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Sun S, Yi C, Ma J, Wang S, Peirats-Llobet M, Lewsey MG, Whelan J, Shou H. Analysis of Spatio-Temporal Transcriptome Profiles of Soybean ( Glycine max) Tissues during Early Seed Development. Int J Mol Sci 2020; 21:E7603. [PMID: 33066688 PMCID: PMC7589660 DOI: 10.3390/ijms21207603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 01/17/2023] Open
Abstract
Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.
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Affiliation(s)
- Shuo Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
| | - Changyu Yi
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
| | - Jing Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
| | - Shoudong Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China;
| | - Marta Peirats-Llobet
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
| | - Mathew G. Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia;
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - James Whelan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
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Redox poise and metabolite changes in bread wheat seeds are advanced by priming with hot steam. Biochem J 2018; 475:3725-3743. [PMID: 30401685 DOI: 10.1042/bcj20180632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/24/2018] [Accepted: 11/02/2018] [Indexed: 12/20/2022]
Abstract
Fast and uniform germination is key to agricultural production and can be achieved by seed 'priming' techniques. Here, we characterised the responses of bread wheat (Triticum aestivum L.) seeds to a hot steam treatment ('BioFlash'), which accelerated water uptake, resulting in faster germination and seedling growth, typical traits of primed seed. Before the completion of germination, metabolite profiling of seeds revealed advanced accumulation of several amino acids (especially cysteine and serine), sugars (ribose, glucose), and organic acids (glycerate, succinate) in hot steam-treated seeds, whereas sugar alcohols (e.g. arabitol, mannitol) and trehalose decreased in all seeds. Tocochromanols (the 'vitamin E family') rose independently of the hot steam treatment. We further assessed shifts in the half-cell reduction potentials of low-molecular-weight (LMW) thiol-disulfide redox couples [i.e. glutathione disulfide (GSSG)/glutathione (GSH) and cystine/cysteine], alongside the activities of the reactive oxygen species (ROS)-processing enzyme superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase. Upon the first 4 h of imbibition, a rapid conversion of LMW disulfides to thiols occurred. Completion of germination was associated with a re-oxidation of the LMW thiol-disulfide cellular redox environment, before more reducing conditions were re-established during seedling growth, accompanied by an increase in all ROS-processing enzyme activities. Furthermore, changes in the thiol-disulfide cellular redox state were associated to specific stages of wheat seed germination. In conclusion, the priming effect of the hot steam treatment advanced the onset of seed metabolism, including redox shifts associated with germination and seedling growth.
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Mateeva Z. Potato Spindle Tuber Viroid (PSTV) does not Inhibit Ribosomal RNA Synthesis in Tomato. BIOTECHNOL BIOTEC EQ 1991. [DOI: 10.1080/13102818.1991.10818639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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6
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Jendrisak J. The use of alpha-amanitin to inhibit in vivo RNA synthesis and germination in wheat embryos. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(18)43529-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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7
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Dependence of protein synthesis on RNA synthesis during the early hours of germination of wheat embryos. Nature 1979. [DOI: 10.1038/277066a0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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CHEUNG CHIP, SUHADOLNIK ROBERTJ. Regulation of RNA synthesis in early germination of isolated wheat (Triticum aestivum L) embryo. Nature 1978. [DOI: 10.1038/271357a0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Brökelmann J. Changes in the morphology of ribosomes in uterine epithelial cells under various hormonal conditions. Cell Tissue Res 1977; 179:517-30. [PMID: 558826 DOI: 10.1007/bf00219853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ultrastructural morphology of "free" cytoplasmic ribosomes of rat uterine epithelial cells was studied during diestrus, estrus, after ovariectomy, and after estradiol-17 beta administration to rats that were ovariectomized 1 to 25 weeks before hormone treatment. A change in size and contrast of ribosomes was observed concomitant with a transition from pre-existing monosomes to polysomes depending on the dose of estradiol and its route of application. In 3 weeks ovariectomized rats these changes in ribosomal granules take place at approximately the same time (30-45 min) when synthesis of "induced protein" was described biochemically. The morphological events after estradiol administration are discussed with respect to a primary site of estrogen action.
