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Xiang L, Zhang X, Lei Y, Wu J, Yan G, Chen W, Li S, Wang W, Jin JM, Liang C, Tang SY. Designing a highly efficient type III polyketide whole-cell catalyst with minimized byproduct formation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:93. [PMID: 38961423 PMCID: PMC11223281 DOI: 10.1186/s13068-024-02545-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Polyketide synthases (PKSs) are classified into three types based on their enzyme structures. Among them, type III PKSs, catalyzing the iterative condensation of malonyl-coenzyme A (CoA) with a CoA-linked starter molecule, are important synthases of valuable natural products. However, low efficiency and byproducts formation often limit their applications in recombinant overproduction. RESULTS Herein, a rapid growth selection system is designed based on the accumulation and derepression of toxic acyl-CoA starter molecule intermediate products, which could be potentially applicable to most type III polyketides biosynthesis. This approach is validated by engineering both chalcone synthases (CHS) and host cell genome, to improve naringenin productions in Escherichia coli. From directed evolution of key enzyme CHS, beneficial mutant with ~ threefold improvement in capability of naringenin biosynthesis was selected and characterized. From directed genome evolution, effect of thioesterases on CHS catalysis is first discovered, expanding our understanding of byproduct formation mechanism in type III PKSs. Taken together, a whole-cell catalyst producing 1082 mg L-1 naringenin in flask with E value (evaluating product specificity) improved from 50.1% to 96.7% is obtained. CONCLUSIONS The growth selection system has greatly contributed to both enhanced activity and discovery of byproduct formation mechanism in CHS. This research provides new insights in the catalytic mechanisms of CHS and sheds light on engineering highly efficient heterologous bio-factories to produce naringenin, and potentially more high-value type III polyketides, with minimized byproducts formation.
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Grants
- 2022M713331 the China Postdoctoral Science Foundation
- Grant No. 31970080, 31971337, 31961133016 and 31971382 the National Natural Science Foundation of China
- Grant No. 31970080, 31971337, 31961133016 and 31971382 the National Natural Science Foundation of China
- Grant No. 31970080, 31971337, 31961133016 and 31971382 the National Natural Science Foundation of China
- Grant 2021YFC2100502, 2021YFC2103300, 2018YFA0900701, and 2021YFC2103901 the National Key Research and Development Program of China
- Grant 2021YFC2100502, 2021YFC2103300, 2018YFA0900701, and 2021YFC2103901 the National Key Research and Development Program of China
- YJKYYQ20210032 Instrument Developing Project of Chinese Academy of Science
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Affiliation(s)
- La Xiang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuanxuan Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyan Lei
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jieyuan Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangru Yan
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shizhong Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenzhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, 100048, China.
| | - Chaoning Liang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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Ding X, Wang H, Huang S, Zhang H, Chen H, Chen P, Wang Y, Yang Z, Wang Y, Peng S, Dai H, Mei W. Molecular evolution and characterization of type III polyketide synthase gene family in Aquilaria sinensis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108571. [PMID: 38604011 DOI: 10.1016/j.plaphy.2024.108571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/24/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
2-(2-Phenylethyl) chromone (PEC) and its derivatives are markers of agarwood formation and are also related to agarwood quality. However, the biosynthetic and regulatory mechanisms of PECs still remain mysterious. Several studies suggested that type III polyketide synthases (PKSs) contribute to PEC biosynthesis in Aquilaria sinensis. Furthermore, systematic studies on the evolution of PKSs in A. sinensis have rarely been reported. Herein, we comprehensively analyzed PKS genes from 12 plant genomes and characterized the AsPKSs in detail. A unique branch contained only AsPKS members was identified through evolutionary analysis, including AsPKS01 that was previously indicated to participate in PEC biosynthesis. AsPKS07 and AsPKS08, two tandem-duplicated genes of AsPKS01 and lacking orthologous genes in evolutionary models, were selected for their transient expression in the leaves of Nicotiana benthamiana. Subsequently, PECs were detected in the extracts of N. benthamiana leaves, suggesting that AsPKS07 and AsPKS08 promote PEC biosynthesis. The interaction between the promoters of AsPKS07, AsPKS08 and five basic leucine zippers (bZIPs) from the S subfamily indicated that their transcripts could be regulated by these transcription factors (TFs) and might further contribute to PECs biosynthesis in A. sinensis. Our findings provide valuable insights into the molecular evolution of the PKS gene family in A. sinensis and serve as a foundation for advancing PEC production through the bioengineering of gene clusters. Ultimately, this contribution is expected to shed light on the mechanism underlying agarwood formation.
