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Davies JG, Menzies GE. Utilizing biological experimental data and molecular dynamics for the classification of mutational hotspots through machine learning. BIOINFORMATICS ADVANCES 2024; 4:vbae125. [PMID: 39239360 PMCID: PMC11377099 DOI: 10.1093/bioadv/vbae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 08/06/2024] [Accepted: 08/23/2024] [Indexed: 09/07/2024]
Abstract
Motivation Benzo[a]pyrene, a notorious DNA-damaging carcinogen, belongs to the family of polycyclic aromatic hydrocarbons commonly found in tobacco smoke. Surprisingly, nucleotide excision repair (NER) machinery exhibits inefficiency in recognizing specific bulky DNA adducts including Benzo[a]pyrene Diol-Epoxide (BPDE), a Benzo[a]pyrene metabolite. While sequence context is emerging as the leading factor linking the inadequate NER response to BPDE adducts, the precise structural attributes governing these disparities remain inadequately understood. We therefore combined the domains of molecular dynamics and machine learning to conduct a comprehensive assessment of helical distortion caused by BPDE-Guanine adducts in multiple gene contexts. Specifically, we implemented a dual approach involving a random forest classification-based analysis and subsequent feature selection to identify precise topological features that may distinguish adduct sites of variable repair capacity. Our models were trained using helical data extracted from duplexes representing both BPDE hotspot and nonhotspot sites within the TP53 gene, then applied to sites within TP53, cII, and lacZ genes. Results We show our optimized model consistently achieved exceptional performance, with accuracy, precision, and f1 scores exceeding 91%. Our feature selection approach uncovered that discernible variance in regional base pair rotation played a pivotal role in informing the decisions of our model. Notably, these disparities were highly conserved among TP53 and lacZ duplexes and appeared to be influenced by the regional GC content. As such, our findings suggest that there are indeed conserved topological features distinguishing hotspots and nonhotpot sites, highlighting regional GC content as a potential biomarker for mutation. Availability and implementation Code for comparing machine learning classifiers and evaluating their performance is available at https://github.com/jdavies24/ML-Classifier-Comparison, and code for analysing DNA structure with Curves+ and Canal using Random Forest is available at https://github.com/jdavies24/ML-classification-of-DNA-trajectories.
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Affiliation(s)
- James G Davies
- Molecular Bioscience Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
| | - Georgina E Menzies
- Molecular Bioscience Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
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2
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Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky A, Schoch E, Gagliani E, Herr A, Gebelein B, Kovall R. Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface. Nucleic Acids Res 2024; 52:7987-8002. [PMID: 38874471 PMCID: PMC11260452 DOI: 10.1093/nar/gkae522] [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: 12/11/2023] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the following question: How do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely 7 bp apart. However, the mechanistic basis for Gsx-DNA binding and cooperativity is poorly understood. Here, we used biochemical, biophysical, structural and modeling approaches to (i) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation, (ii) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions, (iii) solve a high-resolution monomer/DNA structure that reveals that Gsx2 induces a 20° bend in DNA, (iv) identify a Gsx2 protein-protein interface required for cooperative DNA binding and (v) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors.
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Affiliation(s)
- Jordan A Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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3
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Murthy S, Dey U, Olymon K, Abbas E, Yella VR, Kumar A. Discerning the Role of DNA Sequence, Shape, and Flexibility in Recognition by Drosophila Transcription Factors. ACS Chem Biol 2024; 19:1533-1543. [PMID: 38902964 DOI: 10.1021/acschembio.4c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The precise spatial and temporal orchestration of gene expression is crucial for the ontogeny of an organism and is mainly governed by transcription factors (TFs). The mechanism of recognition of cognate sites amid millions of base pairs in the genome by TFs is still incompletely understood. In this study, we focus on DNA sequence composition, shape, and flexibility preferences of 28 quintessential TFs from Drosophila melanogaster that are critical to development and body patterning mechanisms. Our study finds that TFs exhibit distinct predilections for DNA shape, flexibility, and sequence compositions in the proximity of transcription factor binding sites (TFBSs). Notably, certain zinc finger proteins prefer GC-rich areas with less negative propeller twist, while homeodomains mainly seek AT-rich regions with a more negative propeller twist at their sites. Intriguingly, while numerous cofactors share similar binding site preferences and bind closer to each other in the genome, some cofactors that have different preferences bind farther apart. These findings shed light on TF DNA recognition and provide novel insights into possible cofactor binding and transcriptional regulation mechanisms.
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Affiliation(s)
- Smrithi Murthy
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Eshan Abbas
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur 520002, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
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4
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Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VYF, Wang Y, Ghosh G. Transient interactions modulate the affinity of NF-κB transcription factors for DNA. Proc Natl Acad Sci U S A 2024; 121:e2405555121. [PMID: 38805268 PMCID: PMC11161749 DOI: 10.1073/pnas.2405555121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/09/2024] [Indexed: 05/30/2024] Open
Abstract
The dimeric nuclear factor kappa B (NF-κB) transcription factors (TFs) regulate gene expression by binding to a variety of κB DNA elements with conserved G:C-rich flanking sequences enclosing a degenerate central region. Toward defining mechanistic principles of affinity regulated by degeneracy, we observed an unusual dependence of the affinity of RelA on the identity of the central base pair, which appears to be noncontacted in the complex crystal structures. The affinity of κB sites with A or T at the central position is ~10-fold higher than with G or C. The crystal structures of neither the complexes nor the free κB DNAs could explain the differences in affinity. Interestingly, differential dynamics of several residues were revealed in molecular dynamics simulation studies, where simulation replicates totaling 148 μs were performed on NF-κB:DNA complexes and free κB DNAs. Notably, Arg187 and Arg124 exhibited selectivity in transient interactions that orchestrated a complex interplay among several DNA-interacting residues in the central region. Binding and simulation studies with mutants supported these observations of transient interactions dictating specificity. In combination with published reports, this work provides insights into the nuanced mechanisms governing the discriminatory binding of NF-κB family TFs to κB DNA elements and sheds light on cancer pathogenesis of cRel, a close homolog of RelA.