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Grzelczak Z, Buchowicz J. A comparison of the activation of ribosomal RNA synthesis during germination of isolated and non-isolated embryos of Triticum aestivum L. PLANTA 1977; 134:263-265. [PMID: 24419780 DOI: 10.1007/bf00384191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/1976] [Accepted: 12/17/1976] [Indexed: 06/03/2023]
Abstract
Incorporation of [(14)C]uridine into ribosomal RNA and ribosomal RNA precursor fractions was studied in isolated wheat embryos and in embryos remaining within the intact grains during germination. In isolated embryos, radioactive 25S and 18S as well as 31S RNA species appeared already within the first 3 h of germination. In non-isolated embryos, radioactivity could be detected in the mature ribosomal and pre-ribosomal RNA fractions only after 6 h and 12 h germination, respectively. It is concluded that transcription of ribosomal sequences is activated almost immediately in isolated wheat embryos but remains repressed for several hours when the embryo germinates under natural physiological conditions.
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Affiliation(s)
- Z Grzelczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Ul. Rakowiecka 36, P-02-532, Warszawa, Poland
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Hecker M, Köhler KH, Wiedmann M. Reactivation of Ribonucleic Acid Synthesis during Early Germination of Agrostemma githago Embryos. ACTA ACUST UNITED AC 1977. [DOI: 10.1016/s0015-3796(17)30329-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Hecker M. [Studies on stable and during early imbibition phases synthesized poly(A)-RNA of Agrostemma githago embryos (author's transl)]. EXPERIENTIA 1976; 32:50-3. [PMID: 1248588 DOI: 10.1007/bf01932618] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RNA isolated from dry embryos of Agrostemma githago seeds contains poly(A)-sequences, but in very small amounts. In the early phase of imbibition, an intensive synthesis of poly(A)-containing RNA is brought about. The importance of this synthesis of poly(A)-RNA is discussed.
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Bhat SP, Padayatty JD. Transcriptional events during early phase of germination of rice embryos. Nature 1975; 256:227-8. [PMID: 1152993 DOI: 10.1038/256227a0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Sen S, Payne PI, Osborne DJ. Early ribonucleic acid synthesis during the germination of rye (Secale cereale) embryos and the relationship to early protein synthesis. Biochem J 1975; 148:381-7. [PMID: 1200984 PMCID: PMC1165555 DOI: 10.1042/bj1480381] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Incorporation studies with radioactive precursors showed that synthesis of protein and RNA is initiated in germinating embryos of rye within the first hour of imbibition of water. By polyacrylamide-gel fractionations of radioactive nucleic acid components, the appearance of products of transcription of the genome was shown to follow the sequence: heterogeneous (ribonuclease-sensitive) RNA, 4S and 5S RNA by 20min, 31S and 25S rRNA by 40min, and 18S RNA by 60min. "Fingerprint' analysis of T1-ribonuclease digests show that all the large oligonucleotides present in 25S and 18S RNA are present in the 31S species, indicating that 31S RNA is the precursor rRNA molecule to both 25S and 18S RNA. The importance of these early RNA syntheses and in particular the possible template function of the heterogeneous RNA is discussed in relation to the concept of long-lived mRNA and the coding for protein synthesis in the first hours of germination.
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Ahmed ZU, Kamra OP. DNA content of dormant barley leaf nuclei and the synthesis of RNA and DNA during germination. FEBS Lett 1975; 51:277-80. [PMID: 1123062 DOI: 10.1016/0014-5793(75)80906-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Robinson NE, Bryant JA. Onset of nucleic acid synthesis during germination of Pisum sativum L. PLANTA 1975; 127:63-68. [PMID: 24430285 DOI: 10.1007/bf00388863] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/1975] [Accepted: 07/28/1975] [Indexed: 06/03/2023]
Abstract
Measurments of total nucleic acid content of the embryonic axis indicated that massive net synthesis of both DNA and RNA was initiated at approximately 30 h after the onset of germination. The onset of net nucleic acid synthesis was marked by an increase in the rate of incorporation of [(3)H]thymidine into DNA, and of [(3)H]orotic acid and [(3)H]uridine into both DNA and RNA. rRNA was usually more heavily labelled than tRNA, but was not preferentially accumulated, suggesting a grater rate of turnover of rRNA than tRNA. Some incorporation of precursors occurred prior to the onset of net nucleic acid synthesis, particularly into RNA. This was taken to represent nucleic acid turnover. There was no evidence that the "scavenging" pathways for nucleotide biosynthesis were more important than the "normal" pathways in contributing precursors for net nucleic acid synthesis.
