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Andrade-Marcial M, Pacheco-Arjona R, Hernández-Castellano S, Che-Aguilar L, De-la-Peña C. Transcriptome analysis reveals molecular mechanisms underlying chloroplast biogenesis in albino Agave angustifolia plantlets. PHYSIOLOGIA PLANTARUM 2024; 176:e14289. [PMID: 38606618 DOI: 10.1111/ppl.14289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/13/2024]
Abstract
Albino plants display partial or complete loss of photosynthetic pigments and defective thylakoid membrane development, consequently impairing plastid function and development. These distinctive attributes render albino plants excellent models for investigating chloroplast biogenesis. Despite their potential, limited exploration has been conducted regarding the molecular alterations underlying these phenotypes, extending beyond photosynthetic metabolism. In this study, we present a novel de novo transcriptome assembly of an albino somaclonal variant of Agave angustifolia Haw., which spontaneously emerged during the micropropagation of green plantlets. Additionally, RT-qPCR analysis was employed to validate the expression of genes associated with chloroplast biogenesis, and plastome copy numbers were quantified. This research aims to gain insight into the molecular disruptions affecting chloroplast development and ascertain whether the expression of critical genes involved in plastid development and differentiation is compromised in albino tissues of A. angustifolia. Our transcriptomic findings suggest that albino Agave plastids exhibit high proliferation, activation of the protein import machinery, altered transcription directed by PEP and NEP, dysregulation of plastome expression genes, reduced expression of photosynthesis-associated nuclear genes, disruption in the tetrapyrrole and carotenoid biosynthesis pathway, alterations in the plastid ribosome, and an increased number of plastome copies, among other alterations.
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Affiliation(s)
| | - Ramón Pacheco-Arjona
- Consejo Nacional de Ciencia y Tecnología- Universidad Autónoma de Yucatán, Facultad de Medicina Veterinaria y Zootecnia, Mérida, México
| | | | - Ligia Che-Aguilar
- Tecnológico Nacional de México. Instituto Tecnológico de Mérida, Mérida, Yucatán, México
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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Ferl RJ, Zhou M, Strickland HF, Haveman NJ, Callaham JB, Bandla S, Ambriz D, Paul AL. Transcriptomic dynamics in the transition from ground to space are revealed by Virgin Galactic human-tended suborbital spaceflight. NPJ Microgravity 2023; 9:95. [PMID: 38123588 PMCID: PMC10733374 DOI: 10.1038/s41526-023-00340-w] [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: 08/10/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
The Virgin Galactic Unity 22 mission conducted the first astronaut-manipulated suborbital spaceflight experiment. The experiment examined the operationalization of Kennedy Space Center Fixation Tubes (KFTs) as a generalizable approach to preserving biology at various phases of suborbital flight. The biology chosen for this experiment was Arabidopsis thaliana, ecotype Col-0, because of the plant history of spaceflight experimentation within KFTs and wealth of comparative data from orbital experiments. KFTs were deployed as a wearable device, a leg pouch attached to the astronaut, which proved to be operationally effective during the course of the flight. Data from the inflight samples indicated that the microgravity period of the flight elicited the strongest transcriptomic responses as measured by the number of genes showing differential expression. Genes related to reactive oxygen species and stress, as well as genes associated with orbital spaceflight, were highly represented among the suborbital gene expression profile. In addition, gene families largely unaffected in orbital spaceflight were diversely regulated in suborbital flight, including stress-responsive transcription factors. The human-tended suborbital experiment demonstrated the operational effectiveness of the KFTs in suborbital flight and suggests that rapid transcriptomic responses are a part of the temporal dynamics at the beginning of physiological adaptation to spaceflight.
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Affiliation(s)
- Robert J Ferl
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA.
- UF Research, University of Florida, 1523 Union Rd, Grinter Hall, Gainesville, FL, 32611, USA.
| | - Mingqi Zhou
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Hunter F Strickland
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Natasha J Haveman
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Jordan B Callaham
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Sirisha Bandla
- Virgin Galactic, 1700 Flight Way, 3rd Floor, Tustin, CA, 92782, USA
| | - Daniel Ambriz
- Virgin Galactic, 1700 Flight Way, 3rd Floor, Tustin, CA, 92782, USA
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA.
- Interdisciplinary Center for Biotechnology Research, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA.
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Xie W, Xu D, Chen F, Wang Z, Luo J, He Y, Zheng Q, Liu C. Integrated Cytological, Physiological, and Transcriptome Analyses Provide Insight into the Albino Phenotype of Chinese Plum ( Prunus salicina). Int J Mol Sci 2023; 24:14457. [PMID: 37833903 PMCID: PMC10573071 DOI: 10.3390/ijms241914457] [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: 08/22/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Albino seedlings that arise during seed reproduction can have a significant impact on plant growth and breeding. In this research, we present the first report of albino occurrences in the seed reproduction process of Prunus salicina and describe the cytological, physiological, and transcriptomic changes observed in albino seedlings. The albino seedlings which were observed in several plum cultivars exhibited abnormal chloroplast ultrastructure and perturbed stomatal structure. Compared to normal seedlings, the photosynthetic pigment contents in albino seedlings decreased by more than 90%, accompanied by significant reductions in several chlorophyll fluorescence parameters. Furthermore, substantially changed photosynthetic parameters indicated that the photosynthetic capacity and stomatal function were impaired in albino seedlings. Additionally, the activities of the antioxidant enzyme were drastically altered against the background of higher proline and lower ascorbic acid in leaves of albino seedlings. A total of 4048 differentially expressed genes (DEGs) were identified through transcriptomic sequencing, and the downregulated DEGs in albino seedlings were greatly enriched in the pathways for photosynthetic antenna proteins and flavonoid biosynthesis. GLK1 and Ftsz were identified as candidate genes responsible for the impaired chloroplast development and division in albino seedlings. Additionally, the substantial decline in the expression levels of examined photosystem-related chloroplast genes was validated in albino seedlings. Our findings shed light on the intricate physiological and molecular mechanisms driving albino plum seedling manifestation, which will contribute to improving the reproductive and breeding efforts of plums.
