA at different developmental stages. Since microRNAs always negatively regulate their targets, the high number of positively correlated microRNA/target pairs suggests that mutual exclusion could be as widespread as temporal regulation. The change of correlation during development suggests that the type of regulatory circuit directed by a microRNA can change over time and can be different for individual gene family members. Our results also highlight potential problems for expression profiling-based microRNA target identification/validation.
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Affiliation(s)
- Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Román B, González-Verdejo CI, Peña F, Nadal S, Gómez P. Evaluation of different pulverisation methods for RNA extraction in squash fruit: lyophilisation, cryogenic mill and mortar grinding. PHYTOCHEMICAL ANALYSIS : PCA 2012; 23:622-626. [PMID: 22517615 DOI: 10.1002/pca.2364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 02/17/2012] [Accepted: 03/06/2012] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Quality and integrity of RNA are critical for transcription studies in plant molecular biology. In squash fruit and other high water content crops, the grinding of tissue with mortar and pestle in liquid nitrogen fails to produce a homogeneous and fine powered sample desirable to ensure a good penetration of the extraction reagent. OBJECTIVE To develop an improved pulverisation method to facilitate the homogenisation process of squash fruit tissue prior to RNA extraction without reducing quality and yield of the extracted RNA. METHODOLOGY Three methods of pulverisation, each followed by the same extraction protocol, were compared. The first approach consisted of the lyophilisation of the sample in order to remove the excess of water before grinding, the second one used a cryogenic mill and the control one a mortar grinding of frozen tissue. The quality of the isolated RNA was tested by carrying out a quantitative real time downstream amplification. RESULTS In the three situations considered, mean values for A(260) /A(280) indicated minimal interference by proteins and RNA quality indicator (RQI) values were considered appropriate for quantitative real-time polymerase chain reaction (qRT-PCR) amplification. Successful qRT-PCR amplifications were obtained with cDNA isolated with the three protocols. CONCLUSION Both apparatus can improve and facilitate the grinding step in the RNA extraction process in zucchini, resulting in isolated RNA of high quality and integrity as revealed by qRT-PCR downstream application. This is apparently the first time that a cryogenic mill has been used to prepare fruit samples for RNA extraction, thereby improving the sampling strategy because the fine powder obtained represents a homogeneous mix of the organ tissue.
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Affiliation(s)
- Belén Román
- IFAPA-Centro Alameda del Obispo., Área de Mejora y Biotecnología, Avda. Menéndez Pidal s/n, Apdo. 3092, 14080, Córdoba, Spain.
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Matsumoto S, Mizutani M, Sakata K, Shimizu BI. Molecular cloning and functional analysis of the ortho-hydroxylases of p-coumaroyl coenzyme A/feruloyl coenzyme A involved in formation of umbelliferone and scopoletin in sweet potato, Ipomoea batatas (L.) Lam. PHYTOCHEMISTRY 2012; 74:49-57. [PMID: 22169019 DOI: 10.1016/j.phytochem.2011.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/28/2011] [Accepted: 11/21/2011] [Indexed: 05/23/2023]
Abstract
Ortho-hydroxylation of cinnamates is a key step in coumarin biosynthesis in plants. Ortho-hydroxylated cinnamates undergo trans/cis isomerization of the side-chain and then lactonization to form coumarins. Sweet potato [Ipomoea batatas (L.) Lam.] accumulates umbelliferone and scopoletin after biotic and abiotic stresses. To elucidate molecular aspects of ortho-hydroxylation involved in umbelliferone formation in sweet potato, isolation and characterization of cDNAs encoding 2-oxoglutarate-dependent dioxygenases (2OGD) was performed from sweet potato tubers treated with a chitosan elicitor. Five cDNAs (designated as Ib) encoding a protein of 358 amino acid residues were cloned, and these were categorized into two groups, Ib1 and Ib2, based on their amino acid sequences. Whether the recombinant Ib proteins had any enzymatic activity toward cinnamates was examined. Ib1 proteins exhibited ortho-hydroxylation activity toward feruloyl coenzyme A (CoA) to form scopoletin (K(m)=~10 μM, k(cat)=~2.7s(-1)). By contrast, Ib2 proteins catalyzed ortho-hydroxylation of feruloyl-CoA (K(m)=7.3-14.0 μM, k(cat)=0.28-0.55 s(-1)) and also of p-coumaroyl-CoA (K(m)=6.1-15.2 μM, k(cat)=0.28-0.64 s(-1)) to form scopoletin and umbelliferone, respectively. Fungal and chitosan treatments increased levels of umbelliferone and its glucoside (skimmin) in the tubers, and expression of the Ib2 gene was induced concomitantly.
