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Omelyanchuk NA, Lavrekha VV, Bogomolov AG, Dolgikh VA, Sidorenko AD, Zemlyanskaya EV. Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1905. [PMID: 39065433 PMCID: PMC11280061 DOI: 10.3390/plants13141905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.
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Affiliation(s)
- Nadya A. Omelyanchuk
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Viktoriya V. Lavrekha
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton G. Bogomolov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Vladislav A. Dolgikh
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksandra D. Sidorenko
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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López-Ruíz BA, García-Ponce B, de la Paz Sánchez M, Álvarez-Buylla ER, Urrutia AO, Garay-Arroyo A. Genome-wide association studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity. Mol Biol Rep 2024; 51:763. [PMID: 38874813 PMCID: PMC11178574 DOI: 10.1007/s11033-024-09623-1] [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: 01/24/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Arabidopsis thaliana primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth. METHODS AND RESULTS We used 639 accessions from nine different studies under control conditions and performed different GWAS tests. We found that primary root growth changes were associated with 41 genes, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown lines of two genes, Suppressor of Gene Silencing (SGS3), involved in tasiRNA processing, and a gene with a Sterile Alpha Motif (SAM) motif named NOJOCH MOOTS (NOJO), confirmed their role as repressors of primary root growth, none has been shown to participate in this developmental process before. CONCLUSIONS In summary, our GWAS analysis of different available studies identified new genes that participate in primary root growth; two of them were identified as repressors of primary root growth.
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Affiliation(s)
- Brenda Anabel López-Ruíz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México
- Centro de Ciencias de la Complejidad, UNAM, CDMX, México
| | - Araxi O Urrutia
- Laboratorio de Genómica Evolutiva y Funcional, Instituto de Ecología, UNAM, Mexico City, México.
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK.
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Depto. de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), C. U. CDMX, México.
- Centro de Ciencias de la Complejidad, UNAM, CDMX, México.
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Pierre PM, Preyanka M, Zachary H, Zhang L, Lukas B, Matias GF, Kian F, Callum G, Wolfgang B. Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:632-646. [PMID: 37871136 PMCID: PMC10841685 DOI: 10.1111/tpj.16493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/22/2023] [Indexed: 10/25/2023]
Abstract
Plants are sessile organisms that constantly adapt to their changing environment. The root is exposed to numerous environmental signals ranging from nutrients and water to microbial molecular patterns. These signals can trigger distinct responses including the rapid increase or decrease of root growth. Consequently, using root growth as a readout for signal perception can help decipher which external cues are perceived by roots, and how these signals are integrated. To date, studies measuring root growth responses using large numbers of roots have been limited by a lack of high-throughput image acquisition, poor scalability of analytical methods, or low spatiotemporal resolution. Here, we developed the Root Walker pipeline, which uses automated microscopes to acquire time-series images of many roots exposed to controlled treatments with high spatiotemporal resolution, in conjunction with fast and automated image analysis software. We demonstrate the power of Root Walker by quantifying root growth rate responses at different time and throughput scales upon treatment with natural auxin and two mitogen-associated protein kinase cascade inhibitors. We find a concentration-dependent root growth response to auxin and reveal the specificity of one MAPK inhibitor. We further demonstrate the ability of Root Walker to conduct genetic screens by performing a genome-wide association study on 260 accessions in under 2 weeks, revealing known and unknown root growth regulators. Root Walker promises to be a useful toolkit for the plant science community, allowing large-scale screening of root growth dynamics for a variety of purposes, including genetic screens for root sensing and root growth response mechanisms.