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Affiliation(s)
- Weiwei Xie
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.X.); (D.X.); (F.C.); (Z.W.); (J.L.); (Y.H.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Dantong Xu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.X.); (D.X.); (F.C.); (Z.W.); (J.L.); (Y.H.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Fangce Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.X.); (D.X.); (F.C.); (Z.W.); (J.L.); (Y.H.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Zhengpeng Wang
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.X.); (D.X.); (F.C.); (Z.W.); (J.L.); (Y.H.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Jiandong Luo
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.X.); (D.X.); (F.C.); (Z.W.); (J.L.); (Y.H.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Yehua He
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.X.); (D.X.); (F.C.); (Z.W.); (J.L.); (Y.H.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Qianming Zheng
- Institute of Pomology Science, Guizhou Academy of Agricultural Science, Ministry of Agriculture and Rural Affairs Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Region, Guiyang 550006, China
| | - Chaoyang Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (W.X.); (D.X.); (F.C.); (Z.W.); (J.L.); (Y.H.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
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Andrade-Marcial M, Ruíz-May E, Elizalde-Contreras JM, Pacheco N, Herrera-Pool E, De-la-Peña C. Proteome of Agave angustifolia Haw.: Uncovering metabolic alterations, over-accumulation of amino acids, and compensatory pathways in chloroplast-deficient albino plantlets. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107902. [PMID: 37506650 DOI: 10.1016/j.plaphy.2023.107902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
Amino acids (AA) are essential molecules for plant physiology, acting as precursor molecules for proteins and other organic compounds. Chloroplasts play a vital role in AA metabolism, yet little is known about the impact on AA metabolism of albino plants' lack of chloroplasts. In this study, we conducted a quantitative proteome analysis on albino and variegated somaclonal variants of Agave angustifolia Haw. to investigate metabolic alterations in chloroplast-deficient plants, with a focus on AA metabolic pathways. We identified 82 enzymes involved in AA metabolism, with 32 showing differential accumulation between the somaclonal variants. AaCM, AaALS, AaBCAT, AaIPMS1, AaSHMT, AaAST, AaCGS, and AaMS enzymes were particularly relevant in chloroplast-deficient Agave plantlets. Both variegated and albino phenotypes exhibited excessive synthesis of AA typically associated with chloroplasts (aromatic AAs, BCAAs, Asp, Lys, Pro and Met). Consistent trends were observed for AaBCAT and AaCM at mRNA and protein levels in albino plantlets. These findings highlight the critical activation and reprogramming of AA metabolic pathways in plants lacking chloroplasts. This study contributes to unraveling the intricate relationship between AA metabolism and chloroplast absence, offering insights into survival mechanisms of albino plants.
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Affiliation(s)
- M Andrade-Marcial
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - E Ruíz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Congregación el Haya, 91070, Xalapa, Veracruz, México
| | - J M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Congregación el Haya, 91070, Xalapa, Veracruz, México
| | - N Pacheco
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Unidad Sureste, Tablaje Catastral 31264 Km 5.5 Carretera Sierra Papacal-Chuburná Puerto, Parque Científico Tecnológico de Yucatán, CP, 97302, Mérida, Yucatán, México
| | - E Herrera-Pool
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Unidad Sureste, Tablaje Catastral 31264 Km 5.5 Carretera Sierra Papacal-Chuburná Puerto, Parque Científico Tecnológico de Yucatán, CP, 97302, Mérida, Yucatán, México
| | - C De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México.
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Alam I, Manghwar H, Zhang H, Yu Q, Ge L. Identification of GOLDEN2-like transcription factor genes in soybeans and their role in regulating plant development and metal ion stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1052659. [PMID: 36438095 PMCID: PMC9691782 DOI: 10.3389/fpls.2022.1052659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The Golden 2-Like (G2-like or GLK) transcription factors are essential for plant growth, development, and many stress responses as well as heavy metal stress. However, G2-like regulatory genes have not been studied in soybean. This study identified the genes for 130 G2-Like candidates' in the genome of Glycine max (soybean). These GLK genes were located on all 20 chromosomes, and several of them were segmentally duplicated. Most GLK family proteins are highly conserved in Arabidopsis and soybean and were classified into five major groups based on phylogenetic analysis. These GmGLK gene promoters share cis-acting elements involved in plant responses to abscisic acid, methyl jasmonate, auxin signaling, low temperature, and biotic and abiotic stresses. RNA-seq expression data revealed that the GLK genes were classified into 12 major groups and differentially expressed in different tissues or organs. The co-expression network complex revealed that the GmGLK genes encode proteins involved in the interaction of genes related to chlorophyll biosynthesis, circadian rhythms, and flowering regulation. Real-time quantitative PCR analysis confirmed the expression profiles of eight GLK genes in response to cadmium (Cd) and copper (Cu) stress, with some GLK genes significantly induced by both Cd and Cu stress treatments, implying a functional role in defense responsiveness. Thus, we present a comprehensive perspective of the GLK genes in soybean and emphasize their important role in crop development and metal ion stresses.
