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Han Y, Yang R, Zhang X, Wang Q, Wang Y, Li Y, Prusky D, Bi Y. MYB24, MYB144, and MYB168 positively regulate suberin biosynthesis at potato tuber wounds during healing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38776519 DOI: 10.1111/tpj.16845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 04/25/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The essence of wound healing is the accumulation of suberin at wounds, which is formed by suberin polyphenolic (SPP) and suberin polyaliphatic (SPA). The biosynthesis of SPP and SPA monomers is catalyzed by several enzyme classes related to phenylpropanoid metabolism and fatty acid metabolism, respectively. However, how suberin biosynthesis is regulated at the transcriptional level during potato (Solanum tuberosum) tuber wound healing remains largely unknown. Here, 6 target genes and 15 transcription factors related to suberin biosynthesis in tuber wound healing were identified by RNA-seq technology and qRT-PCR. Dual luciferase and yeast one-hybrid assays showed that StMYB168 activated the target genes StPAL, StOMT, and St4CL in phenylpropanoid metabolism. Meanwhile, StMYB24 and StMYB144 activated the target genes StLTP, StLACS, and StCYP in fatty acid metabolism, and StFHT involved in the assembly of SPP and SPA domains in both native and wound periderms. More importantly, virus-induced gene silencing in S. tuberosum and transient overexpression in Nicotiana benthamiana assays confirmed that StMYB168 regulates the biosynthesis of free phenolic acids, such as ferulic acid. Furthermore, StMYB24/144 regulated the accumulation of suberin monomers, such as ferulates, α, ω-diacids, and ω-hydroxy acids. In conclusion, StMYB24, StMYB144, and StMYB168 have an elaborate division of labor in regulating the synthesis of suberin during tuber wound healing.
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Affiliation(s)
- Ye Han
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ruirui Yang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xuejiao Zhang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Qihui Wang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yi Wang
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongcai Li
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
| | - Dov Prusky
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Rishon LeZion, 7505101, Israel
| | - Yang Bi
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, 730070, China
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Xu Y, Fu S, Huang Y, Zhou D, Wu Y, Peng J, Kuang M. Genome-wide expression analysis of LACS gene family implies GhLACS25 functional responding to salt stress in cotton. BMC PLANT BIOLOGY 2024; 24:392. [PMID: 38735932 PMCID: PMC11089787 DOI: 10.1186/s12870-024-05045-0] [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: 12/12/2023] [Accepted: 04/19/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND Long-chain acyl-coenzyme A synthetase (LACS) is a type of acylating enzyme with AMP-binding, playing an important role in the growth, development, and stress response processes of plants. RESULTS The research team identified different numbers of LACS in four cotton species (Gossypium hirsutum, Gossypium barbadense, Gossypium raimondii, and Gossypium arboreum). By analyzing the structure and evolutionary characteristics of the LACS, the GhLACS were divided into six subgroups, and a chromosome distribution map of the family members was drawn, providing a basis for further research classification and positioning. Promoter cis-acting element analysis showed that most GhLACS contain plant hormones (GA, MeJA) or non-biological stress-related cis-elements. The expression patterns of GhLACS under salt stress treatment were analyzed, and the results showed that GhLACS may significantly participate in salt stress response through different mechanisms. The research team selected 12 GhLACSs responsive to salt stress for tissue expression analysis and found that these genes are expressed in different tissues. CONCLUSIONS There is a certain diversity of LACS among different cotton species. Analysis of promoter cis-acting elements suggests that GhLACS may be involved in regulating plant growth, development and stress response processes. GhLACS25 was selected for in-depth study, which confirmed its significant role in salt stress response through virus-induced gene silencing (VIGS) and induced expression in yeast cells.
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Affiliation(s)
- Yuchen Xu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
- Henan University/State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng, Henan, 475004, China
| | - Shouyang Fu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
- Sanya National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Yiwen Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
- Sanya National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Dayun Zhou
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Yuzhen Wu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Jun Peng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China.
- Sanya National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China.
| | - Meng Kuang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China.
- Sanya National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China.
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Yang J, Wang Y, Sun J, Li Y, Zhu R, Yin Y, Wang C, Yin X, Qin L. Metabolome and Transcriptome Association Analysis Reveals Mechanism of Synthesis of Nutrient Composition in Quinoa ( Chenopodium quinoa Willd.) Seeds. Foods 2024; 13:1325. [PMID: 38731698 PMCID: PMC11082971 DOI: 10.3390/foods13091325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) seeds are rich in nutrition, superior to other grains, and have a high market value. However, the biosynthesis mechanisms of protein, starch, and lipid in quinoa grain are still unclear. The objective of this study was to ascertain the nutritional constituents of white, yellow, red, and black quinoa seeds and to employ a multi-omics approach to analyze the synthesis mechanisms of these nutrients. The findings are intended to furnish a theoretical foundation and technical support for the biological breeding of quinoa in China. In this study, the nutritional analysis of white, yellow, red, and black quinoa seeds from the same area showed that the nutritional contents of the quinoa seeds were significantly different, and the protein content increased with the deepening of color. The protein content of black quinoa was the highest (16.1 g/100 g) and the lipid content was the lowest (2.7 g/100 g), among which, linoleic acid was the main fatty acid. A combined transcriptome and metabolome analysis exhibited that differentially expressed genes were enriched in "linoleic acid metabolism", "unsaturated fatty acid biosynthesis", and "amino acid biosynthesis". We mainly identified seven genes involved in starch synthesis (LOC110716805, LOC110722789, LOC110738785, LOC110720405, LOC110730081, LOC110692055, and LOC110732328); five genes involved in lipid synthesis (LOC110701563, LOC110699636, LOC110709273, LOC110715590, and LOC110728838); and nine genes involved in protein synthesis (LOC110710842, LOC110720003, LOC110687170, LOC110716004, LOC110702086, LOC110724454 LOC110724577, LOC110704171, and LOC110686607). The data presented in this study based on nutrient, transcriptome, and metabolome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa, and provide candidate genes for further genetic improvements to improve the nutritional value of quinoa seeds.
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Affiliation(s)
- Jindan Yang
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Yiyun Wang
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Jiayi Sun
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Yuzhe Li
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Renbin Zhu
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230036, China;
| | - Yongjie Yin
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Chuangyun Wang
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
| | - Xuebin Yin
- Suzhou Selenium Valley Technology Co., Ltd., Suzhou 215100, China;
- Anhui Province Key Laboratory of Functional Agriculture and Functional Food, Anhui Science and Technology University, Chuzhou 239000, China
| | - Lixia Qin
- College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China; (J.Y.); (Y.W.); (J.S.); (Y.L.); (Y.Y.); (C.W.)
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230036, China;
- Suzhou Selenium Valley Technology Co., Ltd., Suzhou 215100, China;
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Charital S, Shunmugam S, Dass S, Alazzi AM, Arnold CS, Katris NJ, Duley S, Quansah NA, Pierrel F, Govin J, Yamaryo-Botté Y, Botté CY. The acyl-CoA synthetase TgACS1 allows neutral lipid metabolism and extracellular motility in Toxoplasma gondii through relocation via its peroxisomal targeting sequence (PTS) under low nutrient conditions. mBio 2024; 15:e0042724. [PMID: 38501871 PMCID: PMC11005404 DOI: 10.1128/mbio.00427-24] [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: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Apicomplexa parasites cause major diseases such as toxoplasmosis and malaria that have major health and economic burdens. These unicellular pathogens are obligate intracellular parasites that heavily depend on lipid metabolism for the survival within their hosts. Their lipid synthesis relies on an essential combination of fatty acids (FAs) obtained from both de novo synthesis and scavenging from the host. The constant flux of scavenged FA needs to be channeled toward parasite lipid storage, and these FA storages are timely mobilized during parasite division. In eukaryotes, the utilization of FA relies on their obligate metabolic activation mediated by acyl-co-enzyme A (CoA) synthases (ACSs), which catalyze the thioesterification of FA to a CoA. Besides the essential functions of FA for parasite survival, the presence and roles of ACS are yet to be determined in Apicomplexa. Here, we identified TgACS1 as a Toxoplasma gondii cytosolic ACS that is involved in FA mobilization in the parasite specifically during low host nutrient conditions, especially in extracellular stages where it adopts a different localization. Heterologous complementation of yeast ACS mutants confirmed TgACS1 as being an Acyl-CoA synthetase of the bubble gum family that is most likely involved in β-oxidation processes. We further demonstrate that TgACS1 is critical for gliding motility of extracellular parasite facing low nutrient conditions, by relocating to peroxisomal-like area.IMPORTANCEToxoplasma gondii, causing human toxoplasmosis, is an Apicomplexa parasite and model within this phylum that hosts major infectious agents, such as Plasmodium spp., responsible for malaria. The diseases caused by apicomplexans are responsible for major social and economic burdens affecting hundreds of millions of people, like toxoplasmosis chronically present in about one-third of the world's population. Lack of efficient vaccines, rapid emergence of resistance to existing treatments, and toxic side effects of current treatments all argue for the urgent need to develop new therapeutic tools to combat these diseases. Understanding the key metabolic pathways sustaining host-intracellular parasite interactions is pivotal to develop new efficient ways to kill these parasites. Current consensus supports parasite lipid synthesis and trafficking as pertinent target for novel treatments. Many processes of this essential lipid metabolism in the parasite are not fully understood. The capacity for the parasites to sense and metabolically adapt to the host physiological conditions has only recently been unraveled. Our results clearly indicate the role of acyl-co-enzyme A (CoA) synthetases for the essential metabolic activation of fatty acid (FA) used to maintain parasite propagation and survival. The significance of our research is (i) the identification of seven of these enzymes that localize at different cellular areas in T. gondii parasites; (ii) using lipidomic approaches, we show that TgACS1 mobilizes FA under low host nutrient content; (iii) yeast complementation showed that acyl-CoA synthase 1 (ACS1) is an ACS that is likely involved in peroxisomal β-oxidation; (iv) the importance of the peroxisomal targeting sequence for correct localization of TgACS1 to a peroxisomal-like compartment in extracellular parasites; and lastly, (v) that TgACS1 has a crucial role in energy production and extracellular parasite motility.
