1
|
Trajano-Silva LAM, Mule SN, Palmisano G. Molecular tools to regulate gene expression in Trypanosoma cruzi. Adv Clin Chem 2024; 120:169-190. [PMID: 38762241 DOI: 10.1016/bs.acc.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Developing molecular strategies to manipulate gene expression in trypanosomatids is challenging, particularly with respect to the unique gene expression mechanisms adopted by these unicellular parasites, such as polycistronic mRNA transcription and multi-gene families. In the case of Trypanosoma cruzi (T. cruzi), the causative agent of Chagas Disease, the lack of RNA interference machinery further complicated functional genetic studies important for understanding parasitic biology and developing biomarkers and potential therapeutic targets. Therefore, alternative methods of performing knockout and/or endogenous labelling experiments were developed to identify and understand the function of proteins for survival and interaction with the host. In this review, we present the main tools for the genetic manipulation of T. cruzi, focusing on the Clustered Regularly Interspaced Short Palindromic Repeats Cas9-associated system technique widely used in this organism. Moreover, we highlight the importance of using these tools to elucidate the function of uncharacterized and glycosylated proteins. Further developments of these technologies will allow the identification of new biomarkers, therapeutic targets and potential vaccines against Chagas disease with greater efficiency and speed.
Collapse
Affiliation(s)
- Lays Adrianne M Trajano-Silva
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Simon Ngao Mule
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Glycoproteomic Laboratory, Parasitology Department, Institute of Biomedical Science II, University of Sao Paulo, Sao Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
| |
Collapse
|
2
|
Fang Y, Liu H, Qin L, Qi F, Sun Z, Wu J, Dong W, Huang B, Zhang X. Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.). BMC Genomics 2023; 24:495. [PMID: 37641021 PMCID: PMC10463326 DOI: 10.1186/s12864-023-09568-y] [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: 06/08/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Improving its yield is crucial for sustainable peanut production to meet increasing food and industrial requirements. Deciphering the genetic control underlying peanut kernel weight and size, which are essential components of peanut yield, would facilitate high-yield breeding. A high-density single nucleotide polymorphism (SNP)-based linkage map was constructed using a recombinant inbred lines (RIL) population derived from a cross between the variety Yuanza9102 and a germplasm accession wt09-0023. Kernel weight and size quantitative trait loci (QTLs) were co-localized to a 0.16 Mb interval on Arahy07 using inclusive composite interval mapping (ICIM). Analysis of SNP, and Insertion or Deletion (INDEL) markers in the QTL interval revealed a gene encoding a pentatricopeptide repeat (PPR) superfamily protein as a candidate closely linked with kernel weight and size in cultivated peanut. Examination of the PPR gene family indicated a high degree of collinearity of PPR genes between A. hypogaea and its diploid progenitors, Arachis duranensis and Arachis ipaensis. The candidate PPR gene, Arahy.JX1V6X, displayed a constitutive expression pattern in developing seeds. These findings lay a foundation for further fine mapping of QTLs related to kernel weight and size, as well as validation of candidate genes in cultivated peanut.
Collapse
Affiliation(s)
- Yuanjin Fang
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Hua Liu
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Li Qin
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Feiyan Qi
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Ziqi Sun
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jihua Wu
- Shangqiu Academy of Agriculture and Forestry, Shangqiu, 476002, China
| | - Wenzhao Dong
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Bingyan Huang
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China.
| | - Xinyou Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China.
