1
|
Wang Z, Wang Z, Li X, Chen Z, Liu Y, Zhang F, Dai Q, Yu Q, Li N. Identification and Analysis of the Expression of the PIP5K Gene Family in Tomatoes. Int J Mol Sci 2023; 25:159. [PMID: 38203328 PMCID: PMC10778592 DOI: 10.3390/ijms25010159] [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: 11/10/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
To explore the function of phosphatidylinositol 4-phosphate 5-kinase (PIP5K) in tomatoes, members of the tomato PIP5K family were identified and characterized using bioinformatic methods, and their expression patterns were also analyzed under salt stress and in different tissues. Twenty-one PIP5K members-namely, SlPIP5K1-SlPIP5K21-were identified from ten chromosomes, and these were divided into three groups according to a phylogenetic analysis. Further bioinformatic analysis showed four pairs of collinear relationships and fragment replication events among the SlPIP5K family members. To understand the possible roles of the SlPIP5Ks, a cis-acting element analysis was conducted, which indicated that tomato PIP5Ks could be associated with plant growth, hormones, and stress responses. We further validated the results of the in silico analysis by integrating RNA-seq and qRT-PCR techniques for salt- and hormone-treated tomato plants. Our results showed that SlPIP5K genes exhibited tissue- and treatment-specific patterns, and some of the SlPIP5Ks exhibited significantly altered expressions after our treatments, suggesting that they might be involved in these stresses. We selected one of the SlPIP5Ks that responded to our treatments, SlPIP5K2, to further understand its subcellular localization. Our results showed that SlPIP5K2 was located on the membrane. This study lays a foundation for the analysis of the biological functions of the tomato SlPIP5K genes and can also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation, especially under salt stress.
Collapse
Affiliation(s)
- Zepeng Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zhongyu Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Xianguo Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zhaolong Chen
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yuxiang Liu
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Fulin Zhang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qi Dai
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Qinghui Yu
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Ning Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| |
Collapse
|
2
|
García-Galindo P, Ahnert SE, Martin NS. The non-deterministic genotype-phenotype map of RNA secondary structure. J R Soc Interface 2023; 20:20230132. [PMID: 37608711 PMCID: PMC10445035 DOI: 10.1098/rsif.2023.0132] [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: 03/08/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023] Open
Abstract
Selection and variation are both key aspects in the evolutionary process. Previous research on the mapping between molecular sequence (genotype) and molecular fold (phenotype) has shown the presence of several structural properties in different biological contexts, implying that these might be universal in evolutionary spaces. The deterministic genotype-phenotype (GP) map that links short RNA sequences to minimum free energy secondary structures has been studied extensively because of its computational tractability and biologically realistic nature. However, this mapping ignores the phenotypic plasticity of RNA. We define a GP map that incorporates non-deterministic (ND) phenotypes, and take RNA as a case study; we use the Boltzmann probability distribution of folded structures and examine the structural properties of ND GP maps for RNA sequences of length 12 and coarse-grained RNA structures of length 30 (RNAshapes30). A framework is presented to study robustness, evolvability and neutral spaces in the ND map. This framework is validated by demonstrating close correspondence between the ND quantities and sample averages of their deterministic counterparts. When using the ND framework we observe the same structural properties as in the deterministic GP map, such as bias, negative correlation between genotypic robustness and evolvability, and positive correlation between phenotypic robustness and evolvability.