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Affiliation(s)
- Sarah Charital
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Serena Shunmugam
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Sheena Dass
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Anna Maria Alazzi
- Team Govin, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Christophe-Sébastien Arnold
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Nicholas J. Katris
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Samuel Duley
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Nyamekye A. Quansah
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Fabien Pierrel
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Jérôme Govin
- Team Govin, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Yoshiki Yamaryo-Botté
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
| | - Cyrille Y. Botté
- Apicolipid Team, Institute for Advanced Biosciences, CNRS UMR5309, INSERM U1209, Université Grenoble Alpes, Grenoble, France
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5
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Zhai X, Wu D, Chen C, Yang X, Cheng S, Sha L, Deng S, Cheng Y, Fan X, Kang H, Wang Y, Liu D, Zhou Y, Zhang H. A chromosome level genome assembly of Pseudoroegneria Libanotica reveals a key Kcs gene involves in the cuticular wax elongation for drought resistance. BMC Genomics 2024; 25:253. [PMID: 38448864 PMCID: PMC10916072 DOI: 10.1186/s12864-024-10140-5] [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: 09/11/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae), whose genome symbol was designed as "St", accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome, exhibited strong drought resistance, and was morphologically covered by cuticular wax on the aerial part. Therefore, the St-genome sequencing data could provide fundamental information for studies of genome evolution and reveal its mechanisms of cuticular wax and drought resistance. RESULTS In this study, we reported the chromosome-level genome assembly for the St genome of Pse. libanotica, with a total size of 2.99 Gb. 46,369 protein-coding genes annotated and 71.62% was repeat sequences. Comparative analyses revealed that the genus Pseudoroegneria diverged during the middle and late Miocene. During this period, unique genes, gene family expansion, and contraction in Pse. libanotica were enriched in biotic and abiotic stresses, such as fatty acid biosynthesis which may greatly contribute to its drought adaption. Furthermore, we investigated genes associated with the cuticular wax formation and water deficit and found a new Kcs gene evm.TU.CTG175.54. It plays a critical role in the very long chain fatty acid (VLCFA) elongation from C18 to C26 in Pse. libanotica. The function needs more evidence to be verified. CONCLUSIONS We sequenced and assembled the St genome in Triticeae and discovered a new KCS gene that plays a role in wax extension to cope with drought. Our study lays a foundation for the genome diversification of Triticeae species and deciphers cuticular wax formation genes involved in drought resistance.
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Affiliation(s)
- Xingguang Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Chen Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shaobo Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shuhan Deng
- Glbizzia Biosciences Co., Ltd, Liandong U Valley, Huatuo Road 50, Daxing, Beijing, 102600, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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6
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Wang Y, Bi Y, Jiang F, Shaw RK, Sun J, Hu C, Guo R, Fan X. Mapping and Functional Analysis of QTL for Kernel Number per Row in Tropical and Temperate-Tropical Introgression Lines of Maize ( Zea mays L.). Curr Issues Mol Biol 2023; 45:4416-4430. [PMID: 37232750 DOI: 10.3390/cimb45050281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F7 recombinant inbred line (RIL) populations were created using a temperate-tropical introgression line TML418 and a tropical inbred line CML312 as female parents and a backbone maize inbred line Ye107 as the common male parent. Bi-parental quantitative trait locus (QTL) mapping and genome-wide association analysis (GWAS) were then performed on 399 lines of the two maize RIL populations for KNR in two different environments using 4118 validated single nucleotide polymorphism (SNP) markers. This study aimed to: (1) detect molecular markers and/or the genomic regions associated with KNR; (2) identify the candidate genes controlling KNR; and (3) analyze whether the candidate genes are useful in improving GY. The authors reported a total of 7 QTLs tightly linked to KNR through bi-parental QTL mapping and identified 21 SNPs significantly associated with KNR through GWAS. Among these, a highly confident locus qKNR7-1 was detected at two locations, Dehong and Baoshan, with both mapping approaches. At this locus, three novel candidate genes (Zm00001d022202, Zm00001d022168, Zm00001d022169) were identified to be associated with KNR. These candidate genes were primarily involved in the processes related to compound metabolism, biosynthesis, protein modification, degradation, and denaturation, all of which were related to the inflorescence development affecting KNR. These three candidate genes were not reported previously and are considered new candidate genes for KNR. The progeny of the hybrid Ye107 × TML418 exhibited strong heterosis for KNR, which the authors believe might be related to qKNR7-1. This study provides a theoretical foundation for future research on the genetic mechanism underlying KNR in maize and the use of heterotic patterns to develop high-yielding hybrids.
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Affiliation(s)
- Yuling Wang
- Institute of Resource Plants, Yunnan University, Kunming 650504, China
| | - Yaqi Bi
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Ranjan Kumar Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jiachen Sun
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650500, China
| | - Can Hu
- Institute of Resource Plants, Yunnan University, Kunming 650504, China
| | - Ruijia Guo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
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7
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Zhong Y, Wang Y, Li P, Gong W, Wang X, Yan H, Ge Q, Liu A, Shi Y, Shang H, Zhang Y, Gong J, Yuan Y. Genome-Wide Analysis and Functional Characterization of LACS Gene Family Associated with Lipid Synthesis in Cotton ( Gossypium spp.). Int J Mol Sci 2023; 24:ijms24108530. [PMID: 37239883 DOI: 10.3390/ijms24108530] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Cotton (Gossypium spp.) is the fifth largest oil crop in the world, and cottonseed provides abundant vegetable oil resources and industrial bioenergy fuels for people; therefore, it is of practical significance to increase the oil content of cotton seeds for improving the oil yield and economic benefits of planting cotton. Long-chain acyl-coenzyme A (CoA) synthetase (LACS) capable of catalyzing the formation of acyl-CoAs from free fatty acids has been proven to significantly participate in lipid metabolism, of which whole-genome identification and functional characterization of the gene family have not yet been comprehensively analyzed in cotton. In this study, a total of sixty-five LACS genes were confirmed in two diploid and two tetraploid Gossypium species, which were divided into six subgroups based on phylogenetic relationships with twenty-one other plants. An analysis of protein motif and genomic organizations displayed structural and functional conservation within the same group but diverged among the different group. Gene duplication relationship analysis illustrates the LACS gene family in large scale expansion through WGDs/segmental duplications. The overall Ka/Ks ratio indicated the intense purifying selection of LACS genes in four cotton species during evolution. The LACS genes promoter elements contain numerous light response cis-elements associated with fatty acids synthesis and catabolism. In addition, the expression of almost all GhLACS genes in high seed oil were higher compared to those in low seed oil. We proposed LACS gene models and shed light on their functional roles in lipid metabolism, demonstrating their engineering potential for modulating TAG synthesis in cotton, and the genetic engineering of cottonseed oil provides a theoretical basis.
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Affiliation(s)
- Yike Zhong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yongbo Wang
- Cotton Sciences Research Institute of Hunan, National Hybrid Cotton Research Promotion Center, Changde 415101, China
| | - Pengtao Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyu Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Haoliang Yan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yuanming Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Youlu Yuan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
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Li Y, Jin F, Wu X, Teixeira da Silva JA, Xiong Y, Zhang X, Ma G. Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153866. [PMID: 36399836 DOI: 10.1016/j.jplph.2022.153866] [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: 10/31/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.
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Affiliation(s)
- Yuan Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Feng Jin
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Xiuju Wu
- College of Life Science, Northeast Agricultural University, Harbin, 150040, China.
| | | | - Yuping Xiong
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Xinhua Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
| | - Guohua Ma
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China National Botanical Garden, Guangzhou, 510650, China.
