51
|
Lv Q, Shang Y, Bi H, Yang J, Lin L, Shi C, Wang M, Xie R, Zhu Z, Wang F, Hua L, Chen H, Wu B, Peng Z. Identification of two-component system ArcAB and the universal stress protein E in Pasteurella multocida and their effects on bacterial fitness and pathogenesis. Microbes Infect 2023:105235. [PMID: 37802468 DOI: 10.1016/j.micinf.2023.105235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/28/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
Two-component regulatory system (TCS) is a widespread bacterial signal transduction mechanism and plays a critical role in bacterial adaptation to environments as well as regulating bacterial virulence. However, few studies have reported the actions of TCS in Pasteurella multocida, a zoonotic bacterial pathogen. In this study, genes encoding proteins homologous to the ArcAB TCS were identified in genome sequences of P. multocida belonging to different serogroups, and the transcription of both arcA and arcB was up-regulated in anaerobic and superoxygen environment. Compared to wild type strains, P. multocida arcA-deletion mutants (ΔarcA) displayed a decrease in growing under anaerobic conditions, biofilm formation, as well as the capacities of anti-serum bactericidal effect, cell adherence and invasion, anti-phagocytosis, and virulence in different in vivo models (Galleria mellonella and mice). RNA-Seq identified 70 significantly downregulated genes in ΔarcA compared to the wild type strain, and several of them are associated with P. multocida virulence. Among them, a universal stress protein E encoding gene uspE was characterized in P. multocida for the first time. Electrophoretic mobility shift assay (EMSA) demonstrated that the ArcAB TCS could regulate uspE directly. Deletion of uspE also led to a decrease of P. multocida in growing under anaerobic conditions, biofilm formation, anti-serum bactericidal effect, cell adherence and invasion, anti-phagocytosis, and virulence in mice. The data provided from this study will help further understanding the fitness and pathogenesis of P. multocida.
Collapse
Affiliation(s)
- Qingjie Lv
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yuyao Shang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Haixin Bi
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jie Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lin Lin
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Congcong Shi
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Mixue Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Xie
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhanwei Zhu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Fei Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lin Hua
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bin Wu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Zhong Peng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China; Frontiers Science Center for Animal Breeding and Sustainable Production, The Cooperative Innovation Central for Sustainable Pig Production, Wuhan, China.
| |
Collapse
|
52
|
Wang R, Zhao J, Chen L, Ye J, Wu H, Zhang H. LcbR1, a newly identified GntR family regulator, represses lincomycin biosynthesis in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2023. [DOI: doi.org/10.1007/s00253-023-12756-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 10/09/2023]
|
53
|
Crawford JD, Wang H, Trejo-Zambrano D, Cimbro R, Talbot CC, Thomas MA, Curran AM, Girgis AA, Schroeder JT, Fava A, Goldman DW, Petri M, Rosen A, Antiochos B, Darrah E. The XIST lncRNA is a sex-specific reservoir of TLR7 ligands in SLE. JCI Insight 2023; 8:e169344. [PMID: 37733447 PMCID: PMC10634230 DOI: 10.1172/jci.insight.169344] [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: 02/02/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with a dramatic sex bias, affecting 9 times more women than men. Activation of Toll-like receptor 7 (TLR7) by self-RNA is a central pathogenic process leading to aberrant production of type I interferon (IFN) in SLE, but the specific RNA molecules that serve as TLR7 ligands have not been defined. By leveraging gene expression data and the known sequence specificity of TLR7, we identified the female-specific X-inactive specific transcript (XIST) long noncoding RNA as a uniquely rich source of TLR7 ligands in SLE. XIST RNA stimulated IFN-α production by plasmacytoid DCs in a TLR7-dependent manner, and deletion of XIST diminished the ability of whole cellular RNA to activate TLR7. XIST levels were elevated in blood leukocytes from women with SLE compared with controls, correlated positively with disease activity and the IFN signature, and were enriched in extracellular vesicles released from dying cells in vitro. Importantly, XIST was not IFN inducible, suggesting that XIST is a driver, rather than a consequence, of IFN in SLE. Overall, our work elucidated a role for XIST RNA as a female sex-specific danger signal underlying the sex bias in SLE.
Collapse
Affiliation(s)
| | - Hong Wang
- Division of Rheumatology, Department of Medicine
| | | | | | - C. Conover Talbot
- The Single Cell and Transcriptomics Core, Institute for Basic Biomedical Sciences; and
| | | | | | | | - John T. Schroeder
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrea Fava
- Division of Rheumatology, Department of Medicine
| | | | | | - Antony Rosen
- Division of Rheumatology, Department of Medicine
| | | | - Erika Darrah
- Division of Rheumatology, Department of Medicine
| |
Collapse
|
54
|
Kletzien OA, Wuttke DS, Batey RT. The RNA-binding domain of hnRNP U extends beyond the RGG/RG motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558674. [PMID: 37786719 PMCID: PMC10541603 DOI: 10.1101/2023.09.20.558674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG element within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV crosslinking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing eleven of these identified crosslink sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG element is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG element with RNA-binding properties comparable to the canonical RGG/RG element. These RGG/RG elements serve redundant functions, with neither serving as the primary RBD. While in isolation each RGG/RG element has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling binding of most of the designed RNA set with low to mid-nanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlights the perils of a reductionist approach to defining biochemical activities in this system and paves the way for a detailed investigation of its RNA-binding specificity.
Collapse
Affiliation(s)
- Otto A. Kletzien
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T. Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| |
Collapse
|
55
|
Castillo-Zeledón A, Rivas-Solano O, Villalta-Romero F, Gómez-Espinoza O, Moreno E, Chaves-Olarte E, Guzmán-Verri C. The Brucella abortus two-component system response regulator BvrR binds to three DNA regulatory boxes in the upstream region of omp25. Front Microbiol 2023; 14:1241143. [PMID: 37779712 PMCID: PMC10538546 DOI: 10.3389/fmicb.2023.1241143] [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: 06/16/2023] [Accepted: 08/15/2023] [Indexed: 10/03/2023] Open
Abstract
Brucella abortus is a facultative extracellular-intracellular bacterial zoonotic pathogen worldwide. It is also a major cause of abortion in bovines, generating economic losses. The two-component regulatory system BvrR/BvrS modulates the expression of genes required to transition from extracellular to intracellular lifestyles. However, few regulatory regions of BvrR direct target genes have been studied. In this study, we characterized the regulatory region of omp25, a gene encoding an outer membrane protein that is positively regulated by TCS BvrR/BvrS. By omp25-lacZ reporter fusions and β-galactosidase activity assays, we found that the region between-262 and + 127 is necessary for transcriptional activity, particularly a 111-bp long fragment located from-262 to -152. In addition, we demonstrated the binding of P-BvrR to three sites within the -140 to +1 region. Two of these sites were delimited between -18 to +1 and - 99 to -76 by DNase I footprinting and called DNA regulatory boxes 1 and 2, respectively. The third binding site (box 3) was delimited from -140 to -122 by combining EMSA and fluorescence anisotropy results. A molecular docking analysis with HDOCK predicted BvrR-DNA interactions between 11, 13, and 12 amino acid residue-nucleotide pairs in boxes 1, 2, and 3, respectively. A manual sequence alignment of the three regulatory boxes revealed the presence of inverted and non-inverted repeats of five to eight nucleotides, partially matching DNA binding motifs previously described for BvrR. We propose that P-BvrR binds directly to up to three regulatory boxes and probably interacts with other transcription factors to regulate omp25 expression. This gene regulation model could apply to other BvrR target genes and to orthologs of the TCS BvrR/BvrS and Omp25 in phylogenetically closed Rhizobiales.
Collapse
Affiliation(s)
- Amanda Castillo-Zeledón
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Olga Rivas-Solano
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Campus Tecnológico Central Cartago, Cartago, Costa Rica
| | - Fabián Villalta-Romero
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Campus Tecnológico Central Cartago, Cartago, Costa Rica
| | - Olman Gómez-Espinoza
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, Campus Tecnológico Central Cartago, Cartago, Costa Rica
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| |
Collapse
|
56
|
Cai Y, Liu Y, Fan Y, Li X, Yang M, Xu D, Wang H, Deng XW, Li J. MYB112 connects light and circadian clock signals to promote hypocotyl elongation in Arabidopsis. THE PLANT CELL 2023; 35:3485-3503. [PMID: 37335905 PMCID: PMC10473211 DOI: 10.1093/plcell/koad170] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/05/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
Ambient light and the endogenous circadian clock play key roles in regulating Arabidopsis (Arabidopsis thaliana) seedling photomorphogenesis. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) acts downstream of both light and the circadian clock to promote hypocotyl elongation. Several members of the R2R3-MYB transcription factor (TF) family, the most common type of MYB TF family in Arabidopsis, have been shown to be involved in regulating photomorphogenesis. Nonetheless, whether R2R3-MYB TFs are involved in connecting the light and clock signaling pathways during seedling photomorphogenesis remains unknown. Here, we report that MYB112, a member of the R2R3-MYB family, acts as a negative regulator of seedling photomorphogenesis in Arabidopsis. The light signal promotes the transcription and protein accumulation of MYB112. myb112 mutants exhibit short hypocotyls in both constant light and diurnal cycles. MYB112 physically interacts with PIF4 to enhance the transcription of PIF4 target genes involved in the auxin pathway, including YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19), and IAA29. Furthermore, MYB112 directly binds to the promoter of LUX ARRHYTHMO (LUX), the central component of clock oscillators, to repress its expression mainly in the afternoon and relieve LUX-inhibited expression of PIF4. Genetic evidence confirms that LUX acts downstream of MYB112 in regulating hypocotyl elongation. Thus, the enhanced transcript accumulation and transcriptional activation activity of PIF4 by MYB112 additively promotes the expression of auxin-related genes, thereby increasing auxin synthesis and signaling and fine-tuning hypocotyl growth under diurnal cycles.
Collapse
Affiliation(s)
- Yupeng Cai
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongting Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yangyang Fan
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing 100097, China
| | - Xitao Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- School of Life Science, Huizhou University, Huizhou 516007, China
| | - Maosheng Yang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking–Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
57
|
Hong X, Tong X, Xie J, Liu P, Liu X, Song Q, Liu S, Liu S. An updated dataset and a structure-based prediction model for protein-RNA binding affinity. Proteins 2023; 91:1245-1253. [PMID: 37186412 DOI: 10.1002/prot.26503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/08/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Understanding the process of protein-RNA interaction is essential for structural biology. The thermodynamic process is an important part to uncover the protein-RNA interaction mechanism. The regulatory networks between protein and RNA in organisms are dominated by the binding or dissociation in the cells. Therefore, determining the binding affinity for protein-RNA complexes can help us to understand the regulation mechanism of protein-RNA interaction. Since it is time-consuming and labor-intensive to determine the binding affinity for protein-RNA complexes by experimental methods, it is necessary and urgent to develop computational methods to predict that. To develop a binding affinity prediction model, first we update the dataset of protein-RNA binding affinity benchmark (PRBAB), which includes 145 complexes now. Second, we extract the structural features based on complex structure, and then we analyze and select the representative structural features to train the regression model. Third, we random select the subset from the PRBAB2.0 to fit the protein-RNA binding affinity determined by experiment. In the end, we tested our model on the nonredundant PDBbind dataset, and the results showed that Pearson correlation coefficient r = .57 and RMSE = 2.51 kcal/mol. The Pearson correlation coefficient achieves 0.7 while removing 5 complex structures with modified residues/nucleotides and metal ions. While testing on ProNAB, the results showed that 71.60% of the prediction achieves Pearson correlation coefficient r = .61 and RMSE = 1.56 kcal/mol with experiment values.