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Affiliation(s)
- Xupo Ding
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Hao Wang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shengzhuo Huang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hao Zhang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Huiqin Chen
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Pengwei Chen
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yuguang Wang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Zhuo Yang
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yali Wang
- International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shiqing Peng
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Haofu Dai
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Wenli Mei
- Key Laboratory of Research and Development of Natural Product from Li Folk Medicine of Hainan Province, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; International Joint Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China; Hainan Engineering Research Center of Agarwood, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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Zhang T, Zhou L, Pu Y, Tang Y, Liu J, Yang L, Zhou T, Feng L, Wang X. A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum. BMC PLANT BIOLOGY 2024; 24:261. [PMID: 38594606 PMCID: PMC11005207 DOI: 10.1186/s12870-024-04972-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/01/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Rhubarb is one of common traditional Chinese medicine with a diverse array of therapeutic efficacies. Despite its widespread use, molecular research into rhubarb remains limited, constraining our comprehension of the geoherbalism. RESULTS We assembled the genome of Rheum palmatum L., one of the source plants of rhubarb, to elucidate its genome evolution and unpack the biosynthetic pathways of its bioactive compounds using a combination of PacBio HiFi, Oxford Nanopore, Illumina, and Hi-C scaffolding approaches. Around 2.8 Gb genome was obtained after assembly with more than 99.9% sequences anchored to 11 pseudochromosomes (scaffold N50 = 259.19 Mb). Transposable elements (TE) with a continuous expansion of long terminal repeat retrotransposons (LTRs) is predominant in genome size, contributing to the genome expansion of R. palmatum. Totally 30,480 genes were predicted to be protein-coding genes with 473 significantly expanded gene families enriched in diverse pathways associated with high-altitude adaptation for this species. Two successive rounds of whole genome duplication event (WGD) shared by Fagopyrum tataricum and R. palmatum were confirmed. We also identified 54 genes involved in anthraquinone biosynthesis and other 97 genes entangled in flavonoid biosynthesis. Notably, RpALS emerged as a compelling candidate gene for the octaketide biosynthesis after the key residual screening. CONCLUSION Overall, our findings offer not only an enhanced understanding of this remarkable medicinal plant but also pave the way for future innovations in its genetic breeding, molecular design, and functional genomic studies.
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Affiliation(s)
- Tianyi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lipan Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yang Pu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yadi Tang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jie Liu
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Yang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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4
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Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Somermeyer LG, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov FA, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. A hybrid pathway for self-sustained luminescence. SCIENCE ADVANCES 2024; 10:eadk1992. [PMID: 38457503 PMCID: PMC10923510 DOI: 10.1126/sciadv.adk1992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis-a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors.
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Affiliation(s)
- Kseniia A. Palkina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana A. Karataeva
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maxim M. Perfilov
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Liliia I. Fakhranurova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nadezhda M. Markina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Elena Garcia-Perez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Marta Rodriguez-Rodriguez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Victor Vazquez-Vilriales
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Ekaterina S. Shakhova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Tatiana Mitiouchkina
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey I. Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Anna Alekberova
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alena K. Malyshevskaia
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Elena B. Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
| | - Anastasia Balakireva
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nikita Sytov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | | | - Daria I. Boldyreva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vladislav V. Babenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Fyodor A. Kondrashov
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0412, Japan
| | - Vladimir V. Choob
- Botanical Garden of Lomonosov Moscow State University, Vorobievy Gory 1 b.12, Moscow 119234 Russia
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de Valéncia, 46022 Valencia, Spain
| | - Ilia V. Yampolsky
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow 117997, Russia
- Light Bio Inc., Ketchum, ID, USA
| | - Alexander S. Mishin
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Karen S. Sarkisyan
- Planta LLC, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Light Bio Inc., Ketchum, ID, USA
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
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Nie B, Chen X, Hou Z, Guo M, Li C, Sun W, Ji J, Zang L, Yang S, Fan P, Zhang W, Li H, Tan Y, Li W, Wang L. Haplotype-phased genome unveils the butylphthalide biosynthesis and homoploid hybrid origin of Ligusticum chuanxiong. SCIENCE ADVANCES 2024; 10:eadj6547. [PMID: 38324681 PMCID: PMC10849598 DOI: 10.1126/sciadv.adj6547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
Butylphthalide is one of the first-line drugs for ischemic stroke therapy, while no biosynthetic enzyme for butylphthalide has been reported. Here, we present a haplotype-resolved genome of Ligusticum chuanxiong, a long-cultivated and phthalide-rich medicinal plant in Apiaceae. On the basis of comprehensive screening, four Fe(II)- and 2-oxoglutarate-dependent dioxygenases and two CYPs were mined and further biochemically verified as phthalide C-4/C-5 desaturases (P4,5Ds) that effectively promoted the forming of (S)-3-n-butylphthalide and butylidenephthalide. The substrate promiscuity and functional redundancy featured for P4,5Ds may contribute to the high phthalide diversity in L. chuanxiong. Notably, comparative genomic evidence supported L. chuanxiong as a homoploid hybrid with Ligusticum sinense as a potential parent. The two haplotypes demonstrated exceptional structure variance and diverged around 3.42 million years ago. Our study is an icebreaker for the dissection of phthalide biosynthetic pathway and reveals the hybrid origin of L. chuanxiong, which will facilitate the metabolic engineering for (S)-3-n-butylphthalide production and breeding for L. chuanxiong.