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9
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Huo Z, Xu Y, Yuan S, Chang J, Li S, Wang J, Zhao H, Xu R, Zhong F. The AP2 Transcription Factor BrSHINE3 Regulates Wax Accumulation in Nonheading Chinese Cabbage. Int J Mol Sci 2022; 23:ijms232113454. [PMID: 36362247 PMCID: PMC9656708 DOI: 10.3390/ijms232113454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Wax is an acellular structural substance attached to the surface of plant tissues. It forms a protective barrier on the epidermis of plants and plays an important role in resisting abiotic and biotic stresses. In this paper, nonheading Chinese cabbage varieties with and without wax powder were observed using scanning electron microscopy, and the surface of waxy plants was covered with a layer of densely arranged waxy crystals, thus differentiating them from the surface of waxless plants. A genetic analysis showed that wax powder formation in nonheading Chinese cabbage was controlled by a pair of dominant genes. A preliminary bulked segregant analysis sequencing (BSA-seq) assay showed that one gene was located at the end of chromosome A09. Within this interval, we identified BraA09000626, encoding an AP2 transcription factor homologous to Arabidopsis AtSHINE3, and we named it BrSHINE3. By comparing the CDS of the gene in the two parental plants, a 35 bp deletion in the BrSHINE3 gene of waxless plants resulted in a frameshift mutation. Tissue analysis showed that BrSHINE3 was expressed at significantly higher levels in waxy plant rosette stage petioles and bolting stage stems than in the tissues of waxless plants. We speculate that this deletion in BrSHINE3 bases in the waxless material may inhibit wax synthesis. The overexpression of BrSHINE3 in Arabidopsis induced the accumulation of wax on the stem surface, indicating that BrSHINE3 is a key gene that regulates the formation of wax powder in nonheading Chinese cabbage. The analysis of the subcellular localization showed that BrSHINE3 is mainly located in the nucleus and chloroplast of tobacco leaves, suggesting that the gene may function as a transcription factor. Subsequent transcriptome analysis of the homology of BrSHINE3 downstream genes in nonheading Chinese cabbage showed that these genes were downregulated in waxless materials. These findings provide a basis for a better understanding of the nonheading Chinese cabbage epidermal wax synthesis pathway and provide important information for the molecular-assisted breeding of nonheading Chinese cabbage.
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10
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Wei S, Jiao H, Wang H, Ran K, Dong R, Dong X, Yan W, Wang S. The mechanism analysis of exogenous melatonin in limiting pear fruit aroma decrease under low temperature storage. PeerJ 2022; 10:e14166. [PMID: 36262407 PMCID: PMC9575684 DOI: 10.7717/peerj.14166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/12/2022] [Indexed: 01/21/2023] Open
Abstract
Exogenous melatonin (MT) is widely used in fruit preservation, and can increase the storage time and delay the quality deterioration. Firstly, it was found that 150 μM MT was the optimal concentration to treat 'Xinli No.7' under storage at 4 °C for 60 days. MT could significantly improve oxidase activity and inhibit the reduction of physiological indexes, including pulp hardness, weight loss, titratable acid and soluble solid content. MT could also reduce ethylene release and limit the reduction of fruit aroma. The average content of fruit aroma substance increased by 43.53%. A relevant RNA-Seq database was built to further explore the regulation mechanism of MT. A total of 2,761 differentially expressed genes (DEGs) were identified. DEGs were enriched in 64 functional groups and 191 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. DEGs were mainly enriched in alpha-linolenic acid metabolism, fatty acid metabolism and plant hormone signal transduction pathway. The gene pycom09g05270 belonging to long chain acyl-CoA synthetase family and participating in fatty acid metabolism pathway was identified, and its expression level was consistent with fragments per kilobase per million mapped reads (FPKM) values, implying that pycom09g05270 might play a vital role in maintaining quality during the storage process.
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Affiliation(s)
- Shuwei Wei
- Shandong Institute of Pomology, TaiAn, China
| | - Huijun Jiao
- Shandong Institute of Pomology, TaiAn, China
| | | | - Kun Ran
- Shandong Institute of Pomology, TaiAn, China
| | - Ran Dong
- Shandong Institute of Pomology, TaiAn, China
| | | | - Wenjing Yan
- Shandong Agricultural University, TaiAn, China
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11
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Liang Q, Liu JN, Fang H, Dong Y, Wang C, Bao Y, Hou W, Zhou R, Ma X, Gai S, Wang L, Li S, Yang KQ, Sang YL. Genomic and transcriptomic analyses provide insights into valuable fatty acid biosynthesis and environmental adaptation of yellowhorn. FRONTIERS IN PLANT SCIENCE 2022; 13:991197. [PMID: 36147226 PMCID: PMC9486082 DOI: 10.3389/fpls.2022.991197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 06/01/2023]
Abstract
Yellowhorn (Xanthoceras sorbifolium) is an oil-bearing tree species growing naturally in poor soil. The kernel of yellowhorn contains valuable fatty acids like nervonic acid. However, the genetic basis underlying the biosynthesis of valued fatty acids and adaptation to harsh environments is mainly unexplored in yellowhorn. Here, we presented a haplotype-resolved chromosome-scale genome assembly of yellowhorn with the size of 490.44 Mb containing scaffold N50 of 34.27 Mb. Comparative genomics, in combination with transcriptome profiling analyses, showed that expansion of gene families like long-chain acyl-CoA synthetase and ankyrins contribute to yellowhorn fatty acid biosynthesis and defense against abiotic stresses, respectively. By integrating genomic and transcriptomic data of yellowhorn, we found that the transcription of 3-ketoacyl-CoA synthase gene XS04G00959 was consistent with the accumulation of nervonic and erucic acid biosynthesis, suggesting its critical regulatory roles in their biosynthesis. Collectively, these results enhance our understanding of the genetic basis underlying the biosynthesis of valuable fatty acids and adaptation to harsh environments in yellowhorn and provide foundations for its genetic improvement.
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Affiliation(s)
- Qiang Liang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Jian Ning Liu
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yan Bao
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Wenrui Hou
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Rui Zhou
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xinmei Ma
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Shasha Gai
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Lichang Wang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
| | - Shouke Li
- Worth Agricultural Development Co. Ltd., Weifang, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai’an, Shandong, China
| | - Ya Lin Sang
- College of Forestry, Shandong Agricultural University, Tai’an, Shandong, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Shandong Agricultural University, Tai’an, Shandong, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Tai’an, Shandong, China
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12
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Zhang H, Zhang S, Li M, Wang J, Wu T. The PoLACS4 Gene May Participate in Drought Stress Resistance in Tree Peony (Paeonia ostii ‘Feng Dan Bai’). Genes (Basel) 2022; 13:genes13091591. [PMID: 36140759 PMCID: PMC9498442 DOI: 10.3390/genes13091591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/28/2022] [Accepted: 09/02/2022] [Indexed: 11/20/2022] Open
Abstract
The tree peony (Paeonia ostii ‘Feng Dan Bai’) has excellent drought tolerance. Although it has already been reported that the cuticle is an essential barrier against drought stress, the critical genes for cuticle resistance to drought remain unclear. However, the long-chain acyl-CoA synthetases (LACS) family of genes may be significant for the synthesis of cuticle wax. To test whether the LACS gene family is involved in cuticle response to drought stress in tree peony, we measure the thickness of cuticle stems and leaves alongside LACS enzyme activity. It is found that the cuticle thickens and the LACS enzyme increases with the maturation of stems and leaves, and there is a positive correlation between them. The LACS enzyme increases within 12 h under drought stress induced by polyethylene glycol (PEG). The transcriptome sequencing result (BioProject accession number PRJNA317164) is searched for, and a LACS gene with high expression is cloned. This gene has high homology and similarity with LACS4 from Arabidopsis thaliana. The gene is named PoLACS4. It is show to be highly expressed in mature leaves and peaks within 1 h under drought and salt stresses. All these results suggest that the LACS family of genes may be involved in cuticle response to drought stress and that PoLACS4 is a crucial gene which responds rapidly to drought in the tree peony.
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Affiliation(s)
- Hongye Zhang
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China
- Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Kunming 650224, China
| | - Shan Zhang
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China
- Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Kunming 650224, China
| | - Meng Li
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China
- Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Kunming 650224, China
| | - Juan Wang
- Institute of Ecological Development, Southwest Forestry University, Kunming 650224, China
| | - Tian Wu
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China
- Yunnan Functional Flower Resources and Industrialization Technology Engineering Research Center, Kunming 650224, China
- Correspondence:
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13
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Wei H, Movahedi A, Zhang Y, Aghaei-Dargiri S, Liu G, Zhu S, Yu C, Chen Y, Zhong F, Zhang J. Long-Chain Acyl-CoA Synthetases Promote Poplar Resistance to Abiotic Stress by Regulating Long-Chain Fatty Acid Biosynthesis. Int J Mol Sci 2022; 23:ijms23158401. [PMID: 35955540 PMCID: PMC9369374 DOI: 10.3390/ijms23158401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023] Open
Abstract
Long-chain acyl-CoA synthetases (LACSs) catalyze fatty acids (FAs) to form fatty acyl-CoA thioesters, which play essential roles in FA and lipid metabolisms and cuticle wax biosynthesis. Although LACSs from Arabidopsis have been intensively studied, the characterization and function of LACSs from poplar are unexplored. Here, 10 poplar PtLACS genes were identified from the poplar genome and distributed to eight chromosomes. A phylogenetic tree indicated that PtLACSs are sorted into six clades. Collinearity analysis and duplication events demonstrated that PtLACSs expand through segmental replication events and experience purifying selective pressure during the evolutionary process. Expression patterns revealed that PtLACSs have divergent expression changes in response to abiotic stress. Interaction proteins and GO analysis could enhance the understanding of putative interactions among protein and gene regulatory networks related to FA and lipid metabolisms. Cluster networks and long-chain FA (LCFA) and very long-chain FA (VLCFA) content analysis revealed the possible regulatory mechanism in response to drought and salt stresses in poplar. The present study provides valuable information for the functional identification of PtLACSs in response to abiotic stress metabolism in poplar.