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Affiliation(s)
- Tianjie Li
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region999077, China
| | - Shandy Shahabi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
| | - Wenfei Pan
- Faculty of Health Sciences, University of Macau, Taipa, Macau Special Administrative Region999078, China
| | - De-Bin Huang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau Special Administrative Region999078, China
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region999077, China
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
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5
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Gupta S, Kesarwani V, Bhati U, Jyoti, Shankar R. PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants. Brief Bioinform 2024; 25:bbae324. [PMID: 39013383 PMCID: PMC11250369 DOI: 10.1093/bib/bbae324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024] Open
Abstract
Unlike animals, variability in transcription factors (TFs) and their binding regions (TFBRs) across the plants species is a major problem that most of the existing TFBR finding software fail to tackle, rendering them hardly of any use. This limitation has resulted into underdevelopment of plant regulatory research and rampant use of Arabidopsis-like model species, generating misleading results. Here, we report a revolutionary transformers-based deep-learning approach, PTFSpot, which learns from TF structures and their binding regions' co-variability to bring a universal TF-DNA interaction model to detect TFBR with complete freedom from TF and species-specific models' limitations. During a series of extensive benchmarking studies over multiple experimentally validated data, it not only outperformed the existing software by >30% lead but also delivered consistently >90% accuracy even for those species and TF families that were never encountered during the model-building process. PTFSpot makes it possible now to accurately annotate TFBRs across any plant genome even in the total lack of any TF information, completely free from the bottlenecks of species and TF-specific models.
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Affiliation(s)
- Sagar Gupta
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Veerbhan Kesarwani
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Umesh Bhati
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Jyoti
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, The Himalayan Centre for High-throughput Computational Biology, (HiCHiCoB, A BIC supported by DBT, India), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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Zheng M, Sun G, Li X, Fan Y. EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion. Brief Bioinform 2024; 25:bbae330. [PMID: 38975896 PMCID: PMC11229037 DOI: 10.1093/bib/bbae330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/08/2024] [Accepted: 06/26/2024] [Indexed: 07/09/2024] Open
Abstract
Mechanisms of protein-DNA interactions are involved in a wide range of biological activities and processes. Accurately identifying binding sites between proteins and DNA is crucial for analyzing genetic material, exploring protein functions, and designing novel drugs. In recent years, several computational methods have been proposed as alternatives to time-consuming and expensive traditional experiments. However, accurately predicting protein-DNA binding sites still remains a challenge. Existing computational methods often rely on handcrafted features and a single-model architecture, leaving room for improvement. We propose a novel computational method, called EGPDI, based on multi-view graph embedding fusion. This approach involves the integration of Equivariant Graph Neural Networks (EGNN) and Graph Convolutional Networks II (GCNII), independently configured to profoundly mine the global and local node embedding representations. An advanced gated multi-head attention mechanism is subsequently employed to capture the attention weights of the dual embedding representations, thereby facilitating the integration of node features. Besides, extra node features from protein language models are introduced to provide more structural information. To our knowledge, this is the first time that multi-view graph embedding fusion has been applied to the task of protein-DNA binding site prediction. The results of five-fold cross-validation and independent testing demonstrate that EGPDI outperforms state-of-the-art methods. Further comparative experiments and case studies also verify the superiority and generalization ability of EGPDI.
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Affiliation(s)
- Mengxin Zheng
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Guicong Sun
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Xueping Li
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
| | - Yongxian Fan
- School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin 541004, China
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7
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Paul S, Olymon K, Martinez GS, Sarkar S, Yella VR, Kumar A. MLDSPP: Bacterial Promoter Prediction Tool Using DNA Structural Properties with Machine Learning and Explainable AI. J Chem Inf Model 2024; 64:2705-2719. [PMID: 38258978 DOI: 10.1021/acs.jcim.3c02017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Bacterial promoters play a crucial role in gene expression by serving as docking sites for the transcription initiation machinery. However, accurately identifying promoter regions in bacterial genomes remains a challenge due to their diverse architecture and variations. In this study, we propose MLDSPP (Machine Learning and Duplex Stability based Promoter prediction in Prokaryotes), a machine learning-based promoter prediction tool, to comprehensively screen bacterial promoter regions in 12 diverse genomes. We leveraged biologically relevant and informative DNA structural properties, such as DNA duplex stability and base stacking, and state-of-the-art machine learning (ML) strategies to gain insights into promoter characteristics. We evaluated several machine learning models, including Support Vector Machines, Random Forests, and XGBoost, and assessed their performance using accuracy, precision, recall, specificity, F1 score, and MCC metrics. Our findings reveal that XGBoost outperformed other models and current state-of-the-art promoter prediction tools, namely Sigma70pred and iPromoter2L, achieving F1-scores >95% in most systems. Significantly, the use of one-hot encoding for representing nucleotide sequences complements these structural features, enhancing our XGBoost model's predictive capabilities. To address the challenge of model interpretability, we incorporated explainable AI techniques using Shapley values. This enhancement allows for a better understanding and interpretation of the predictions of our model. In conclusion, our study presents MLDSPP as a novel, generic tool for predicting promoter regions in bacteria, utilizing original downstream sequences as nonpromoter controls. This tool has the potential to significantly advance the field of bacterial genomics and contribute to our understanding of gene regulation in diverse bacterial systems.