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Affiliation(s)
- Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xueqing Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Miaoxian Guo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenkai Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lanlan Zang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Song Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Pengxiang Fan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310063, China
| | - Wenhao Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuzhu Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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6
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Lv Y, Zhu J, Huang S, Xing X, Zhou S, Yao H, Yang Z, Liu L, Huang S, Miao Y, Liu X, Fernie AR, Ding Y, Luo J. Metabolome profiling and transcriptome analysis filling the early crucial missing steps of piperine biosynthesis in Piper nigrum L. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:107-120. [PMID: 37753665 DOI: 10.1111/tpj.16476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023]
Abstract
Black pepper (Piper nigrum L.), the world renown as the King of Spices, is not only a flavorsome spice but also a traditional herb. Piperine, a species-specific piper amide, is responsible for the major bioactivity and pungent flavor of black pepper. However, several key steps for the biosynthesis of piperoyl-CoA (acyl-donor) and piperidine (acyl-acceptor), two direct precursors for piperine, remain unknown. In this study, we used guilt-by-association analysis of the combined metabolome and transcriptome, to identify two feruloyldiketide-CoA synthases responsible for the production of the C5 side chain scaffold feruloyldiketide-CoA intermediate, which is considered the first and important step to branch metabolic fluxes from phenylpropanoid pathway to piperine biosynthesis. In addition, we also identified the first two key enzymes for piperidine biosynthesis derived from lysine in P. nigrum, namely a lysine decarboxylase and a copper amine oxidase. These enzymes catalyze the production of cadaverine and 1-piperideine, the precursors of piperidine. In vivo and in vitro experiments verified the catalytic capability of them. In conclusion, our findings revealed enigmatic key steps of piperine biosynthetic pathway and thus provide a powerful reference for dissecting the biosynthetic logic of other piper amides.
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Affiliation(s)
- Yuanyuan Lv
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Yazhouwan National Laboratory (YNL), Sanya, 572025, China
| | - Jinjin Zhu
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Sihui Huang
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Xiaoli Xing
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Shen Zhou
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Hui Yao
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Zhuang Yang
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Ling Liu
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Sishu Huang
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Yuanyuan Miao
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Xianqing Liu
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Yuanhao Ding
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Jie Luo
- School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Yazhouwan National Laboratory (YNL), Sanya, 572025, China
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7
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Brasileiro ACM, Gimenes MA, Pereira BM, Mota APZ, Aguiar MN, Martins ACQ, Passos MAS, Guimaraes PM. The Stilbene Synthase Family in Arachis: A Genome-Wide Study and Functional Characterization in Response to Stress. Genes (Basel) 2023; 14:2181. [PMID: 38137003 PMCID: PMC10742623 DOI: 10.3390/genes14122181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Peanut (Arachis hypogaea) and its wild relatives are among the few species that naturally synthesize resveratrol, a well-known stilbenoid phytoalexin that plays a crucial role in plant defense against biotic and abiotic stresses. Resveratrol has received considerable attention due to its health benefits, such as preventing and treating various human diseases and disorders. Chalcone (CHS) and Stilbene (STS) Synthases are plant-specific type III Polyketide Synthases (PKSs) that share the same substrates and are key branch enzymes in the biosynthesis of flavonoids and stilbenoids, respectively. Although resveratrol accumulation in response to external stimulus has been described in peanut, there are no comprehensive studies of the CHS and STS gene families in the genus Arachis. In the present study, we identified and characterized 6 CHS and 46 STS genes in the tetraploid peanut and an average of 4 CHS and 22 STS genes in three diploid wild species (Arachis duranensis, Arachis ipaënsis and Arachis stenosperma). The CHS and STS gene and protein structures, chromosomal distributions, phylogenetic relationships, conserved amino acid domains, and cis-acting elements in the promoter regions were described for all Arachis species studied. Based on gene expression patterns of wild A. stenosperma STS genes in response to different biotic and abiotic stresses, we selected the candidate AsSTS4 gene, which is strongly induced by ultraviolet (UV) light exposure, for further functional investigation. The AsSTS4 overexpression in peanut hairy roots significantly reduced (47%) root-knot nematode infection, confirming that stilbene synthesis activation in transgenic plants can increase resistance to pathogens. These findings contribute to understanding the role of resveratrol in stress responses in Arachis species and provide the basis for genetic engineering for improved production of valuable secondary metabolites in plants.