Collapse
Affiliation(s)
- Xu Hong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoxue Tong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Juan Xie
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Pinyu Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xudong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Song
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Sen Liu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China
| | - Shiyong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China
| |
Collapse
|
58
|
Antika TR, Nazilah KR, Chrestella DJ, Wang TL, Tseng YK, Wang SC, Hsu HL, Wang SW, Chuang TH, Pan HC, Horng JC, Wang CC. Sequence-specific targeting of Caenorhabditis elegans C-Ala to the D-loop of tRNA Ala. J Biol Chem 2023; 299:105149. [PMID: 37567477 PMCID: PMC10485164 DOI: 10.1016/j.jbc.2023.105149] [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] [Received: 03/13/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Alanyl-tRNA synthetase retains a conserved prototype structure throughout its biology. Nevertheless, its C-terminal domain (C-Ala) is highly diverged and has been shown to play a role in either tRNA or DNA binding. Interestingly, we discovered that Caenorhabditis elegans cytoplasmic C-Ala (Ce-C-Alac) robustly binds both ligands. How Ce-C-Alac targets its cognate tRNA and whether a similar feature is conserved in its mitochondrial counterpart remain elusive. We show that the N- and C-terminal subdomains of Ce-C-Alac are responsible for DNA and tRNA binding, respectively. Ce-C-Alac specifically recognized the conserved invariant base G18 in the D-loop of tRNAAla through a highly conserved lysine residue, K934. Despite bearing little resemblance to other C-Ala domains, C. elegans mitochondrial C-Ala robustly bound both tRNAAla and DNA and maintained targeting specificity for the D-loop of its cognate tRNA. This study uncovers the underlying mechanism of how C. elegans C-Ala specifically targets the D-loop of tRNAAla.
Collapse
Affiliation(s)
- Titi Rindi Antika
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | | | | | - Tzu-Ling Wang
- Graduate Institute of Mathematics and Science Education, National Tsing Hua University, Hsinchu City, Taiwan
| | - Yi-Kuan Tseng
- Graduate Institute of Statistics, National Central University, Taoyuan, Taiwan
| | - Sun-Chong Wang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Hsin-Ling Hsu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Shao-Win Wang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Miaoli, Taiwan
| | - Hung-Chuan Pan
- Department of Neurosurgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, Taoyuan, Taiwan.
| |
Collapse
|
59
|
Guan S, Zou Q, Wu H, Ding Y. Protein-DNA Binding Residues Prediction Using a Deep Learning Model With Hierarchical Feature Extraction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2619-2628. [PMID: 35834447 DOI: 10.1109/tcbb.2022.3190933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biologically important effects occur when proteins bind to other substances, of which binding to DNA is a crucial one. Therefore, accurate identification of protein-DNA binding residues is important for further understanding of the protein-DNA interaction mechanism. Although wet-lab methods can accurately obtain the location of bound residues, it requires significant human, financial and time costs. There is thus an urgent need to develop efficient computational-based methods. Most current state-of-the-art methods are two-step approaches: the first step uses a sliding window technique to extract residue features; the second step uses each residue as an input to the model for prediction. This has a negative impact on the efficiency of prediction and ease of use. In this study, we propose a sequence-to-sequence (seq2seq) model that can input the entire protein sequence of variable length and use two modules, Transformer Encoder Block and Feature Extracting Block, for hierarchical feature extraction, where Transformer Encoder Block is used to extract global features, and then Feature Extracting Block is used to extract local features to further improve the recognition capability of the model. The comparison results on two benchmark datasets, namely PDNA-543 and PDNA-41, prove the effectiveness of our method in identifying protein-DNA binding residues.
Collapse
|
60
|
Barbagallo C, Stella M, Ferrara C, Caponnetto A, Battaglia R, Barbagallo D, Di Pietro C, Ragusa M. RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases. EXPLORATION OF MEDICINE 2023:504-540. [DOI: 10.37349/emed.2023.00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
The idea that proteins are the main determining factors in the functioning of cells and organisms, and their dysfunctions are the first cause of pathologies, has been predominant in biology and biomedicine until recently. This protein-centered view was too simplistic and failed to explain the physiological and pathological complexity of the cell. About 80% of the human genome is dynamically and pervasively transcribed, mostly as non-protein-coding RNAs (ncRNAs), which competitively interact with each other and with coding RNAs generating a complex RNA network regulating RNA processing, stability, and translation and, accordingly, fine-tuning the gene expression of the cells. Qualitative and quantitative dysregulations of RNA-RNA interaction networks are strongly involved in the onset and progression of many pathologies, including cancers and degenerative diseases. This review will summarize the RNA species involved in the competitive endogenous RNA network, their mechanisms of action, and involvement in pathological phenotypes. Moreover, it will give an overview of the most advanced experimental and computational methods to dissect and rebuild RNA networks.
Collapse
Affiliation(s)
- Cristina Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | | | - Angela Caponnetto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Rosalia Battaglia
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Davide Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Cinzia Di Pietro
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| |
Collapse
|
61
|
Liao YC, Huang YT, Tseng CH, Liu CW, Liu PY. Comparative Genomics Identified PenR E151V Substitution Associated with Carbapenem-Resistance Burkholderia cepacia Complex and a Novel Burkholderia cepacia Complex Specific OXA-1043 Subgroup. Infect Drug Resist 2023; 16:5627-5635. [PMID: 37662974 PMCID: PMC10473398 DOI: 10.2147/idr.s418969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Purpose Burkholderia cepacia complex (Bcc) is a known significant opportunistic pathogen causing morbidity and mortality, particularly in those with cystic fibrosis, chronic granulomatous disease, or immunocompromising host. Mortality of Bcc bloodstream infections among non-cystic fibrosis patients remained high. The antibiotic treatment for Bcc infection is quite challenging due to its intrinsic resistance to most antibiotics, and the resistance to carbapenems was the biggest concern among them. We aimed to realize the mechanism of carbapenem resistance in Bcc. Patients and Methods Ten strains of Bcc were identified by the MALDI-TOF MS, and the drug susceptibility test was using VITEK 2 system. The Burkholderia cepacia complex genomes were sequenced via Nanopore GridIon. We also downloaded another ninety-five strains of Bcc from the National Center for Biotechnology Information database to evaluate the divergence between carbapenem-resistance and carbapenem-sensitive strains. Results The genetic organization between carbapenem-sensitive and carbapenem-resistant strains of Bcc showed no difference. However, in the carbapenem-sensitive strain, E151V substitution in PenR was detected. In addition, a novel specific OXA family subgroup, blaOXA-1043 in Burkholderia cenocepacia was discovered. Conclusion The E151V substitution in PenR may be associated with carbapenem-sensitive in Bcc. Moreover, the V151E mutation in PenR may be related to the activation of PenB, leading to Bcc resistance to carbapenems. Besides, a novel OXA family subgroup, blaOXA-1043, was found in Burkholderia cenocepacia, which differs from the previous OXA family.
Collapse
Affiliation(s)
- Ya-Chun Liao
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chia-Wei Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, National Chung Hsing University, Taichung, Taiwan
- Genome Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
| |
Collapse
|
62
|
Kwon EB, Kim SG, Kim YS, Kim B, Han SM, Lee HJ, Choi HM, Choi JG. Castanea crenata honey reduces influenza infection by activating the innate immune response. Front Immunol 2023; 14:1157506. [PMID: 37711616 PMCID: PMC10497975 DOI: 10.3389/fimmu.2023.1157506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/31/2023] [Indexed: 09/16/2023] Open
Abstract
Influenza is an acute respiratory disorder caused by the influenza virus and is associated with prolonged hospitalization and high mortality rates in older individuals and chronically ill patients. Vaccination is the most effective preventive strategy for ameliorating seasonal influenza. However, the vaccine is not fully effective in cases of antigenic mismatch with the viral strains circulating in the community. The emergence of resistance to antiviral drugs aggravates the situation. Therefore, developing new vaccines and antiviral drugs is essential. Castanea crenata honey (CH) is an extensively cultivated food worldwide and has been used as a nutritional supplement or herbal medicine. However, the potential anti-influenza properties of CH remain unexplored. In this study, the in vitro and in vivo antiviral effects of CH were assessed. CH significantly prevented influenza virus infection in mouse Raw264.7 macrophages. CH pretreatment inhibited the expression of the viral proteins M2, PA, and PB1 and enhanced the secretion of proinflammatory cytokines and type-I interferon (IFN)-related proteins in vitro. CH increased the expression of RIG-1, mitochondrial antiviral signaling (MAVS) protein, and IFN-inducible transmembrane protein, which interferes with virus replication. CH reduced body weight loss by 20.9%, increased survival by 60%, and decreased viral replication and inflammatory response in the lungs of influenza A virus-infected mice. Therefore, CH stimulates an antiviral response in murine macrophages and mice by preventing viral infection through the RIG-1-mediated MAVS pathway. Further investigation is warranted to understand the molecular mechanisms involved in the protective effects of CH on influenza virus infection.
Collapse
Affiliation(s)
- Eun-Bin Kwon
- Korean Medicine Application Center, Korea Institute of Oriental Medicine, Daegu, Republic of Korea
| | - Se-Gun Kim
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Young Soo Kim
- Korean Medicine Application Center, Korea Institute of Oriental Medicine, Daegu, Republic of Korea
| | - Buyun Kim
- Korean Medicine Application Center, Korea Institute of Oriental Medicine, Daegu, Republic of Korea
| | - Sang Mi Han
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Hye Jin Lee
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Hong Min Choi
- Department of Agricultural Biology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Jang-Gi Choi
- Korean Medicine Application Center, Korea Institute of Oriental Medicine, Daegu, Republic of Korea
| |
Collapse
|
63
|
Li J, Qiu JX, Zeng QH, Zhang N, Xu SX, Jin J, Dong ZC, Chen L, Huang W. OsTOC1 plays dual roles in the regulation of plant circadian clock by functioning as a direct transcription activator or repressor. Cell Rep 2023; 42:112765. [PMID: 37421622 DOI: 10.1016/j.celrep.2023.112765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/28/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
Plant clock function relies on precise timing of gene expression through complex regulatory networks consisting of activators and repressors at the core of oscillators. Although TIMING OF CAB EXPRESSION 1 (TOC1) has been recognized as a repressor involved in shaping oscillations and regulating clock-driven processes, its potential to directly activate gene expression remains unclear. In this study, we find that OsTOC1 primarily acts as a transcriptional repressor for core clock components, including OsLHY and OsGI. Here, we show that OsTOC1 possesses the ability to directly activate the expression of circadian target genes. Through binding to the promoters of OsTGAL3a/b, transient activation of OsTOC1 induces the expression of OsTGAL3a/b, indicating its role as an activator contributing to pathogen resistance. Moreover, TOC1 participates in regulating multiple yield-related traits in rice. These findings suggest that TOC1's function as a transcriptional repressor is not inherent, providing flexibility to circadian regulations, particularly in outputs.