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Affiliation(s)
- Subhojit Paul
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Gustavo Sganzerla Martinez
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
| | - Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur 522302, Andhra Pradesh, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
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8
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Stellwagen E, Stellwagen NC. Flanking AT base pairs affect the localization of monovalent cations in DNA A-tracts. Electrophoresis 2024; 45:528-536. [PMID: 38087830 DOI: 10.1002/elps.202300220] [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: 10/07/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 03/20/2024]
Abstract
Capillary electrophoresis has been used to measure the free solution mobilities of a series of 26-base pair (bp) DNA oligomers containing two phased A4T1in-tracts embedded in flanking sequences containing 0 to 11 additional AT bps. A random-sequence 26-bp oligomer with 12 isolated AT bps was used as the reference. Mobility ratios (A-tract/reference) were measured in background electrolytes (BGEs) containing mixtures of small monovalent cations and tetrabutylammonium (TBA+ ) or tetrapropylammonium (TPA+ ) ions. The mobility ratios observed in 0.3 M TBA+ were >1.00, suggesting that the TBA+ ions had formed electrostatic contact pairs with the AT bp in the reference and in the A-tract flanking sequences, decreasing the mobilities of both oligomers. The TBA-AT pairing interactions could be eliminated by increasing the concentration of small monovalent cations in the BGE. In 0.3 M TPA+ , electrostatic contact pairs were formed with the AT bps in the flanking sequences and in the A-tracts. Interestingly, the shapes of the mobility ratio profiles observed for the A4T1in-tract oligomers depended on the total number of A + T residues in the oligomer.
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Affiliation(s)
- Earle Stellwagen
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA
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9
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Zhu X, Huang Q, Huang L, Luo J, Li Q, Kong D, Deng B, Gu Y, Wang X, Li C, Kong S, Zhang Y. MAE-seq refines regulatory elements across the genome. Nucleic Acids Res 2024; 52:e9. [PMID: 38038259 PMCID: PMC10810209 DOI: 10.1093/nar/gkad1129] [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: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
Proper cell fate determination relies on precise spatial and temporal genome-wide cooperation between regulatory elements (REs) and their targeted genes. However, the lengths of REs defined using different methods vary, which indicates that there is sequence redundancy and that the context of the genome may be unintelligible. We developed a method called MAE-seq (Massive Active Enhancers by Sequencing) to experimentally identify functional REs at a 25-bp scale. In this study, MAE-seq was used to identify 626879, 541617 and 554826 25-bp enhancers in mouse embryonic stem cells (mESCs), C2C12 and HEK 293T, respectively. Using ∼1.6 trillion 25 bp DNA fragments and screening 12 billion cells, we identified 626879 as active enhancers in mESCs as an example. Comparative analysis revealed that most of the histone modification datasets were annotated by MAE-Seq loci. Furthermore, 33.85% (212195) of the identified enhancers were identified as de novo ones with no epigenetic modification. Intriguingly, distinct chromatin states dictate the requirement for dissimilar cofactors in governing novel and known enhancers. Validation results show that these 25-bp sequences could act as a functional unit, which shows identical or similar expression patterns as the previously defined larger elements, Enhanced resolution facilitated the identification of numerous cell-specific enhancers and their accurate annotation as super enhancers. Moreover, we characterized novel elements capable of augmenting gene activity. By integrating with high-resolution Hi-C data, over 55.64% of novel elements may have a distal association with different targeted genes. For example, we found that the Cdh1 gene interacts with one novel and two known REs in mESCs. The biological effects of these interactions were investigated using CRISPR-Cas9, revealing their role in coordinating Cdh1 gene expression and mESC proliferation. Our study presents an experimental approach to refine the REs at 25-bp resolution, advancing the precision of genome annotation and unveiling the underlying genome context. This novel approach not only advances our understanding of gene regulation but also opens avenues for comprehensive exploration of the genomic landscape.
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Affiliation(s)
- Xiusheng Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qitong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Department of animal sciences, Wageningen University & Research, Wageningen, 6708PB, Netherlands
| | - Lei Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qing Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dashuai Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Biao Deng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yi Gu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xueyan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Chenying Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Siyuan Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528225, China
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10
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Silva EC, Quinde CA, Cieza B, Basu A, Vila MMDC, Balcão VM. Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes (Basel) 2024; 15:113. [PMID: 38255005 PMCID: PMC10815195 DOI: 10.3390/genes15010113] [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: 12/09/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but they are both highly toxic to the environment and stimulate the appearance of bacterial resistance. Herein, we report the molecular characterization and mechanical features of the genome of two newly isolated (putative polyvalent) lytic phages for Psg. The isolated phages belong to class Caudoviricetes and present a myovirus-like morphotype belonging to the genuses Tequatrovirus (PsgM02F) and Phapecoctavirus (PsgM04F) of the subfamilies Straboviridae (PsgM02F) and Stephanstirmvirinae (PsgM04F), according to recent bacterial viruses' taxonomy, based on their complete genome sequences. The 165,282 bp (PsgM02F) and 151,205 bp (PsgM04F) genomes do not feature any lysogenic-related (integrase) genes and, hence, can safely be assumed to follow a lytic lifestyle. While phage PsgM02F produced a morphogenesis yield of 124 virions per host cell, phage PsgM04F produced only 12 virions per host cell, indicating that they replicate well in Psg with a 50 min latency period. Genome mechanical analyses established a relationship between genome bendability and virion morphogenesis yield within infected host cells.
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Affiliation(s)
- Erica C. Silva
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Carlos A. Quinde
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA;
| | - Basilio Cieza
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Aakash Basu
- Department of Biosciences, Durham University, Durham DH1 3LE, UK;
| | - Marta M. D. C. Vila
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
| | - Victor M. Balcão
- VBlab—Laboratory of Bacterial Viruses, University of Sorocaba, Sorocaba 18023-000, SP, Brazil; (E.C.S.); (M.M.D.C.V.)