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Affiliation(s)
- Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (S.Z.)
- College of Arts and Sciences, Arlington International University, Wilmington, DE 19804, USA
- Correspondence: (A.M.); (J.Z.)
| | - Yanyan Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (S.Z.)
| | - Soheila Aghaei-Dargiri
- Department of Horticulture, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas 47916193145, Iran;
| | - Guoyuan Liu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Sheng Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (S.Z.)
| | - Chunmei Yu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Yanhong Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Fei Zhong
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Jian Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
- Correspondence: (A.M.); (J.Z.)
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14
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Bengtsson JD, Wallis JG, Browse J. Expression of Physaria longchain acyl-CoA synthetases and hydroxy fatty acid accumulation in transgenic Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2022; 274:153717. [PMID: 35584570 PMCID: PMC9494924 DOI: 10.1016/j.jplph.2022.153717] [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: 04/07/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Hydroxy fatty acids (HFA) are industrially useful chemical feedstocks that accumulate in seed-storage triacylglycerols (TAG) of several plant species, including castor (Ricinus communis) and Physaria (Physaria fendleri). For researchers, HFA also offer a unique opportunity to trace fatty acid metabolism and modification. Past work producing HFA in Arabidopsis (Arabidopsis thaliana) has demonstrated the importance of isozymes of TAG synthesis from plants that evolved to store HFA and as a result have a high degree of specificity towards HFA substrates. Castor phospholipase A2α (RcPLA2) has specificity for HFA-containing phosphatidylcholine. However, expression of RcPLA2 in HFA-accumulating Arabidopsis line CL37-PLA2 reduced HFA content of TAG. This loss was interpreted as being due to poor ability of Arabidopsis longchain acyl-CoA synthetases (LACSs) to utilize HFAs substrates. LACS enzymes are essential to activate HFA to HFA-CoA for TAG synthesis. Physaria is a close relative of Arabidopsis in the Brassicaceae family. To test the hypothesis that this close relatedness would allow Physaria LACSs to interface successfully with Arabidopsis enzymes of seed lipid metabolism and thereby restore HFA accumulation, we transformed PfLACS4 and PfLACS8 constructs into the CL37-PLA2 line. However, HFA content was not recovered, and biochemical characterization of recombinant PfLACS4 and PfLACS8 indicated that these isozymes have substrate specificities and selectivities that are similar to their Arabidopsis orthologues. These and other results pose an important question about how HFA synthesized on phosphatidylcholine can be transferred into the acyl-CoA pool for TAG synthesis.
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Affiliation(s)
- Jesse D Bengtsson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - James G Wallis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA.
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15
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Kim J, Kim RJ, Lee SB, Suh MC. Protein-protein interactions in fatty acid elongase complexes are important for very-long-chain fatty acid synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3004-3017. [PMID: 35560210 DOI: 10.1093/jxb/erab543] [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: 05/12/2021] [Accepted: 12/10/2021] [Indexed: 06/15/2023]
Abstract
Fatty acid elongase (FAE), which catalyzes the synthesis of very-long-chain fatty acids (VLCFAs), is a multiprotein complex; however, little is known about its quaternary structure. In this study, bimolecular fluorescence complementation and/or yeast two-hybrid assays showed that homo-interactions were observed in β-ketoacyl-CoA synthases (KCS2, KCS9, and KCS6), Eceriferum2-like proteins [CER2 and CER2-Like2 (C2L2)], and FAE complex proteins (KCR1, PAS2, ECR, and PAS1), except for CER2-Like1 (C2L1). Hetero-interactions were observed between KCSs (KCS2, KCS9, and KCS6), between CER2-LIKEs (CER2, C2L2, and C2L1), and between FAE complex proteins (KCR1, PAS2, ECR, and PAS1). PAS1 interacts with FAE complex proteins (KCR1, PAS2, and ECR), but not with KCSs (KCS2, KCS9, and KCS6) and CER2-LIKEs (CER2, C2L2, and C2L1). Asp308 and Arg309-Arg311 of KCS9 were essential for the homo-interactions of KCS9 and hetero-interactions between KCS9 and PAS2 or ECR. Asp339 of KCS9 is involved in its homo- and hetero-interactions with ECR. Complementation analysis of the Arabidopsis kcs9 mutant by the expression of amino acid-substituted KCS9 mutant genes showed that Asp308 and Asp339 of KCS9 are involved in the synthesis of C24 VLCFAs from C22. This study suggests that protein-protein interaction in FAE complexes is important for VLCFA synthesis and provides insight into the quaternary structure of FAE complexes for efficient synthesis of VLCFAs.
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Affiliation(s)
- Juyoung Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ryeo Jin Kim
- Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
| | - Saet Buyl Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Mi Chung Suh
- Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
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16
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Lee SB, Suh MC. Regulatory mechanisms underlying cuticular wax biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2799-2816. [PMID: 35560199 DOI: 10.1093/jxb/erab509] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/18/2021] [Indexed: 05/24/2023]
Abstract
Plants are sessile organisms that have developed hydrophobic cuticles that cover their aerial epidermal cells to protect them from terrestrial stresses. The cuticle layer is mainly composed of cutin, a polyester of hydroxy and epoxy fatty acids, and cuticular wax, a mixture of very-long-chain fatty acids (>20 carbon atoms) and their derivatives, aldehydes, alkanes, ketones, alcohols, and wax esters. During the last 30 years, forward and reverse genetic, transcriptomic, and biochemical approaches have enabled the identification of key enzymes, transporters, and regulators involved in the biosynthesis of cutin and cuticular waxes. In particular, cuticular wax biosynthesis is significantly influenced in an organ-specific manner or by environmental conditions, and is controlled using a variety of regulators. Recent studies on the regulatory mechanisms underlying cuticular wax biosynthesis have enabled us to understand how plants finely control carbon metabolic pathways to balance between optimal growth and development and defense against abiotic and biotic stresses. In this review, we summarize the regulatory mechanisms underlying cuticular wax biosynthesis at the transcriptional, post-transcriptional, post-translational, and epigenetic levels.
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Affiliation(s)
- Saet Buyl Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Korea
| | - Mi Chung Suh
- Department of Life Science, Sogang University, Seoul, 04107, Korea
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17
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Huang C, Li Y, Wang K, Xi J, Xu Y, Hong J, Si X, Ye H, Lyu S, Xia G, Wang J, Li P, Xing Y, Wang Y, Huang J. Integrated transcriptome and proteome analysis of developing embryo reveals the mechanisms underlying the high levels of oil accumulation in Carya cathayensis Sarg. TREE PHYSIOLOGY 2022; 42:684-702. [PMID: 34409460 DOI: 10.1093/treephys/tpab112] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Hickory (Carya cathayensis Sarg.) is an extraordinary nut-bearing deciduous arbor with high content of oil in its embryo. However, the molecular mechanism underlying high oil accumulation is mostly unknown. Here, we reported that the lipid droplets and oil accumulation gradually increased with the embryo development and the oil content was up to ~76% at maturity. Furthermore, transcriptome and proteome analysis of developing hickory embryo identified 32,907 genes and 9857 proteins. Time-series analysis of gene expressions showed that these genes were divided into 12 clusters and lipid metabolism-related genes were enriched in Cluster 3, with the highest expression levels at 95 days after pollination (S2). Differentially expressed genes and proteins indicated high correlation, and both were enriched in the lipid metabolism. Notably, the genes involved in biosynthesis, transport of fatty acid/lipid and lipid droplets formation had high expression levels at S2, while the expression levels of other genes required for suberin/wax/cutin biosynthesis and lipid degradation were very low at all the sampling time points, ultimately promoting the accumulation of oil. Quantitative reverse-transcription PCR analysis also verified the results of RNA-seq. The co-regulatory networks of lipid metabolism were further constructed and WRINKLED1 (WRI1) was a core transcriptional factor located in the nucleus. Of note, CcWRI1A/B could directly activate the expression of some genes (CcBCCP2A, CcBCCP2B, CcFATA and CcFAD3) required for fatty acid synthesis. These results provided in-depth evidence for revealing the molecular mechanism of high oil accumulation in hickory embryo.