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Affiliation(s)
- Seitaro Matsumoto
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 6110011, Japan
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Condori J, Nopo-Olazabal C, Medrano G, Medina-Bolivar F. Selection of reference genes for qPCR in hairy root cultures of peanut. BMC Res Notes 2011; 4:392. [PMID: 21985172 PMCID: PMC3199266 DOI: 10.1186/1756-0500-4-392] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/10/2011] [Indexed: 11/10/2022] Open
Abstract
Background Hairy root cultures produced via Agrobacterium rhizogenes-mediated transformation have emerged as practical biological models to elucidate the biosynthesis of specialized metabolites. To effectively understand the expression patterns of the genes involved in the metabolic pathways of these compounds, reference genes need to be systematically validated under specific experimental conditions as established by the MIQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines. In the present report we describe the first validation of reference genes for RT-qPCR in hairy root cultures of peanut which produce stilbenoids upon elicitor treatments. Results A total of 21 candidate reference genes were evaluated. Nineteen genes were selected based on previous qPCR studies in plants and two were from the T-DNAs transferred from A. rhizogenes. Nucleotide sequences of peanut candidate genes were obtained using their homologous sequences in Arabidopsis. To identify the suitable primers, calibration curves were obtained for each candidate reference gene. After data analysis, 12 candidate genes meeting standard efficiency criteria were selected. The expression stability of these genes was analyzed using geNorm and NormFinder algorithms and a ranking was established based on expression stability of the genes. Candidate reference gene expression was shown to have less variation in methyl jasmonate (MeJA) treated root cultures than those treated with sodium acetate (NaOAc). Conclusions This work constitutes the first effort to validate reference genes for RT-qPCR in hairy roots. While these genes were selected under conditions of NaOAc and MeJA treatment, we anticipate these genes to provide good targets for reference genes for hairy roots under a variety of stress conditions. The lead reference genes were a gene encoding for a TATA box binding protein (TBP2) and a gene encoding a ribosomal protein (RPL8C). A commonly used reference gene GAPDH showed low stability of expression suggesting that its use may lead to inaccurate gene expression profiles when used for data normalization in stress-stimulated hairy roots. Likewise the A. rhizogenes transgene rolC showed less expression stability than GAPDH. This study proposes that a minimum of two reference genes should be used for a normalization procedure in gene expression profiling using elicited hairy roots.
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Affiliation(s)
- Jose Condori
- Arkansas Biosciences Institute, Arkansas State University, P,O, Box 639, State University, AR 72467, USA.
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Abstract
Small RNAs (sRNAs) play fundamental roles in modifying the transcriptomes and proteomes of organisms. sRNAs can be classified according to their origin and way of action into classes such as microRNAs, trans-acting siRNAs, heterochromatin siRNAs, Piwi-interacting RNAs, and natural antisense siRNAs, although microRNAs are the most conserved and studied class. The expression pattern of a sRNA can be indicative of its biological function. Northern blotting is one of the most widely used methods to identify, validate, and study the expression profile of sRNAs because it is a quantitative, relatively inexpensive technique that is readily available for most laboratories. This chapter describes a protocol for sRNA Northern blot analysis, which includes RNA extraction, polyacrylamide gel electrophoresis, hybridisation, or the detection of sRNA using oligonucleotide probes.