Collapse
Affiliation(s)
- Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jia-Xin Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Qing-Hua Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Ning Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Shu-Xuan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China
| | - Jian Jin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Zhi-Cheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
64
|
Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL. Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA. RSC Chem Biol 2023; 4:486-493. [PMID: 37415868 PMCID: PMC10320839 DOI: 10.1039/d3cb00053b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/09/2023] [Indexed: 07/08/2023] Open
Abstract
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide-DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins.
Collapse
Affiliation(s)
- Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| |
Collapse
|
65
|
Watkin SAJ, Bennie RZ, Gilkes JM, Nock VM, Pearce FG, Dobson RCJ. On the utility of microfluidic systems to study protein interactions: advantages, challenges, and applications. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:459-471. [PMID: 36583735 PMCID: PMC9801160 DOI: 10.1007/s00249-022-01626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
Within the complex milieu of a cell, which comprises a large number of different biomolecules, interactions are critical for function. In this post-reductionist era of biochemical research, the 'holy grail' for studying biomolecular interactions is to be able to characterize them in native environments. While there are a limited number of in situ experimental techniques currently available, there is a continuing need to develop new methods for the analysis of biomolecular complexes that can cope with the additional complexities introduced by native-like solutions. We think approaches that use microfluidics allow researchers to access native-like environments for studying biological problems. This review begins with a brief overview of the importance of studying biomolecular interactions and currently available methods for doing so. Basic principles of diffusion and microfluidics are introduced and this is followed by a review of previous studies that have used microfluidics to measure molecular diffusion and a discussion of the advantages and challenges of this technique.
Collapse
Affiliation(s)
- Serena A J Watkin
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel Z Bennie
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jenna M Gilkes
- Protein Science and Engineering Team, Callaghan Innovation, Christchurch, New Zealand
| | - Volker M Nock
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand.
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia.
| |
Collapse
|
66
|
Zhang X, Cao Y, Liu Y, Lei Y, Zhai R, Chen W, Shi G, Jin JM, Liang C, Tang SY. Designing glucose utilization "highway" for recombinant biosynthesis. Metab Eng 2023; 78:235-247. [PMID: 37394056 DOI: 10.1016/j.ymben.2023.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
cAMP receptor protein (CRP) is known as a global regulatory factor mainly mediating carbon source catabolism. Herein, we successfully engineered CRP to develop microbial chassis cells with improved recombinant biosynthetic capability in minimal medium with glucose as single carbon source. The obtained best-performing cAMP-independent CRPmu9 mutant conferred both faster cell growth and a 133-fold improvement in expression level of lac promoter in presence of 2% glucose, compared with strain under regulation of CRPwild-type. Promoters free from "glucose repression" are advantageous for recombinant expression, as glucose is a frequently used inexpensive carbon source in high-cell-density fermentations. Transcriptome analysis demonstrated that the CRP mutant globally rewired cell metabolism, displaying elevated tricarboxylic acid cycle activity; reduced acetate formation; increased nucleotide biosynthesis; and improved ATP synthesis, tolerance, and stress-resistance activity. Metabolites analysis confirmed the enhancement of glucose utilization with the upregulation of glycolysis and glyoxylate-tricarboxylic acid cycle. As expected, an elevated biosynthetic capability was demonstrated with vanillin, naringenin and caffeic acid biosynthesis in strains regulated by CRPmu9. This study has expanded the significance of CRP optimization into glucose utilization and recombinant biosynthesis, beyond the conventionally designated carbon source utilization other than glucose. The Escherichiacoli cell regulated by CRPmu9 can be potentially used as a beneficial chassis for recombinant biosynthesis.
Collapse
Affiliation(s)
- Xuanxuan Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufeng Cao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Liu
- Yingsheng (Beijing) Biotechnology Co., Ltd., Beijing, 100081, China
| | - Yanyan Lei
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruixue Zhai
- Yingsheng (Beijing) Biotechnology Co., Ltd., Beijing, 100081, China
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guizhi Shi
- Yingsheng (Beijing) Biotechnology Co., Ltd., Beijing, 100081, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing, 100048, China.
| | - Chaoning Liang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
67
|
de Souza-Neto RR, Vasconcelos FNDC, Teper D, Carvalho IGB, Takita MA, Benedetti CE, Wang N, de Souza AA. The Expansin Gene CsLIEXP1 Is a Direct Target of CsLOB1 in Citrus. PHYTOPATHOLOGY 2023; 113:1266-1277. [PMID: 36825333 DOI: 10.1094/phyto-11-22-0424-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Transcription activator-like effectors are key virulence factors of Xanthomonas. They are secreted into host plant cells and mimic transcription factors inducing the expression of host susceptibility (S) genes. In citrus, CsLOB1 is a direct target of PthA4, the primary effector associated with citrus canker symptoms. CsLOB1 is a transcription factor, and its expression is required for canker symptoms induced by Xanthomonas citri subsp. citri. Several genes are up-regulated by PthA4; however, only CsLOB1 was described as an S gene induced by PthA4. Here, we investigated whether other up-regulated genes could be direct targets of PthA4 or CsLOB1. Seven up-regulated genes by PthA4 were investigated; however, an expansin-coding gene was more induced than CsLOB1. In Nicotiana benthamiana transient expression experiments, we demonstrate that the expansin-coding gene, referred here to as CsLOB1-INDUCED EXPANSIN 1 (CsLIEXP1), is not a direct target of PthA4, but CsLOB1. Interestingly, CsLIEXP1 was induced by CsLOB1 even without the predicted CsLOB1 binding site, which suggested that CsLOB1 has other unknown binding sites. We also investigated the minimum promoter regulated by CsLOB1, and this region and LOB1 domain were conserved among citrus species and relatives, which suggests that the interaction PthA4-CsLOB1-CsLIEXP1 is conserved in citrus species and relatives. This is the first study that experimentally demonstrated a CsLOB1 downstream target and lays the foundation to identify other new targets. In addition, we demonstrated that the CsLIEXP1 is a putative S gene indirectly induced by PthA4, which may serve as the target for genome editing to generate citrus canker-resistant varieties.
Collapse
Affiliation(s)
- Reinaldo Rodrigues de Souza-Neto
- Citrus Research Center "Sylvio Moreira", Agronomic Institute-IAC, Brazil
- Departament of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Brazil
| | | | - Doron Teper
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, Volcani Center, Israel
| | | | | | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Brazil
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, U.S.A
| | | |
Collapse
|
68
|
Miller LG, Demny M, Tamamis P, Contreras LM. Characterization of epitranscriptome reader proteins experimentally and in silico: Current knowledge and future perspectives beyond the YTH domain. Comput Struct Biotechnol J 2023; 21:3541-3556. [PMID: 37501707 PMCID: PMC10371769 DOI: 10.1016/j.csbj.2023.06.018] [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: 04/20/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
To date, over 150 chemical modifications to the four canonical RNA bases have been discovered, known collectively as the epitranscriptome. Many of these modifications have been implicated in a variety of cellular processes and disease states. Additional work has been done to identify proteins known as "readers" that selectively interact with RNAs that contain specific chemical modifications. Protein interactomes with N6-methyladenosine (m6A), N1-methyladenosine (m1A), N5-methylcytosine (m5C), and 8-oxo-7,8-dihydroguanosine (8-oxoG) have been determined, mainly through experimental advances in proteomics techniques. However, relatively few proteins have been confirmed to bind directly to RNA containing these modifications. Furthermore, for many of these protein readers, the exact binding mechanisms as well as the exclusivity for recognition of modified RNA species remain elusive, leading to questions regarding their roles within different cellular processes. In the case of the YT-521B homology (YTH) family of proteins, both experimental and in silico techniques have been leveraged to provide valuable biophysical insights into the mechanisms of m6A recognition at atomic resolution. To date, the YTH family is one of the best characterized classes of readers. Here, we review current knowledge about epitranscriptome recognition of the YTH domain proteins from previously published experimental and computational studies. We additionally outline knowledge gaps for proteins beyond the well-studied human YTH domains and the current in silico techniques and resources that can enable investigation of protein interactions with modified RNA outside of the YTH-m6A context.
Collapse
Affiliation(s)
- Lucas G. Miller
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Madeline Demny
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
69
|
Khan D, Terenzi F, Liu G, Ghosh PK, Ye F, Nguyen K, China A, Ramachandiran I, Chakraborty S, Stefan J, Khan K, Vasu K, Dong F, Willard B, Karn J, Gack MU, Fox PL. A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon. Nat Commun 2023; 14:3385. [PMID: 37296097 PMCID: PMC10250186 DOI: 10.1038/s41467-023-39091-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, generates multiple protein-coding, subgenomic RNAs (sgRNAs) from a longer genomic RNA, all bearing identical termini with poorly understood roles in regulating viral gene expression. Insulin and interferon-gamma, two host-derived, stress-related agents, and virus spike protein, induce binding of glutamyl-prolyl-tRNA synthetase (EPRS1), within an unconventional, tetra-aminoacyl-tRNA synthetase complex, to the sgRNA 3'-end thereby enhancing sgRNA expression. We identify an EPRS1-binding sarbecoviral pan-end activating RNA (SPEAR) element in the 3'-end of viral RNAs driving agonist-induction. Translation of another co-terminal 3'-end feature, ORF10, is necessary for SPEAR-mediated induction, independent of Orf10 protein expression. The SPEAR element enhances viral programmed ribosomal frameshifting, thereby expanding its functionality. By co-opting noncanonical activities of a family of essential host proteins, the virus establishes a post-transcriptional regulon stimulating global viral RNA translation. A SPEAR-targeting strategy markedly reduces SARS-CoV-2 titer, suggesting a pan-sarbecoviral therapeutic modality.
Collapse
Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic Foundation, Port St. Lucie, FL, 34987, USA
| | - Prabar K Ghosh
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Fengchun Ye
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kien Nguyen
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Shruti Chakraborty
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Jennifer Stefan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Franklin Dong
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Belinda Willard
- Lerner Research Institute Proteomics and Metabolomics Core, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic Foundation, Port St. Lucie, FL, 34987, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
| |
Collapse
|
70
|
Vega-Badillo J, Zamore PD, Jouravleva K. Protocol to measure protein-RNA binding using double filter-binding assays followed by phosphorimaging or high-throughput sequencing. STAR Protoc 2023; 4:102336. [PMID: 37270783 DOI: 10.1016/j.xpro.2023.102336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/29/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2023] Open
Abstract
Binding affinity quantitatively describes the strength of a molecular interaction and is reported by the equilibrium dissociation constant (KD). Here, we present a protocol to measure KD of mammalian microRNA-loaded Argonaute2 protein by double filter binding. We describe steps for radiolabeling target RNA, measuring concentration of binding-competent protein, setting up binding reactions, separating protein-bound RNA from protein-unbound RNA, preparing library for Illumina sequencing, and performing data analysis. Our protocol is easily applied to other RNA- or DNA-binding proteins. For complete details on the use and execution of this protocol, please refer to Jouravleva et al.1.