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Affiliation(s)
- Ana Cristina Miranda Brasileiro
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
| | - Marcos Aparecido Gimenes
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Bruna Medeiros Pereira
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Ana Paula Zotta Mota
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Matheus Nascimento Aguiar
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Andressa Cunha Quintana Martins
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
| | - Mario Alfredo Saraiva Passos
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
| | - Patricia Messenberg Guimaraes
- Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, DF, Brazil; (M.A.G.); (B.M.P.); (A.P.Z.M.); (M.N.A.); (A.C.Q.M.); (M.A.S.P.); (P.M.G.)
- National Institute of Science and Technology-INCT PlantStress Biotech-Embrapa, Brasília 70770-917, DF, Brazil
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8
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Watanabe M, Tohge T. Species-specific 'specialized' genomic region provides the new insights into the functional genomics characterizing metabolic polymorphisms in plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102427. [PMID: 37517136 DOI: 10.1016/j.pbi.2023.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/19/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
Functional genomics approaches with comparative omics analyses of wild-accessions and cultivars/wild species, as well as comparative genomic analyses in plant species focusing on gene clusters, have successfully detected key metabolic polymorphisms in plant specialized metabolism. In recent decades, (i) intra-species specific metabolic polymorphisms, (ii) new functionalization of tandem duplicated genes, and (iii) metabolic gene clusters were found as the main factors creating metabolic diversity of specialized metabolites in plants. However, given findings aware us that the identification of genes in plant specialized metabolism requires strategic approaches depending on the target metabolic pathways. The increasing availability of plant genome sequences and transcriptome data has facilitated inter-specific comparative analyses, including genomic analysis and gene co-expression network analysis. Here, we introduce functional genomics approaches with the integration of inter-/intra-species comparative metabolomics, their key roles in providing genomic signatures of metabolic evolution, and discuss future prospects of functional genomics on plant specialized metabolism.
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Affiliation(s)
- Mutsumi Watanabe
- Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Takayama-cho 8916-5, Ikoma, Nara 630-0192, Japan
| | - Takayuki Tohge
- Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), Takayama-cho 8916-5, Ikoma, Nara 630-0192, Japan.
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9
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Berman P, de Haro LA, Jozwiak A, Panda S, Pinkas Z, Dong Y, Cveticanin J, Barbole R, Livne R, Scherf T, Shimoni E, Levin-Zaidman S, Dezorella N, Petrovich-Kopitman E, Meir S, Rogachev I, Sonawane PD, Aharoni A. Parallel evolution of cannabinoid biosynthesis. NATURE PLANTS 2023; 9:817-831. [PMID: 37127748 DOI: 10.1038/s41477-023-01402-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Modulation of the endocannabinoid system is projected to have therapeutic potential in almost all human diseases. Accordingly, the high demand for novel cannabinoids stimulates the discovery of untapped sources and efficient manufacturing technologies. Here we explored Helichrysum umbraculigerum, an Asteraceae species unrelated to Cannabis sativa that produces Cannabis-type cannabinoids (for example, 4.3% cannabigerolic acid). In contrast to Cannabis, cannabinoids in H. umbraculigerum accumulate in leaves' glandular trichomes rather than in flowers. The integration of de novo whole-genome sequencing data with unambiguous chemical structure annotation, enzymatic assays and pathway reconstitution in Nicotiana benthamiana and in Saccharomyces cerevisiae has uncovered the molecular and chemical features of this plant. Apart from core biosynthetic enzymes, we reveal tailoring ones producing previously unknown cannabinoid metabolites. Orthology analyses demonstrate that cannabinoid synthesis evolved in parallel in H. umbraculigerum and Cannabis. Our discovery provides a currently unexploited source of cannabinoids and tools for engineering in heterologous hosts.