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Kumar GNM, Lulai EC, Suttle JC, Knowles NR. Age-induced loss of wound-healing ability in potato tubers is partly regulated by ABA. PLANTA 2010; 232:1433-45. [PMID: 20839005 DOI: 10.1007/s00425-010-1269-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 08/30/2010] [Indexed: 05/20/2023]
Abstract
Wounding of potato (Solanum tuberosum L.) tubers induces the development of a suberized closing layer and wound periderm that resists desiccation and microbial invasion. Wound-healing ability declines with tuber age (storage period). The mechanism of loss in healing capacity with age is not known; however, upregulation of superoxide production, increased ABA biosynthesis and phenylalanine ammonia lyase (PAL) activity in response to wounding are processes critical to the development of a suberized closing layer and wound periderm. Therefore, the role of ABA in modulating the age-induced loss of wound-healing ability of tubers was examined. Non-wounded older tubers had 86% less ABA (dry matter basis) than younger tubers. PAL transcript increased in younger tubers within 24 h of wounding, but transcription was delayed by 5 days in older tubers. Wound-induced PAL activity increased more rapidly in younger than older tubers. ABA treatment increased PAL expression and activity in tissue from both ages of tubers and restored the 24 h transcription time line in older tubers. Moreover, ABA treatment of wounded older tubers enhanced their resistance to water vapor loss following a 6-day wound-healing period. Wound-induced accumulation of suberin poly(phenolic(s)) (SPP) and suberin poly(aliphatic(s)) (SPA) was measurably slower in older versus younger tubers. ABA treatment hastened SPP accumulation in older tubers to match that in younger tubers, but only enhanced SPA accumulations over the initial 4 days of healing. Age-induced loss of wound-healing ability is thus partly due to reduced ability to accumulate ABA and modulate the production of SPP through PAL in response to wounding and to dysfunction in the downstream signaling events that couple SPA biosynthesis and/or deposition to ABA. ABA treatment partly restored the healing ability of older tubers by enhancing the accumulation of SPP without restoring wound-induced superoxide forming ability to the level of younger tubers. The coupling of phenolic monomers into the poly(phenolic) domain of suberin was therefore not limited by the diminished wound-induced superoxide production of older tubers.
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Affiliation(s)
- G N Mohan Kumar
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture and Landscape Architecture, Washington State University, P.O. Box 646414, Pullman, WA 99164-6414, USA
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Van Eck J, Zhou X, Lu S, Li L. Modulation of carotenoid accumulation in transgenic potato by inducing chromoplast formation with enhanced sink strength. Methods Mol Biol 2010; 643:77-93. [PMID: 20552445 DOI: 10.1007/978-1-60761-723-5_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
An increasing interest in carotenoids as nutritional sources of provitamin A and health-promoting compounds has prompted a significant effort in metabolic engineering of carotenoid content and composition in food crops. The strategy commonly used in plants is to increase the biosynthetic capacity by altering the carotenogenic enzyme activities. The recent isolation of the Or gene from a cauliflower orange mutant has brought a new endeavor for carotenoid enhancement by increasing the sink strength to sequester and store the synthesized carotenoids. Potato as one of the major staple crops usually accumulates low levels of carotenoids. In this chapter, we describe a detailed protocol for metabolic engineering of carotenoids in potato plants with the Or gene and the analysis of the Or transformants.
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MESH Headings
- Agrobacterium tumefaciens/genetics
- Blotting, Northern
- Blotting, Southern
- Brassica/genetics
- Carotenoids/metabolism
- Chromatography, High Pressure Liquid
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Genes, Plant/genetics
- Genetic Engineering/methods
- Microscopy
- Plant Tubers/cytology
- Plant Tubers/genetics
- Plant Tubers/metabolism
- Plants, Genetically Modified
- Plastids/metabolism
- RNA, Plant/genetics
- RNA, Plant/isolation & purification
- Reverse Transcriptase Polymerase Chain Reaction
- Solanum tuberosum/cytology
- Solanum tuberosum/genetics
- Solanum tuberosum/metabolism
- Transformation, Genetic
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Affiliation(s)
- Joyce Van Eck
- Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
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Weeda SM, Mohan Kumar GN, Richard Knowles N. Developmentally linked changes in proteases and protease inhibitors suggest a role for potato multicystatin in regulating protein content of potato tubers. PLANTA 2009; 230:73-84. [PMID: 19347354 DOI: 10.1007/s00425-009-0928-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Accepted: 03/22/2009] [Indexed: 05/08/2023]
Abstract
The soluble protein fraction of fully developed potato (Solanum tuberosum L.) tubers is dominated by patatin, a 40 kD storage glycoprotein, and protease inhibitors. Potato multicystatin (PMC) is a multidomain Cys-type protease inhibitor. PMC effectively inhibits degradation of patatin by tuber proteases in vitro. Herein we show that changes in PMC, patatin concentration, activities of various proteases, and their gene expression are temporally linked during tuber development, providing evidence that PMC has a role in regulating tuber protein content in vivo. PMC was barely detectable in non-tuberized stolons. PMC transcript levels increased progressively during tuberization, concomitant with a 40-fold increase in PMC concentration (protein basis) as tubers developed to 10 g fresh wt. Further increases in PMC were comparatively modest (3.7-fold) as tubers developed to full maturity (250 g). Protease activity declined precipitously as PMC levels increased during tuberization. Proteolytic activity was highest in non-tuberized stolons and fell substantially through the 10-g fresh wt stage. Cys-type proteases dominated the pre-tuberization and earliest stages of tuber development. Increases in patatin transcript levels during tuberization were accompanied by a notable lag in patatin accumulation. Patatin did not begin to accumulate substantially on a protein basis until tubers had reached the 10-g stage, wherein protease activity had been inhibited by approximately 60%. These results indicate that a threshold level of PMC (ca. 3 microg tuber(-1), 144 ng mg(-1) protein) is needed to favor patatin accumulation. Collectively, these results are consistent with a role for PMC in facilitating the accumulation of proteins in developing tubers by inhibiting Cys-type proteases.
