Relevant bibliographies by topics / Plant development, Microproteins, Molecular Biology / Journal articles

Journal articles on the topic 'Plant development, Microproteins, Molecular Biology'

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Author: Grafiati
Published: 11 March 2023

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1

Bhati, Kaushal Kumar, Valdeko Kruusvee, Daniel Straub, Anil Kumar Nalini Chandran, Ki-Hong Jung, and Stephan Wenkel. "Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation." G3: Genes|Genomes|Genetics 10, no. 10 (August 6, 2020): 3709–17. http://dx.doi.org/10.1534/g3.120.400794.

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MicroProteins are a class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or which they relate to. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterized microProteins in Arabidopsis thaliana, studies from more complex plant genomes are still missing. We have previously developed miPFinder, a software for identifying microProteins from annotated genomes. Here we present an improved version where we have updated the algorithm to increase its accuracy and speed, and used it to analyze five cereal crop genomes – wheat, rice, barley, maize and sorghum. We found 20,064 potential microProteins from a total of 258,029 proteins in these five organisms, of which approximately 2000 are high-confidence, i.e., likely to function as actual microProteins. Gene ontology analysis of these 2000 microProtein candidates revealed their roles in stress, light and growth responses, hormone signaling and transcriptional regulation. Using a recently developed rice gene co-expression database, we analyzed 347 potential rice microProteins that are also conserved in other cereal crops and found over 50 of these rice microProteins to be co-regulated with their identified interaction partners. Overall, our study reveals a rich source of biotechnologically interesting small proteins that regulate fundamental plant processes such a growth and stress response that could be utilized in crop bioengineering.
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2

Aviña-Padilla, Katia, Octavio Zambada-Moreno, Gabriel Emilio Herrera-Oropeza, Marco A. Jimenez-Limas, Peter Abrahamian, Rosemarie W. Hammond, and Maribel Hernández-Rosales. "Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches." International Journal of Molecular Sciences 23, no. 11 (May 26, 2022): 5983. http://dx.doi.org/10.3390/ijms23115983.

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Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.
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3

Bhati, Kaushal Kumar, Ulla Dolde, and Stephan Wenkel. "MicroProteins: Expanding functions and novel modes of regulation." Molecular Plant 14, no. 5 (May 2021): 705–7. http://dx.doi.org/10.1016/j.molp.2021.01.006.

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4

Wu, Qingqing, Shangwei Zhong, and Hui Shi. "MicroProteins: Dynamic and accurate regulation of protein activity." Journal of Integrative Plant Biology 64, no. 4 (February 28, 2022): 812–20. http://dx.doi.org/10.1111/jipb.13229.

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5

Eguen, Tenai, Jorge Gomez Ariza, Vittoria Brambilla, Bin Sun, Kaushal Kumar Bhati, Fabio Fornara, and Stephan Wenkel. "Control of flowering in rice through synthetic microProteins." Journal of Integrative Plant Biology 62, no. 6 (October 16, 2019): 730–36. http://dx.doi.org/10.1111/jipb.12865.

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6

Scheres, B. "Rooting plant development." Development 140, no. 5 (February 12, 2013): 939–41. http://dx.doi.org/10.1242/dev.093559.

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7

Clark, Steven. "Plant Development." Cell 114, no. 1 (July 2003): 11–12. http://dx.doi.org/10.1016/s0092-8674(03)00516-6.

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8

Wu, Gang. "Plant MicroRNAs and Development." Journal of Genetics and Genomics 40, no. 5 (May 2013): 217–30. http://dx.doi.org/10.1016/j.jgg.2013.04.002.

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9

Hanke, David E. "Plant growth and development: A molecular approach." Trends in Cell Biology 4, no. 11 (November 1994): 406–7. http://dx.doi.org/10.1016/0962-8924(94)90056-6.

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10

Leyser, Ottoline. "Plant development: a Special Issue." Development 143, no. 18 (September 13, 2016): 3223. http://dx.doi.org/10.1242/dev.143594.

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11

Kieber, Joseph J., and G. Eric Schaller. "Cytokinin signaling in plant development." Development 145, no. 4 (February 15, 2018): dev149344. http://dx.doi.org/10.1242/dev.149344.

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12

Reski, R. "Development, Genetics and Molecular Biology of Mosses." Botanica Acta 111, no. 1 (February 1998): 1–15. http://dx.doi.org/10.1111/j.1438-8677.1998.tb00670.x.

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13

Duckett, Catherine M., and John C. Gray. "Illuminating plant development." BioEssays 17, no. 2 (February 1995): 101–3. http://dx.doi.org/10.1002/bies.950170204.

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14

Trewavas, A. J. "Signalling Plant Development." BioEssays 21, no. 10 (September 23, 1999): 893. http://dx.doi.org/10.1002/(sici)1521-1878(199910)21:10<893::aid-bies14>3.0.co;2-6.

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15

Pickersgill, H. "Asymmetric Division in Plant Development." Science Signaling 2, no. 56 (February 3, 2009): ec45-ec45. http://dx.doi.org/10.1126/scisignal.256ec45.