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, P-3810-193 Aveiro, Portugal
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11
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Jiang Y, Chiu TP, Mitra R, Rohs R. Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding. Biophys J 2024; 123:248-259. [PMID: 38130056 PMCID: PMC10808038 DOI: 10.1016/j.bpj.2023.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/22/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
DNA recognition and targeting by transcription factors (TFs) through specific binding are fundamental in biological processes. Furthermore, the histidine protonation state at the TF-DNA binding interface can significantly influence the binding mechanism of TF-DNA complexes. Nevertheless, the role of histidine in TF-DNA complexes remains underexplored. Here, we employed all-atom molecular dynamics simulations using AlphaFold2-modeled complexes based on previously solved co-crystal structures to probe the role of the His-12 residue in the Extradenticle (Exd)-Sex combs reduced (Scr)-DNA complex when binding to Scr and Ultrabithorax (Ubx) target sites. Our results demonstrate that the protonation state of histidine notably affected the DNA minor-groove width profile and binding free energy. Examining flanking sequences of various binding affinities derived from SELEX-seq experiments, we analyzed the relationship between binding affinity and specificity. We uncovered how histidine protonation leads to increased binding affinity but can lower specificity. Our findings provide new mechanistic insights into the role of histidine in modulating TF-DNA binding.
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Affiliation(s)
- Yibei Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Raktim Mitra
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California; Department of Chemistry, University of Southern California, Los Angeles, California; Department of Physics and Astronomy, University of Southern California, Los Angeles, California; Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, California.
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12
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Buechel ER, Pinkett HW. Activity of the pleiotropic drug resistance transcription factors Pdr1p and Pdr3p is modulated by binding site flanking sequences. FEBS Lett 2024; 598:169-186. [PMID: 37873734 PMCID: PMC10843404 DOI: 10.1002/1873-3468.14762] [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: 08/11/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
The transcription factors Pdr1p and Pdr3p regulate pleiotropic drug resistance (PDR) in Saccharomyces cerevisiae via the PDR responsive elements (PDREs) to modulate gene expression. However, the exact mechanisms underlying the differences in their regulons remain unclear. Employing genomic occupancy profiling (CUT&RUN), binding assays, and transcription studies, we characterized the differences in sequence specificity between transcription factors. Findings reveal distinct preferences for core PDRE sequences and the flanking sequences for both proteins. While flanking sequences moderately alter DNA binding affinity, they significantly impact Pdr1/3p transcriptional activity. Notably, both proteins demonstrated the ability to bind half sites, showing potential enhancement of transcription from adjacent PDREs. This insight sheds light on ways Pdr1/3p can differentially regulate PDR.
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Affiliation(s)
- Evan R. Buechel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Heather W. Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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13
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Faltejsková K, Vondrášek J. PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction. BMC Bioinformatics 2023; 24:487. [PMID: 38114921 PMCID: PMC10731698 DOI: 10.1186/s12859-023-05613-5] [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: 09/29/2022] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger context of the binding site. In this work, we present a novel heuristic algorithm that can reconstruct the unique binding sites captured in a sequencing experiment without using the reference genome. RESULTS We present PAPerFly, the Partial Assembly-based Peak Finder, a tool for the binding site and binding context reconstruction from the sequencing data without any prior knowledge. This tool operates without the need to know the reference genome of the respective organism. We employ algorithmic approaches that are used during genome assembly. The proposed algorithm constructs a de Bruijn graph from the sequencing data. Based on this graph, sequences and their enrichment are reconstructed using a novel heuristic algorithm. The reconstructed sequences are aligned and the peaks in the sequence enrichment are identified. Our approach was tested by processing several ChIP-seq experiments available in the ENCODE database and comparing the results of Paperfly and standard methods. CONCLUSIONS We show that PAPerFly, an algorithm tailored for experiment analysis without the reference genome, yields better results than an aggregation of ChIP-seq agnostic tools. Our tool is freely available at https://github.com/Caeph/paperfly/ or on Zenodo ( https://doi.org/10.5281/zenodo.7116424 ).
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Affiliation(s)
- Kateřina Faltejsková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00, Prague, Czech Republic.
- Computer Science Institute, Faculty of Mathematics and Physics, Charles University, Malostranské náměstí 25, 118 00, Prague, Czech Republic.
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00, Prague, Czech Republic.
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14
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Webb JA, Farrow E, Cain B, Yuan Z, Yarawsky AE, Schoch E, Gagliani EK, Herr AB, Gebelein B, Kovall RA. Cooperative Gsx2-DNA Binding Requires DNA Bending and a Novel Gsx2 Homeodomain Interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570805. [PMID: 38106145 PMCID: PMC10723402 DOI: 10.1101/2023.12.08.570805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The conserved Gsx homeodomain (HD) transcription factors specify neural cell fates in animals from flies to mammals. Like many HD proteins, Gsx factors bind A/T-rich DNA sequences prompting the question - how do HD factors that bind similar DNA sequences in vitro regulate specific target genes in vivo? Prior studies revealed that Gsx factors bind DNA both as a monomer on individual A/T-rich sites and as a cooperative homodimer to two sites spaced precisely seven base pairs apart. However, the mechanistic basis for Gsx DNA binding and cooperativity are poorly understood. Here, we used biochemical, biophysical, structural, and modeling approaches to (1) show that Gsx factors are monomers in solution and require DNA for cooperative complex formation; (2) define the affinity and thermodynamic binding parameters of Gsx2/DNA interactions; (3) solve a high-resolution monomer/DNA structure that reveals Gsx2 induces a 20° bend in DNA; (4) identify a Gsx2 protein-protein interface required for cooperative DNA binding; and (5) determine that flexible spacer DNA sequences enhance Gsx2 cooperativity on dimer sites. Altogether, our results provide a mechanistic basis for understanding the protein and DNA structural determinants that underlie cooperative DNA binding by Gsx factors, thereby providing a deeper understanding of HD specificity.
