1
|
Yokomori M, Gotoh O, Murakami Y, Fujimoto K, Suyama A. A multiplex RNA quantification method to determine the absolute amounts of mRNA without reverse transcription. Anal Biochem 2017; 539:96-103. [PMID: 29029978 DOI: 10.1016/j.ab.2017.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 01/16/2023]
Abstract
We have developed a highly sensitive microarray-based method that determines the absolute amounts of mRNA in a total RNA sample in a multiplex manner without reverse transcription. This direct mRNA measurement promotes high-throughput testing and reduces bias in transcriptome analyses. Furthermore, quantification of the absolute amount of mRNA allows transcriptome analysis without common controls or additional, complicated normalization. The method, called Photo-DEAN, was validated using chemically synthesized RNAs of known quantities and mouse liver total RNA samples. We found that the absolute amounts of mRNA were successfully measured without the cDNA synthesis step, with a sensitivity of 15 zmol achieved in 7 h.
Collapse
Affiliation(s)
- Maasa Yokomori
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Osamu Gotoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yasufumi Murakami
- Department of Biological Science and Technology, Graduate School of Industrial Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan
| | - Akira Suyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
| |
Collapse
|
2
|
Song T, Kale SD, Arredondo FD, Shen D, Su L, Liu L, Wu Y, Wang Y, Dou D, Tyler BM. Two RxLR avirulence genes in Phytophthora sojae determine soybean Rps1k-mediated disease resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:711-20. [PMID: 23530601 DOI: 10.1094/mpmi-12-12-0289-r] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Resistance to Phytophthora sojae (Rps) genes have been widely used in soybean against root and stem rot diseases caused by this oomycete. Among 15 known soybean Rps genes, Rps1k has been the most widely used in the past four decades. Here, we show that the products of two distinct but closely linked RxLR effector genes are detected by Rps1k-containing plants, resulting in disease resistance. One of the genes is Avr1b-1, that confers avirulence in the presence of Rps1b. Three lines of evidence, including overexpression and gene silencing of Avr1b-1 in stable P. sojae transformants, as well as transient expression of this gene in soybean, indicated that Avr1b could trigger an Rps1k-mediated defense response. Some isolates of P. sojae that do not express Avr1b are nevertheless unable to infect Rps1k plants. In those isolates, we identified a second RxLR effector gene (designated Avr1k), located 5 kb away from Avr1b-1. Silencing or overexpression of Avr1k in P. sojae stable transformants resulted in the loss or gain, respectively, of the avirulence phenotype in the presence of Rps1k. Only isolates of P. sojae with mutant alleles of both Avr1b-1 and Avr1k could evade perception by the soybean plants carrying Rps1k.
Collapse
Affiliation(s)
- Tianqiao Song
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Dong S, Kong G, Qutob D, Yu X, Tang J, Kang J, Dai T, Wang H, Gijzen M, Wang Y. The NLP toxin family in Phytophthora sojae includes rapidly evolving groups that lack necrosis-inducing activity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:896-909. [PMID: 22397404 DOI: 10.1094/mpmi-01-12-0023-r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Necrosis- and ethylene-inducing-like proteins (NLP) are widely distributed in eukaryotic and prokaryotic plant pathogens and are considered to be important virulence factors. We identified, in total, 70 potential Phytophthora sojae NLP genes but 37 were designated as pseudogenes. Sequence alignment of the remaining 33 NLP delineated six groups. Three of these groups include proteins with an intact heptapeptide (Gly-His-Arg-His-Asp-Trp-Glu) motif, which is important for necrosis-inducing activity, whereas the motif is not conserved in the other groups. In total, 19 representative NLP genes were assessed for necrosis-inducing activity by heterologous expression in Nicotiana benthamiana. Surprisingly, only eight genes triggered cell death. The expression of the NLP genes in P. sojae was examined, distinguishing 20 expressed and 13 nonexpressed NLP genes. Real-time reverse-transcriptase polymerase chain reaction results indicate that most NLP are highly expressed during cyst germination and infection stages. Amino acid substitution ratios (Ka/Ks) of 33 NLP sequences from four different P. sojae strains resulted in identification of positive selection sites in a distinct NLP group. Overall, our study indicates that expansion and pseudogenization of the P. sojae NLP family results from an ongoing birth-and-death process, and that varying patterns of expression, necrosis-inducing activity, and positive selection suggest that NLP have diversified in function.