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Affiliation(s)
- Intikhab Alam
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- College of Life Sciences, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- Guangdong Subcenter of the National Center for Soybean Improvement, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
| | - Hakim Manghwar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
| | - Hanyin Zhang
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- Guangdong Subcenter of the National Center for Soybean Improvement, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
| | - Qianxia Yu
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- Guangdong Subcenter of the National Center for Soybean Improvement, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
- Guangdong Subcenter of the National Center for Soybean Improvement, South China Agricultural University (SCAU), Guangzhou, Guangdong, China
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Yan J, Liu B, Cao Z, Chen L, Liang Z, Wang M, Liu W, Lin Y, Jiang B. Cytological, genetic and transcriptomic characterization of a cucumber albino mutant. FRONTIERS IN PLANT SCIENCE 2022; 13:1047090. [PMID: 36340338 PMCID: PMC9630852 DOI: 10.3389/fpls.2022.1047090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Photosynthesis, a fundamental process for plant growth and development, is dependent on chloroplast formation and chlorophyll synthesis. Severe disruption of chloroplast structure results in albinism of higher plants. In the present study, we report a cucumber albino alc mutant that presented white cotyledons under normal light conditions and was unable to produce first true leaf. Meanwhile, alc mutant could grow creamy green cotyledons under dim light conditions but died after exposure to normal light irradiation. No chlorophyll and carotenoid were detected in the alc mutant grown under normal light conditions. Using transmission electron microscopy, impaired chloroplasts were observed in this mutant. The genetic analysis indicated that the albino phenotype was recessively controlled by a single locus. Comparative transcriptomic analysis between the alc mutant and wild type revealed that genes involved in chlorophyll metabolism and the methylerythritol 4-phosphate pathway were affected in the alc mutant. In addition, three genes involved in chloroplast development, including two FtsH genes and one PPR gene, were found to have negligible expression in this mutant. The quality of RNA sequencing results was further confirmed by real-time quantitative PCR analysis. We also examined 12 homologous genes from alc mutant in other plant species, but no genetic variation in the coding sequences of these genes was found between alc mutant and wild type. Taken together, we characterized a cucumber albino mutant with albinism phenotype caused by chloroplast development deficiency and this mutant can pave way for future studies on plastid development.
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Affiliation(s)
- Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Bin Liu
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Zhenqiang Cao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Lin Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zhaojun Liang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yu'e Lin
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Andrade-Marcial M, Pacheco-Arjona R, Góngora-Castillo E, De-la-Peña C. Chloroplastic pentatricopeptide repeat proteins (PPR) in albino plantlets of Agave angustifolia Haw. reveal unexpected behavior. BMC PLANT BIOLOGY 2022; 22:352. [PMID: 35850575 PMCID: PMC9295523 DOI: 10.1186/s12870-022-03742-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pentatricopeptide repeat (PPR) proteins play an essential role in the post-transcriptional regulation of genes in plastid genomes. Although important advances have been made in understanding the functions of these genes, there is little information available on chloroplastic PPR genes in non-model plants and less in plants without chloroplasts. In the present study, a comprehensive and multifactorial bioinformatic strategy was applied to search for putative PPR genes in the foliar and meristematic tissues of green and albino plantlets of the non-model plant Agave angustifolia Haw. RESULTS A total of 1581 PPR transcripts were identified, of which 282 were chloroplastic. Leaf tissue in the albino plantlets showed the highest levels of expression of chloroplastic PPRs. The search for hypothetical targets of 12 PPR sequences in the chloroplast genes of A. angustifolia revealed their action on transcripts related to ribosomes and translation, photosystems, ATP synthase, plastid-encoded RNA polymerase and RuBisCO. CONCLUSIONS Our results suggest that the expression of PPR genes depends on the state of cell differentiation and plastid development. In the case of the albino leaf tissue, which lacks functional chloroplasts, it is possible that anterograde and retrograde signaling networks are severely compromised, leading to a compensatory anterograde response characterized by an increase in the expression of PPR genes.
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Affiliation(s)
- M Andrade-Marcial
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - R Pacheco-Arjona
- Facultad de Medicina Veterinaria y Zootecnia, Consejo Nacional de Ciencia y Tecnología- Universidad Autónoma de Yucatán, Mérida, Mexico
| | - E Góngora-Castillo
- Consejo Nacional de Ciencia y Tecnología-Unidad De Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico
| | - C De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34. Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, Mexico.