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Affiliation(s)
- Platre Matthieu Pierre
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Mehta Preyanka
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Halvorson Zachary
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Ling Zhang
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Brent Lukas
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Gleason F. Matias
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Faizi Kian
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Goulding Callum
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Busch Wolfgang
- Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
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Zheng L, Zhou P, Pan Y, Li B, Shen R, Lan P. Proteomic profile of the germinating seeds reveals enhanced seedling growth in Arabidopsis rpp1a mutant. PLANT MOLECULAR BIOLOGY 2023; 113:105-120. [PMID: 37804450 DOI: 10.1007/s11103-023-01378-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
Ribosomal phosphoprotein P1 (RPP1) is an integral component of the P-protein stalk in the 60S subunit of eukaryotic ribosomes and is required for the efficient elongation of translation. Previously, Arabidopsis RPP1A was revealed to be involved in the regulation of seed size and seed storage protein accumulation. In this work, the seedling growth analysis shows that the knockout mutation of Arabidopsis RPP1A significantly promoted seedling growth, particularly in the shoots. The label-free quantitative proteomic analysis demonstrated that a total of 593 proteins were differentially accumulated between the germinating seeds of the wild-type Col-0 and rpp1a mutant. And these proteins were significantly enriched in the intracellular transport, nitrogen compound transport, protein transport, and organophosphate metabolic process. The abundance of proteins involved in the RNA and protein processing processes, including ncRNA processing and protein folding, were significantly increased in the rpp1a mutant. Mutation in RPP1A highlighted the effects on the ribosome, energy metabolism, and nitrogen metabolism. The abundance of enzymes involved in glycolysis and pyruvate mechanism was decreased in the germinating seeds of the rpp1a mutant. Whereas the processes of amino acid biosynthesis, protein processing in endoplasmic reticulum, and biosynthesis of cofactors were enhanced in the germinating seeds of the rpp1a mutant. Taken together, the lack of RPP1A triggered changes in other ribosomal proteins, and the higher amino acid contents in the seedlings of the rpp1a mutant probably contributed to enhanced biosynthesis, processing, and transport of proteins, resulting in accelerated growth. Our results show the novel role of a P-protein and shed new light on the regulatory mechanism of seedling growth.
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Affiliation(s)
- Lu Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Peijun Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yilin Pan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingjuan Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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López-Ruiz BA, Quezada-Rodríguez EH, Piñeyro-Nelson A, Tovar H, García-Ponce B, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate in Arabidopsis thaliana Primary Root Development Using Cellular Measurements and Primary Root Length. PLANTS (BASEL, SWITZERLAND) 2022; 11:3162. [PMID: 36432890 PMCID: PMC9697774 DOI: 10.3390/plants11223162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Genome-wide association studies (GWAS) have allowed the identification of different loci associated with primary root (PR) growth, and Arabidopsis is an excellent model for these studies. The PR length is controlled by cell proliferation, elongation, and differentiation; however, the specific contribution of proliferation and differentiation in the control of PR growth is still poorly studied. To this end, we analyzed 124 accessions and used a GWAS approach to identify potential causal genomic regions related to four traits: PR length, growth rate, cell proliferation and cell differentiation. Twenty-three genes and five statistically significant SNPs were identified. The SNP with the highest score mapped to the fifth exon of NAC048 and this change makes a missense variant in only 33.3% of the accessions with a large PR, compared with the accessions with a short PR length. Moreover, we detected five more SNPs in this gene and in NAC3 that allow us to discover closely related accessions according to the phylogenetic tree analysis. We also found that the association between genetic variants among the 18 genes with the highest scores in our GWAS and the phenotypic classes into which we divided our accessions are not straightforward and likely follow historical patterns.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Elsa H. Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México 04510, Mexico
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Hugo Tovar
- División de Genómica Computacional, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México 14610, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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Abbas M, Abid MA, Meng Z, Abbas M, Wang P, Lu C, Askari M, Akram U, Ye Y, Wei Y, Wang Y, Guo S, Liang C, Zhang R. Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway. PHYSIOLOGIA PLANTARUM 2022; 174:e13787. [PMID: 36169590 DOI: 10.1111/ppl.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.