| |
Collapse
|
3
|
Deng Z, Yang Z, Liu X, Dai X, Zhang J, Deng K. Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato ( Solanum tuberosum L.). Int J Mol Sci 2023; 24:12888. [PMID: 37629069 PMCID: PMC10454627 DOI: 10.3390/ijms241612888] [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: 07/10/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Transcription factors containing a CCCH structure (C3H) play important roles in plant growth and development, and their stress response, but research on the C3H gene family in potato has not been reported yet. In this study, we used bioinformatics to identify 50 C3H genes in potato and named them StC3H-1 to StC3H-50 according to their location on chromosomes, and we analyzed their physical and chemical properties, chromosome location, phylogenetic relationship, gene structure, collinearity relationship, and cis-regulatory element. The gene expression pattern analysis showed that many StC3H genes are involved in potato growth and development, and their response to diverse environmental stresses. Furthermore, RT-qPCR data showed that the expression of many StC3H genes was induced by high temperatures, indicating that StC3H genes may play important roles in potato response to heat stress. In addition, Some StC3H genes were predominantly expressed in the stolon and developing tubers, suggesting that these StC3H genes may be involved in the regulation of tuber development. Together, these results provide new information on StC3H genes and will be helpful for further revealing the function of StC3H genes in the heat stress response and tuber development in potato.
Collapse
Affiliation(s)
- Zeyi Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Zhijiang Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xinyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
| | - Xiumei Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiankui Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kexuan Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China; (Z.D.); (Z.Y.); (X.L.); (X.D.); (J.Z.)
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| |
Collapse
|
4
|
Xu W, Jian S, Li J, Wang Y, Zhang M, Xia K. Genomic Identification of CCCH-Type Zinc Finger Protein Genes Reveals the Role of HuTZF3 in Tolerance of Heat and Salt Stress of Pitaya (Hylocereus polyrhizus). Int J Mol Sci 2023; 24:ijms24076359. [PMID: 37047333 PMCID: PMC10094633 DOI: 10.3390/ijms24076359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Pitaya (Hylocereus polyrhizus) is cultivated in a broad ecological range, due to its tolerance to drought, heat, and poor soil. The zinc finger proteins regulate gene expression at the transcriptional and post-transcriptional levels, by interacting with DNA, RNA, and proteins, to play roles in plant growth and development, and stress response. Here, a total of 81 CCCH-type zinc finger protein genes were identified from the pitaya genome. Transcriptomic analysis showed that nine of them, including HuTZF3, responded to both salt and heat stress. RT-qPCR results showed that HuTZF3 is expressed in all tested organs of pitaya, with a high level in the roots and stems, and confirmed that expression of HuTZF3 is induced by salt and heat stress. Subcellular localization showed that HuTZF3 is targeted in the processing bodies (PBs) and stress granules (SGs). Heterologous expression of HuTZF3 could improve both salt and heat tolerance in Arabidopsis, reduce oxidative stress, and improve the activity of catalase and peroxidase. Therefore, HuTZF3 may be involved in post-transcriptional regulation via localizing to PBs and SGs, contributing to both salt and heat tolerance in pitaya.
Collapse
Affiliation(s)
- Weijuan Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuguang Jian
- South China National Botanical Garden, Guangzhou 510650, China
- CAS Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jianyi Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yusang Wang
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- Correspondence: (M.Z.); (K.X.); Tel./Fax: +86-20-37252891 (M.Z.)
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- Correspondence: (M.Z.); (K.X.); Tel./Fax: +86-20-37252891 (M.Z.)
| |
Collapse
|
5
|
Wei W, Lu L, Bian XH, Li QT, Han JQ, Tao JJ, Yin CC, Lai YC, Li W, Bi YD, Man WQ, Chen SY, Zhang JS, Zhang WK. Zinc-finger protein GmZF351 improves both salt and drought stress tolerance in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36866859 DOI: 10.1111/jipb.13474] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Abiotic stress is one of the most important factors reducing soybean yield. It is essential to identify regulatory factors contributing to stress responses. A previous study found that the tandem CCCH zinc-finger protein GmZF351 is an oil level regulator. In this study, we discovered that the GmZF351 gene is induced by stress and that the overexpression of GmZF351 confers stress tolerance to transgenic soybean. GmZF351 directly regulates the expression of GmCIPK9 and GmSnRK, leading to stomata closing, by binding to their promoter regions, which carry two CT(G/C)(T/A)AA elements. Stress induction of GmZF351 is mediated through reduction in the H3K27me3 level at the GmZF351 locus. Two JMJ30-demethylase-like genes, GmJMJ30-1 and GmJMJ30-2, are involved in this demethylation process. Overexpression of GmJMJ30-1/2 in transgenic hairy roots enhances GmZF351 expression mediated by histone demethylation and confers stress tolerance to soybean. Yield-related agronomic traits were evaluated in stable GmZF351-transgenic plants under mild drought stress conditions. Our study reveals a new mode of GmJMJ30-GmZF351 action in stress tolerance, in addition to that of GmZF351 in oil accumulation. Manipulation of the components in this pathway is expected to improve soybean traits and adaptation under unfavorable environments.