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Affiliation(s)
- Paula Berman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Luis Alejandro de Haro
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Adam Jozwiak
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Zoe Pinkas
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Younghui Dong
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jelena Cveticanin
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ranjit Barbole
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rotem Livne
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Scherf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Smadar Levin-Zaidman
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Nili Dezorella
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | | | - Sagit Meir
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Rogachev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Prashant D Sonawane
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
- Department of Natural Product Biosynthesis, Max-Planck Institute for Chemical Ecology, Jena, Germany.
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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10
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Jiang W, Tong T, Li W, Huang Z, Chen G, Zeng F, Riaz A, Amoanimaa-Dede H, Pan R, Zhang W, Deng F, Chen ZH. Molecular Evolution of Plant 14-3-3 Proteins and Function of Hv14-3-3A in Stomatal Regulation and Drought Tolerance. PLANT & CELL PHYSIOLOGY 2023; 63:1857-1872. [PMID: 35323970 DOI: 10.1093/pcp/pcac034] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Drought significantly affects stomatal regulation, leading to the reduced growth and productivity of plants. Plant 14-3-3 proteins were reported to participate in drought response by regulating the activities of a wide array of target proteins. However, the molecular evolution, expression pattern and physiological functions of 14-3-3s under drought stress remain unclear. In this study, a comparative genomic analysis and the tissue-specific expression of 14-3-3s revealed the highly conserved and early evolution of 14-3-3s in green plants and duplication and expansion of the 14-3-3s family members in angiosperms. Using barley (Hordeum vulgare) for the functional characterization of 14-3-3 proteins, the transcripts of five members out of six Hv14-3-3s were highly induced by drought in the drought-tolerant line, XZ141. Suppression of the expression of Hv14-3-3A through barley stripe mosaic virus-virus induced gene silencing resulted in significantly increased drought sensitivity and stomatal density as well as significantly reduced net CO2 assimilation (A) and stomatal conductance (gs) in barley. Moreover, we showed the functional interactions between Hv14-3-3s and key proteins in drought and stomatal responses in plants-such as Open Stomata 1 (HvOST1), Slow Anion Channel 1 (HvSLAC1), three Heat Shock Proteins (HvHSP90-1/2/5) and Dehydration-Responsive Element-Binding 3 (HvDREB3). Taken together, we propose that 14-3-3s are highly evolutionarily conserved proteins and that Hv14-3-3s represent a group of the core regulatory components for the rapid stomatal response to drought in barley. This study will provide important evolutionary and molecular evidence for future applications of 14-3-3 proteins in breeding drought-tolerant crops in a changing global climate.
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Affiliation(s)
- Wei Jiang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Tao Tong
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Wen Li
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Zhenghong Huang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Fanrong Zeng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Adeel Riaz
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Hanna Amoanimaa-Dede
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Fenglin Deng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
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11
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Davies KM, Andre CM. All roads lead to Rome: alternative biosynthetic routes in plant specialised metabolism. THE NEW PHYTOLOGIST 2023; 237:371-373. [PMID: 36412921 PMCID: PMC10099233 DOI: 10.1111/nph.18577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This article is a Commentary on T‐T. Zhu et al. (2023), 237: 515–531.