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Affiliation(s)
- Chunying Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Ketao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Jianwei Xi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Yifan Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Junyan Hong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Xiaolin Si
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Hongyu Ye
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Shiheng Lyu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Guohua Xia
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Jianhua Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Peipei Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Yulin Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Yige Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St, Lin'an District, Hangzhou, Zhejiang 311300, China
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Woolfson KN, Esfandiari M, Bernards MA. Suberin Biosynthesis, Assembly, and Regulation. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040555. [PMID: 35214889 PMCID: PMC8875741 DOI: 10.3390/plants11040555] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 05/03/2023]
Abstract
Suberin is a specialized cell wall modifying polymer comprising both phenolic-derived and fatty acid-derived monomers, which is deposited in below-ground dermal tissues (epidermis, endodermis, periderm) and above-ground periderm (i.e., bark). Suberized cells are largely impermeable to water and provide a critical protective layer preventing water loss and pathogen infection. The deposition of suberin is part of the skin maturation process of important tuber crops such as potato and can affect storage longevity. Historically, the term "suberin" has been used to describe a polyester of largely aliphatic monomers (fatty acids, ω-hydroxy fatty acids, α,ω-dioic acids, 1-alkanols), hydroxycinnamic acids, and glycerol. However, exhaustive alkaline hydrolysis, which removes esterified aliphatics and phenolics from suberized tissue, reveals a core poly(phenolic) macromolecule, the depolymerization of which yields phenolics not found in the aliphatic polyester. Time course analysis of suberin deposition, at both the transcriptional and metabolite levels, supports a temporal regulation of suberin deposition, with phenolics being polymerized into a poly(phenolic) domain in advance of the bulk of the poly(aliphatics) that characterize suberized cells. In the present review, we summarize the literature describing suberin monomer biosynthesis and speculate on aspects of suberin assembly. In addition, we highlight recent advances in our understanding of how suberization may be regulated, including at the phytohormone, transcription factor, and protein scaffold levels.
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19
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Hao X, Chen W, Amato A, Jouhet J, Maréchal E, Moog D, Hu H, Jin H, You L, Huang F, Moosburner M, Allen AE, Gong Y. Multiplexed CRISPR/Cas9 editing of the long-chain acyl-CoA synthetase family in the diatom Phaeodactylum tricornutum reveals that mitochondrial ptACSL3 is involved in the synthesis of storage lipids. THE NEW PHYTOLOGIST 2022; 233:1797-1812. [PMID: 34882804 DOI: 10.1111/nph.17911] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
Long-chain acyl-CoA synthetases (LACS) play diverse and fundamentally important roles in lipid metabolism. While their functions have been well established in bacteria, yeast and plants, the mechanisms by which LACS isozymes regulate lipid metabolism in unicellular oil-producing microalgae, including the diatom Phaeodactylum tricornutum, remain largely unknown. In P. tricornutum, a family of five genes (ptACSL1-ptACSL5) encodes LACS activities. We generated single lacs knockout/knockdown mutants using multiplexed CRISPR/Cas9 method, and determined their substrate specificities towards different fatty acids (FAs) and subcellular localisations. ptACSL3 is localised in the mitochondria and its disruption led to compromised growth and reduced triacylglycerol (TAG) content when cells were bubbled with air. The ptACSL3 mutants showed altered FA profiles in two galactoglycerolipids and phosphatidylcholine (PC) with significantly reduced distribution of 16:0 and 16:1. ptACSL5 is localised in the peroxisome and its knockdown resulted in reduced growth rate and altered molecular species of PC and TAG, indicating a role in controlling the composition of acyl-CoAs for lipid synthesis. Our work demonstrates the potential of generating gene knockout mutants with the mutation of large fragment deletion using multiplexed CRISPR/Cas9 and provides insight into the functions of LACS isozymes in lipid metabolism in the oleaginous microalgae.
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Affiliation(s)
- Xiahui Hao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wenchao Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, Grenoble, F-38041, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, Grenoble, F-38041, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de la Recherche Agronomique, Université Grenoble Alpes, UMR 5168, Grenoble, F-38041, France
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps-University Marburg, Marburg, D-35032, Germany
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Hu Jin
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lingjie You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Fenghong Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Mark Moosburner
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Andrew E Allen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yangmin Gong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
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20
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Bai F, Yu L, Shi J, Li-Beisson Y, Liu J. Long-chain acyl-CoA synthetases activate fatty acids for lipid synthesis, remodeling and energy production in Chlamydomonas. THE NEW PHYTOLOGIST 2022; 233:823-837. [PMID: 34665469 DOI: 10.1111/nph.17813] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Long-chain acyl-CoA synthetases (LACSs) play many roles in mammals, yeasts and plants, but knowledge on their functions in microalgae remains fragmented. Here via genetic, biochemical and physiological analyses, we unraveled the function and roles of LACSs in the model microalga Chlamydomonas reinhardtii. In vitro assays on purified recombinant proteins revealed that CrLACS1, CrLACS2 and CrLACS3 all exhibited bona fide LACS activities toward a broad range of free fatty acids. The Chlamydomonas mutants compromised in CrLACS1, CrLACS2 or CrLACS3 did not show any obvious phenotypes in lipid content or growth under nitrogen (N)-replete condition. But under N-deprivation, CrLACS1 or CrLACS2 suppression resulted in c. 50% less oil, yet with a higher amount of chloroplast lipids. By contrast, CrLACS3 suppression impaired oil remobilization and cell growth severely during N-recovery, supporting its role in fatty acid β-oxidation to provide energy and carbon sources for regrowth. Transcriptomics analysis suggested that the observed lipid phenotypes are likely not due to transcriptional reprogramming but rather a shift in metabolic adjustment. Taken together, this study provided solid experimental evidence for essential roles of the three Chlamydomonas LACS enzymes in lipid synthesis, remodeling and catabolism, and highlighted the importance of lipid homeostasis in cell growth under nutrient fluctuations.
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Affiliation(s)
- Fan Bai
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Lihua Yu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Jianan Shi
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing, 100871, China
| | - Yonghua Li-Beisson
- CEA, CNRS, BIAM, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, Aix Marseille Université, Saint Paul-Lez-Durance, 13108, France
| | - Jin Liu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing, 100871, China
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21
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Ferik F, Ates D, Ercisli S, Erdogan A, Orhan E, Tanyolac MB. Genome-wide association links candidate genes to fruit firmness, fruit flesh color, flowering time, and soluble solid content in apricot (Prunus armeniaca L.). Mol Biol Rep 2021; 49:5283-5291. [PMID: 34741707 DOI: 10.1007/s11033-021-06856-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Apricots originated from China, Central Asia and the Near East and arrived in Anatolia, and particularly in their second homeland of Malatya province in Turkey. Apricots are outstanding summer fruits, with their beautiful attractive color, delicious sweet taste, aroma and high vitamin and mineral content. METHODS AND RESULTS In the current study, a total of 259 apricots genotypes from different geographical origins in Turkey were used. Significant variations were detected in fruit firmness (FF), fruit flesh color (FFC), flowering time (FT), and soluble solid content (SSC). A total of 11,532 SNPs based on DArT were developed and used in the analyses of population structure and association mapping (AM). According to the STRUCTURE (v.2.2) analysis, the apricot genotypes were divided into three groups. The mixed linear model with Q and K matrixes were used to detect the associations between the SNPs and four traits. A total of 131 SNPs were associated with FF, FFC and SSC. No SNP marker was detected associated with FT. CONCLUSION The results demonstrated that AM had high potential of revealing the markers associated with economically important traits in apricot. The SNPs identified in the study can be used in future breeding programs for marker-assisted selection in apricot.
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Affiliation(s)
- Filiz Ferik
- Engineering Faculty, Department of Bioengineering, Ege University, Bornova, 35040, Izmir, Turkey
| | - Duygu Ates
- Engineering Faculty, Department of Bioengineering, Ege University, Bornova, 35040, Izmir, Turkey
| | - Sezai Ercisli
- Agriculture Faculty, Department of Horticulture, Ataturk University, Yakutiye, 25030, Erzurum, Turkey
| | - Abdullah Erdogan
- Institute for Apricot Research of Malatya, 44090, Malatya, Turkey
| | - Emine Orhan
- Agriculture Faculty, Department of Horticulture, Ataturk University, Yakutiye, 25030, Erzurum, Turkey
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22
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Jamsheer K M, Kumar M, Srivastava V. SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6042-6065. [PMID: 33693699 DOI: 10.1093/jxb/erab079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/17/2021] [Indexed: 05/03/2023]
Abstract
The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy. Along with the well-characterized molecular interaction in SnRK1 signaling, our analysis highlights several unchartered regions of SnRK1 signaling in plants such as its possible communication with chromatin remodelers, histone modifiers, and inositol phosphate signaling. We also discuss potential reciprocal interactions of SnRK1 signaling with other signaling pathways and cellular processes, which could be involved in maintaining flexibility and homeostasis under different environmental conditions. Overall, this review provides a comprehensive overview of the SnRK1 signaling network in plants and suggests many novel directions for future research.
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Affiliation(s)
- Muhammed Jamsheer K
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Manoj Kumar
- Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
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23
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Ayaz A, Huang H, Zheng M, Zaman W, Li D, Saqib S, Zhao H, Lü S. Molecular Cloning and Functional Analysis of GmLACS2-3 Reveals Its Involvement in Cutin and Suberin Biosynthesis along with Abiotic Stress Tolerance. Int J Mol Sci 2021; 22:9175. [PMID: 34502106 PMCID: PMC8430882 DOI: 10.3390/ijms22179175] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
Cutin and wax are the main precursors of the cuticle that covers the aerial parts of plants and provide protection against biotic and abiotic stresses. Long-chain acyl-CoA synthetases (LACSs) play diversified roles in the synthesis of cutin, wax, and triacylglycerol (TAG). Most of the information concerned with LACS functions is obtained from model plants, whereas the roles of LACS genes in Glycine max are less known. Here, we have identified 19 LACS genes in Glycine max, an important crop plant, and further focused our attention on 4 LACS2 genes (named as GmLACS2-1, 2, 3, 4, respectively). These GmLACS2 genes display different expression patterns in various organs and also show different responses to abiotic stresses, implying that these genes might play diversified functions during plant growth and against stresses. To further identify the role of GmLACS2-3, greatly induced by abiotic stresses, we transformed a construct containing its full length of coding sequence into Arabidopsis. The expression of GmLACS2-3 in an Arabidopsis atlacs2 mutant greatly suppressed its phenotype, suggesting it plays conserved roles with that of AtLACS2. The overexpression of GmLACS2-3 in wild-type plants significantly increased the amounts of cutin and suberin but had little effect on wax amounts, indicating the specific role of GmLACS2-3 in the synthesis of cutin and suberin. In addition, these GmLACS2-3 overexpressing plants showed enhanced drought tolerance. Taken together, our study deepens our understanding of the functions of LACS genes in different plants and also provides a clue for cultivating crops with strong drought resistance.