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Affiliation(s)
- Jordan A. Webb
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Edward Farrow
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children’s Hospital Research Foundation, Cincinnati, OH 45229, USA
- Medical-Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Brittany Cain
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Zhenyu Yuan
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Alexander E. Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Ave, Cincinnati, OH 45229, USA
| | - Emma Schoch
- Department of Medical Education, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ellen K. Gagliani
- Department of Chemistry, Xavier University, Cincinnati, OH 45207, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, 3333, Burnet Ave, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A. Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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15
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Back G, Walther D. Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility. NAR Genom Bioinform 2023; 5:lqad097. [PMID: 37954573 PMCID: PMC10632188 DOI: 10.1093/nargab/lqad097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Mechanical properties of DNA have been implied to influence many of its biological functions. Recently, a new high-throughput method, called loop-seq, which allows measuring the intrinsic bendability of DNA fragments, has been developed. Using loop-seq data, we created a deep learning model to explore the biological significance of local DNA flexibility in a range of different species from different kingdoms. Consistently, we observed a characteristic and largely dinucleotide-composition-driven change of local flexibility near transcription start sites. In the presence of a TATA-box, a pronounced peak of high flexibility can be observed. Furthermore, depending on the transcription factor investigated, flanking-sequence-dependent DNA flexibility was identified as a potential factor influencing DNA binding. Compared to randomized genomic sequences, depending on species and taxa, actual genomic sequences were observed both with increased and lowered flexibility. Furthermore, in Arabidopsis thaliana, mutation rates, both de novo and fixed, were found to be associated with relatively rigid sequence regions. Our study presents a range of significant correlations between characteristic DNA mechanical properties and genomic features, the significance of which with regard to detailed molecular relevance awaits further theoretical and experimental exploration.
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Affiliation(s)
- Georg Back
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
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16
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Al Masri C, Wan B, Yu J. Nonspecific vs. specific DNA binding free energetics of a transcription factor domain protein. Biophys J 2023; 122:4476-4487. [PMID: 37897044 PMCID: PMC10722393 DOI: 10.1016/j.bpj.2023.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Transcription factor (TF) proteins regulate gene expression by binding to specific sites on the genome. In the facilitated diffusion model, an optimized search process is achieved by the TF alternating between 3D diffusion in the bulk and 1D diffusion along DNA. While undergoing 1D diffusion, the protein can switch from a search mode for fast diffusion along nonspecific DNA to a recognition mode for stable binding to specific DNA. It was recently noticed that, for a small TF domain protein, reorientations on DNA happen between the nonspecific and specific DNA binding. We here conducted all-atom molecular dynamics simulations with steering forces to reveal the protein-DNA binding free energetics, confirming that the search and recognition modes are distinguished primarily by protein orientations on the DNA. As the binding free energy difference between the specific and nonspecific DNA system slightly deviates from that being estimated directly from dissociation constants on 15-bp DNA constructs, we hypothesize that the discrepancy can come from DNA sequences flanking the 6-bp central binding sites that impact on the dissociation kinetics measurements. The hypothesis is supported by a simplified spherical protein-DNA model along with stochastic simulations and kinetic modeling.
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Affiliation(s)
- Carmen Al Masri
- Department of Physics and Astronomy, University of California, Irvine, California
| | - Biao Wan
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Jin Yu
- Department of Physics and Astronomy, University of California, Irvine, California; Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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17
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Kazimierska M, Podralska M, Żurawek M, Woźniak T, Kasprzyk ME, Sura W, Łosiewski W, Ziółkowska‐Suchanek I, Kluiver J, van den Berg A, Rozwadowska N, Dzikiewicz‐Krawczyk A. CRISPR/Cas9 screen for genome-wide interrogation of essential MYC-bound E-boxes in cancer cells. Mol Oncol 2023; 17:2295-2313. [PMID: 37519063 PMCID: PMC10620128 DOI: 10.1002/1878-0261.13493] [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: 02/10/2023] [Revised: 04/28/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate gene expression in a cell-type- and developmental-stage-specific manner. To date, a combined analysis of essential MYC-bound E-boxes and their downstream target genes important for growth of different types of cancer is missing. In this study, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knock out protein-coding genes. We performed high-throughput screens with these libraries in four MYC-dependent cancer cell lines-K562, ST486, HepG2, and MCF7-which revealed several essential E-boxes and genes. Among them, we pinpointed crucial common and cell-type-specific MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach confirmed that E-box disruption affects MYC binding, target-gene expression, and cell proliferation in vitro as well as tumor growth in vivo. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.
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Affiliation(s)
- Marta Kazimierska
- Institute of Human GeneticsPolish Academy of SciencesPoznańPoland
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznańPoland
| | - Marta Podralska
- Institute of Human GeneticsPolish Academy of SciencesPoznańPoland
| | | | - Tomasz Woźniak
- Institute of Human GeneticsPolish Academy of SciencesPoznańPoland
| | | | - Weronika Sura
- Institute of Human GeneticsPolish Academy of SciencesPoznańPoland
| | | | | | - Joost Kluiver
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenThe Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenThe Netherlands
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18
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Zhang P, Wang H, Xu H, Wei L, Liu L, Hu Z, Wang X. Deep flanking sequence engineering for efficient promoter design using DeepSEED. Nat Commun 2023; 14:6309. [PMID: 37813854 PMCID: PMC10562447 DOI: 10.1038/s41467-023-41899-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023] Open
Abstract
Designing promoters with desirable properties is essential in synthetic biology. Human experts are skilled at identifying strong explicit patterns in small samples, while deep learning models excel at detecting implicit weak patterns in large datasets. Biologists have described the sequence patterns of promoters via transcription factor binding sites (TFBSs). However, the flanking sequences of cis-regulatory elements, have long been overlooked and often arbitrarily decided in promoter design. To address this limitation, we introduce DeepSEED, an AI-aided framework that efficiently designs synthetic promoters by combining expert knowledge with deep learning techniques. DeepSEED has demonstrated success in improving the properties of Escherichia coli constitutive, IPTG-inducible, and mammalian cell doxycycline (Dox)-inducible promoters. Furthermore, our results show that DeepSEED captures the implicit features in flanking sequences, such as k-mer frequencies and DNA shape features, which are crucial for determining promoter properties.
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Affiliation(s)
- Pengcheng Zhang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, China
| | - Haochen Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, China
| | - Hanwen Xu
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, China
| | - Lei Wei
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, China
| | - Liyang Liu
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, China
| | - Zhirui Hu
- Center for Statistical Science, Tsinghua University, Beijing, China
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, China.