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Affiliation(s)
- Kevin M. Davies
- The New Zealand Institute for Plant and Food Research LimitedPrivate Bag 11600Palmerston North4442New Zealand
| | - Christelle M. Andre
- The New Zealand Institute for Plant and Food Research LimitedPrivate Bag 92169, Auckland Mail CentreAuckland1142New Zealand
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12
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Zhu TT, Sun CJ, Liu XY, Zhang JZ, Hou XB, Ni R, Zhang J, Cheng AX, Lou HX. Interaction of PKR with STCS1: an indispensable step in the biosynthesis of lunularic acid in Marchantia polymorpha. THE NEW PHYTOLOGIST 2023; 237:515-531. [PMID: 36062450 DOI: 10.1111/nph.18408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Unlike bibenzyls derived from the vascular plants, lunularic acid (LA), a key precursor for macrocyclic bisbibenzyl synthesis in nonvascular liverworts, exhibits the absence of one hydroxy group within the A ring. It was hypothesized that both polyketide reductase (PKR) and stilbenecarboxylate synthase 1 (STCS1) were involved in the LA biosynthesis, but the underlined mechanisms have not been clarified. This study used bioinformatics analysis with molecular, biochemical and physiological approaches to characterize STCS1s and PKRs involved in the biosynthesis of LA. The results indicated that MpSTCS1s from Marchantia polymorpha catalyzed both C2→C7 aldol-type and C6→C1 Claisen-type cyclization using dihydro-p-coumaroyl-coenzyme A (CoA) and malonyl-CoA as substrates to yield a C6-C2-C6 skeleton of dihydro-resveratrol following decarboxylation and the C6-C3-C6 type of phloretin in vitro. The protein-protein interaction of PKRs with STCS1 (PPI-PS) was revealed and proved essential for LA accumulation when transiently co-expressed in Nicotiana benthamiana. Moreover, replacement of the active domain of STCS1 with an 18-amino-acid fragment from the chalcone synthase led to the PPI-PS greatly decreasing and diminishing the formation of LA. The replacement also increased the chalcone formation in STCS1s. Our results highlight a previously unrecognized PPI in planta that is indispensable for the formation of LA.
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Affiliation(s)
- Ting-Ting Zhu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chun-Jing Sun
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xin-Yan Liu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jiao-Zhen Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xu-Ben Hou
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Rong Ni
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jing Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
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13
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Suh DY, Ashton NW. A sporopollenin definition for the genomics age. THE NEW PHYTOLOGIST 2022; 236:2009-2013. [PMID: 36098674 DOI: 10.1111/nph.18484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Dae-Yeon Suh
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Neil W Ashton
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
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14
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Davies KM, Landi M, van Klink JW, Schwinn KE, Brummell DA, Albert NW, Chagné D, Jibran R, Kulshrestha S, Zhou Y, Bowman JL. Evolution and function of red pigmentation in land plants. ANNALS OF BOTANY 2022; 130:613-636. [PMID: 36070407 PMCID: PMC9670752 DOI: 10.1093/aob/mcac109] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/05/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Land plants commonly produce red pigmentation as a response to environmental stressors, both abiotic and biotic. The type of pigment produced varies among different land plant lineages. In the majority of species they are flavonoids, a large branch of the phenylpropanoid pathway. Flavonoids that can confer red colours include 3-hydroxyanthocyanins, 3-deoxyanthocyanins, sphagnorubins and auronidins, which are the predominant red pigments in flowering plants, ferns, mosses and liverworts, respectively. However, some flowering plants have lost the capacity for anthocyanin biosynthesis and produce nitrogen-containing betalain pigments instead. Some terrestrial algal species also produce red pigmentation as an abiotic stress response, and these include both carotenoid and phenolic pigments. SCOPE In this review, we examine: which environmental triggers induce red pigmentation in non-reproductive tissues; theories on the functions of stress-induced pigmentation; the evolution of the biosynthetic pathways; and structure-function aspects of different pigment types. We also compare data on stress-induced pigmentation in land plants with those for terrestrial algae, and discuss possible explanations for the lack of red pigmentation in the hornwort lineage of land plants. CONCLUSIONS The evidence suggests that pigment biosynthetic pathways have evolved numerous times in land plants to provide compounds that have red colour to screen damaging photosynthetically active radiation but that also have secondary functions that provide specific benefits to the particular land plant lineage.
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Affiliation(s)
| | - Marco Landi
- Department of Agriculture, Food and Environment, University of Pisa, Italy
| | - John W van Klink
- The New Zealand Institute for Plant and Food Research Limited, Department of Chemistry, Otago University, Dunedin, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David A Brummell
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Nick W Albert
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Rubina Jibran
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Samarth Kulshrestha
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Yanfei Zhou
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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15
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Zhu L, Pietiäinen M, Kontturi J, Turkkelin A, Elomaa P, Teeri TH. Polyketide reductases in defense-related parasorboside biosynthesis in Gerbera hybrida share processing strategies with microbial polyketide synthase systems. THE NEW PHYTOLOGIST 2022; 236:296-308. [PMID: 35719102 PMCID: PMC9541798 DOI: 10.1111/nph.18328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/13/2022] [Indexed: 05/14/2023]
Abstract
Plant polyketides are well-known for their crucial functions in plants and their importance in the context of human health. They are synthesized by type III polyketide synthases (PKSs) and their final functional diversity is determined by post-PKS tailoring enzymes. Gerbera hybrida is rich in two defense-related polyketides: gerberin and parasorboside. Their synthesis is known to be initiated by GERBERA 2-PYRONE SYNTHASE 1 (G2PS1), but the polyketide reductases (PKRs) that determine their final structure have not yet been identified. We identified two PKR candidates in the pathway, GERBERA REDUCTASE 1 (GRED1) and GRED2. Gene expression and metabolite analysis of different gerbera tissues, cultivars, and transgenic gerbera plants, and in vitro enzyme assays, were performed for functional characterization of the enzymes. GRED1 and GRED2 catalyze the second reduction step in parasorboside biosynthesis. They reduce the proximal keto domain of the linear CoA bound intermediate before lactonization. We identified a crucial tailoring step in an important gerbera PKS pathway and show that plant polyketide biosynthesis shares processing strategies with fungi and bacteria. The two tailoring enzymes are recruited from the ancient sporopollenin biosynthetic pathway to a defense-related PKS pathway in gerbera. Our data provide an example of how plants recruit conserved genes to new functions in secondary metabolism that are important for environmental adaptation.