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16

De Coninck, Tibo, Koen Gistelinck, Henry C. Janse van Rensburg, Wim Van den Ende, and Els J. M. Van Damme. "Sweet Modifications Modulate Plant Development." Biomolecules 11, no. 5 (May 18, 2021): 756. http://dx.doi.org/10.3390/biom11050756.

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Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants’ perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.
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17

Trewavas, A. J. "Plant growth substances and development." Trends in Biochemical Sciences 12 (January 1987): 258. http://dx.doi.org/10.1016/0968-0004(87)90127-7.

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18

Walton, Jonathan D. "Renaissance of Plant Biology The Molecular Basis of Plant Development Robert Goldberg." BioScience 40, no. 3 (March 1990): 208–9. http://dx.doi.org/10.2307/1311368.

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19

de Folter, Stefan. "Plant Biology: Gynoecium Development with Style." Current Biology 30, no. 23 (December 2020): R1420—R1422. http://dx.doi.org/10.1016/j.cub.2020.10.040.

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20

Trewavas, A. J. "Molecular and Cellular Aspects of Calcium in Plant Development." Development 103, no. 4 (August 1, 1988): 619–23. http://dx.doi.org/10.1242/dev.103.4.619_3.

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21

Ruan, Yong-Ling, John W. Patrick, and Hans Weber. "Assimilate Partitioning and Plant Development." Molecular Plant 3, no. 6 (November 2010): 941. http://dx.doi.org/10.1093/mp/ssq069.

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22

Yeoman, M. M. "An introduction to plant cell development." Trends in Biochemical Sciences 11, no. 3 (March 1986): 123. http://dx.doi.org/10.1016/0968-0004(86)90055-1.

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23

Ljung, K. "Auxin metabolism and homeostasis during plant development." Development 140, no. 5 (February 12, 2013): 943–50. http://dx.doi.org/10.1242/dev.086363.

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24

Godin, Christophe, Christophe Golé, and Stéphane Douady. "Phyllotaxis as geometric canalization during plant development." Development 147, no. 19 (October 1, 2020): dev165878. http://dx.doi.org/10.1242/dev.165878.

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ABSTRACTWhy living forms develop in a relatively robust manner, despite various sources of internal or external variability, is a fundamental question in developmental biology. Part of the answer relies on the notion of developmental constraints: at any stage of ontogenesis, morphogenetic processes are constrained to operate within the context of the current organism being built. One such universal constraint is the shape of the organism itself, which progressively channels the development of the organism toward its final shape. Here, we illustrate this notion with plants, where strikingly symmetric patterns (phyllotaxis) are formed by lateral organs. This Hypothesis article aims first to provide an accessible overview of phyllotaxis, and second to argue that the spiral patterns in plants are progressively canalized from local interactions of nascent organs. The relative uniformity of the organogenesis process across all plants then explains the prevalence of certain patterns in plants, i.e. Fibonacci phyllotaxis.
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25

Lam, Eric. "Controlled cell death, plant survival and development." Nature Reviews Molecular Cell Biology 5, no. 4 (April 2004): 305–15. http://dx.doi.org/10.1038/nrm1358.

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26

Considine, Michael J., and Christine H. Foyer. "Redox Regulation of Plant Development." Antioxidants & Redox Signaling 21, no. 9 (September 20, 2014): 1305–26. http://dx.doi.org/10.1089/ars.2013.5665.

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27

Bergmann, Dominique C. "Asymmetry and patterning in plant epidermal development." Developmental Biology 319, no. 2 (July 2008): 472. http://dx.doi.org/10.1016/j.ydbio.2008.05.027.

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28

Vasil, Indra K. "Plant tissue culture and molecular biology as tools in understanding plant development and in plant improvement." Current Opinion in Biotechnology 2, no. 2 (April 1991): 158–63. http://dx.doi.org/10.1016/0958-1669(91)90004-o.

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29

Murray, J. "Integrating cell division and plant development." Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 150, no. 3 (July 2008): S141. http://dx.doi.org/10.1016/j.cbpa.2008.04.350.

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30

Hala, M., R. Cole, L. Synek, E. Drdova, I. Kulich, T. Pecenkova, F. Hochholdinger, F. Cvrckova, J. Fowler, and V. Zarsky. "Exocyst complex functions in plant development." Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 150, no. 3 (July 2008): S189. http://dx.doi.org/10.1016/j.cbpa.2008.04.511.

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31

Prusinkiewicz, Przemyslaw. "Constraints of space in plant development." Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 153, no. 2 (June 2009): S219. http://dx.doi.org/10.1016/j.cbpa.2009.04.539.

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32

Hathway, D. E. "PLANT GROWTH AND DEVELOPMENT IN MOLECULAR PERSPECTIVE." Biological Reviews 65, no. 4 (November 1990): 473–515. http://dx.doi.org/10.1111/j.1469-185x.1990.tb01234.x.