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Luo T, Zhou Z, Deng Y, Fan Y, Qiu L, Chen R, Yan H, Zhou H, Lakshmanan P, Wu J, Chen Q. Transcriptome and metabolome analyses reveal new insights into chlorophyll, photosynthesis, metal ion and phenylpropanoids related pathways during sugarcane ratoon chlorosis. BMC PLANT BIOLOGY 2022; 22:222. [PMID: 35484490 PMCID: PMC9052583 DOI: 10.1186/s12870-022-03588-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Ratoon sugarcane is susceptible to chlorosis, characterized by chlorophyll loss, poor growth, and a multitude of nutritional deficiency mainly occurring at young stage. Chlorosis would significantly reduce the cane production. The molecular mechanism underlying this phenomenon remains unknown. We analyzed the transcriptome and metabolome of chlorotic and non-chlorotic sugarcane leaves of the same age from the same field to gain molecular insights into this phenomenon. RESULTS The agronomic traits, such as plant height and the number of leaf, stalk node, and tillers declined in chlorotic sugarcane. Chlorotic leaves had substantially lower chlorophyll content than green leaves. A total of 11,776 differentially expressed genes (DEGs) were discovered in transcriptome analysis. In the KEGG enriched chlorophyll metabolism pathway, sixteen DEGs were found, eleven of which were down-regulated. Two photosynthesis pathways were also enriched with 32 genes downregulated and four genes up-regulated. Among the 81 enriched GO biological processes, there were four categories related to metal ion homeostasis and three related to metal ion transport. Approximately 400 metabolites were identified in metabolome analysis. The thirteen differentially expressed metabolites (DEMs) were all found down-regulated. The phenylpropanoid biosynthesis pathway was enriched in DEGs and DEMs, indicating a potentially vital role for phenylpropanoids in chlorosis. CONCLUSIONS Chlorophyll production, metal ion metabolism, photosynthesis, and some metabolites in the phenylpropanoid biosynthesis pathway were considerably altered in chlorotic ratoon sugarcane leaves. Our finding revealed the relation between chlorosis and these pathways, which will help expand our mechanistic understanding of ratoon sugarcane chlorosis.
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Affiliation(s)
- Ting Luo
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Zhongfeng Zhou
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Yuchi Deng
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Yegeng Fan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Lihang Qiu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Rongfa Chen
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Haifeng Yan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Huiwen Zhou
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Prakash Lakshmanan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, 400716, China
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, QLD, St Lucia, 4067, Australia
| | - Jianming Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China.
- Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, China.
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi, China.
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China.
| | - Qi Chen
- Nanning New Technology Entrepreneur Center, Nanning, Guangxi, China
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Cui Q, Huang J, Wu F, Li DZ, Zheng L, Hu G, Hu S, Zhang L. Biochemical and transcriptomic analyses reveal that critical genes involved in pigment biosynthesis influence leaf color changes in a new sweet osmanthus cultivar 'Qiannan Guifei'. PeerJ 2021; 9:e12265. [PMID: 34707941 PMCID: PMC8504463 DOI: 10.7717/peerj.12265] [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: 05/21/2020] [Accepted: 09/16/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Osmanthus fragrans (Oleaceae) is one of the most important ornamental plant species in China. Many cultivars with different leaf color phenotypes and good ornamental value have recently been developed. For example, a new cultivar 'Qiannan Guifei', presents a rich variety of leaf colors, which change from red to yellow-green and ultimately to green as leaves develop, making this cultivar valuable for landscaping. However, the biochemical characteristics and molecular mechanisms underlying leaf color changes of these phenotypes have not been elucidated. It has been hypothesized that the biosynthesis of different pigments in O. fragrans might change during leaf coloration. Here, we analyzed transcriptional changes in genes involved in chlorophyll (Chl), flavonoid, and carotenoid metabolic pathways and identified candidate genes responsible for leaf coloration in the new cultivar 'Qiannan Guifei'. METHODS Leaf samples were collected from 'Qiannan Guifei' plants at the red (R), yellow-green (YG) and green (G) leaf stages. We compared the different-colored leaves via leaf pigment concentrations, chloroplast ultrastructure, and transcriptomic data. We further analyzed differentially expressed genes (DEGs) involved in the Chl, flavonoid, and carotenoid metabolic pathways. In addition, we used qRT-PCR to validate expression patterns of the DEGs at the three stages. RESULTS We found that, compared with those at the G stage, chloroplasts at the R and YG stages were less abundant and presented abnormal morphologies. Pigment analyses revealed that the leaves had higher flavonoid and anthocyanin levels at the R stage but lower Chl and carotenoid concentrations. Similarly, Chl and carotenoid concentrations were lower at the YG stage than at the G stage. By using transcriptomic sequencing, we further identified 61 DEGs involved in the three pigment metabolic pathways. Among these DEGs, seven structural genes (OfCHS, OfCHI, OfF3H, OfDFR, OfANS, OfUGT andOf3AT) involved in the flavonoid biosynthesis pathway were expressed at the highest level at the R stage, thereby increasing the biosynthesis of flavonoids, especially anthocyanins. Six putativeOfMYB genes, including three flavonoid-related activators and three repressors, were also highly expressed at the R stage, suggesting that they might coordinately regulate the accumulation of flavonoids, including anthocyanins. Additionally, expressions of the Chl biosynthesis-related genes OfHEMA, OfCHLG and OfCAO and the carotenoid biosynthesis-related genes OfHYB and OfZEP were upregulated from the R stage to the G stage, which increased the accumulation of Chl and carotenoids throughout leaf development. In summary, we screened the candidate genes responsible for the leaf color changes of 'Qiannan Guifei', improved current understanding of the regulatory mechanisms underlying leaf coloration and provided potential targets for future leaf color improvement in O. fragrans.