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Affiliation(s)
- Sarah M Weeda
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture and Landscape Architecture, Washington State University, P.O. Box 646414, Pullman, WA 99164-6414, USA
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Yu YJ, Majumdar APN, Nechvatal JM, Ram JL, Basson MD, Heilbrun LK, Kato I. Exfoliated cells in stool: a source for reverse transcription-PCR-based analysis of biomarkers of gastrointestinal cancer. Cancer Epidemiol Biomarkers Prev 2008; 17:455-8. [PMID: 18268130 DOI: 10.1158/1055-9965.epi-07-2515] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Because the colonic mucosa is in direct contact with digesta, luminal exposure to potentially carcinogenic or chemopreventive agents may be important in colorectal carcinogenesis, independently of the effects of systemic exposure through the circulation. To date, few biomarkers for luminal exposure have been identified, and isolation of reasonably good quality fecal human RNA remains difficult. In this study, we assessed the yield and quality of RNA extracted from 10 human stool samples after storage with several commercially available preservatives compared with stool samples immediately frozen in liquid nitrogen. This study shows that careful design of primer pairs which amplify a short length of DNA is key to obtaining interpretable and reproducible results. Moreover, the use of commercially available RNA preservation kits enables investigators to collect usable fecal samples from large populations. Of all the preservative methods tested, RNAlater had the best performance in terms of overall quality, quantity, and level of genomic DNA contamination, and thus deserves further investigation.
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Affiliation(s)
- Ying Jie Yu
- Department of Internal Medicine, Wayne State University, Detroit, MI 48201, USA
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Kumar GNM, Iyer S, Knowles NR. Strboh A homologue of NADPH oxidase regulates wound-induced oxidative burst and facilitates wound-healing in potato tubers. PLANTA 2007; 227:25-36. [PMID: 17653758 DOI: 10.1007/s00425-007-0589-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 07/06/2007] [Indexed: 05/16/2023]
Abstract
During 30-months of storage at 4 degrees C, potato (Solanum tuberosum L.) tubers progressively lose the ability to produce superoxide in response to wounding, resist microbial infection, and develop a suberized wound periderm. Using differentially aged tubers, we demonstrate that Strboh A is responsible for the wound-induced oxidative burst in potato and aging attenuates its expression. In vivo superoxide production and NADPH oxidase (NOX) activity from 1-month-old tubers increased to a maximum 18-24 h after wounding and then decreased to barely detectable levels by 72 h. Wounding also induced a 68% increase in microsomal protein within 18 h. These wound-induced responses were lost over a 25- to 30-month storage period. Superoxide production and NOX activity were inhibited by diphenylene iodonium chloride, a specific inhibitor of NOX, which in turn effectively inhibited wound-healing and increased susceptibility to microbial infection and decay in 1-month-old tubers. Wound-induced superoxide production was also inhibited by EGTA-mediated destabilization of membranes. The ability to restore superoxide production to EGTA-treated tissue with Ca(+2) declined with advancing tuber age, likely a consequence of age-related changes in membrane architecture. Of the five homologues of NOX (Strboh A-D and F), wounding induced the expression of Strboh A in 6-month-old tubers but this response was absent in tubers stored for 25-30 months. Strboh A thus mediates the initial burst of superoxide in response to wounding of potato tubers; loss of its expression increases the susceptibility to microbial infection and contributes to the age-induced loss of wound-healing ability.
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Affiliation(s)
- G N Mohan Kumar
- Postharvest Physiology and Biochemistry Laboratory, Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164-6414, USA
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