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Affiliation(s)
- Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ali Abid
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Askari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Umar Akram
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yulu Ye
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Mahmoud A, Qi R, Zhao H, Yang H, Liao N, Ali A, Malangisha GK, Ma Y, Zhang K, Zhou Y, Xia Y, Lyu X, Yang J, Zhang M, Hu Z. An allelic variant in the ACS7 gene promotes primary root growth in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3357-3373. [PMID: 35980402 DOI: 10.1007/s00122-022-04173-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Gene mining in a C. lanatus × C. amarus population revealed one gene, ACS7, linked to primary root elongation in watermelon. Watermelon is a xerophytic crop characterized by a long primary root and robust lateral roots. Therefore, watermelon serves as an excellent model for studying root elongation and development. However, the genetic mechanism underlying the primary root elongation in watermelon remains unknown. Herein, through bulk segregant analysis we identified a genetic locus, qPRL.Chr03, controlling primary root length (PRL) using two different watermelon species (Citrullus lanatus and Citrullus amarus) that differ in their root architecture. Fine mapping revealed that xaa-Pro dipeptidase and 1-aminocyclopropane-1-carboxylate synthase 7 (ACS7) are candidate regulators of the primary root growth. Allelic variation in the delimited region among 193 watermelon accessions indicated that the long-root alleles might only exist in C. amarus. Interestingly, the discrepancy in PRL among the C. amarus accessions was clearly associated with a nonsynonymous single nucleotide polymorphism variant within the ACS7 gene. The ACS7 expression and ethylene levels in the primary root tips suggested that ethylene is a negative regulator of root elongation in watermelon, as supported by the application of 1-aminocyclopropane-1-carboxylate (ACC, the ethylene precursor) or 2-aminoethoxyvinyl glycine (AVG, an ACS inhibitor). To the best of our knowledge, these findings provide the first description of the genetic basis of root elongation in watermelon. The detected markers of the ACS7 gene will facilitate marker-assisted selection for the PRL trait to improve water and nutrient use efficacy in watermelon and beyond.
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Affiliation(s)
- Ahmed Mahmoud
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Agriculture Research Center, Horticulture Research Institute, 9 Gmaa St, Giza, 12619, Egypt
| | - Rui Qi
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
| | - Haoshun Zhao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Haiyang Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Nanqiao Liao
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Abid Ali
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Guy Kateta Malangisha
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yuyuan Ma
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Kejia Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yimei Zhou
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yuelin Xia
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China.
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
- Hainan Institute of Zhejiang University, Yazhou District, Sanya, 572025, People's Republic of China.
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou, Zhejiang, People's Republic of China.
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Longkumer T, Chen CY, Biancucci M, Bhaskara GB, Verslues PE. Spatial differences in stoichiometry of EGR phosphatase and Microtubule-associated Stress Protein 1 control root meristem activity during drought stress. THE PLANT CELL 2022; 34:742-758. [PMID: 34865106 PMCID: PMC8824564 DOI: 10.1093/plcell/koab290] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/18/2021] [Indexed: 05/16/2023]
Abstract
During moderate severity drought and low water potential (ψw) stress, poorly understood signaling mechanisms restrict both meristem cell division and subsequent cell expansion. We found that the Arabidopsis thaliana Clade E Growth-Regulating 2 (EGR2) protein phosphatase and Microtubule-Associated Stress Protein 1 (MASP1) differed in their stoichiometry of protein accumulation across the root meristem and had opposing effects on root meristem activity at low ψw. Ectopic MASP1 or EGR expression increased or decreased, respectively, root meristem size and root elongation during low ψw stress. This, along with the ability of phosphomimic MASP1 to overcome the EGR-mediated suppression of root meristem size and the observation that ectopic EGR expression had no effect on unstressed plants, indicated that during low ψw EGR activation and attenuation of MASP1 phosphorylation in their overlapping zone of expression determines root meristem size and activity. Ectopic EGR expression also decreased root cell size at low ψw. Conversely, both the egr1-1 egr2-1 and egr1-1 egr2-1 masp1-1 mutants had similarly increased root cell size but only egr1-1egr2-1 had increased cell division. These observations demonstrated that EGRs affect meristem activity via MASP1 but affect cell expansion via other mechanisms. Interestingly, EGR2 was highly expressed in the root cortex, a cell type important for growth regulation and environmental response.