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Affiliation(s)
- Qi Cui
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Junhua Huang
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Fan Wu
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Dong-ze Li
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Liqun Zheng
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Guang Hu
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Shaoqing Hu
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
| | - Lu Zhang
- School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, China
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The identification of key candidate genes mediating yellow seedling lethality in a Lilium regale mutant. Mol Biol Rep 2020; 47:2487-2499. [PMID: 32124168 DOI: 10.1007/s11033-020-05323-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
Abstract
Leaf color mutants are ideal materials for exploring plant photosynthesis mechanisms, chlorophyll biosynthetic pathways and chloroplast development. The yellow seedling lethal mutant lrysl1 was discovered from self-bred progenies of Lilium regale; however, the mechanism of leaf color mutation remains unclear. In this study, the ultrastructural and physiological features and de novo RNA-Seq data of a L. regale leaf color mutant and wild-type L. regale were investigated. Genetic analysis indicated that the characteristics of the lrysl1 mutant were controlled by a recessive nuclear gene. The chlorophyll a, chlorophyll b and carotenoid contents in the mutant leaves were lower than those in the wild-type leaves. Furthermore, the contents of the chlorophyll precursors aminolevulinic acid (ALA), porphobilinogen (PBG), protoporphyrin IX (ProtoIX), Mg-protoporphyrin IX (Mg-ProtoIX), and protochlorophyll (Pchl) decreased significantly in mutant leaves. Transcriptome data from the mutant and wild type showed that a total of 892 differentially expressed genes were obtained, of which 668 and 224 were upregulated genes and downregulated genes in the mutant, respectively. Almost all genes in the photosynthesis pathway and chlorophyll biosynthetic pathway were downregulated in the mutant, which corroborated the differences in the physiological features mentioned above. Further research indicated that the chloroplasts of the mutant leaves exhibited an abnormal morphology and distribution and that the expression of a gene related to chloroplast development was downregulated. It was concluded that abnormal chloroplast development was the main cause of leaf color mutation in the mutant lrysl1 and that LrGLK was a gene related to chloroplast development in L. regale. This research provides a foundation for further research on the mechanism by which LrGLK regulates chloroplast development in L. regale.
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Xue Y, Ma J, He Y, Yu S, Lin Z, Xiong Y, Rafique F, Jiang F, Sun L, Ma M, Zhou Y, Li X, Huang Z. Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus. PeerJ 2019; 7:e7261. [PMID: 31333908 PMCID: PMC6626515 DOI: 10.7717/peerj.7261] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/31/2019] [Indexed: 11/20/2022] Open
Abstract
Background Ananas comosus var. bracteatus has high ornamental value due to its chimeric leaves. However, the chimeric trait is very unstable in red pineapple plants, and transcriptional variation between the two types of cells (white/green cells) and the molecular mechanism responsible for their albino phenotype remain poorly understood. Methods Comparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of chimeric leaves were performed. Results In total, 1,685 differentially expressed genes (DEGs) (712 upregulated and 973 downregulated) and 1,813 differentially abundant proteins (DAPs) (1,018 with low abundance and 795 with high abundance) were identified. Based on Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the DEGs were mostly involved in carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolism and oxidative phosphorylation, while proteomic analysis revealed that DAPs were mostly related to ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed increased mRNA levels but low abundance of nine proteins level in Whs /Grs related to photosynthetic pigment and photosynthesis. Transcriptional changes, posttranscriptional regulation and translational alterations of key enzymes involved in chlorophyll biosynthesis and photosynthesis may play important roles in the albino parts of chimeric leaves.
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Affiliation(s)
- Yanbin Xue
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yehua He
- Horticultural Biotechnology College of South China Agricultural University, South China Agricultural University, Guangzhou, Guangdong, China
| | - Sanmiao Yu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhen Lin
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yingyuan Xiong
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fatima Rafique
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fuxing Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lingxia Sun
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingdong Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yujue Zhou
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuo Huang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, Sichuan, China
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Zhu L, Wang D, Sun J, Mu Y, Pu W, Ma B, Ren F, Yan W, Zhang Z, Li G, Li Y, Pan Y. Phenotypic and proteomic characteristics of sorghum (Sorghum bicolor) albino lethal mutant sbe6-a1. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:400-410. [PMID: 30981156 DOI: 10.1016/j.plaphy.2019.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 04/01/2019] [Indexed: 05/27/2023]
Abstract
Leaf color mutants are ideal materials for chloroplast development and photosynthetic mechanism research. Here, we characterized an EMS (ethyl methane sulfonate)-mutagenized sorghum (Sorghum bicolor) mutant, sbe6-a1, in which the severe disruption in chloroplast structure and a chlorophyll deficiency promote an albino leaf phenotype and lead to premature death. The proteomic analyses of mutant and its progenitor wild-type (WT) were performed using a Q Exactive plus Orbitrap mass spectrometer and 4,233 proteins were accurately quantitated. The function analysis showed that most of up-regulated proteins in mutant sbe6-a1 had not been well characterized. GO-enrichment analysis of the differentially abundant proteins (DAPs) showed that up-regulated DAPs were significantly enriched in catabolic process and located in mitochondria, while down regulated DAPs were located in chloroplasts and participated in photosynthesis and some other processes. KEGG pathway-enrichment analyses indicated that the degradation and metabolic pathways of fatty acids, as well as some amino acids and secondary metabolites, were significantly enhanced in the mutant sbe6-a1, while photosynthesis-related pathways, some secondary metabolites' biosynthesis and ribosomal pathways were significantly inhibited. Analysis also shows that some DAPs, such as FBAs, MDHs, PEPC, ATP synthase, CABs, CHLM, PRPs, pathogenesis-related protein, sHSP, ACP2 and AOX may be closely associated with the albino phenotype. Our analysis will promote the understanding of the molecular phenomena that result in plant albino phenotypes.