Collapse
Affiliation(s)
- Joel Vega-Badillo
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Karina Jouravleva
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| |
Collapse
|
71
|
Martins JR, Pinheiro DG, Ahmed ACC, Giuliatti S, Mizzen CA, Bitondi MMG. Genome-wide analysis of the chromatin sites targeted by HEX 70a storage protein in the honeybee brain and fat body. INSECT MOLECULAR BIOLOGY 2023; 32:277-304. [PMID: 36630080 DOI: 10.1111/imb.12830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/12/2022] [Indexed: 05/15/2023]
Abstract
Hexamerins, the proteins massively stored in the larval haemolymph of insects, are gradually used throughout metamorphosis as a source of raw material and energy for the development of adult tissues. Such behaviour defined hexamerins as storage proteins. Immunofluorescence experiments coupled with confocal microscopy show a hexamerin, HEX 70a, in the nucleus of the brain and fat body cells from honeybee workers, an unexpected localization for a storage protein. HEX 70a colocalizes with fibrillarin, a nucleolar-specific protein and H3 histone, thus suggesting a potential role as a chromatin-binding protein. This was investigated through chromatin immunoprecipitation and high-throughput DNA sequencing (ChIP-seq). The significant HEX 70a-DNA binding sites were mainly localized at the intergenic, promoter and intronic regions. HEX 70a targeted DNA stretches mapped to the genomic regions encompassing genes with relevant functional attributes. Several HEX 70a targeted genes were associated with H3K27ac or/and H3K27me3, known as active and repressive histone marks. Brain and fat body tissues shared a fraction of the HEX 70 targeted genes, and tissue-specific targets were also detected. The presence of overrepresented DNA motifs in the binding sites is consistent with specific HEX 70a-chromatin association. In addition, a search for HEX 70a targets in RNA-seq public libraries of fat bodies from nurses and foragers revealed differentially expressed targets displaying hex 70a-correlated developmental expression, thus supporting a regulatory activity for HEX 70a. Our results support the premise that HEX 70a is a moonlighting protein that binds chromatin and has roles in the brain and fat body cell nuclei, apart from its canonical role as a storage protein.
Collapse
Affiliation(s)
- Juliana R Martins
- Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, Brazil
| | - Daniel G Pinheiro
- Departamento de Biotecnologia Agropecuária e Ambiental, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, Brazil
| | - Amy C C Ahmed
- University of Illinois at Urbana-Champaign, Carl R. Woese Institute for Genomic Biology, Urbana, Illinois, USA
| | - Silvana Giuliatti
- Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, Brazil
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Márcia M G Bitondi
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Ribeirão Preto, Brazil
| |
Collapse
|
72
|
López Rodríguez M, Arasu UT, Kaikkonen MU. Exploring the genetic basis of coronary artery disease using functional genomics. Atherosclerosis 2023; 374:87-98. [PMID: 36801133 DOI: 10.1016/j.atherosclerosis.2023.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Genome-wide Association Studies (GWAS) have identified more than 300 loci associated with coronary artery disease (CAD), defining the genetic risk map of the disease. However, the translation of the association signals into biological-pathophysiological mechanisms constitute a major challenge. Through a group of examples of studies focused on CAD, we discuss the rationale, basic principles and outcomes of the main methodologies implemented to prioritize and characterize causal variants and their target genes. Additionally, we highlight the strategies as well as the current methods that integrate association and functional genomics data to dissect the cellular specificity underlying the complexity of disease mechanisms. Despite the limitations of existing approaches, the increasing knowledge generated through functional studies helps interpret GWAS maps and opens novel avenues for the clinical usability of association data.
Collapse
Affiliation(s)
- Maykel López Rodríguez
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland; Department of Pathology and Laboratory Medicine, University of California, UCLA, Los Angeles, USA.
| | - Uma Thanigai Arasu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland.
| |
Collapse
|
73
|
Wu YH, Huang YA, Li JQ, You ZH, Hu PW, Hu L, Leung VCM, Du ZH. Knowledge graph embedding for profiling the interaction between transcription factors and their target genes. PLoS Comput Biol 2023; 19:e1011207. [PMID: 37339154 PMCID: PMC10313080 DOI: 10.1371/journal.pcbi.1011207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 06/30/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Interactions between transcription factor and target gene form the main part of gene regulation network in human, which are still complicating factors in biological research. Specifically, for nearly half of those interactions recorded in established database, their interaction types are yet to be confirmed. Although several computational methods exist to predict gene interactions and their type, there is still no method available to predict them solely based on topology information. To this end, we proposed here a graph-based prediction model called KGE-TGI and trained in a multi-task learning manner on a knowledge graph that we specially constructed for this problem. The KGE-TGI model relies on topology information rather than being driven by gene expression data. In this paper, we formulate the task of predicting interaction types of transcript factor and target genes as a multi-label classification problem for link types on a heterogeneous graph, coupled with solving another link prediction problem that is inherently related. We constructed a ground truth dataset as benchmark and evaluated the proposed method on it. As a result of the 5-fold cross experiments, the proposed method achieved average AUC values of 0.9654 and 0.9339 in the tasks of link prediction and link type classification, respectively. In addition, the results of a series of comparison experiments also prove that the introduction of knowledge information significantly benefits to the prediction and that our methodology achieve state-of-the-art performance in this problem.
Collapse
Affiliation(s)
- Yang-Han Wu
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China
| | - Yu-An Huang
- School of Computer Science, Northwesterm Polytechnical University, Xi’an, Shaanxi, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China
| | - Zhu-Hong You
- School of Computer Science, Northwesterm Polytechnical University, Xi’an, Shaanxi, China
| | - Peng-Wei Hu
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China
| | - Lun Hu
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China
| | - Victor C. M. Leung
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China
| | - Zhi-Hua Du
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China
| |
Collapse
|
74
|
Nandavaram A, Nandakumar A, Kashif GM, Sagar AL, Shailaja G, Ramesh A, Siddavattam D. Unusual Relationship between Iron Deprivation and Organophosphate Hydrolase Expression. Appl Environ Microbiol 2023; 89:e0190322. [PMID: 37074175 PMCID: PMC10231211 DOI: 10.1128/aem.01903-22] [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: 11/15/2022] [Accepted: 03/08/2023] [Indexed: 04/20/2023] Open
Abstract
Organophosphate hydrolases (OPH), hitherto known to hydrolyze the third ester bond of organophosphate (OP) insecticides and nerve agents, have recently been shown to interact with outer membrane transport components, namely, TonB and ExbB/ExbD. In an OPH negative background, Sphingopyxis wildii cells failed to transport ferric enterobactin and showed retarded growth under iron-limiting conditions. We now show the OPH-encoding organophosphate degradation (opd) gene from Sphingobium fuliginis ATCC 27551 to be part of the iron regulon. A fur-box motif found to be overlapping with the transcription start site (TSS) of the opd gene coordinates with an iron responsive element (IRE) RNA motif identified in the 5' coding region of the opd mRNA to tightly regulate opd gene expression. The fur-box motif serves as a target for the Fur repressor in the presence of iron. A decrease in iron concentration leads to the derepression of opd. IRE RNA inhibits the translation of opd mRNA and serves as a target for apo-aconitase (IRP). The IRP recruited by the IRE RNA abrogates IRE-mediated translational inhibition. Our findings establish a novel, multilayered, iron-responsive regulation that is crucial for OPH function in the transport of siderophore-mediated iron uptake. IMPORTANCE Sphingobium fuliginis, a soil-dwelling microbe isolated from agricultural soils, was shown to degrade a variety of insecticides and pesticides. These synthetic chemicals function as potent neurotoxins, and they belong to a class of chemicals termed organophosphates. S. fuliginis codes for OPH, an enzyme that has been shown to be involved in the metabolism of several organophosphates and their derivatives. Interestingly, OPH has also been shown to facilitate siderophore-mediated iron uptake in S. fuliginis and in another Sphingomonad, namely, Sphingopyxis wildii, implying that this organophosphate-metabolizing protein has a role in iron homeostasis, as well. Our research dissects the underlying molecular mechanisms linking iron to the expression of OPH, prompting a reconsideration of the role of OPH in Sphingomonads and a reevaluation of the evolutionary origins of the OPH proteins from soil bacteria.
Collapse
Affiliation(s)
- Aparna Nandavaram
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Anirudh Nandakumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
- The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bengaluru, Karnataka, India
| | - G. M. Kashif
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - G. Shailaja
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Arati Ramesh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru, India
| | - Dayananda Siddavattam
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
- Department of Biochemistry, School of Sciences, GITAM University, Visakhapatnam, India
| |
Collapse
|
75
|
Wang JE, Zhou YC, Wu BH, Chen XC, Zhai J, Tan JH, Huang ZS, Chen SB. A rapid and highly sensitive immunosorbent assay to monitor helicases unwinding diverse nucleic acid structures. Analyst 2023; 148:2343-2351. [PMID: 37185609 DOI: 10.1039/d2an01989b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Helicases are crucial enzymes in DNA and RNA metabolism and function by unwinding particular nucleic acid structures. However, most convenient and high-throughput helicase assays are limited to the typical duplex DNA. Herein, we developed an immunosorbent assay to monitor the Werner syndrome (WRN) helicase unwinding a wide range of DNA structures, such as a replication fork, a bubble, Holliday junction, G-quadruplex and hairpin. This assay could sensitively detect the unwinding of DNA structures with detection limits around 0.1 nM, and accurately monitor the substrate-specificity of WRN with a comparatively less time-consuming and high throughput process. Remarkably, we have established that this new assay was compatible in evaluating helicase inhibitors and revealed that the inhibitory effect was substrate-dependent, suggesting that diverse substrate structures other than duplex structures should be considered in discovering new inhibitors. Our study provided a foundational example for using this new assay as a powerful tool to study helicase functions and discover potent inhibitors.
Collapse
Affiliation(s)
- Jia-En Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Ying-Chen Zhou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Bi-Han Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Xiu-Cai Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Junqiu Zhai
- Guangzhou University of Chinese Medicine, Guangzhou, Guangzhou 510330, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| |
Collapse
|
76
|
Yang S, Gong W, Zhou T, Sun X, Chen L, Zhou W, Li C. emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model. Brief Bioinform 2023:7165253. [PMID: 37193676 DOI: 10.1093/bib/bbad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/18/2023] Open
Abstract
Protein-deoxyribonucleic acid (DNA) interactions are important in a variety of biological processes. Accurately predicting protein-DNA binding affinity has been one of the most attractive and challenging issues in computational biology. However, the existing approaches still have much room for improvement. In this work, we propose an ensemble model for Protein-DNA Binding Affinity prediction (emPDBA), which combines six base models with one meta-model. The complexes are classified into four types based on the DNA structure (double-stranded or other forms) and the percentage of interface residues. For each type, emPDBA is trained with the sequence-based, structure-based and energy features from binding partners and complex structures. Through feature selection by the sequential forward selection method, it is found that there do exist considerable differences in the key factors contributing to intermolecular binding affinity. The complex classification is beneficial for the important feature extraction for binding affinity prediction. The performance comparison of our method with other peer ones on the independent testing dataset shows that emPDBA outperforms the state-of-the-art methods with the Pearson correlation coefficient of 0.53 and the mean absolute error of 1.11 kcal/mol. The comprehensive results demonstrate that our method has a good performance for protein-DNA binding affinity prediction. Availability and implementation: The source code is available at https://github.com/ChunhuaLiLab/emPDBA/.