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Affiliation(s)
- Asma Ayaz
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (A.A.); (H.H.); (M.Z.); (D.L.); (H.Z.)
| | - Haodong Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (A.A.); (H.H.); (M.Z.); (D.L.); (H.Z.)
| | - Minglü Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (A.A.); (H.H.); (M.Z.); (D.L.); (H.Z.)
| | - Wajid Zaman
- Lushan Botanical Garden, Chinese Academy of Sciences, Nanchang 332900, China;
| | - Donghai Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (A.A.); (H.H.); (M.Z.); (D.L.); (H.Z.)
| | - Saddam Saqib
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huayan Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (A.A.); (H.H.); (M.Z.); (D.L.); (H.Z.)
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (A.A.); (H.H.); (M.Z.); (D.L.); (H.Z.)
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24
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Renard J, Martínez-Almonacid I, Queralta Castillo I, Sonntag A, Hashim A, Bissoli G, Campos L, Muñoz-Bertomeu J, Niñoles R, Roach T, Sánchez-León S, Ozuna CV, Gadea J, Lisón P, Kranner I, Barro F, Serrano R, Molina I, Bueso E. Apoplastic lipid barriers regulated by conserved homeobox transcription factors extend seed longevity in multiple plant species. THE NEW PHYTOLOGIST 2021; 231:679-694. [PMID: 33864680 DOI: 10.1111/nph.17399] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
Cutin and suberin are lipid polyesters deposited in specific apoplastic compartments. Their fundamental roles in plant biology include controlling the movement of gases, water and solutes, and conferring pathogen resistance. Both cutin and suberin have been shown to be present in the Arabidopsis seed coat where they regulate seed dormancy and longevity. In this study, we use accelerated and natural ageing seed assays, glutathione redox potential measures, optical and transmission electron microscopy and gas chromatography-mass spectrometry to demonstrate that increasing the accumulation of lipid polyesters in the seed coat is the mechanism by which the AtHB25 transcription factor regulates seed permeability and longevity. Chromatin immunoprecipitation during seed maturation revealed that the lipid polyester biosynthetic gene long-chain acyl-CoA synthetase 2 (LACS2) is a direct AtHB25 binding target. Gene transfer of this transcription factor to wheat and tomato demonstrated the importance of apoplastic lipid polyesters for the maintenance of seed viability. Our work establishes AtHB25 as a trans-species regulator of seed longevity and has identified the deposition of apoplastic lipid barriers as a key parameter to improve seed longevity in multiple plant species.
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Affiliation(s)
- Joan Renard
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Irene Martínez-Almonacid
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Indira Queralta Castillo
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, P6A 2G4, Canada
| | - Annika Sonntag
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, P6A 2G4, Canada
| | - Aseel Hashim
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, P6A 2G4, Canada
| | - Gaetano Bissoli
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Laura Campos
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Jesús Muñoz-Bertomeu
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Regina Niñoles
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Thomas Roach
- Institute of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Susana Sánchez-León
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, 14004, Spain
| | - Carmen V Ozuna
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, 14004, Spain
| | - José Gadea
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Ilse Kranner
- Institute of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Francisco Barro
- Department of Plant Breeding, Institute for Sustainable Agriculture (IAS-CSIC), Córdoba, 14004, Spain
| | - Ramón Serrano
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
| | - Isabel Molina
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, P6A 2G4, Canada
| | - Eduardo Bueso
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Camino de Vera, Valencia, 46022, Spain
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25
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Ayaz A, Saqib S, Huang H, Zaman W, Lü S, Zhao H. Genome-wide comparative analysis of long-chain acyl-CoA synthetases (LACSs) gene family: A focus on identification, evolution and expression profiling related to lipid synthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:1-11. [PMID: 33556720 DOI: 10.1016/j.plaphy.2021.01.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/25/2021] [Indexed: 05/27/2023]
Abstract
In plants, Long-chain acyl-CoA synthetases (LACSs) play key roles in activating fatty acids to fatty acyl-CoA thioesters, which are then further involved in lipid synthesis and fatty acid catabolism. LACSs have been intensively studied in Arabidopsis, but its evolutionary relationship in green plants is unexplored. In this study, we performed a comprehensive genome-wide analysis of the LACS gene family across green plants followed by phylogenetic clustering analysis, gene structure determination, detection of conserved motifs, gene expression in tissues and subcellular localization. Our results identified LACS genes in 122 plant species including algae, low land plants (i.e., mosses and lycophytes), monocots, and eudicots. In total, 697 sequences were identified, and 629 sequences were selected because of alignment and some duplication errors. The retrieved amino acid sequences ranged from 271 to 1056 residues and diversified in intron/exon patterns in different LACSs. Phylogenetic clustering grouped LACS gene family into six major clades with distinct potential functions. This classification is well supported by examining gene structure and conserved motifs. Also, gene expression analysis and subcellular localization substantiate with clade division in the phylogeny, indicating that the evolutionary pattern is visible in their functionality. Additionally, experimental analysis of lacs2 mutant validated that LACS2 plays key roles in suberin synthesis. Thus, our study not only provides an evolutionary mechanism underlying functional diversification but also lays the foundation for further elucidation of the LACS gene family.
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Affiliation(s)
- Asma Ayaz
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Saddam Saqib
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Haodong Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Wajid Zaman
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Huayan Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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26
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González-Thuillier I, Pellny TK, Tosi P, Mitchell RA, Haslam R, Shewry PR. Accumulation and deposition of triacylglycerols in the starchy endosperm of wheat grain. J Cereal Sci 2021; 98:103167. [PMID: 33897098 PMCID: PMC8047771 DOI: 10.1016/j.jcs.2021.103167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/19/2022]
Abstract
A combination of lipidomics, transcriptomics and bioimaging has been used to study triacylglycerol synthesis and deposition in the developing starchy endosperm of wheat. The content of TAG increased between 14 and 34 days after anthesis, from 50 to 115 mg/100 g dry wt and from about 35 to 175 mg/100 g dry wt in two experiments. The major fatty acids were C16 (palmitic C16:0 and palmitoleic C16:1) and C18 (stearic C18:0, oleic C18:1, linoleic C18:2 and linolenic C18:3), with unsaturated fatty acids accounting for about 75-80% of the total throughout development. Linoleic acid (C18:2) was the major component at all stages and the proportion increased during development. Transcript profiling indicated that predominant route to TAG synthesis and oil accumulation is via the Kennedy pathway and diacylglycerol acyltransferase (DGAT) activity. Confocal microscopy of stained tissue sections showed that TAG accumulated in droplets which are associated with protein and concentrated in the starchy endosperm cells below the sub-aleurone cells. Transcripts encoding 16kd oleosins were also expressed, indicating that the oil droplets are in part stabilised by oleosin proteins.
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Affiliation(s)
| | - Till K. Pellny
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Paola Tosi
- School of Agriculture, Policy and Development, University of Reading, Whiteknights Campus, Early Gate, RG6 6AR, UK
| | | | - Richard Haslam
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
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Jawahir V, Zolman BK. Long chain acyl CoA synthetase 4 catalyzes the first step in peroxisomal indole-3-butyric acid to IAA conversion. PLANT PHYSIOLOGY 2021; 185:120-136. [PMID: 33631795 PMCID: PMC8133310 DOI: 10.1093/plphys/kiaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/08/2020] [Indexed: 06/12/2023]
Abstract
Indole-3-butyric acid (IBA) is an endogenous storage auxin important for maintaining appropriate indole-3-acetic acid (IAA) levels, thereby influencingprimary root elongation and lateral root development. IBA is metabolized into free IAA in peroxisomes in a multistep process similar to fatty acid β-oxidation. We identified LONG CHAIN ACYL-COA SYNTHETASE 4 (LACS4) in a screen for enhanced IBA resistance in primary root elongation in Arabidopsis thaliana. LACSs activate substrates by catalyzing the addition of CoA, the necessary first step for fatty acids to participate in β-oxidation or other metabolic pathways. Here, we describe the novel role of LACS4 in hormone metabolism and postulate that LACS4 catalyzes the addition of CoA onto IBA, the first step in its β-oxidation. lacs4 is resistant to the effects of IBA in primary root elongation and dark-grown hypocotyl elongation, and has reduced lateral root density. lacs6 also is resistant to IBA, although both lacs4 and lacs6 remain sensitive to IAA in primary root elongation, demonstrating that auxin responses are intact. LACS4 has in vitro enzymatic activity on IBA, but not IAA or IAA conjugates, and disruption of LACS4 activity reduces the amount of IBA-derived IAA in planta. We conclude that, in addition to activity on fatty acids, LACS4 and LACS6 also catalyze the addition of CoA onto IBA, the first step in IBA metabolism and a necessary step in generating IBA-derived IAA.