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Affiliation(s)
- Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Daoping Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jiusheng Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; Research Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, PR China
| | - Yongying Mu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Weijun Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Bo Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Fuli Ren
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Wenxiu Yan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Guiying Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Yubin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Yinghong Pan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; The National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, PR China.
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Zhou M, Sng NJ, LeFrois CE, Paul AL, Ferl RJ. Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana. BMC Genomics 2019; 20:205. [PMID: 30866818 PMCID: PMC6416986 DOI: 10.1186/s12864-019-5554-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/21/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of spaceflight aboard the International Space Station (ISS), an environment completely outside their evolutionary history, they respond with unique alterations to their gene expression profile. Identifying the genes important for physiological adaptation to spaceflight and dissecting the biological processes and pathways engaged by plants during spaceflight has helped reveal spaceflight adaptation, and has furthered understanding of terrestrial growth processes. However, the underlying regulatory mechanisms responsible for these changes in gene expression patterns are just beginning to be explored. Epigenetic modifications, such as DNA methylation at position five in cytosine, has been shown to play a role in the physiological adaptation to adverse terrestrial environments, and may play a role in spaceflight as well. RESULTS Whole Genome Bisulfite Sequencing of DNA of Arabidopsis grown on the ISS from seed revealed organ-specific patterns of differential methylation compared to ground controls. The overall levels of methylation in CG, CHG, and CHH contexts were similar between flight and ground DNA, however, thousands of specifically differentially methylated cytosines were discovered, and there were clear organ-specific differences in methylation patterns. Spaceflight leaves had higher methylation levels in CHG and CHH contexts within protein-coding genes in spaceflight; about a fifth of the leaf genes were also differentially regulated in spaceflight, almost half of which were associated with reactive oxygen signaling. CONCLUSIONS The physiological adaptation of plants to spaceflight is likely nuanced by epigenomic modification. This is the first examination of differential genomic methylation from plants grown completely in the spaceflight environment of the ISS in plant growth hardware developed for informing exploration life support strategies. Yet even in this optimized plant habitat, plants respond as if stressed. These data suggest that gene expression associated with physiological adaptation to spaceflight is regulated in part by methylation strategies similar to those engaged with familiar terrestrial stress responses. The differential methylation maps generated here provide a useful reference for elucidating the layers of regulation of spaceflight responses.
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Affiliation(s)
- Mingqi Zhou
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Natasha J. Sng
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Collin E. LeFrois
- 0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Anna-Lisa Paul
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Robert J. Ferl
- 0000 0004 1936 8091grid.15276.37Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Horticultural Sciences Department, University of Florida, Gainesville, FL USA ,0000 0004 1936 8091grid.15276.37Interdisciplinary Center for Biotechnology, University of Florida, Gainesville, FL USA
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Cao P, Ren Y, Liu X, Zhang T, Zhang P, Xiao L, Zhang F, Liu S, Jiang L, Wan J. Purine nucleotide biosynthetic gene GARS controls early chloroplast development in rice (Oryza sativa L.). PLANT CELL REPORTS 2019; 38:183-194. [PMID: 30499032 DOI: 10.1007/s00299-018-2360-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
GARS encodes an enzyme catalyzing the second step of purine nucleotide biosynthesis and plays an important role to maintain the development of chloroplasts in juvenile plants by affecting the expression of plastid-encoded genes. A series of rice white striped mutants were previously described. In this research, we characterized a novel gars mutant with white striped leaves at the seedling stage. By positional cloning, we identified the mutated gene, which encodes a glycinamide ribonucleotide synthetase (GARS) that catalyzes the second step of purine nucleotide biosynthesis. Thylakoid membranes were less abundant in the albinic sectors of mutant seedling leaves compared to the wild type. The expression levels of genes involved in chlorophyll synthesis and photosynthesis were changed. Contents of ATP, ADP, AMP, GTP and GDP, which are crucial for plant growth and development, were decreased in the mutant seedlings. Complementation and CrispR tests confirmed the role of the GARS allele, which was expressed in all rice tissues, especially in the leaves. GARS protein displayed a typical chloroplast location pattern in rice protoplasts. Our results indicated that GARS was involved in chloroplast development at early leaf development by affecting the expression of plastid-encoded genes.