Collapse
Affiliation(s)
- Shuang Yang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Tong Zhou
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Xiaohan Sun
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Lei Chen
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Wenxue Zhou
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| |
Collapse
|
77
|
Gautam P, Sinha SK. Theoretical investigation of functional responses of bio-molecular assembly networks. SOFT MATTER 2023; 19:3803-3817. [PMID: 37191191 DOI: 10.1039/d2sm01530g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cooperative protein-protein and protein-DNA interactions form programmable complex assemblies, often performing non-linear gene regulatory operations involved in signal transductions and cell fate determination. The apparent structure of those complex assemblies is very similar, but their functional response strongly depends on the topology of the protein-DNA interaction networks. Here, we demonstrate how the coordinated self-assembly creates gene regulatory network motifs that corroborate the existence of a precise functional response at the molecular level using thermodynamic and dynamic analyses. Our theoretical and Monte Carlo simulations show that a complex network of interactions can form a decision-making loop, such as feedback and feed-forward circuits, only by a few molecular mechanisms. We characterize each possible network of interactions by systematic variations of free energy parameters associated with the binding among biomolecules and DNA looping. We also find that the higher-order networks exhibit alternative steady states from the stochastic dynamics of each network. We capture this signature by calculating stochastic potentials and attributing their multi-stability features. We validate our findings against the Gal promoter system in yeast cells. Overall, we show that the network topology is vital in phenotype diversity in regulatory circuits.
Collapse
Affiliation(s)
- Pankaj Gautam
- Theoretical and Computational Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India.
| | - Sudipta Kumar Sinha
- Theoretical and Computational Biophysical Chemistry Group, Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India.
| |
Collapse
|
78
|
Yang C, Liu C, Li S, Zhang Y, Zhang Y, Wang X, Xiang W. The Transcription Factors WRKY41 and WRKY53 Mediate Early Flowering Induced by the Novel Plant Growth Regulator Guvermectin in Arabidopsis thaliana. Int J Mol Sci 2023; 24:ijms24098424. [PMID: 37176133 PMCID: PMC10178944 DOI: 10.3390/ijms24098424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/19/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Flowering is a crucial stage for plant reproductive success; therefore, the regulation of plant flowering has been widely researched. Although multiple well-defined endogenous and exogenous flowering regulators have been reported, new ones are constantly being discovered. Here, we confirm that a novel plant growth regulator guvermectin (GV) induces early flowering in Arabidopsis. Interestingly, our genetic experiments newly demonstrated that WRKY41 and its homolog WRKY53 were involved in GV-accelerated flowering as positive flowering regulators. Overexpression of WRKY41 or WRKY53 resulted in an early flowering phenotype compared to the wild type (WT). In contrast, the w41/w53 double mutants showed a delay in GV-accelerated flowering. Gene expression analysis showed that flowering regulatory genes SOC1 and LFY were upregulated in GV-treated WT, 35S:WRKY41, and 35S:WRKY53 plants, but both declined in w41/w53 mutants with or without GV treatment. Meanwhile, biochemical assays confirmed that SOC1 and LFY were both direct targets of WRKY41 and WRKY53. Furthermore, the early flowering phenotype of 35S:WRKY41 lines was abolished in the soc1 or lfy background. Together, our results suggest that GV plays a function in promoting flowering, which was co-mediated by WRKY41 and WRKY53 acting as new flowering regulators by directly activating the transcription of SOC1 and LFY in Arabidopsis.
Collapse
Affiliation(s)
- Chenyu Yang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chongxi Liu
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin 150030, China
| | - Shanshan Li
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanyan Zhang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yi Zhang
- Department of Biology, School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiangjing Wang
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin 150030, China
| | - Wensheng Xiang
- The State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Agriculture Biological Functional Gene of Heilongjiang Provincial Education Committee, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin 150030, China
| |
Collapse
|
79
|
Song Q, Gong W, Yu X, Ji K, Jiang Y, Chang Y, Yuan D. Transcriptome and Anatomical Comparisons Reveal the Effects of Methyl Jasmonate on the Seed Development of Camellia oleifera. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6747-6762. [PMID: 37026572 DOI: 10.1021/acs.jafc.3c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Seed is a major storage organ that determines the yield and quality of Camellia oleifera (C. oleifera). Methyl jasmonate (MeJA) is a signaling molecule involved in plant growth and development. However, the role of MeJA in the development of C. oleifera seeds remains a mystery. This study demonstrated that the larger seeds induced by MeJA resulted from more cell numbers and a larger cell area in the outer seed coat and embryo at the cellular level. At the molecular level, MeJA could regulate the expression of factors in the known signaling pathways of seed size control as well as cell proliferation and expansion, resulting in larger seeds. Furthermore, the accumulation of oil and unsaturated fatty acids due to MeJA-inducement was attributed to the increased expression of fatty acid biosynthesis-related genes but reduced expression of fatty acid degradation-related genes. CoMYC2, a key regulator in jasmonate signaling, was considered a potential hub regulator which directly interacted with three hub genes (CoCDKB2-3, CoCYCB2-3, and CoXTH9) related to the seed size and two hub genes (CoACC1 and CoFAD2-3) related to oil accumulation and fatty acid biosynthesis by binding to their promoters. These findings provide an excellent target for the improvement of the yield and quality in C. oleifera.
Collapse
Affiliation(s)
- Qiling Song
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Wenfang Gong
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Xinran Yu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Ke Ji
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Yi Jiang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Yihong Chang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| |
Collapse
|
80
|
Wang R, Zhou T, Kong F, Hou B, Ye J, Wu H, Zhang H. AflQ1-Q2 represses lincomycin biosynthesis via multiple cascades in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2023; 107:2933-2945. [DOI: doi.org/10.1007/s00253-023-12429-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 10/09/2023]
|
81
|
Lechable M, Tang X, Siebert S, Feldbacher A, Fernández-Quintero ML, Breuker K, Juliano CE, Liedl KR, Hobmayer B, Hartl M. High Intrinsic Oncogenic Potential in the Myc-Box-Deficient Hydra Myc3 Protein. Cells 2023; 12:cells12091265. [PMID: 37174665 PMCID: PMC10177328 DOI: 10.3390/cells12091265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
The proto-oncogene myc has been intensively studied primarily in vertebrate cell culture systems. Myc transcription factors control fundamental cellular processes such as cell proliferation, cell cycle control and stem cell maintenance. Myc interacts with the Max protein and Myc/Max heterodimers regulate thousands of target genes. The genome of the freshwater polyp Hydra encodes four myc genes (myc1-4). Previous structural and biochemical characterization showed that the Hydra Myc1 and Myc2 proteins share high similarities with vertebrate c-Myc, and their expression patterns suggested a function in adult stem cell maintenance. In contrast, an additional Hydra Myc protein termed Myc3 is highly divergent, lacking the common N-terminal domain and all conserved Myc-boxes. Single cell transcriptome analysis revealed that the myc3 gene is expressed in a distinct population of interstitial precursor cells committed to nerve- and gland-cell differentiation, where the Myc3 protein may counteract the stemness actions of Myc1 and Myc2 and thereby allow the implementation of a differentiation program. In vitro DNA binding studies showed that Myc3 dimerizes with Hydra Max, and this dimer efficiently binds to DNA containing the canonical Myc consensus motif (E-box). In vivo cell transformation assays in avian fibroblast cultures further revealed an unexpected high potential for oncogenic transformation in the conserved Myc3 C-terminus, as compared to Hydra Myc2 or Myc1. Structure modeling of the Myc3 protein predicted conserved amino acid residues in its bHLH-LZ domain engaged in Myc3/Max dimerization. Mutating these amino acid residues in the human c-Myc (MYC) sequence resulted in a significant decrease in its cell transformation potential. We discuss our findings in the context of oncogenic transformation and cell differentiation, both relevant for human cancer, where Myc represents a major driver.
Collapse
Affiliation(s)
- Marion Lechable
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Xuechen Tang
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Angelika Feldbacher
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Bert Hobmayer
- Institute of Zoology, University of Innsbruck, 6020 Innsbruck, Austria
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus Hartl
- Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
- Institute of Biochemistry, University of Innsbruck, 6020 Innsbruck, Austria
| |
Collapse
|
82
|
Gupta P, Gupta RK, Gandhi BS, Singh P. Differential binding of CREB and REST/NRSF to NMDAR1 promoter is associated with the sex-selective cognitive deficit following postnatal PBDE-209 exposure in mice. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-26107-0. [PMID: 37002525 DOI: 10.1007/s11356-023-26107-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Neonatal exposure to decabromodiphenyl ether (PBDE-209), a widely used flame retardant, affects cognitive performances in the later stage of life in a sex-dependent manner. PBDE-209 interferes with glutamatergic signaling and N-methyl-D-aspartate receptor (NMDAR) subunits with unresolved regulatory mechanisms. This study exposed male and female mice pups through postnatal day (PND) 3-10 to PBDE-209 (oral dose: 0, 6, or 20 mg/kg body weight). The frontal cortex and hippocampus, collected from neonate (PND 11) and young (PND 60) mice, were analyzed for cAMP response element-binding protein (CREB) and RE1-silencing transcription factor/ Neuron-restrictive silencer factor (REST/NRSF) binding to NMDAR1 promoter and expression of NMDAR1 gene by electrophoretic mobility shift assay and semi-quantitative RT-PCR respectively. Behavioral changes were assessed using spontaneous alternation behavior and novel object recognition tests in young mice. In neonates, the binding of CREB was increased, while REST/NRSF was decreased significantly to their cognate NMDAR1 promoter sequences at the high dose of PBDE-209 in both the sexes. This reciprocal pattern of CREB and REST/NRSF interactions correlates with the up-regulation of NMDAR1 expression. Young males followed a similar pattern of CREB and REST/NRSF binding and NMDAR1 expression as in neonates. Surprisingly, young females did not show any alteration when compared to age-matched controls. Also, we found that only young males showed working and recognition memory deficits. These results indicate that early exposure to PBDE-209 interferes with CREB- and REST/NRSF-dependent regulation of the NMDAR1 gene in an acute setting. However, long-term effects persist only in young males that could be associated with cognitive impairment.