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33

Kaufmann, Kerstin, Cezary Smaczniak, Sacco de Vries, Gerco C. Angenent, and Rumyana Karlova. "Proteomics insights into plant signaling and development." PROTEOMICS 11, no. 4 (January 17, 2011): 744–55. http://dx.doi.org/10.1002/pmic.201000418.

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34

Dolan, L. "New insights into plant development in New England." Development 131, no. 21 (November 1, 2004): 5215–20. http://dx.doi.org/10.1242/dev.01439.

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35

Venugopala Reddy, G. "Interplay between cell cycle regulation and plant development." Development 135, no. 24 (December 15, 2008): 3980–81. http://dx.doi.org/10.1242/dev.023499.

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36

Long, J. A. "Plant development: new models and approaches bring progress." Development 133, no. 23 (November 1, 2006): 4609–12. http://dx.doi.org/10.1242/dev.02676.

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37

Surpin, Marci, and Natasha Raikhel. "Traffic jams affect plant development and signal transduction." Nature Reviews Molecular Cell Biology 5, no. 2 (February 1, 2004): 100–109. http://dx.doi.org/10.1038/nrm1311.

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38

Laux, Thomas. "Can Genetics Explain Plant Development?" Cell 96, no. 4 (February 1999): 466–67. http://dx.doi.org/10.1016/s0092-8674(00)80640-6.

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39

Hake, Sarah. "Tissue interactions in plant development." BioEssays 6, no. 2 (February 1987): 58–60. http://dx.doi.org/10.1002/bies.950060204.

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40

Dolan, Liam. "Plant Evolution: TALES of Development." Cell 133, no. 5 (May 2008): 771–73. http://dx.doi.org/10.1016/j.cell.2008.05.016.

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41

Goldberg, Robert B. "Emerging patterns of plant development." Cell 49, no. 3 (May 1987): 298–300. http://dx.doi.org/10.1016/0092-8674(87)90278-9.

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42

Huelskamp, Martin. "Book review:Mechanisms in plant development." BioEssays 26, no. 1 (2003): 106. http://dx.doi.org/10.1002/bies.10396.

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43

Agustí, Javier, and Miguel A. Blázquez. "Plant vascular development: mechanisms and environmental regulation." Cellular and Molecular Life Sciences 77, no. 19 (March 19, 2020): 3711–28. http://dx.doi.org/10.1007/s00018-020-03496-w.

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44

POETHIG, R. S., A. PERAGINE, M. YOSHIKAWA, C. HUNTER, M. WILLMANN, and G. WU. "The Function of RNAi in Plant Development." Cold Spring Harbor Symposia on Quantitative Biology 71 (January 1, 2006): 165–70. http://dx.doi.org/10.1101/sqb.2006.71.030.

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45

Ahmad, Ayaz, Yong Zhang, and Xiao-Feng Cao. "Decoding the Epigenetic Language of Plant Development." Molecular Plant 3, no. 4 (July 2010): 719–28. http://dx.doi.org/10.1093/mp/ssq026.

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46

Jin, Danfeng, Yue Wang, Yuhua Zhao, and Ming Chen. "MicroRNAs and Their Cross-Talks in Plant Development." Journal of Genetics and Genomics 40, no. 4 (April 2013): 161–70. http://dx.doi.org/10.1016/j.jgg.2013.02.003.

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47

Planas-Riverola, Ainoa, Aditi Gupta, Isabel Betegón-Putze, Nadja Bosch, Marta Ibañes, and Ana I. Caño-Delgado. "Brassinosteroid signaling in plant development and adaptation to stress." Development 146, no. 5 (March 1, 2019): dev151894. http://dx.doi.org/10.1242/dev.151894.

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48

Surpin, Marci, and Natasha Raikhel. "Correction: Traffic jams affect plant development and signal transduction." Nature Reviews Molecular Cell Biology 5, no. 4 (April 2004): 329. http://dx.doi.org/10.1038/nrm1383.

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49

The Plant Ontology Consortium. "The Plant Ontology™Consortium and Plant Ontologies." Comparative and Functional Genomics 3, no. 2 (2002): 137–42. http://dx.doi.org/10.1002/cfg.154.

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The goal of the Plant Ontology™Consortium is to produce structured controlled vocabularies, arranged in ontologies, that can be applied to plant-based database information even as knowledge of the biology of the relevant plant taxa (e.g. development, anatomy, morphology, genomics, proteomics) is accumulating and changing. The collaborators of the Plant Ontology™Consortium (POC) represent a number of core participant database groups. The Plant Ontology™Consortium is expanding the paradigm of the Gene Ontology™Consortium (http://www.geneontology.org). Various trait ontologies (agronomic traits, mutant phenotypes, phenotypes, traits, and QTL) and plant ontologies (plant development, anatomy [incl. morphology]) for several taxa (Arabidopsis, maize/corn/Zea mays and rice/Oryza) are under development. The products of the Plant Ontology™Consortium will be open-source.
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50

Loughman, B. C. "Second messengers in plant growth and development." FEBS Letters 253, no. 1-2 (August 14, 1989): 299. http://dx.doi.org/10.1016/0014-5793(89)80991-3.

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