Collapse
Affiliation(s)
- Suomeng Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Dong S, Yin W, Kong G, Yang X, Qutob D, Chen Q, Kale SD, Sui Y, Zhang Z, Dou D, Zheng X, Gijzen M, M. Tyler B, Wang Y. Phytophthora sojae avirulence effector Avr3b is a secreted NADH and ADP-ribose pyrophosphorylase that modulates plant immunity. PLoS Pathog 2011; 7:e1002353. [PMID: 22102810 PMCID: PMC3213090 DOI: 10.1371/journal.ppat.1002353] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 09/19/2011] [Indexed: 11/18/2022] Open
Abstract
Plants have evolved pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) to protect themselves from infection by diverse pathogens. Avirulence (Avr) effectors that trigger plant ETI as a result of recognition by plant resistance (R) gene products have been identified in many plant pathogenic oomycetes and fungi. However, the virulence functions of oomycete and fungal Avr effectors remain largely unknown. Here, we combined bioinformatics and genetics to identify Avr3b, a new Avr gene from Phytophthora sojae, an oomycete pathogen that causes soybean root rot. Avr3b encodes a secreted protein with the RXLR host-targeting motif and C-terminal W and Nudix hydrolase motifs. Some isolates of P. sojae evade perception by the soybean R gene Rps3b through sequence mutation in Avr3b and lowered transcript accumulation. Transient expression of Avr3b in Nicotiana benthamiana increased susceptibility to P. capsici and P. parasitica, with significantly reduced accumulation of reactive oxygen species (ROS) around invasion sites. Biochemical assays confirmed that Avr3b is an ADP-ribose/NADH pyrophosphorylase, as predicted from the Nudix motif. Deletion of the Nudix motif of Avr3b abolished enzyme activity. Mutation of key residues in Nudix motif significantly impaired Avr3b virulence function but not the avirulence activity. Some Nudix hydrolases act as negative regulators of plant immunity, and thus Avr3b might be delivered into host cells as a Nudix hydrolase to impair host immunity. Avr3b homologues are present in several sequenced Phytophthora genomes, suggesting that Phytophthora pathogens might share similar strategies to suppress plant immunity.
Collapse
Affiliation(s)
- Suomeng Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, China
| | - Weixiao Yin
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guanghui Kong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xinyu Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Dinah Qutob
- Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Qinghe Chen
- Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - Shiv D. Kale
- Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - Yangyang Sui
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhengguang Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, China
| | - Xiaobo Zheng
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, China
| | - Mark Gijzen
- Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Brett M. Tyler
- Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
| | - Yuanchao Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, China
| |
Collapse
|
5
|
Wang Q, Han C, Ferreira AO, Yu X, Ye W, Tripathy S, Kale SD, Gu B, Sheng Y, Sui Y, Wang X, Zhang Z, Cheng B, Dong S, Shan W, Zheng X, Dou D, Tyler BM, Wang Y. Transcriptional programming and functional interactions within the Phytophthora sojae RXLR effector repertoire. THE PLANT CELL 2011; 23:2064-86. [PMID: 21653195 PMCID: PMC3160037 DOI: 10.1105/tpc.111.086082] [Citation(s) in RCA: 293] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 04/05/2011] [Accepted: 05/25/2011] [Indexed: 05/18/2023]
Abstract
The genome of the soybean pathogen Phytophthora sojae contains nearly 400 genes encoding candidate effector proteins carrying the host cell entry motif RXLR-dEER. Here, we report a broad survey of the transcription, variation, and functions of a large sample of the P. sojae candidate effectors. Forty-five (12%) effector genes showed high levels of polymorphism among P. sojae isolates and significant evidence for positive selection. Of 169 effectors tested, most could suppress programmed cell death triggered by BAX, effectors, and/or the PAMP INF1, while several triggered cell death themselves. Among the most strongly expressed effectors, one immediate-early class was highly expressed even prior to infection and was further induced 2- to 10-fold following infection. A second early class, including several that triggered cell death, was weakly expressed prior to infection but induced 20- to 120-fold during the first 12 h of infection. The most strongly expressed immediate-early effectors could suppress the cell death triggered by several early effectors, and most early effectors could suppress INF1-triggered cell death, suggesting the two classes of effectors may target different functional branches of the defense response. In support of this hypothesis, misexpression of key immediate-early and early effectors severely reduced the virulence of P. sojae transformants.