Collapse
Affiliation(s)
- Paula García-Galindo
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
| | - Sebastian E. Ahnert
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
- The Alan Turing Institute, 96 Euston Road, London NW1 2DB, UK
| | - Nora S. Martin
- Rudolf Peierls Centre for Theoretical Physics, Beecroft Building, Parks Road, Oxford OX1 3PU, UK
| |
Collapse
|
3
|
Dreher Y, Fichtler J, Karfusehr C, Jahnke K, Xin Y, Keller A, Göpfrich K. Genotype-phenotype mapping with polyominos made from DNA origami tiles. Biophys J 2022; 121:4840-4848. [PMID: 36088535 PMCID: PMC9811662 DOI: 10.1016/j.bpj.2022.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/18/2022] [Accepted: 09/06/2022] [Indexed: 01/07/2023] Open
Abstract
The correlation between genetic information and characteristics of a living cell-its genotype and its phenotype-constitutes the basis of genetics. Here, we experimentally realize a primitive form of genotype-phenotype mapping with DNA origami. The DNA origami can polymerize into two-dimensional lattices (phenotype) via blunt-end stacking facilitated by edge staples at the seam of the planar DNA origami. There are 80 binding positions for edge staples, which allow us to translate an 80-bit long binary code (genotype) onto the DNA origami. The presence of an edge staple thus corresponds to a "1" and its absence to a "0." The interactions of our DNA-based system can be reproduced by a polyomino model. Polyomino growth simulations qualitatively reproduce our experimental results. We show that not only the absolute number of base stacks but also their sequence position determine the cluster size and correlation length of the orientation of single DNA origami within the cluster. Importantly, the mutation of a few bits can result in major morphology changes of the DNA origami cluster, while more often, major sequence changes have no impact. Our experimental realization of a correlation between binary information ("genotype") and cluster morphology ("phenotype") thus reproduces key properties of genotype-phenotype maps known from living systems.
Collapse
Affiliation(s)
- Yannik Dreher
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Julius Fichtler
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany
| | - Christoph Karfusehr
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Max Planck School Matter to Life, Heidelberg University, Heidelberg, Germany
| | - Kevin Jahnke
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Yang Xin
- Paderborn University, Technical and Macromolecular Chemistry, Paderborn, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Paderborn, Germany
| | - Kerstin Göpfrich
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
4
|
Yu Z, Zhang D, Zeng B, Liu X, Yang J, Gao W, Ma X. Characterization of the WRKY gene family reveals its contribution to the adaptability of almond ( Prunus dulcis). PeerJ 2022; 10:e13491. [PMID: 35811825 PMCID: PMC9261925 DOI: 10.7717/peerj.13491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/03/2022] [Indexed: 01/17/2023] Open
Abstract
Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT-PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
Collapse
Affiliation(s)
- Zhenfan Yu
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Dongdong Zhang
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Bin Zeng
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Xingyue Liu
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China,GuangZhou Institute of Forestry and Landscape Architecture, GuangZhou, China
| | - Jiahui Yang
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Wenwen Gao
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| | - Xintong Ma
- College of Horticulture, Xinjiang Agriculture University, Urumqi, China
| |
Collapse
|
5
|
Martin NS, Ahnert SE. Fast free-energy-based neutral set size estimates for the RNA genotype-phenotype map. J R Soc Interface 2022; 19:20220072. [PMID: 35702868 PMCID: PMC9198509 DOI: 10.1098/rsif.2022.0072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The genotype–phenotype (GP) map of RNA secondary structure links each RNA sequence to its corresponding secondary structure. Previous research has shown that the large-scale structural properties of GP maps, such as the size of neutral sets in genotype space, can influence evolutionary outcomes. In order to use neutral set sizes, efficient and accurate computational methods are needed to compute them. Here, we propose a new method, which is based on free energy estimates and is much faster than existing sample-based methods. Moreover, this approach can give insight into the reasons behind neutral set size variations, for example, why structures with fewer stacks tend to have larger neutral set sizes. In addition, we generalize neutral set size calculations from the previously studied many-to-one framework, where each sequence folds into a single energetically preferred structure, to a fuller many-to-many framework, where several low-energy structures are included. We find that structures with high neutral sets in one framework also tend to have large neutral sets in the other framework for a range of parameters and thus the choice of GP map does not fundamentally affect which structures have the largest neutral set sizes.
Collapse
Affiliation(s)
- Nora S Martin
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.,Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Sebastian E Ahnert
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK.,The Alan Turing Institute, British Library, Euston Road, London NW1 2DB, UK
| |
Collapse
|