Collapse
Affiliation(s)
- Priya Gupta
- Department of Zoology, Women's College, Banaras Hindu University, Varanasi, UP, India
| | - Rajaneesh K Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, UP, India
| | - Behrose S Gandhi
- Department of Zoology, Women's College, Banaras Hindu University, Varanasi, UP, India
| | - Poonam Singh
- Department of Zoology, Women's College, Banaras Hindu University, Varanasi, UP, India.
| |
Collapse
|
83
|
Verma D, Hegde V, Kirkpatrick J, Carlomagno T. The EJC disassembly factor PYM is an intrinsically disordered protein and forms a fuzzy complex with RNA. Front Mol Biosci 2023; 10:1148653. [PMID: 37065448 PMCID: PMC10098021 DOI: 10.3389/fmolb.2023.1148653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
The discovery of several functional interactions where one or even both partners remain disordered has demonstrated that specific interactions do not necessarily require well-defined intermolecular interfaces. Here we describe a fuzzy protein–RNA complex formed by the intrinsically unfolded protein PYM and RNA. PYM is a cytosolic protein, which has been reported to bind the exon junction complex (EJC). In the process of oskar mRNA localization in Drosophila melanogaster, removal of the first intron and deposition of the EJC are essential, while PYM is required to recycle the EJC components after localization has been accomplished. Here we demonstrate that the first 160 amino acids of PYM (PYM1–160) are intrinsically disordered. PYM1–160 binds RNA independently of its nucleotide sequence, forming a fuzzy protein–RNA complex that is incompatible with PYM’s function as an EJC recycling factor. We propose that the role of RNA binding consists in down-regulating PYM activity by blocking the EJC interaction surface of PYM until localization has been accomplished. We suggest that the largely unstructured character of PYM may act to enable binding to a variety of diverse interaction partners, such as multiple RNA sequences and the EJC proteins Y14 and Mago.
Collapse
Affiliation(s)
- Deepshikha Verma
- Laboratory of NMR-based Integrative Structural Biology, Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Hanover, Germany
| | - Veena Hegde
- Laboratory of NMR-based Integrative Structural Biology, Centre for Biomolecular Drug Research (BMWZ) and Institute of Organic Chemistry, Leibniz University Hannover, Hanover, Germany
| | - John Kirkpatrick
- Laboratory of Integrative Structural Biology, School of Biosciences, College of LES, University of Birmingham, Birmingham, United Kingdom
| | - Teresa Carlomagno
- Laboratory of Integrative Structural Biology, School of Biosciences, College of LES, University of Birmingham, Birmingham, United Kingdom
- *Correspondence: Teresa Carlomagno,
| |
Collapse
|
84
|
Khatoon H, Raza RZ, Saleem S, Batool F, Arshad S, Abrar M, Ali S, Hussain I, Shubin NH, Abbasi AA. Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. BMC Mol Cell Biol 2023; 24:13. [PMID: 36991330 PMCID: PMC10053400 DOI: 10.1186/s12860-023-00474-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Abstract
Background
Human accelerated regions (HARs) are short conserved genomic sequences that have acquired significantly more nucleotide substitutions than expected in the human lineage after divergence from chimpanzees. The fast evolution of HARs may reflect their roles in the origin of human-specific traits. A recent study has reported positively-selected single nucleotide variants (SNVs) within brain-exclusive human accelerated enhancers (BE-HAEs) hs1210 (forebrain), hs563 (hindbrain) and hs304 (midbrain/forebrain). By including data from archaic hominins, these SNVs were shown to be Homo sapiens-specific, residing within transcriptional factors binding sites (TFBSs) for SOX2 (hs1210), RUNX1/3 (hs563), and FOS/JUND (hs304). Although these findings suggest that the predicted modifications in TFBSs may have some role in present-day brain structure, work is required to verify the extent to which these changes translate into functional variation.
Results
To start to fill this gap, we investigate the SOX2 SNV, with both forebrain expression and strong signal of positive selection in humans. We demonstrate that the HMG box of SOX2 binds in vitro with Homo sapiens-specific derived A-allele and ancestral T-allele carrying DNA sites in BE-HAE hs1210. Molecular docking and simulation analysis indicated highly favourable binding of HMG box with derived A-allele containing DNA site when compared to site carrying ancestral T-allele.
Conclusion
These results suggest that adoptive changes in TF affinity within BE-HAE hs1210 and other HAR enhancers in the evolutionary history of Homo sapiens might.
have brought about changes in gene expression patterns and have functional consequences on forebrain formation and evolution.
Methods
The present study employ electrophoretic mobility shift assays (EMSA) and molecular docking and molecular dynamics simulations approaches.
Collapse
|
85
|
Yang X, Luo X, Zhang Y, Zhang Z, OuYang X, Shi X, Lv X, Li F, Zhang S, Liu Y, Zhang D. Tomato chlorosis virus CPm protein is a pathogenicity determinant and suppresses host local RNA silencing induced by single-stranded RNA. Front Microbiol 2023; 14:1151747. [PMID: 37056753 PMCID: PMC10086252 DOI: 10.3389/fmicb.2023.1151747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
IntroductionTomato chlorosis virus (ToCV) is a typical member of the genus Crinivirus, which severely threatens Solanaceae crops worldwide. The CPm protein encoded by ToCV has been reported to be associated with virus transmission by vectors and is involved in RNA silencing suppression, while the mechanisms remain ambiguous.MethodsHere, ToCV CPm was ectopically expressed by a Potato virus X (PVX) vector and infiltrated into Nicotiana benthamiana wild-type and GFP-transgenic16c plants.ResultsThe phylogenetic analysis showed that the CPm proteins encoded by criniviruses were distinctly divergent in amino acid sequences and predicted conserved domains, and the ToCV CPm protein possesses a conserved domain homologous to the TIGR02569 family protein, which does not occur in other criniviruses. Ectopic expression of ToCV CPm using a PVX vector resulted in severe mosaic symptoms followed by a hypersensitive-like response in N. benthamiana. Furthermore, agroinfiltration assays in N. benthamiana wilt type or GFP-transgenic 16c indicated that ToCV CPm protein effectively suppressed local RNA silencing induced by single-stranded but not double-stranded RNA, which probably resulted from the activity of binding double-stranded but not single-stranded RNA by ToCV CPm protein.ConclusionTaken together, the results of this study suggest that the ToCV CPm protein possesses the dual activities of pathogenicity and RNA silencing, which might inhibit host post-transcriptional gene silencing (PTGS)-mediated resistance and is pivotal in the primary process of ToCV infecting hosts.
Collapse
Affiliation(s)
- Xiao Yang
- Longping Branch, College of Biology, Hunan University, Changsha, Hunan, China
| | - Xiangwen Luo
- Longping Branch, College of Biology, Hunan University, Changsha, Hunan, China
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
| | - Yu Zhang
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
| | - Zhanhong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha, Hunan, China
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
| | - Xian OuYang
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
| | - Xiaobin Shi
- Longping Branch, College of Biology, Hunan University, Changsha, Hunan, China
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
| | - Xiaoyuan Lv
- Technical Center of Changsha Customs, Changsha, Hunan, China
| | - Fan Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Songbai Zhang
- Longping Branch, College of Biology, Hunan University, Changsha, Hunan, China
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
- *Correspondence: Songbai Zhang,
| | - Yong Liu
- Longping Branch, College of Biology, Hunan University, Changsha, Hunan, China
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
- Yong Liu,
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha, Hunan, China
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
- Deyong Zhang,
| |
Collapse
|
86
|
Wang R, Zhou T, Kong F, Hou B, Ye J, Wu H, Zhang H. AflQ1-Q2 represses lincomycin biosynthesis via multiple cascades in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2023; 107:2933-2945. [PMID: 36930277 DOI: 10.1007/s00253-023-12429-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 03/18/2023]
Abstract
Lincomycin is a broad-spectrum antibiotic and particularly effective against Gram-positive pathogens. Albeit familiar with the biosynthetic mechanism of lincomycin, we know less about its regulation, limiting the rational design for strain improvement. We therefore analyzed two-component systems (TCSs) in Streptomyces lincolnensis, and selected eight TCS gene(s) to construct their deletion mutants utilizing CRISPR/Cas9 system. Among them, lincomycin yield increased in two strains (Δ3900-3901 and Δ5290-5291) while decreased in other four strains (Δ3415-3416, Δ4153-4154, Δ4985, and Δ7949). Considering the conspicuous effect, SLINC_5291-5290 (AflQ1-Q2) was subsequently studied in detail. Its repression on lincomycin biosynthesis was further proved by gene complementation and overexpression. By binding to a 16-bp palindromic motif, the response regulator AflQ1 inhibits the transcription of its encoding gene and the expression of eight operons inside the lincomycin synthetic cluster (headed by lmbA, lmbJ, lmbK, lmbV, lmbW, lmbU, lmrA, and lmrC), as demonstrated by quantitative RT-PCR and electrophoretic mobility shift assays. Besides, the regulatory genes including bldD, glnR, lcbR1, and ramR are also regulated by the TCS. According to the screening towards nitrogen sources, aspartate affects the regulatory behavior of histidine kinase AflQ2. And in return, AflQ1 accelerates aspartate metabolism via ask-asd, asd2, and thrA. In summary, we acquired six novel regulators related to lincomycin biosynthesis, and elucidated the regulatory mechanism of AflQ1-Q2. This highly conserved TCS is a promising target for the construction of antibiotic high-yield strains. KEY POINTS: • AflQ1-Q2 is a repressor for lincomycin production. • AflQ1 modulates the expression of lincomycin biosynthetic and regulatory genes. • Aspartate affects the behavior of AflQ2, and its metabolism is promoted by AflQ1.
Collapse
Affiliation(s)
- Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Tianyu Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Fanjing Kong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Department of Applied Biology, East China University of Science and Technology, Shanghai, 200237, China
| |
Collapse
|
87
|
Xu X, Ji S, Chen Y, Xia S, Li Y, Chen L, Li Y, Zhang F, Zhang Z, Zheng S. Induction of DNMT1-dependent demethylation of SHP-1 by the natural flavonoid compound Baicalein overcame Imatinib-resistance in CML CD34 + cells. Cell Commun Signal 2023; 21:47. [PMID: 36869331 PMCID: PMC9985268 DOI: 10.1186/s12964-023-01049-9] [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: 07/23/2022] [Accepted: 01/14/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND The most significant cause of treatment failure in chronic myeloid leukemia (CML) is a persistent population of minimal residual cells. Emerging evidences showed that methylation of SHP-1 contributed to Imatinib (IM) resistance. Baicalein was reported to have an effect on reversal of chemotherapeutic agents resistance. However, the molecular mechanism of Baicalein on JAK2/STAT5 signaling inhibition against drug resistance in bone marrow (BM) microenvironment that had not been clearly revealed. METHODS We co-cultured hBMSCs and CML CD34+ cells as a model of SFM-DR. Further researches were performed to clarify the reverse mechanisms of Baicalein on SFM-DR model and engraftment model. The apoptosis, cytotoxicity, proliferation, GM-CSF secretion, JAK2/STAT5 activity, the expression of SHP-1 and DNMT1 were analyzed. To validate the role of SHP-1 on the reversal effect of Baicalein, the SHP-1 gene was over-expressed by pCMV6-entry shp-1 and silenced by SHP-1 shRNA, respectively. Meanwhile, the DNMT1 inhibitor decitabine was used. The methylation extent of SHP-1 was evaluated using MSP and BSP. The molecular docking was replenished to further explore the binding possibility of Baicalein and DNMT1. RESULTS BCR/ABL-independent activation of JAK2/STAT5 signaling was involved in IM resistance in CML CD34+ subpopulation. Baicalein significantly reversed BM microenvironment-induced IM resistance not through reducing GM-CSF secretion, but interfering DNMT1 expression and activity. Baicalein induced DNMT1-mediated demethylation of the SHP-1 promoter region, and subsequently activated SHP-1 re-expression, which resulted in an inhibition of JAK2/STAT5 signaling in resistant CML CD34+ cells. Molecular docking model indicated that DNMT1 and Baicalein had binding pockets in 3D structures, which further supported Baicalein might be a small-molecule inhibitor targeting DNMT1. CONCLUSIONS The mechanism of Baicalein on improving the sensitivity of CD34+ cells to IM might be correlated with SHP-1 demethylation by inhibition of DNMT1 expression. These findings suggested that Baicalein could be a promising candidate by targeting DNMT1 to eradicate minimal residual disease in CML patients. Video Abstract.