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Affiliation(s)
- Lingping Zhu
- Department of Agricultural Sciences, Viikki Plant Science CentreUniversity of HelsinkiHelsinki00014 UHFinland
| | - Milla Pietiäinen
- Department of Agricultural Sciences, Viikki Plant Science CentreUniversity of HelsinkiHelsinki00014 UHFinland
| | - Juha Kontturi
- Department of Agricultural Sciences, Viikki Plant Science CentreUniversity of HelsinkiHelsinki00014 UHFinland
| | - Anna Turkkelin
- Department of Agricultural Sciences, Viikki Plant Science CentreUniversity of HelsinkiHelsinki00014 UHFinland
| | - Paula Elomaa
- Department of Agricultural Sciences, Viikki Plant Science CentreUniversity of HelsinkiHelsinki00014 UHFinland
| | - Teemu H. Teeri
- Department of Agricultural Sciences, Viikki Plant Science CentreUniversity of HelsinkiHelsinki00014 UHFinland
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16
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Guo D, Wang H, Zhang S, Lan T. The type III polyketide synthase supergene family in plants: complex evolutionary history and functional divergence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:414-428. [PMID: 36004534 DOI: 10.1111/tpj.15953] [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: 04/06/2022] [Revised: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Type III polyketide synthases (PKSs) are key enzymes involved in the biosynthesis of a variety of plant specialized metabolites, including flavonoids, stilbenes, and sporopollenin, to name a few. These enzymes likely played vital roles in plant adaptation during their transition from aquatic to terrestrial habitats and their colonization of specific ecological environments. Members of this supergene family have diverse functions, but how type III PKSs and their functions have evolved remains poorly understood. Here, we conducted comprehensive phylogenomics analysis of the type III PKS supergene family in 60 species representing the major plant lineages and elucidated the classification, origin, and evolutionary history of each class. Molecular evolutionary analysis of the typical chalcone synthase and stilbene synthase types revealed evidence for strong positive natural selection in both the Pinaceae and Fabaceae lineages. The positively selected sites of these proteins include residues at the catalytic tunnel entrance and homodimer interface, which might have driven the functional divergence between the two types. Our results also suggest that convergent evolution of enzymes involved in plant flavonoid biosynthesis is quite common. The results of this study provide new insights into the origin, evolution, and functional diversity of plant type III PKSs. In addition, they serve as a guide for the enzymatic engineering of plant polyketides.