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Affiliation(s)
- Vanessica Jawahir
- Department of Biology, University of Missouri – St Louis, St Louis, Missouri 63121, USA
| | - Bethany Karlin Zolman
- Department of Biology, University of Missouri – St Louis, St Louis, Missouri 63121, USA
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Aragón W, Formey D, Aviles-Baltazar NY, Torres M, Serrano M. Arabidopsis thaliana Cuticle Composition Contributes to Differential Defense Response to Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2021; 12:738949. [PMID: 34804086 PMCID: PMC8603936 DOI: 10.3389/fpls.2021.738949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/06/2021] [Indexed: 05/10/2023]
Abstract
The chemical composition of a plant cuticle can change in response to various abiotic or biotic stresses and plays essential functions in disease resistance responses. Arabidopsis thaliana mutants altered in cutin content are resistant to Botrytis cinerea, presumably because of increased cuticular water and solute permeability, allowing for faster induction of defense responses. Within this context, our knowledge of wax mutants is limited against this pathogen. We tested the contribution of cuticular components to immunity to B. cinerea using mutants altered in either cutin or wax alone, or in both cutin and wax contents. We found that even all the tested mutants showed increased permeability and reactive oxygen species (ROS) accumulation in comparison with wild-type plants and that only cutin mutants showed resistance. To elucidate the early molecular mechanisms underlying cuticle-related immunity, we performed a transcriptomic analysis. A set of upregulated genes involved in cell wall integrity and accumulation of ROS were shared by the cutin mutants bdg, lacs2-3, and eca2, but not by the wax mutants cer1-4 and cer3-6. Interestingly, these genes have recently been shown to be required in B. cinerea resistance. In contrast, we found the induction of genes involved in abiotic stress shared by the two wax mutants. Our study reveals new insight that the faster recognition of a pathogen by changes in cuticular permeability is not enough to induce resistance to B. cinerea, as has previously been hypothesized. In addition, our data suggest that mutants with resistant phenotype can activate other defense pathways, different from those canonical immune ones.
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Affiliation(s)
- Wendy Aragón
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Wendy Aragón, ; Mario Serrano,
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Martha Torres
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Wendy Aragón, ; Mario Serrano,
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Jin JF, He QY, Li PF, Lou HQ, Chen WW, Yang JL. Genome-Wide Identification and Gene Expression Analysis of Acyl-Activating Enzymes Superfamily in Tomato ( Solanum lycopersicum) Under Aluminum Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:754147. [PMID: 34925406 PMCID: PMC8674732 DOI: 10.3389/fpls.2021.754147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/04/2021] [Indexed: 05/06/2023]
Abstract
In response to changing environments, plants regulate gene expression and subsequent metabolism to acclimate and survive. A superfamily of acyl-activating enzymes (AAEs) has been observed in every class of creatures on planet. Some of plant AAE genes have been identified and functionally characterized to be involved in growth, development, biotic, and abiotic stresses via mediating diverse metabolic pathways. However, less information is available about AAEs superfamily in tomato (Solanum lycopersicum), the highest value fruit and vegetable crop globally. In this study, we aimed to identify tomato AAEs superfamily and investigate potential functions with respect to aluminum (Al) stress that represents one of the major factors limiting crop productivity on acid soils worldwide. Fifty-three AAE genes of tomato were identified and named on the basis of phylogenetic relationships between Arabidopsis and tomato. The phylogenetic analysis showed that AAEs could be classified into six clades; however, clade III contains no AAE genes of tomato. Synteny analyses revealed tomato vegetable paralogs and Arabidopsis orthologs. The RNA-seq and quantitative reverse-transcriptase PCR (qRT-PCR) analysis indicated that 9 out of 53 AAEs genes were significantly up- or downregulated by Al stress. Numerous cis-acting elements implicated in biotic and abiotic stresses were detected in the promoter regions of SlAAEs. As the most abundantly expressed gene in root apex and highly induced by Al, there are many potential STOP1 cis-acting elements present in the promoter of SlAAE3-1, and its expression in root apex was specific to Al. Finally, transgenic tobacco lines overexpressing SlAAE3-1 displayed increased tolerance to Al. Altogether, our results pave the way for further studies on the functional characterization of SlAAE genes in tomato with a wish of improvement in tomato crop in the future.
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Affiliation(s)
- Jian Feng Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qi Yu He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Peng Fei Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - He Qiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Wei Wei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- *Correspondence: Wei Wei Chen,
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- Jian Li Yang,
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Zhao H, Kosma DK, Lü S. Functional Role of Long-Chain Acyl-CoA Synthetases in Plant Development and Stress Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:640996. [PMID: 33828572 PMCID: PMC8019973 DOI: 10.3389/fpls.2021.640996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/04/2021] [Indexed: 05/03/2023]
Abstract
Fatty acids (FAs) play vital roles in plants as components of lipid membranes that demarcate cells and organelles, as sources of stored energy in the form of neutral lipids, and as signaling molecules that elicit plant responses to adverse conditions. The activation of FAs through the formation of acyl-CoA intermediates by acyl-CoA synthetase (ACS) family enzymes is required for their synthesis and degradation. Long-chain ACSs (LACSs) represent a small subgroup of ACS enzymes that specifically convert long-chain or very-long-chain FAs into corresponding thioesters for multiple lipid-associated processes. Alteration of LACS activity often results in pleiotropic phenotypes such as male sterility, organ fusion, aberrant cuticular structure, delayed seed germination, altered seed oil content, and plant capacity to respond to various environmental stresses. This review provides a comprehensive analysis of LACS family enzymes including substrate specificity, tissue-specific expression patterns, and distinct subcellular localization highlighting their specific roles in lipid synthesis and degradation, the effects of altered LACS activity on plant development, the relationship between LACS activity and stress resistance, and the regulation of LACS activity. Finally, we pose several major questions to be addressed, which would advance our current understanding of LACS function in plants.
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Affiliation(s)
- Huayan Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Dylan K. Kosma
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, United States
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- *Correspondence: Shiyou Lü,
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Jia S, Yobi A, Naldrett MJ, Alvarez S, Angelovici R, Zhang C, Holding DR. Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5880-5895. [PMID: 32667993 DOI: 10.1093/jxb/eraa325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Opaque kernels in maize may result from mutations in many genes, such as OPAQUE-2. In this study, a maize null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4) showed an opaque kernel phenotype, as well as plant developmental delay, male sterility, and altered response to cold stress. We found that in opaque kernels, all zein proteins were reduced and amino acid content was changed, including increased lysine. Transcriptomic and proteomic analysis confirmed the zein reduction and proteomic rebalancing of non-zein proteins, which was quantitatively and qualitatively different from opaque-2. Global transcriptional changes were found in endosperm and leaf, including many transcription factors and tissue-specific expressed genes. Furthermore, of the more than 8000 significantly differentially expressed genes in wild type in response to cold, a significant proportion (25.9% in moderate cold stress and 40.8% in near freezing stress) were not differentially expressed in response to cold in rdm4, suggesting RDM4 may participate in regulation of abiotic stress tolerance. This initial characterization of maize RDM4 provides a basis for further investigating its function in endosperm and leaf, and as a regulator of normal and stress-responsive development.
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Affiliation(s)
- Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Pratacultural Science, Beijing Municipality, Beijing, China
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
| | - Abou Yobi
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Core facility, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Core facility, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ruthie Angelovici
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
| | - David R Holding
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
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Zhang G, Ahmad MZ, Chen B, Manan S, Zhang Y, Jin H, Wang X, Zhao J. Lipidomic and transcriptomic profiling of developing nodules reveals the essential roles of active glycolysis and fatty acid and membrane lipid biosynthesis in soybean nodulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1351-1371. [PMID: 32412123 DOI: 10.1111/tpj.14805] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/16/2020] [Accepted: 04/28/2020] [Indexed: 05/11/2023]
Abstract
Symbiotic rhizobia-legume interactions are energy-demanding processes, and the carbon supply from host cells that is critically required for nodulation and nitrogen fixation is not fully understood. Investigation of the lipidomic and carbohydrate profiles with the transcriptome of developing nodules revealed highly activated glycolysis, fatty acid (FA), 2-monoacylglycerol (2-MAG), and membrane lipid biosynthesis and transport during nodule development. RNA-sequence profiling of metabolic genes in roots and developing nodules highlighted the enhanced expression of genes involved in the biosynthesis and transport of FAs, membrane lipids, and 2-MAG in rhizobia-soybean symbioses via the RAML-WRI-FatM-GPAT-STRL pathway, which is similar to that in legume-arbuscular mycorrhizal fungi symbiosis. The essential roles of the metabolic pathway during soybean nodulation were further supported by analysis of transgenic hairy roots overexpressing soybean GmWRI1b-OE and GmLEC2a-OE. GmLEC2a-OE hairy roots produced fewer nodules, in contrast to GmWRI1b-OE hairy roots. GmLEC2a-OE hairy roots displayed different or even opposite expression patterns of the genes involved in glycolysis and the synthesis of FAs, 2-MAG, TAG, and membrane lipids compared to GmWRI1b-OE hairy roots. Glycolysis, FA and membrane lipid biosynthesis were repressed in GmLEC2a-OE but increased in GmWRI1b-OE hairy roots, which may account for the reduced nodulation in GmLEC2a-OE hairy roots but increased nodulation in GmWRI1b-OE hairy roots. These data show that active FA, 2-MAG and membrane lipid biosynthesis are essential for nodulation and rhizobia-soybean symbioses. These data shed light on essential and complex lipid metabolism for soybean nodulation and nodule development, laying the foundation for the future detailed investigation of soybean nodulation.