Collapse
Affiliation(s)
- Xuefen Xu
- Department of Pharmacology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, No.138, Xianlin Road, Nanjing, Jiangsu, People's Republic of China. .,Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.
| | - Shufan Ji
- Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Yuan Chen
- Department of Pharmacology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, No.138, Xianlin Road, Nanjing, Jiangsu, People's Republic of China
| | - Siwei Xia
- Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Yang Li
- Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Li Chen
- Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Yujia Li
- Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Feng Zhang
- Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Zili Zhang
- Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Shizhong Zheng
- Jangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.
| |
Collapse
|
88
|
Chang PK, Scharfenstein LL, Mahoney N, Kong Q. Kojic Acid Gene Clusters and the Transcriptional Activation Mechanism of Aspergillus flavus KojR on Expression of Clustered Genes. J Fungi (Basel) 2023; 9:jof9020259. [PMID: 36836373 PMCID: PMC9961346 DOI: 10.3390/jof9020259] [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: 12/02/2022] [Revised: 02/08/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
Kojic acid (KA) is a fungal metabolite and has a variety of applications in the cosmetics and food industries. Aspergillus oryzae is a well-known producer of KA, and its KA biosynthesis gene cluster has been identified. In this study, we showed that nearly all section Flavi aspergilli except for A. avenaceus had complete KA gene clusters, and only one Penicillium species, P. nordicum, contained a partial KA gene cluster. Phylogenetic inference based on KA gene cluster sequences consistently grouped section Flavi aspergilli into clades as prior studies. The Zn(II)2Cys6 zinc cluster regulator KojR transcriptionally activated clustered genes of kojA and kojT in Aspergillus flavus. This was evidenced by the time-course expression of both genes in kojR-overexpressing strains whose kojR expression was driven by a heterologous Aspergillus nidulans gpdA promoter or a homologous A. flavus gpiA promoter. Using sequences from the kojA and kojT promoter regions of section Flavi aspergilli for motif analyses, we identified a consensus KojR-binding motif to be an 11-bp palindromic sequence of 5'-CGRCTWAGYCG-3' (R = A/G, W = A/T, Y = C/T). A CRISPR/Cas9-mediated gene-targeting technique showed that the motif sequence, 5'-CGACTTTGCCG-3', in the kojA promoter was critical for KA biosynthesis in A. flavus. Our findings may facilitate strain improvement and benefit future kojic acid production.
Collapse
Affiliation(s)
- Perng-Kuang Chang
- Southern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, 1100 Allen Toussaint Boulevard, New Orleans, LA 70124, USA
- Correspondence: ; Tel.: +1-504-286-4208; Fax: +1-504-286-4419
| | - Leslie L. Scharfenstein
- Southern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, 1100 Allen Toussaint Boulevard, New Orleans, LA 70124, USA
| | - Noreen Mahoney
- Western Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA
| | - Qing Kong
- School of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| |
Collapse
|
89
|
Using Restriction Endonuclease, Protection, Selection, and Amplification to Identify Preferred DNA-Binding Sequences of Microbial Transcription Factors. Microbiol Spectr 2023; 11:e0439722. [PMID: 36602370 PMCID: PMC9927371 DOI: 10.1128/spectrum.04397-22] [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] [Indexed: 01/06/2023] Open
Abstract
Regulation of gene expression is a vital component of cellular biology. Transcription factor proteins often bind regulatory DNA sequences upstream of transcription start sites to facilitate the activation or repression of RNA polymerase. Research laboratories have devoted many projects to understanding the transcription regulatory networks for transcription factors, as these regulated genes provide critical insight into the biology of the host organism. Various in vivo and in vitro assays have been developed to elucidate transcription regulatory networks. Several assays, including SELEX-seq and ChIP-seq, capture DNA-bound transcription factors to determine the preferred DNA-binding sequences, which can then be mapped to the host organism's genome to identify candidate regulatory genes. In this protocol, we describe an alternative in vitro, iterative selection approach to ascertaining DNA-binding sequences of a transcription factor of interest using restriction endonuclease, protection, selection, and amplification (REPSA). Contrary to traditional antibody-based capture methods, REPSA selects for transcription factor-bound DNA sequences by challenging binding reactions with a type IIS restriction endonuclease. Cleavage-resistant DNA species are amplified by PCR and then used as inputs for the next round of REPSA. This process is repeated until a protected DNA species is observed by gel electrophoresis, which is an indication of a successful REPSA experiment. Subsequent high-throughput sequencing of REPSA-selected DNAs accompanied by motif discovery and scanning analyses can be used for determining transcription factor consensus binding sequences and potential regulated genes, providing critical first steps in determining organisms' transcription regulatory networks. IMPORTANCE Transcription regulatory proteins are an essential class of proteins that help maintain cellular homeostasis by adapting the transcriptome based on environmental cues. Dysregulation of transcription factors can lead to diseases such as cancer, and many eukaryotic and prokaryotic transcription factors have become enticing therapeutic targets. Additionally, in many understudied organisms, the transcription regulatory networks for uncharacterized transcription factors remain unknown. As such, the need for experimental techniques to establish transcription regulatory networks is paramount. Here, we describe a step-by-step protocol for REPSA, an inexpensive, iterative selection technique to identify transcription factor-binding sequences without the need for antibody-based capture methods.
Collapse
|
90
|
Tsuji Y. Optimization of Biotinylated RNA or DNA Pull-Down Assays for Detection of Binding Proteins: Examples of IRP1, IRP2, HuR, AUF1, and Nrf2. Int J Mol Sci 2023; 24:3604. [PMID: 36835018 PMCID: PMC9965622 DOI: 10.3390/ijms24043604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Investigation of RNA- and DNA-binding proteins to a defined regulatory sequence, such as an AU-rich RNA and a DNA enhancer element, is important for understanding gene regulation through their interactions. For in vitro binding studies, an electrophoretic mobility shift assay (EMSA) was widely used in the past. In line with the trend toward using non-radioactive materials in various bioassays, end-labeled biotinylated RNA and DNA oligonucleotides can be more practical probes to study protein-RNA and protein-DNA interactions; thereby, the binding complexes can be pulled down with streptavidin-conjugated resins and identified by Western blotting. However, setting up RNA and DNA pull-down assays with biotinylated probes in optimum protein binding conditions remains challenging. Here, we demonstrate the step-by step optimization of pull-down for IRP (iron-responsive-element-binding protein) with a 5'-biotinylated stem-loop IRE (iron-responsive element) RNA, HuR, and AUF1 with an AU-rich RNA element and Nrf2 binding to an antioxidant-responsive element (ARE) enhancer in the human ferritin H gene. This study was designed to address key technical questions in RNA and DNA pull-down assays: (1) how much RNA and DNA probes we should use; (2) what binding buffer and cell lysis buffer we can use; (3) how to verify the specific interaction; (4) what streptavidin resin (agarose or magnetic beads) works; and (5) what Western blotting results we can expect from varying to optimum conditions. We anticipate that our optimized pull-down conditions can be applicable to other RNA- and DNA-binding proteins along with emerging non-coding small RNA-binding proteins for their in vitro characterization.
Collapse
Affiliation(s)
- Yoshiaki Tsuji
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Campus Box 7633, Raleigh, NC 27695, USA
| |
Collapse
|
91
|
Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
Collapse
Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
92
|
Mok J, Kim E, Kang M, Jeon J, Ban C. Development of an optical sandwich ELONA using a pair of DNA aptamers for yellow fever virus NS1. Talanta 2023; 253:123979. [PMID: 36208558 DOI: 10.1016/j.talanta.2022.123979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022]
Abstract
Here, we proposed an enzyme-linked oligonucleotide assay (ELONA) for yellow fever (YF) diagnosis that uses a pair of aptamers, YFns1-4 and YFns1-31. The aptamers were selected to specifically bind to nonstructural protein 1 (NS1), which is secreted at a high concentration after YF infection. We applied the aptamers which did not interfere with each other on binding to the NS1 in a sandwich ELONA. In the assay, the best detection sensitivity was obtained when the combination of YFns1-31 as a capture aptamer and YFns1-4 as a detect aptamer was used. The sensitivity could be attributed to the results of the direct ELONA with each YFns1-4 and YFns1-31; a great absorbance intensity and a broad detectable range of NS1, respectively. The sandwich ELONA achieved a low detection limit of 0.85 nM in buffer and was highly specific to the YFV-NS1 as its detection signals were significantly distinct from those of other flavivirus-derived NS1. In addition, the assay showed a desirable sensitivity in serum-spiked condition. Our developed sandwich ELONA can be a new practical and applicable serological diagnostics in YF endemic regions where other flaviviruses coexist and facilities for complex diagnostic tests are lacking.
Collapse
Affiliation(s)
- Jihyun Mok
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea
| | - Eunseon Kim
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea
| | - Minji Kang
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea
| | - Jinseong Jeon
- POSTECH Biotech Center, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77, Cheongam-Ro, Nam-Gu, Pohang, Gyeong-buk, 790-784, Republic of Korea.
| |
Collapse
|
93
|
Zhao W, Huang H, Wang J, Wang X, Xu B, Yao X, Sun L, Yang R, Wang J, Sun A, Wang S. Jasmonic acid enhances osmotic stress responses by MYC2-mediated inhibition of protein phosphatase 2C1 and response regulators 26 transcription factor in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:546-561. [PMID: 36534116 DOI: 10.1111/tpj.16067] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The jasmonic acid (JA) signaling pathway is involved in the plant response to drought stress. JA and other hormones synergistically regulate the drought response in plants. However, the molecular mechanism underlying this synergism remains poorly defined. In the present study, transcriptome analyses of guard cells and quantitative PCR experiments revealed that MYC2 negatively regulated the negative regulator of ABA signaling, SlPP2C1, and the type-B response regulator in the cytokinin pathway, SlRR26, and this negative regulation was direct. SlRR26 overexpression reduced drought tolerance in transgenic tomatoes, whereas slrr26cr lines were more tolerant to drought. SlRR26 negatively modulated reactive oxygen species levels in stomata and stomatal closure through RobhB. Moreover, SlRR26 overexpression counteracted JA-mediated stomatal closure, suggesting that SlRR26 played a negative role in the JA-mediated drought response. These findings suggest that MYC2 plays a key role in JA-regulated stomatal closure under drought stress by inhibiting SlPP2C1 and SlRR26.