Collapse
Affiliation(s)
- Wei Wei
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Long Lu
- Key Lab of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiao-Hua Bian
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing-Tian Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jia-Qi Han
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Jun Tao
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cui-Cui Yin
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong-Cai Lai
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wei Li
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ying-Dong Bi
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wei-Qun Man
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, 150086, China
| | - Shou-Yi Chen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jin-Song Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan-Ke Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, INASEED, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
6
|
Comparative Transcriptome Analysis of CCCH Family in Roles of Flower Opening and Abiotic Stress in Osmanthus fragrans. Int J Mol Sci 2022; 23:ijms232315363. [PMID: 36499688 PMCID: PMC9735588 DOI: 10.3390/ijms232315363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
CCCH is a zinc finger family with a typical CCCH-type motif which performs a variety of roles in plant growth and development and responses to environmental stressors. However, the information about this family has not been reported for Osmanthus fragrans. In this study, a total of 66 CCCH predicted genes were identified from the O. fragrans genome, the majority of which had multiple CCCH motifs. The 66 OfCCCHs were found to be unevenly distributed on 21 chromosomes and were clustered into nine groups based on their phylogenetic analysis. In each group, the gene structure and domain makeup were comparatively conserved. The expression profiles of the OfCCCH genes were examined in various tissues, the flower-opening processes, and under various abiotic stresses using transcriptome sequencing and qRT-PCR (quantitative real-time PCR). The results demonstrated the widespread expression of OfCCCHs in various tissues, the differential expression of 22 OfCCCHs during flower-opening stages, and the identification of 4, 5, and 13 OfCCCHs after ABA, salt, and drought stress treatment, respectively. Furthermore, characterization of the representative OfCCCHs (OfCCCH8, 23, 27, and 36) revealed that they were all localized in the nucleus and that the majority of them had transcriptional activation in the yeast system. Our research offers the first thorough examination of the OfCCCH family and lays the groundwork for future investigations regarding the functions of CCCH genes in O. fragrans.
Collapse
|
7
|
Hu X, Zuo J. Population Genomics and Haplotype Analysis in Bread Wheat Identify a Gene Regulating Glume Pubescence. FRONTIERS IN PLANT SCIENCE 2022; 13:897772. [PMID: 35909788 PMCID: PMC9328021 DOI: 10.3389/fpls.2022.897772] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Glume hairiness or pubescence is an important morphological trait with high heritability to distinguish/characterize wheat and is related to the resistance to biotic and abiotic stresses. Hg1 (formerly named Hg) on chromosome arm 1AS controlled glume hairiness in wheat. Its genetic analysis and mapping have been widely studied, yet more useful and accurate information for fine mapping of Hg1 and identification of its candidate gene is lacking. The cloning of this gene has not yet been reported for the large complex wheat genome. Here, we performed a GWAS between SNP markers and glume pubescence (Gp) in a wheat population with 352 lines and further demonstrated the gene expression and haplotype analysis approach for isolating the Hg1 gene. One gene, TraesCSU02G143200 (TaELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was identified as the most promising candidate gene of Hg1. The gene annotation, expression pattern, function SNP variation, haplotype analysis, and co-expression analysis in floral organ (spike) development indicated that it is likely to be involved in the regulation of glume pubescence. Our study demonstrates the importance of high-quality reference genomes and annotation information, as well as bioinformatics analysis, for gene cloning in wheat.
Collapse
Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Jianfang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|