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Affiliation(s)
- Penghui Cao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yakun Ren
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tianyu Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lianjie Xiao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fulin Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight. Int J Mol Sci 2019; 20:ijms20020390. [PMID: 30658467 PMCID: PMC6359015 DOI: 10.3390/ijms20020390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/29/2018] [Accepted: 01/11/2019] [Indexed: 11/16/2022] Open
Abstract
Heat Shock Factor A2 (HsfA2) is part of the Heat Shock Factor (HSF) network, and plays an essential role beyond heat shock in environmental stress responses and cellular homeostatic control. Arabidopsis thaliana cell cultures derived from wild type (WT) ecotype Col-0 and a knockout line deficient in the gene encoding HSFA2 (HSFA2 KO) were grown aboard the International Space Station (ISS) to ascertain whether the HSF network functions in the adaptation to the novel environment of spaceflight. Microarray gene expression data were analyzed using a two-part comparative approach. First, genes differentially expressed between the two environments (spaceflight to ground) were identified within the same genotype, which represented physiological adaptation to spaceflight. Second, gene expression profiles were compared between the two genotypes (HSFA2 KO to WT) within the same environment, which defined genes uniquely required by each genotype on the ground and in spaceflight-adapted states. Results showed that the endoplasmic reticulum (ER) stress and unfolded protein response (UPR) define the HSFA2 KO cells' physiological state irrespective of the environment, and likely resulted from a deficiency in the chaperone-mediated protein folding machinery in the mutant. Results further suggested that additional to its universal stress response role, HsfA2 also has specific roles in the physiological adaptation to spaceflight through cell wall remodeling, signal perception and transduction, and starch biosynthesis. Disabling HsfA2 altered the physiological state of the cells, and impacted the mechanisms induced to adapt to spaceflight, and identified HsfA2-dependent genes that are important to the adaption of wild type cells to spaceflight. Collectively these data indicate a non-thermal role for the HSF network in spaceflight adaptation.
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Liu Z, Lv J, Zhang Z, Li H, Yang B, Chen W, Dai X, Li X, Yang S, Liu L, Ou L, Ma Y, Zou X. Integrative Transcriptome and Proteome Analysis Identifies Major Metabolic Pathways Involved in Pepper Fruit Development. J Proteome Res 2019; 18:982-994. [DOI: 10.1021/acs.jproteome.8b00673] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhoubin Liu
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Junheng Lv
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Zhuqing Zhang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Heng Li
- Shanghai Applied Protein Technology Co. Ltd, Shanghai 200233, P.R. China
| | - Bozhi Yang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Wenchao Chen
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Xiongze Dai
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Xuefeng Li
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Sha Yang
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Li Liu
- Shanghai Applied Protein Technology Co. Ltd, Shanghai 200233, P.R. China
| | - Lijun Ou
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Yanqing Ma
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Xuexiao Zou
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China
- Vegetable Institution of Hunan Academy of Agricultural Science, Changsha 410125, China
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Herranz R, Vandenbrink JP, Villacampa A, Manzano A, Poehlman WL, Feltus FA, Kiss JZ, Medina FJ. RNAseq Analysis of the Response of Arabidopsis thaliana to Fractional Gravity Under Blue-Light Stimulation During Spaceflight. FRONTIERS IN PLANT SCIENCE 2019; 10:1529. [PMID: 31850027 PMCID: PMC6889863 DOI: 10.3389/fpls.2019.01529] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/01/2019] [Indexed: 05/17/2023]
Abstract
Introduction: Traveling to nearby extraterrestrial objects having a reduced gravity level (partial gravity) compared to Earth's gravity is becoming a realistic objective for space agencies. The use of plants as part of life support systems will require a better understanding of the interactions among plant growth responses including tropisms, under partial gravity conditions. Materials and Methods: Here, we present results from our latest space experiments on the ISS, in which seeds of Arabidopsis thaliana were germinated, and seedlings grew for six days under different gravity levels, namely micro-g, several intermediate partial-g levels, and 1g, and were subjected to irradiation with blue light for the last 48 h. RNA was extracted from 20 samples for subsequent RNAseq analysis. Transcriptomic analysis was performed using the HISAT2-Stringtie-DESeq pipeline. Differentially expressed genes were further characterized for global responses using the GEDI tool, gene networks and for Gene Ontology (GO) enrichment. Results: Differential gene expression analysis revealed only one differentially expressed gene (AT4G21560, VPS28-1 a vacuolar protein) across all gravity conditions using FDR correction (q < 0.05). However, the same 14 genes appeared differentially expressed when comparing either micro-g, low-g level (< 0.1g) or the Moon g-level with 1g control conditions. Apart from these 14-shared genes, the number of differentially expressed genes was similar in microgravity and the Moon g-level and increased in the intermediate g-level (< 0.1g), but it was then progressively reduced as the difference with the Earth gravity became smaller. The GO groups were differentially affected at each g-level: light and photosynthesis GO under microgravity, genes belonged to general stress, chemical and hormone responses under low-g, and a response related to cell wall and membrane structure and function under the Moon g-level. Discussion: Transcriptional analyses of plants under blue light stimulation suggests that root blue-light phototropism may be enough to reduce the gravitational stress response caused by the lack of gravitropism in microgravity. Competition among tropisms induces an intense perturbation at the micro-g level, which shows an extensive stress response that is progressively attenuated. Our results show a major effect on cell wall/membrane remodeling (detected at the interval from the Moon to Mars gravity), which can be potentially related to graviresistance mechanisms.