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19
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Mondal S, Banerjee S, Dey D, Lahiri H, Mana T, Jana SS, Mukhopadhyay R. Impact of HMGB1 binding on the structural alterations of platinum drug-treated single dsDNA molecule. Biochimie 2023; 213:168-175. [PMID: 37211256 DOI: 10.1016/j.biochi.2023.05.012] [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: 02/15/2023] [Revised: 04/24/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
High mobility group B1 (HMGB1) is an architectural protein that recognizes the DNA damage sites formed by the platinum anticancer drugs. However, the impact of HMGB1 binding on the structural alterations of the platinum drug-treated single dsDNA molecules has remained largely unknown. Herein, the structural alterations induced by the platinum drugs, the mononuclear cisplatin and it's analog the trinuclear BBR3464, have been probed in presence of HMGB1, by atomic force microscopy (AFM) and AFM-based force spectroscopy. It is observed that the drug-induced DNA loop formation enhanced upon HMGB1 binding, most likely as a result of HMGB1-induced increase in DNA conformational flexibility that allowed the drug-binding sites to come close and form double adducts, thereby resulting in enhanced loop formation via inter-helix cross-linking. Since HMGB1 enhances DNA flexibility, the near-reversible structural transitions as observed in the force-extension curves (for 1 h drug treatment), generally occurred at lower forces in presence of HMGB1. The DNA structural integrity was largely lost after 24 h drug treatment as no reversible transition could be observed. The Young's modulus of the dsDNA molecules, as estimated from the force-extension analysis, increased upon drug treatment, due to formation of the drug-induced covalent cross-links and consequent reduction in DNA flexibility. The Young's modulus increased further in presence of HMGB1 due to HMGB1-induced enhancement in DNA flexibility that could ease formation of the drug-induced covalent cross-links. To our knowledge, this is the first report that shows an increase in the stiffness of the platinum drug-treated DNA molecules in presence of HMGB1.
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Affiliation(s)
- Sourav Mondal
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Siddhartha Banerjee
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Debapriya Dey
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Tanushree Mana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Siddhartha S Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India.
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20
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Buechel ER, Pinkett HW. Unraveling the Half and Full Site Sequence Specificity of the Saccharomyces cerevisiae Pdr1p and Pdr3p Transcription Factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.553033. [PMID: 37609128 PMCID: PMC10441396 DOI: 10.1101/2023.08.11.553033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The transcription factors Pdr1p and Pdr3p regulate pleotropic drug resistance (PDR) in Saccharomyces cerevisiae , via the PDR responsive elements (PDREs) to modulate gene expression. However, the exact mechanisms underlying the differences in their regulons remain unclear. Employing genomic occupancy profiling (CUT&RUN), binding assays, and transcription studies, we characterized the differences in sequence specificity between transcription factors. Findings reveal distinct preferences for core PDRE sequences and the flanking sequences for both proteins. While flanking sequences moderately alter DNA binding affinity, they significantly impact Pdr1/3p transcriptional activity. Notably, both proteins demonstrated the ability to bind half sites, showing potential enhancement of transcription from adjacent PDREs. This insight sheds light on ways Pdr1/3 can differentially regulate PDR.
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21
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Cain B, Webb J, Yuan Z, Cheung D, Lim HW, Kovall R, Weirauch MT, Gebelein B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Res 2023; 51:6055-6072. [PMID: 37114997 PMCID: PMC10325903 DOI: 10.1093/nar/gkad318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/12/2023] [Accepted: 04/25/2023] [Indexed: 04/29/2023] Open
Abstract
Homeodomain proteins constitute one of the largest families of metazoan transcription factors. Genetic studies have demonstrated that homeodomain proteins regulate many developmental processes. Yet, biochemical data reveal that most bind highly similar DNA sequences. Defining how homeodomain proteins achieve DNA binding specificity has therefore been a long-standing goal. Here, we developed a novel computational approach to predict cooperative dimeric binding of homeodomain proteins using High-Throughput (HT) SELEX data. Importantly, we found that 15 of 88 homeodomain factors form cooperative homodimer complexes on DNA sites with precise spacing requirements. Approximately one third of the paired-like homeodomain proteins cooperatively bind palindromic sequences spaced 3 bp apart, whereas other homeodomain proteins cooperatively bind sites with distinct orientation and spacing requirements. Combining structural models of a paired-like factor with our cooperativity predictions identified key amino acid differences that help differentiate between cooperative and non-cooperative factors. Finally, we confirmed predicted cooperative dimer sites in vivo using available genomic data for a subset of factors. These findings demonstrate how HT-SELEX data can be computationally mined to predict cooperativity. In addition, the binding site spacing requirements of select homeodomain proteins provide a mechanism by which seemingly similar AT-rich DNA sequences can preferentially recruit specific homeodomain factors.
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Affiliation(s)
- Brittany Cain
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45221, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
| | - Jordan Webb
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhenyu Yuan
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David Cheung
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Divisions of Human Genetics, Biomedical Informatics and Developmental Biology, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave, MLC 7007, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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22
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Dey U, Olymon K, Banik A, Abbas E, Yella VR, Kumar A. DNA structural properties of DNA binding sites for 21 transcription factors in the mycobacterial genome. Front Cell Infect Microbiol 2023; 13:1147544. [PMID: 37396305 PMCID: PMC10312376 DOI: 10.3389/fcimb.2023.1147544] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/19/2023] [Indexed: 07/04/2023] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, has evolved over time into a multidrug resistance strain that poses a serious global pandemic health threat. The ability to survive and remain dormant within the host macrophage relies on multiple transcription factors contributing to virulence. To date, very limited structural insights from crystallographic and NMR studies are available for TFs and TF-DNA binding events. Understanding the role of DNA structure in TF binding is critical to deciphering MTB pathogenicity and has yet to be resolved at the genome scale. In this work, we analyzed the compositional and conformational preference of 21 mycobacterial TFs, evident at their DNA binding sites, in local and global scales. Results suggest that most TFs prefer binding to genomic regions characterized by unique DNA structural signatures, namely, high electrostatic potential, narrow minor grooves, high propeller twist, helical twist, intrinsic curvature, and DNA rigidity compared to the flanking sequences. Additionally, preference for specific trinucleotide motifs, with clear periodic signals of tetranucleotide motifs, are observed in the vicinity of the TF-DNA interactions. Altogether, our study reports nuanced DNA shape and structural preferences of 21 TFs.