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Razavi M, Saberi Fathi SM, Tuszynski JA. The Effect of the Protein Synthesis Entropy Reduction on the Cell Size Regulation and Division Size of Unicellular Organisms. ENTROPY 2022; 24:e24010094. [PMID: 35052120 PMCID: PMC8775074 DOI: 10.3390/e24010094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/04/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
The underlying mechanism determining the size of a particular cell is one of the fundamental unknowns in cell biology. Here, using a new approach that could be used for most of unicellular species, we show that the protein synthesis and cell size are interconnected biophysically and that protein synthesis may be the chief mechanism in establishing size limitations of unicellular organisms. This result is obtained based on the free energy balance equation of protein synthesis and the second law of thermodynamics. Our calculations show that protein synthesis involves a considerable amount of entropy reduction due to polymerization of amino acids depending on the cytoplasmic volume of the cell. The amount of entropy reduction will increase with cell growth and eventually makes the free energy variations of the protein synthesis positive (that is, forbidden thermodynamically). Within the limits of the second law of thermodynamics we propose a framework to estimate the optimal cell size at division.
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Affiliation(s)
- Mohammad Razavi
- Department of Physics, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran;
| | - Seyed Majid Saberi Fathi
- Department of Physics, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran;
- Correspondence:
| | - Jack Adam Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada;
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, 10129 Torino, Italy
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Zhang J, Gao X, Cai G, Wang Y, Li J, Du H, Wang R, Zhang H, Huang J. An Adenylate Kinase OsAK3 Involves Brassinosteroid Signaling and Grain Length in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2021; 14:105. [PMID: 34962599 PMCID: PMC8714616 DOI: 10.1186/s12284-021-00546-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/17/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Grain size is one of the major determinants of cereal crop yield. As a class of plant polyhydroxysteroids, brassinosteroids (BRs) play essential roles in the regulation of grain size and plant architecture in rice. In a previous research, we cloned qGL3/OsPPKL1 encoding a protein phosphatase with Kelch-like repeat domains, which negatively regulates BR signaling and grain length in rice. RESULTS Here, we screened qGL3-interacting proteins (GIPs) via yeast two-hybrid assay and analyzed the phenotypes of the T-DNA insertion mutants of GIPs. Among these mutants, mutant osak3 presents shorter grain length and dwarfing phenotype. OsAK3 encodes an adenylate kinase, which regulates grain size by controlling cell expansion of rice spikelet glume. Overexpression of OsAK3 resulted in longer grain length. OsAK3 interacts with qGL3 in vivo and in vitro. Lamina inclination, coleoptile elongation and root inhibition experiments showed that the osak3 mutant was less sensitive to exogenous brassinolide (BL) treatment. The transcriptional level of OsAK3 was up-regulated under BL induction. In addition, RNA-Seq data indicate that OsAK3 is involved in a variety of biological processes that regulate BR signaling and grain development in rice. CONCLUSIONS Our study reveals a novel BR signaling component OsAK3 in the regulation of grain length, and provides novel clues for uncovering the potential functions of OsAK3 in rice growth and development.
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Affiliation(s)
- Jiaqi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Xiuying Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Guang Cai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Yuji Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Jianbo Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Huaying Du
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Ruqin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China
| | - Ji Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Jiangsu Provincial Engineering Research Center of Seed Industry Science and Technology, Nanjing, 210095, China.
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Xu R, Yang Y, Zheng X. Unique structural features of the adenylate kinase hCINAP/AK6 and its multifaceted functions in carcinogenesis and tumor progression. FEBS Lett 2021; 595:2071-2084. [PMID: 34245011 DOI: 10.1002/1873-3468.14158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/30/2022]
Abstract
Human coilin-interacting nuclear ATPase protein (hCINAP), also known as adenylate kinase 6 (AK6), is an atypical adenylate kinase with critical roles in many biological processes, including gene transcription, ribosome synthesis, cell metabolism, cell proliferation and apoptosis, DNA damage responses, and genome stability. Furthermore, hCINAP/AK6 dysfunction is associated with cancer and various inflammatory diseases. In this review, we summarize the structural features and biological roles of hCINAP in several important signaling pathways, as well as its connection with tumor onset and progression.