Collapse
Affiliation(s)
- Wenchao Zhao
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Huang Huang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Jingjing Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiaoyun Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Bingqin Xu
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Xuehui Yao
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Lulu Sun
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Rui Yang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Jianli Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| | - Aidong Sun
- Beijing Key Laboratory of Forest Food Processing and Safety, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083, China
| | - Shaohui Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, 102206, China
| |
Collapse
|
94
|
Liu J, Wang Y, He H, Dong S, Tang L, Yang E, Wang W, Zhang B. The leucine-responsive regulatory protein SCAB_Lrp modulates thaxtomin biosynthesis, pathogenicity, and morphological development in Streptomyces scabies. MOLECULAR PLANT PATHOLOGY 2023; 24:167-178. [PMID: 36478143 PMCID: PMC9831280 DOI: 10.1111/mpp.13285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/16/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Streptomyces scabies is the best-characterized plant-pathogenic streptomycete, which is a special species among the large genus Streptomyces. The pathogenicity of S. scabies relies on the production of the secondary metabolite thaxtomin A. Little is known about the molecular mechanisms underlying the regulation of thaxtomin biosynthesis in S. scabies beyond the pathway-specific activator TxtR and the cellulose utilization repressor CebR. The leucine-responsive regulatory protein (Lrp) family modulates secondary metabolism in nonpathogenic streptomycetes. However, the regulatory relationship between the Lrp and pathogenic streptomycetes remains unknown. In this study, we demonstrated that SCAB_Lrp (SCAB_77931) from S. scabies significantly affects thaxtomin biosynthesis, pathogenicity, and morphological development. SCAB_Lrp deletion resulted in a dramatic decline in thaxtomin A production and a low-virulence phenotype of S. scabies. An in-depth dissection of the regulatory mechanism of SCAB_Lrp revealed that it positively regulates the transcription of the thaxtomin biosynthetic gene cluster by directly binding to the promoter of the cluster-situated regulator gene txtR. SCAB_Lrp also controls the morphological development of S. scabies by directly activating the transcription of amfC, whiB, and ssgB. SCAB_Lrp directly controls the transcription of its own gene by binding a specific sequence (5'-GGACAGTCGCCGTGCTACG-3'). Moreover, phenylalanine and methionine have been characterized as SCAB_Lrp effectors by strengthening the binding affinity and complex status between SCAB_Lrp and DNA. Our findings characterize a multifunctional regulatory protein, SCAB_Lrp, that controls secondary metabolism, pathogenicity, and sporulation in S. scabies and provide new insights into the complex regulatory network that modulates thaxtomin phytotoxins in pathogenic Streptomyces.
Collapse
Affiliation(s)
- Jing Liu
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Yunxia Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Haoyang He
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Shengnan Dong
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Lijuan Tang
- Institute of Physical Science and Information Technology, School of Life SciencesAnhui UniversityHefeiChina
| | - Endong Yang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Weiyun Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiChina
| | - Buchang Zhang
- Institute of Physical Science and Information Technology, School of Life SciencesAnhui UniversityHefeiChina
| |
Collapse
|
95
|
Ji S, Tian X, Li X, She Q. Identification and structural analysis of a carbohydrate-binding module specific to alginate, a representative of a new family, CBM96. J Biol Chem 2023; 299:102854. [PMID: 36592931 PMCID: PMC9971899 DOI: 10.1016/j.jbc.2022.102854] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
Carbohydrate-binding modules (CBMs) are the noncatalytic modules that assist functions of the catalytic modules in carbohydrate-active enzymes, and they are usually discrete structural domains in larger multimodular enzymes. CBMs often occur in tandem in different alginate lyases belonging to the CBM families 13, 16, and 32. However, none of the currently known CBMs in alginate lyases specifically bind to an internal alginate chain. In our investigation of the multidomain alginate lyase Dp0100 carrying several ancillary domains, we identified an alginate-binding domain denoted TM6-N4 using protein truncation analysis. The structure of this CBM domain was determined at 1.35 Å resolution. TM6-N4 exhibited an overall β-sandwich fold architecture with two antiparallel β-sheets. We identified an extended binding groove in the CBM using site-directed mutagenesis, docking, and surface electrostatic potential analysis. Affinity analysis revealed that residues of Lys10, Lys22, Lys25, Lys27, Lys31, Arg36, and Tyr159 located on the bottom or the wall of the shallow groove are responsible for alginate binding, and isothermal titration calorimetry analyses indicated that the binding cleft consists of six subsites for sugar recognition. This substrate binding pattern is typical for type B CBM, and it represents the first CBM domain that specifically binds internal alginate chain. Phylogenetic analysis supports that TM6-N4 constitutes the founding member of a new CBM family denoted as CBM96. Our reported structure not only facilitates the investigation of the CBM-alginate ligand recognition mechanism but also inspires the utilization of the CBM domain in biotechnical applications.
Collapse
Affiliation(s)
- Shiqi Ji
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
| | - Xuhui Tian
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Xin Li
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.
| |
Collapse
|
96
|
Lightfoot HL, Smith GF. Targeting RNA with small molecules-A safety perspective. Br J Pharmacol 2023. [PMID: 36631428 DOI: 10.1111/bph.16027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/30/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
RNA is a major player in cellular function, and consequently can drive a number of disease pathologies. Over the past several years, small molecule-RNA targeting (smRNA targeting) has developed into a promising drug discovery approach. Numerous techniques, tools, and assays have been developed to support this field, and significant investments have been made by pharmaceutical and biotechnology companies. To date, the focus has been on identifying disease validated primary targets for smRNA drug development, yet RNA as a secondary (off) target for all small molecule drug programs largely has been unexplored. In this perspective, we discuss structure, target, and mechanism-driven safety aspects of smRNAs and highlight how these parameters can be evaluated in drug discovery programs to produce potentially safer drugs.
Collapse
Affiliation(s)
- Helen L Lightfoot
- Safety and Mechanistic Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Graham F Smith
- Data Science and AI, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| |
Collapse
|
97
|
SPARC is a decoy counterpart for c‑Fos and is associated with osteoblastic differentiation of bone marrow stromal cells by inhibiting adipogenesis. Mol Med Rep 2023; 27:50. [PMID: 36633137 PMCID: PMC9879077 DOI: 10.3892/mmr.2023.12937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/13/2022] [Indexed: 01/11/2023] Open
Abstract
Secreted protein acidic and rich in cysteine (SPARC), also called basement‑membrane protein 40 or osteonectin, is a matricellular protein that is abundant not only in bone tissue as a non‑collagenous protein but is also ubiquitously expressed in non‑calcified tissue. SPARC is located intracellularly and disruption of the Sparc gene has been reported to reduce bone formation and increase fat tissue; however, the mechanism by which SPARC inhibits adipogenesis remains unclear. The present study evaluated the intracellular function of SPARC in adipogenesis using the bone marrow stromal cell line ST2. When ST2 cells with low SPARC production were cloned, intrinsic activator protein‑1 (AP‑1) activity was markedly higher, mineralized nodule formation was significantly lower and lipid accumulation was significantly increased compared with in the parental ST2 cells. Forced expression of secreted SPARC with the signal peptide‑coding sequences of wild‑type Sparc or preprotrypsin in SPARC‑low ST2 cells significantly reduced AP‑1 transcription activity; however, these reductions were not observed in the absence of signal peptide sequences. Recombinant SPARC, produced using Brevibacillus brevis, specifically bound to c‑Fos but not c‑Jun and inhibited the binding of c‑Fos/c‑Jun to a TPA‑response element sequence. These data suggested that SPARC was incorporated into the cells from the extracellular spaces and serves an intracellular role as a decoy counterpart for c‑Fos, as well as being associated with osteoblastogenesis through the inhibition of adipogenesis. These findings may provide new insights into regenerative medicine.
Collapse
|
98
|
Yan Y, Huang T. The Interactome of Protein, DNA, and RNA. Methods Mol Biol 2023; 2695:89-110. [PMID: 37450113 DOI: 10.1007/978-1-0716-3346-5_6] [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: 07/18/2023]
Abstract
Proteins participate in many processes of the organism and are very important for maintaining the health of the organism. However, proteins cannot function independently in the body. They must interact with proteins, DNA, RNA, and other substances to perform biological functions and maintain the body's health. At present, there are many experimental methods and software tools that can detect and predict the interaction between proteins and other substances. There are also many databases that record the interaction between proteins and other substances. This article mainly describes protein-protein, protein-DNA, and protein-RNA interactions in detail by introducing some commonly used experimental methods, the software tools produced with the accumulation of experimental data and the rapid development of machine learning, and the related databases that record the relationship between proteins and some substances. By this review, we hope that through the analysis and summary of various aspects, it will be convenient for researchers to conduct further research on protein interactions.
Collapse
Affiliation(s)
- Yuyao Yan
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
99
|
Cai W, Lu M, Cheng X, Dai W. Improved probe detection sensitivity by flexible tandem biotin labeling. J Microbiol Methods 2023; 204:106654. [PMID: 36509134 DOI: 10.1016/j.mimet.2022.106654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
We develop a biotin-based tandem labeling approach to improve detection sensitivity of DNA probe. Through DNA polymerase-mediated overhand filling, the 3'end of DNA probe was tandemly labeled with biotin molecules. The intensity of biotin signals could be flexibly manipulated by controlling the introduced length of poly(A) in the 5' overhang.
Collapse
Affiliation(s)
- Wenjie Cai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Mingqi Lu
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoyan Cheng
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Weijun Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; College of Plant Protection, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
100
|
A metabolic puzzle: Consumption of C 1 compounds and thiosulfate in Hyphomicrobium denitrificans X T. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148932. [PMID: 36367491 DOI: 10.1016/j.bbabio.2022.148932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Many obligately heterotrophic methylotrophs oxidize thiosulfate as an additional electron source during growth on C1 compounds. Although two different pathways of thiosulfate oxidation are implemented in Hyphomicrobium denitrificans XT, a pronounced negative effect on growth rate is observed when it is cultured in the simultaneous presence of methanol and thiosulfate. In this model organism, periplasmic thiosulfate dehydrogenase TsdA catalyzes formation of the dead-end product tetrathionate. By reverse genetics we verified the second pathway that also starts in the periplasm where SoxXA catalyzes the oxidative fusion of thiosulfate to SoxYZ, from which sulfate is released by SoxB. Sulfane sulfur is then further oxidized in the cytoplasm by the sulfur-oxidizing heterodisulfide reductase-like system (sHdr) which is produced constitutively in a strain lacking the transcriptional repressor sHdrR. When exposed to thiosulfate, the ΔshdrR strain exhibited a strongly reduced growth rate even without thiosulfate in the pre-cultures. When grown on methanol, cells exhibit significantly increased NAD+/NADH ratios in the presence of thiosulfate. In contrast, thiosulfate did not exert any negative effect on growth rate or increase NAD+ levels during growth on formate. On both C1 substrates, excretion of up to 0.5 mM sulfite as an intermediate of thiosulfate (2 mM) oxidation was recorded. Sulfite is known to form adducts with pyrroloquinoline quinone, the cofactor of periplasmic methanol dehydrogenase. We rationalize that this causes specific inhibition of methanol degradation in the presence of thiosulfate while formate metabolism in the cytoplasm remains unaffected.
Collapse
|