Collapse
Affiliation(s)
- Qunqing Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Changzhi Han
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Adriana O. Ferreira
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061
| | - Xiaoli Yu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Sucheta Tripathy
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061
| | - Shiv D. Kale
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061
| | - Biao Gu
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuting Sheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangyang Sui
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoli Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengguang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Baoping Cheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weixing Shan
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China
| | - Brett M. Tyler
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China
| |
Collapse
|
6
|
Lemuth K, Steuer K, Albermann C. Engineering of a plasmid-free Escherichia coli strain for improved in vivo biosynthesis of astaxanthin. Microb Cell Fact 2011; 10:29. [PMID: 21521516 PMCID: PMC3111352 DOI: 10.1186/1475-2859-10-29] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/26/2011] [Indexed: 11/26/2022] Open
Abstract
Background The xanthophyll astaxanthin is a high-value compound with applications in the nutraceutical, cosmetic, food, and animal feed industries. Besides chemical synthesis and extraction from naturally producing organisms like Haematococcus pluvialis, heterologous biosynthesis in non-carotenogenic microorganisms like Escherichia coli, is a promising alternative for sustainable production of natural astaxanthin. Recent achievements in the metabolic engineering of E. coli strains have led to a significant increase in the productivity of carotenoids like lycopene or β-carotene by increasing the metabolic flux towards the isoprenoid precursors. For the heterologous biosynthesis of astaxanthin in E. coli, however, the conversion of β-carotene to astaxanthin is obviously the most critical step towards an efficient biosynthesis of astaxanthin. Results Here we report the construction of the first plasmid-free E. coli strain that produces astaxanthin as the sole carotenoid compound with a yield of 1.4 mg/g cdw (E. coli BW-ASTA). This engineered E. coli strain harbors xanthophyll biosynthetic genes from Pantoea ananatis and Nostoc punctiforme as individual expression cassettes on the chromosome and is based on a β-carotene-producing strain (E. coli BW-CARO) recently developed in our lab. E. coli BW-CARO has an enhanced biosynthesis of the isoprenoid precursor isopentenyl diphosphate (IPP) and produces β-carotene in a concentration of 6.2 mg/g cdw. The expression of crtEBIY along with the β-carotene-ketolase gene crtW148 (NpF4798) and the β-carotene-hydroxylase gene (crtZ) under controlled expression conditions in E. coli BW-ASTA directed the pathway exclusively towards the desired product astaxanthin (1.4 mg/g cdw). Conclusions By using the λ-Red recombineering technique, genes encoding for the astaxanthin biosynthesis pathway were stably integrated into the chromosome of E. coli. The expression levels of chromosomal integrated recombinant biosynthetic genes were varied and adjusted to improve the ratios of carotenoids produced by this E. coli strain. The strategy presented, which combines chromosomal integration of biosynthetic genes with the possibility of adjusting expression by using different promoters, might be useful as a general approach for the construction of stable heterologous production strains synthesizing natural products. This is the case especially for heterologous pathways where excessive protein overexpression is a hindrance.
Collapse
Affiliation(s)
- Karin Lemuth
- Institute of Microbiology, Universität Stuttgart, Stuttgart, Germany
| | | | | |
Collapse
|
7
|
Siemann-Herzberg M, Hardiman T, Takors R, Reuss M. Predicting Gene Expression Profiles from Sequence Information - Challenges for Measuring and Modeling. CHEM-ING-TECH 2010. [DOI: 10.1002/cite.201050734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|