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Affiliation(s)
- Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Anikesh Banik
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Eshan Abbas
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, India
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23
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Recio PS, Mitra NJ, Shively CA, Song D, Jaramillo G, Lewis KS, Chen X, Mitra R. Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode. Nucleic Acids Res 2023; 51:5006-5021. [PMID: 37125648 PMCID: PMC10250231 DOI: 10.1093/nar/gkad320] [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: 12/09/2022] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 05/02/2023] Open
Abstract
Gene expression changes are orchestrated by transcription factors (TFs), which bind to DNA to regulate gene expression. It remains surprisingly difficult to predict basic features of the transcriptional process, including in vivo TF occupancy. Existing thermodynamic models of TF function are often not concordant with experimental measurements, suggesting undiscovered biology. Here, we analyzed one of the most well-studied TFs, the yeast zinc cluster Gal4, constructed a Shea-Ackers thermodynamic model to describe its binding, and compared the results of this model to experimentally measured Gal4p binding in vivo. We found that at many promoters, the model predicted no Gal4p binding, yet substantial binding was observed. These outlier promoters lacked canonical binding motifs, and subsequent investigation revealed Gal4p binds unexpectedly to DNA sequences with high densities of its half site (CGG). We confirmed this novel mode of binding through multiple experimental and computational paradigms; we also found most other zinc cluster TFs we tested frequently utilize this binding mode, at 27% of their targets on average. Together, these results demonstrate a novel mode of binding where zinc clusters, the largest class of TFs in yeast, bind DNA sequences with high densities of half sites.
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Affiliation(s)
- Pamela S Recio
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Nikhil J Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Christian A Shively
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - David Song
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Grace Jaramillo
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Kristine Shady Lewis
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Xuhua Chen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
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24
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Chun I, Kim HJ, Hong S, Kim YG, Kim MS. Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence. PLANT COMMUNICATIONS 2023; 4:100510. [PMID: 36564947 DOI: 10.1016/j.xplc.2022.100510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/02/2022] [Accepted: 12/21/2022] [Indexed: 05/11/2023]
Abstract
Plants use sophisticated mechanisms of gene expression to control senescence in response to environmental stress or aging. ORE1 (Arabidopsis thaliana NAC092) is a master regulator of senescence that belongs to the plant-specific NAC transcription factor protein family. ORE1 has been reported to bind to multiple DNA targets to orchestrate leaf senescence, yet the mechanistic basis for recognition of the cognate gene sequence remains unclear. Here, we report the crystal structure of the ORE1-NAC domain alone and its DNA-binding form. The structure of DNA-bound ORE1-NAC revealed the molecular basis for nucleobase recognition and phosphate backbone interactions. We show that local versatility in the DNA-binding site, in combination with domain flexibility of the ORE-NAC homodimer, is crucial for the maintenance of binding to intrinsically flexible DNA. Our results provide a platform for understanding other plant-specific NAC protein-DNA interactions as well as insight into the structural basis of NAC regulators in plants of agronomic and scientific importance.
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Affiliation(s)
- Inseop Chun
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Hyo Jung Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Sunghyun Hong
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Min-Sung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea.
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25
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Sievers A, Sauer L, Bisch M, Sprengel J, Hausmann M, Hildenbrand G. Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes. Genes (Basel) 2023; 14:genes14030755. [PMID: 36981025 PMCID: PMC10048725 DOI: 10.3390/genes14030755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Dinucleotides are known as determinants for various structural and physiochemical properties of DNA and for binding affinities of proteins to DNA. These properties (e.g., stiffness) and bound proteins (e.g., transcription factors) are known to influence important biological functions, such as transcription regulation and 3D chromatin organization. Accordingly, the question arises of how the considerable variations in dinucleotide contents of eukaryotic chromosomes could still provide consistent DNA properties resulting in similar functions and 3D conformations. In this work, we investigate the hypothesis that coupled dinucleotide contents influence DNA properties in opposite directions to moderate each other's influences. Analyzing all 2478 chromosomes of 155 eukaryotic species, considering bias from coding sequences and enhancers, we found sets of correlated and anti-correlated dinucleotide contents. Using computational models, we estimated changes of DNA properties resulting from this coupling. We found that especially pure A/T dinucleotides (AA, TT, AT, TA), known to influence histone positioning and AC/GT contents, are relevant moderators and that, e.g., the Roll property, which is known to influence histone affinity of DNA, is preferably moderated. We conclude that dinucleotide contents might indirectly influence transcription and chromatin 3D conformation, via regulation of histone occupancy and/or other mechanisms.