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Affiliation(s)
- Ruidan Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Yongfeng Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
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Pujari I, Thomas A, Rai PS, Satyamoorthy K, Babu VS. Cell size: a key determinant of meristematic potential in plant protoplasts. ABIOTECH 2021; 2:96-104. [PMID: 36304480 PMCID: PMC9590549 DOI: 10.1007/s42994-020-00033-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/18/2020] [Indexed: 06/16/2023]
Abstract
Metabolic pathway reconstruction and gene edits for native natural product synthesis in single plant cells are considered to be less complicated when compared to the production of non-native metabolites. Being an efficient eukaryotic system, plants encompass suitable post-translational modifications. However, slow cell division rate and heterogeneous nature is an impediment for consistent product retrieval from plant cells. Plant cell synchrony can be attained in cultures developed in vitro. Isolated plant protoplasts capable of division, can potentially enhance the unimpaired yield of target bioactives, similar to microbes and unicellular eukaryotes. Evidence from yeast experiments suggests that 'critical cell size' and division rates for enhancement machinery, primarily depend on culture conditions and nutrient availability. The cell size control mechanisms in Arabidopsis shoot apical meristem is analogous to yeast notably, fission yeast. If protoplasts isolated from plants are subjected to cell size studies and cell cycle progression in culture, it will answer the underlying molecular mechanisms such as, unicellular to multicellular transition states, longevity, senescence, 'cell-size resetting' during organogenesis, and adaptation to external cues.
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Affiliation(s)
- Ipsita Pujari
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576 104 India
| | - Abitha Thomas
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576 104 India
| | - Padmalatha S. Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Vidhu Sankar Babu
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576 104 India
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Kleczkowski LA, Igamberdiev AU. Magnesium Signaling in Plants. Int J Mol Sci 2021; 22:1159. [PMID: 33503839 PMCID: PMC7865908 DOI: 10.3390/ijms22031159] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/16/2021] [Accepted: 01/19/2021] [Indexed: 01/02/2023] Open
Abstract
Free magnesium (Mg2+) is a signal of the adenylate (ATP+ADP+AMP) status in the cells. It results from the equilibrium of adenylate kinase (AK), which uses Mg-chelated and Mg-free adenylates as substrates in both directions of its reaction. The AK-mediated primary control of intracellular [Mg2+] is finely interwoven with the operation of membrane-bound adenylate- and Mg2+-translocators, which in a given compartment control the supply of free adenylates and Mg2+ for the AK-mediated equilibration. As a result, [Mg2+] itself varies both between and within the compartments, depending on their energetic status and environmental clues. Other key nucleotide-utilizing/producing enzymes (e.g., nucleoside diphosphate kinase) may also be involved in fine-tuning of the intracellular [Mg2+]. Changes in [Mg2+] regulate activities of myriads of Mg-utilizing/requiring enzymes, affecting metabolism under both normal and stress conditions, and impacting photosynthetic performance, respiration, phloem loading and other processes. In compartments controlled by AK equilibrium (cytosol, chloroplasts, mitochondria, nucleus), the intracellular [Mg2+] can be calculated from total adenylate contents, based on the dependence of the apparent equilibrium constant of AK on [Mg2+]. Magnesium signaling, reflecting cellular adenylate status, is likely widespread in all eukaryotic and prokaryotic organisms, due simply to the omnipresent nature of AK and to its involvement in adenylate equilibration.
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Affiliation(s)
- Leszek A. Kleczkowski
- Department of Plant Physiology, Umeå Plant Science Centre, University of Umeå, 901 87 Umeå, Sweden
| | - Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1B3X9, Canada;
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