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Affiliation(s)
- Dongmei Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
| | - Hanyan Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
| | - Shumin Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
| | - Ting Lan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
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Nimmy MS, Kumar V, Suthanthiram B, Subbaraya U, Nagar R, Bharadwaj C, Jain PK, Krishnamurthy P. A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:774885. [PMID: 35371145 PMCID: PMC8970042 DOI: 10.3389/fpls.2022.774885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Multidrug and toxic compound extrusion (MATE) transporters comprise a multigene family that mediates multiple functions in plants through the efflux of diverse substrates including organic molecules, specialized metabolites, hormones, and xenobiotics. MATE classification based on genome-wide studies remains ambiguous, likely due to a lack of large-scale phylogenomic studies and/or reference sequence datasets. To resolve this, we established a phylogeny of the plant MATE gene family using a comprehensive kingdom-wide phylogenomic analysis of 74 diverse plant species. We identified more than 4,000 MATEs, which were classified into 14 subgroups based on a systematic bioinformatics pipeline using USEARCH, blast+ and synteny network tools. Our classification was performed using a four-step process, whereby MATEs sharing ≥ 60% protein sequence identity with a ≤ 1E-05 threshold at different sequence lengths (either full-length, ≥ 60% length, or ≥ 150 amino acids) or retaining in the similar synteny blocks were assigned to the same subgroup. In this way, we assigned subgroups to 95.8% of the identified MATEs, which we substantiated using synteny network clustering analysis. The subgroups were clustered under four major phylogenetic groups and named according to their clockwise appearance within each group. We then generated a reference sequence dataset, the usefulness of which was demonstrated in the classification of MATEs in additional species not included in the original analysis. Approximately 74% of the plant MATEs exhibited synteny relationships with angiosperm-wide or lineage-, order/family-, and species-specific conservation. Most subgroups evolved independently, and their distinct evolutionary trends were likely associated with the development of functional novelties or the maintenance of conserved functions. Together with the systematic classification and synteny network profiling analyses, we identified all the major evolutionary events experienced by the MATE gene family in plants. We believe that our findings and the reference dataset provide a valuable resource to guide future functional studies aiming to explore the key roles of MATEs in different aspects of plant physiology. Our classification framework can also be readily extendable to other (super) families.
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Affiliation(s)
| | - Vinod Kumar
- Department of Molecular Biology and Genetic Engineering, Bihar Agricultural University, Bhagalpur, India
| | | | - Uma Subbaraya
- Crop Improvement Division, ICAR–National Research Centre for Banana, Tiruchirappalli, India
| | - Ramawatar Nagar
- ICAR–National Institute for Plant Biotechnology, New Delhi, India
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Aneklaphakij C, Saigo T, Watanabe M, Naake T, Fernie AR, Bunsupa S, Satitpatipan V, Tohge T. Diversity of Chemical Structures and Biosynthesis of Polyphenols in Nut-Bearing Species. FRONTIERS IN PLANT SCIENCE 2021; 12:642581. [PMID: 33889165 PMCID: PMC8056029 DOI: 10.3389/fpls.2021.642581] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/25/2021] [Indexed: 05/27/2023]
Abstract
Nuts, such as peanut, almond, and chestnut, are valuable food crops for humans being important sources of fatty acids, vitamins, minerals, and polyphenols. Polyphenols, such as flavonoids, stilbenoids, and hydroxycinnamates, represent a group of plant-specialized (secondary) metabolites which are characterized as health-beneficial antioxidants within the human diet as well as physiological stress protectants within the plant. In food chemistry research, a multitude of polyphenols contained in culinary nuts have been studied leading to the identification of their chemical properties and bioactivities. Although functional elucidation of the biosynthetic genes of polyphenols in nut species is crucially important for crop improvement in the creation of higher-quality nuts and stress-tolerant cultivars, the chemical diversity of nut polyphenols and the key biosynthetic genes responsible for their production are still largely uncharacterized. However, current technical advances in whole-genome sequencing have facilitated that nut plant species became model plants for omics-based approaches. Here, we review the chemical diversity of seed polyphenols in majorly consumed nut species coupled to insights into their biological activities. Furthermore, we present an example of the annotation of key genes involved in polyphenolic biosynthesis in peanut using comparative genomics as a case study outlining how we are approaching omics-based approaches of the nut plant species.
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Affiliation(s)
- Chaiwat Aneklaphakij
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Tomoki Saigo
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Mutsumi Watanabe
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Thomas Naake
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Somnuk Bunsupa
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Veena Satitpatipan
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Takayuki Tohge
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
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19
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Scossa F, Fernie AR. Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants? Comput Struct Biotechnol J 2021; 19:1579-1594. [PMID: 33868595 PMCID: PMC8039532 DOI: 10.1016/j.csbj.2021.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.
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Key Words
- APR, ancestral protein resurrection
- ASR, ancestral sequence reconstruction
- Ancestral sequence reconstruction
- CDS, coding sequence
- Evolution
- GR, glucocorticoid receptor
- GWAS, genome wide association study
- Genomics
- InDel, insertion/deletion
- MCMC, Markov Chain Monte Carlo
- ML, maximum likelihood
- MP, maximum parsimony
- MR, mineralcorticoid receptor
- MSA, multiple sequence alignment
- Metabolism
- NJ, neighbor-joining
- Phylogenetics
- Plants
- SFS, site frequency spectrum
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institute of Molecular Plant Physiology (MPI-MP), 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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