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Affiliation(s)
- Raúl Herranz
- Plant Microgravity Lab, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
- *Correspondence: Raúl Herranz,
| | - Joshua P. Vandenbrink
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
- School of Biological Sciences, Louisiana Tech University, Ruston, LA, United States
| | - Alicia Villacampa
- Plant Microgravity Lab, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Aránzazu Manzano
- Plant Microgravity Lab, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - William L. Poehlman
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
| | - Frank Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
| | - John Z. Kiss
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
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Wu H, Shi N, An X, Liu C, Fu H, Cao L, Feng Y, Sun D, Zhang L. Candidate Genes for Yellow Leaf Color in Common Wheat ( Triticum aestivum L.) and Major Related Metabolic Pathways according to Transcriptome Profiling. Int J Mol Sci 2018; 19:ijms19061594. [PMID: 29843474 PMCID: PMC6032196 DOI: 10.3390/ijms19061594] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 01/05/2023] Open
Abstract
The photosynthetic capacity and efficiency of a crop depends on the biosynthesis of photosynthetic pigments and chloroplast development. However, little is known about the molecular mechanisms of chloroplast development and chlorophyll (Chl) biosynthesis in common wheat because of its huge and complex genome. Ygm, a spontaneous yellow-green leaf color mutant of winter wheat, exhibits reduced Chl contents and abnormal chloroplast development. Thus, we searched for candidate genes associated with this phenotype. Comparative transcriptome profiling was performed using leaves from the yellow leaf color type (Y) and normal green color type (G) of the Ygm mutant progeny. We identified 1227 differentially expressed genes (DEGs) in Y compared with G (i.e., 689 upregulated genes and 538 downregulated genes). Gene ontology and pathway enrichment analyses indicated that the DEGs were involved in Chl biosynthesis (i.e., magnesium chelatase subunit H (CHLH) and protochlorophyllide oxidoreductase (POR) genes), carotenoid biosynthesis (i.e., β-carotene hydroxylase (BCH) genes), photosynthesis, and carbon fixation in photosynthetic organisms. We also identified heat shock protein (HSP) genes (sHSP, HSP70, HSP90, and DnaJ) and heat shock transcription factor genes that might have vital roles in chloroplast development. Quantitative RT-PCR analysis of the relevant DEGs confirmed the RNA-Seq results. Moreover, measurements of seven intermediate products involved in Chl biosynthesis and five carotenoid compounds involved in carotenoid-xanthophyll biosynthesis confirmed that CHLH and BCH are vital enzymes for the unusual leaf color phenotype in Y type. These results provide insights into leaf color variation in wheat at the transcriptional level.
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Affiliation(s)
- Huiyu Wu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Narong Shi
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Xuyao An
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Cong Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Hongfei Fu
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
| | - Li Cao
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Yi Feng
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Daojie Sun
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
| | - Lingli Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China.
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Xie F, Yuan JL, Li YX, Wang CJ, Tang HY, Xia JH, Yang QY, Wan ZJ. Transcriptome Analysis Reveals Candidate Genes Associated with Leaf Etiolation of a Cytoplasmic Male Sterility Line in Chinese Cabbage (Brassica Rapa L. ssp. Pekinensis). Int J Mol Sci 2018; 19:E922. [PMID: 29561749 PMCID: PMC5979472 DOI: 10.3390/ijms19040922] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 12/26/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is universally utilized in cruciferous vegetables. However, the Chinese cabbage hau CMS lines, obtained by interspecific hybridization and multiple backcrosses of the Brassica juncea (B. juncea) CMS line and Chinese cabbage, show obvious leaf etiolation, and the molecular mechanism of etiolation remains elusive. Here, the ultrastructural and phenotypic features of leaves from the Chinese cabbage CMS line 1409A and maintainer line 1409B are analyzed. The results show that chloroplasts of 1409A exhibit abnormal morphology and distribution. Next, RNA-sequencing (RNA-Seq) is used to identify 485 differentially expressed genes (DEGs) between 1409A and 1409B, and 189 up-regulated genes and 296 down-regulated genes are found. Genes that affect chloroplasts development, such as GLK1 and GLK2, and chlorophyll biosynthesis, such as PORB, are included in the down-regulated DEGs. Quantitative real-time PCR (qRT-PCR) analysis validate that the expression levels of these genes are significantly lower in 1409A than in 1409B. Taken together, these results demonstrate that leaf etiolation is markedly affected by chloroplast development and pigment biosynthesis. This study provides an effective foundation for research on the molecular mechanisms of leaf etiolation of the hau CMS line in Chinese cabbage (Brassica rapa L. ssp. pekinensis).
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Affiliation(s)
- Fei Xie
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jia-Lan Yuan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yi-Xiao Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Can-Jie Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hong-Yu Tang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jun-Hui Xia
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qing-Yong Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zheng-Jie Wan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
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