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Affiliation(s)
- Gaoyang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Z Ahmad
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Beibei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sehrish Manan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuliang Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanan Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St Louis, MO, 63121, USA
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, 230036, China
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Zhang CL, Zhang YL, Hu X, Xiao X, Wang GL, You CX, Li YY, Hao YJ. An apple long-chain acyl-CoA synthetase, MdLACS4, induces early flowering and enhances abiotic stress resistance in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110529. [PMID: 32563467 DOI: 10.1016/j.plantsci.2020.110529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 05/08/2023]
Abstract
The aerial parts of apple are protected against environmental stress by cuticular wax. Although it has been suggested that several long-chain acyl-CoA synthetases are involved in wax biosynthesis, the molecular pathway of apple cuticular wax biosynthesis remains unclear. In this study, an MdLACS4 protein with long-chain acyl-CoA synthetase activity was isolated from apple. The MdLACS4 gene was highly expressed in pericarp, stem, and mature leaf tissues. Ectopic expression of MdLACS4 in Arabidopsis induced early flowering. Compared with wild-type plants, MdLACS4 transgenic Arabidopsis exhibited lower water loss rates, reduced epidermal permeability, increased cuticular wax in stems and leaves, and altered cuticular ultrastructure. Furthermore, the accumulation of cuticular wax enhanced the resistance of MdLACS4 transgenic plants to drought and salt stress. Finally, predicted protein functional interaction networks for LACS4 suggested that the molecular regulation pathway of MdLACS4 mediates wax biosynthesis in apple.
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Affiliation(s)
- Chun-Ling Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Ya-Li Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xing Hu
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xu Xiao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Gui-Luan Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Yu-Jin Hao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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Lewandowska M, Keyl A, Feussner I. Wax biosynthesis in response to danger: its regulation upon abiotic and biotic stress. THE NEW PHYTOLOGIST 2020; 227:698-713. [PMID: 32242934 DOI: 10.1111/nph.16571] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/12/2020] [Indexed: 05/18/2023]
Abstract
The plant cuticle is the first physical barrier between land plants and their terrestrial environment. It consists of the polyester scaffold cutin embedded and sealed with organic, solvent-extractable cuticular waxes. Cuticular wax ultrastructure and chemical composition differ with plant species, developmental stage and physiological state. Despite this complexity, cuticular wax consistently serves a critical role in restricting nonstomatal water loss. It also protects the plant against other environmental stresses, including desiccation, UV radiation, microorganisms and insects. Within the broader context of plant responses to abiotic and biotic stresses, our knowledge of the explicit roles of wax crystalline structures and chemical compounds is lacking. In this review, we summarize our current knowledge of wax biosynthesis and regulation in relation to abiotic and biotic stresses and stress responses.
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Affiliation(s)
- Milena Lewandowska
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
| | - Alisa Keyl
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, D-37077, Goettingen, Germany
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35
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Philippe G, Sørensen I, Jiao C, Sun X, Fei Z, Domozych DS, Rose JK. Cutin and suberin: assembly and origins of specialized lipidic cell wall scaffolds. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:11-20. [PMID: 32203682 DOI: 10.1016/j.pbi.2020.01.008] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 05/19/2023]
Abstract
Cutin and suberin are hydrophobic lipid biopolyester components of the cell walls of specialized plant tissue and cell-types, where they facilitate adaptation to terrestrial habitats. Many steps in their biosynthetic pathways have been characterized, but the basis of their spatial deposition and precursor trafficking is not well understood. Members of the GDSL lipase/esterase family catalyze cutin polymerization, and candidate proteins have been proposed to mediate interactions between cutin or suberin and other wall components. Comparative genomic studies of charophyte algae and early diverging land plants, combined with knowledge of the biosynthesis, trafficking and assembly mechanisms, suggests an origin for the capacity to secrete waxes, as well as aliphatic and phenolic compounds before the first colonization of true terrestrial habitats.
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Affiliation(s)
- Glenn Philippe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Iben Sørensen
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Chen Jiao
- Boyce Thompson Institute, Ithaca, NY, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA; U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - David S Domozych
- Department of Biology, Skidmore College, Saratoga Springs, NY, USA
| | - Jocelyn Kc Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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Wu T, Fu Y, Shi Y, Li Y, Kou Y, Mao X, Liu J. Functional Characterization of Long-Chain Acyl-CoA Synthetase Gene Family from the Oleaginous Alga Chromochloris zofingiensis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4473-4484. [PMID: 32208653 DOI: 10.1021/acs.jafc.0c01284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Long-chain acyl-coenzyme A (CoA) synthetase (LACS) catalyzes the formation of acyl-CoAs from free fatty acids, which is pivotal for lipid metabolism. Here, we confirmed the presence of six CzLACS genes in Chromochloris zofingiensis. Functional complementation and in vitro enzymatic assay indicated that CzLACS2 through CzLACS5 rather than CzLACS1 or CzLACS6 are bona fide LACS enzymes and they have overlapping yet distinct substrate preference. The results of the subcellular colocalization experiment and different expression patterns under three triacylglycerol (TAG)-inducing conditions showed that CzLACS2 through CzLACS4 reside at endoplasmic reticulum (ER) and are involved in TAG biosynthesis, while CzLACS5 resides in peroxisome and participates in fatty acid β-oxidation. The yeast one-hybrid assay using a library of 50 transcription factors (TFs) constructed in our study identified 12 TFs potentially involved in regulating the expression of CzLACSs. Moreover, heterologous expression of CzLACSs demonstrated their engineering potential for modulating TAG synthesis in yeast and algal cells.
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Affiliation(s)
- Tao Wu
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China
- BIC-ESAT, College of Engineering, Peking University, Beijing 100871, China
| | - Yunlei Fu
- BIC-ESAT, College of Engineering, Peking University, Beijing 100871, China
| | - Ying Shi
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Yuelian Li
- BIC-ESAT, College of Engineering, Peking University, Beijing 100871, China
| | - Yaping Kou
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Xuemei Mao
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China
- BIC-ESAT, College of Engineering, Peking University, Beijing 100871, China
| | - Jin Liu
- Laboratory for Algae Biotechnology & Innovation, College of Engineering, Peking University, Beijing 100871, China
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Kalinger RS, Pulsifer IP, Hepworth SR, Rowland O. Fatty Acyl Synthetases and Thioesterases in Plant Lipid Metabolism: Diverse Functions and Biotechnological Applications. Lipids 2020; 55:435-455. [PMID: 32074392 DOI: 10.1002/lipd.12226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Plants use fatty acids to synthesize acyl lipids for many different cellular, physiological, and defensive roles. These roles include the synthesis of essential membrane, storage, or surface lipids, as well as the production of various fatty acid-derived metabolites used for signaling or defense. Fatty acids are activated for metabolic processing via a thioester linkage to either coenzyme A or acyl carrier protein. Acyl synthetases metabolically activate fatty acids to their thioester forms, and acyl thioesterases deactivate fatty acyl thioesters to free fatty acids by hydrolysis. These two enzyme classes therefore play critical roles in lipid metabolism. This review highlights the surprisingly complex and varying roles of fatty acyl synthetases in plant lipid metabolism, including roles in the intracellular trafficking of fatty acids. This review also surveys the many specialized fatty acyl thioesterases characterized to date in plants, which produce a great diversity of fatty acid products in a tissue-specific manner. While some acyl thioesterases produce fatty acids that clearly play roles in plant-insect or plant-microbial interactions, most plant acyl thioesterases have yet to be fully characterized both in terms of their substrate specificities and their functions. The biotechnological applications of plant acyl thioesterases and synthetases are also discussed, as there is significant interest in these enzymes as catalysts for the sustainable production of fatty acids and their derivatives for industrial uses.
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Affiliation(s)
- Rebecca S Kalinger
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ian P Pulsifer
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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Hui WK, Zhao FY, Wang JY, Chen XY, Li JW, Zhong Y, Li HY, Zheng JX, Zhang LZ, Que QM, Wu AM, Gong W. De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism. BMC Genomics 2020; 21:81. [PMID: 31992199 PMCID: PMC6986037 DOI: 10.1186/s12864-020-6521-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species. Results Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). Conclusions The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.
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Affiliation(s)
- Wen-Kai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fei-Yan Zhao
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing-Yan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Yang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jue-Wei Li
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Zhong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hong-Yun Li
- Agricultural Technology Extension Center in Yantan District, Zigong, 643030, China
| | - Jun-Xing Zheng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liang-Zhen Zhang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qing-Min Que
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
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