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Affiliation(s)
- N E Robinson
- Nottingham University School of Agriculture, Sutton Bonington, LE12 5RD, Loughborough, U.K
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Dobrzanska M, Tomaszewski M, Grzelczak Z, Rejman E, Buchowicz J. Cascade activation of genome transcription in wheat. Nature 1973; 244:507-9. [PMID: 4583114 DOI: 10.1038/244507a0] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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21
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Spore germination and ribosomal activity in the rust fungi. II. Variable properties of ribosomes in the Uredinales. ACTA ACUST UNITED AC 1973. [DOI: 10.1016/0048-4059(73)90030-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Verma DP, Marcus A. Regulation of RNA synthesis in plant cell culture: delayed synthesis of ribosomal RNA during transition from the stationary phase to active growth. Dev Biol 1973; 30:104-14. [PMID: 4697743 DOI: 10.1016/0012-1606(73)90050-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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23
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Hallam ND, Roberts BE, Osborne DJ. Embryogenesis and germination in rye (Secale cereale L.) : II. Biochemical and fine structural changes during germination. PLANTA 1972; 105:293-309. [PMID: 24477844 DOI: 10.1007/bf00386767] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/1972] [Indexed: 06/03/2023]
Abstract
When rye embryos imbibe water they rapidly return to a condition of biochemical and structural complexity. Three stages of imbibition can be recognised: Phase I a short period (10 min) of physical wetting; Phase II a longer period (1 h) when little further imbibition occurs, followed by Phase III a continuous phase of active water uptake. The latter coincides with an increase in respiration rate and an increase both in the number of mitochondria and of cristae within them. Changes in fine structure become evident in all organelles in Phase III, after 2 h of imbibition. In the unimbibed embryo endoplasmic reticulum is present only as short crescents associated with electron lucent bodies, but in Phase III the endoplasmic reticulum proliferates to form many surrounding cirlets. After 6 h these circlets become fewer and instead the endoplasmic reticulum is seen in close association with the nuclear membrane. Concurrently incorporation of radioactive uridine and thymidine is first detectible. This suggests that the large increase in protein synthesis occurs on new ribosomes present on the reticulum associated with the nuclear membrane. For the first 6 h protein synthesis must occur either on polysomes within the dense packing of ribosomes or on these circlets of endoplasmic reticulum associated with electron lucent bodies.
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Affiliation(s)
- N D Hallam
- Agricultural Research Council Unit of Developmental Botany, Cambridge, UK
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24
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Seitz U, Seitz U. [Transport of newly synthesized rRNA from the nucleus to the cytoplasm in freely suspended cells of parsley (Petroselinum sativum)]. PLANTA 1972; 106:141-148. [PMID: 24477955 DOI: 10.1007/bf00383993] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/1972] [Indexed: 06/03/2023]
Abstract
A rapidly labelled rRNA precursor can be detected in callus cells of Petroselinum sativum grown on a liquid synthetic medium. Its molecular weight has been calculated to be 2.3×10(6). This value agrees with that of the rRNA precursor from other plant material. In order to follow the synthesis and processing of rRNA in time and to correlate single steps in this process with cell organelles it was necessary to obtain pure fractions of nuclei and ribosomes. The isolation method for nuclei is given in detail. The nucleic acids are separated on polyacrylamide gels of low acrylamide concentration. Pulse-chase experiments show that the rRNA precursor is split into two fragments within the nucleus: an 18S and a 25S component. The 18S RNA leaves the nucleus rapidly. It is already found quantitatively in the ribosomal fraction after 30-60 min chase. At that time the 25S RNA is still within the nucleus; it appears much later in the ribosomes. Since the increase in ribosomal label occurs simultaneously with the decrease in nuclear label, it is concluded that there is no degradation of 18S RNA within the nucleus. Apparently there are two distinct transport mechanisms with different kinetics for the two RNA components.
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Affiliation(s)
- U Seitz
- Institut für Biologie der Universität Tübingen, Tübingen, Deutschland
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Takahashi N, Shimada T, Higo M, Higo S, Tanifuji S. Ribosomal precursor particles from plant nucleoli. BIOCHIMICA ET BIOPHYSICA ACTA 1972; 262:502-13. [PMID: 4623046 DOI: 10.1016/0005-2787(72)90494-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Ssymank V. Influence of nitrogen deficiency on uridine incorporation into ribosomes in the green alga Chlorella. ARCHIV FUR MIKROBIOLOGIE 1972; 82:311-24. [PMID: 5025910 DOI: 10.1007/bf00424935] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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