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Affiliation(s)
- Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, INF 366, 69117 Heidelberg, Germany
| | - Liane Sauer
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, INF 366, 69117 Heidelberg, Germany
| | - Marc Bisch
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Jan Sprengel
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Faculty of Engeneering, University of Applied Science Aschaffenburg, Würzburger Str. 45, 63743 Aschaffenburg, Germany
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26
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Nagarajan H, Vetrivel U. Deciphering the structural and functional impact of missense mutations in Egr1-DNA interacting interface: an integrative computational approach. J Biomol Struct Dyn 2022; 40:11758-11770. [PMID: 34402752 DOI: 10.1080/07391102.2021.1965030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Early growth response-1 (Egr1) is a zinc-finger transcription factor that plays a critical role in controlling cell growth, proliferation, differentiation, angiogenesis, and apoptosis. Egr1 is induced by many growth factors, cytokines, and stress signals and is also known to be involved in several pathological conditions like cancer, neurological and ocular disorders. The DNA binding domain of Egr1 is a highly conserved Cys2His2 (C2H2) zinc finger (ZNF) domain which specifically binds to GC-rich consensus sequence GcG (G/T) GGGCG and activates transcription. As the C2H2 domain specifically recognizes its DNA target, the mutations spanning this region shall perturb DNA recognition and may hinder transcription of target genes. Therefore, in this study, the missense mutations occurring specifically at the DNA binding domain (DBD) of Egr1 were probed by computational approaches involving in silico screening of pathogenic and functional mutants coupled with extensive molecular dynamics simulations, to determine the mutants that affect its structural stability and interactions with DNA. From the pathogenicity analysis of 38 missense mutations spanning Egr1-DBD, 17 were predicted as pathogenic, and 7 amongst these were found to have functional impact on Egr1. On combined analysis of molecular dynamics simulation, Residue interaction analysis and Egr1-DNA interaction analysis results, the mutants R371C and R375C showed least impact, whilst, H382R tend to increase the structural stability, whereas R360H, H390R, E393V, and H414Y conferred greater impact by altering the structural stability and DNA interactions. Hence, this study exposes the prospects of considering these 4 deleterious mutations for clinical significance, but needs further experimental validation.HighlightsEgr1's DNA binding domain is a highly conserved Cys2His2 (C2H2) zinc finger domain that specifically recognizes its DNA target.Mutations spanning in the DNA binding domain shall perturb DNA recognition and may hinder transcription.Among the missense mutations, mutants R360H, H390R, E393V, and H414Y were inferred to have a greater impact on Egr1 by altering the structural stability and DNA interactions.
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Affiliation(s)
- Hemavathy Nagarajan
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India.,National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research (Govt. of India), Belagavi, Karnataka, India
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27
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Fernandez-Lopez R, Ruiz R, del Campo I, Gonzalez-Montes L, Boer D, de la Cruz F, Moncalian G. Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors. Nucleic Acids Res 2022; 50:11938-11947. [PMID: 36370103 PMCID: PMC9723621 DOI: 10.1093/nar/gkac1024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix-turn-helix domains. We then probed and confirmed that ArdK shows affinity for an inverted repeat, which, surprisingly, is also recognized by a non-symmetrical dimer. Our results indicate that structural flexibility at different positions in the dimerization interface constrains transcription factors to bind DNA sequences with one of these two alternative DNA topologies.
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Affiliation(s)
- Raul Fernandez-Lopez
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Raul Ruiz
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Irene del Campo
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - Lorena Gonzalez-Montes
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, 39011, Santander, Spain
| | - D Roeland Boer
- Alba Synchrotron, Cerdanyola del Vallès, 08290, Barcelona, Spain
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28
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Chiu TP, Li J, Jiang Y, Rohs R. It is in the flanks: Conformational flexibility of transcription factor binding sites. Biophys J 2022; 121:3765-3767. [PMID: 36182667 PMCID: PMC9674972 DOI: 10.1016/j.bpj.2022.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Jinsen Li
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Yibei Jiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California; Departments of Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, California.
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29
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Ghoshdastidar D, Bansal M. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif. Biophys J 2022; 121:3987-4000. [PMID: 35978548 PMCID: PMC9674967 DOI: 10.1016/j.bpj.2022.08.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/02/2022] Open
Abstract
Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. A DNA sequence has intrinsic shape and flexibility features. While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. Overall, this study suggests that flexibility-guided DNA shape, and not merely the static shape, is a key unexplored component of the complex DNA-TF recognition code.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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30
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Yang MG, Ling E, Cowley CJ, Greenberg ME, Vierbuchen T. Characterization of sequence determinants of enhancer function using natural genetic variation. eLife 2022; 11:76500. [PMID: 36043696 PMCID: PMC9662815 DOI: 10.7554/elife.76500] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 08/30/2022] [Indexed: 02/04/2023] Open
Abstract
Sequence variation in enhancers that control cell-type-specific gene transcription contributes significantly to phenotypic variation within human populations. However, it remains difficult to predict precisely the effect of any given sequence variant on enhancer function due to the complexity of DNA sequence motifs that determine transcription factor (TF) binding to enhancers in their native genomic context. Using F1-hybrid cells derived from crosses between distantly related inbred strains of mice, we identified thousands of enhancers with allele-specific TF binding and/or activity. We find that genetic variants located within the central region of enhancers are most likely to alter TF binding and enhancer activity. We observe that the AP-1 family of TFs (Fos/Jun) are frequently required for binding of TEAD TFs and for enhancer function. However, many sequence variants outside of core motifs for AP-1 and TEAD also impact enhancer function, including sequences flanking core TF motifs and AP-1 half sites. Taken together, these data represent one of the most comprehensive assessments of allele-specific TF binding and enhancer function to date and reveal how sequence changes at enhancers alter their function across evolutionary timescales.
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Affiliation(s)
- Marty G Yang
- Department of Neurobiology, Harvard Medical School, Boston, United States.,Program in Neuroscience, Harvard Medical School, Boston, United States
| | - Emi Ling
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | | | | | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, United States.,Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, United States
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31
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Rohac R, Crack JC, de Rosny E, Gigarel O, Le Brun NE, Fontecilla-Camps JC, Volbeda A. Structural determinants of DNA recognition by the NO sensor NsrR and related Rrf2-type [FeS]-transcription factors. Commun Biol 2022; 5:769. [PMID: 35908109 PMCID: PMC9338935 DOI: 10.1038/s42003-022-03745-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/21/2022] [Indexed: 11/20/2022] Open
Abstract
Several transcription factors of the Rrf2 family use an iron-sulfur cluster to regulate DNA binding through effectors such as nitric oxide (NO), cellular redox status and iron levels. [4Fe-4S]-NsrR from Streptomyces coelicolor (ScNsrR) modulates expression of three different genes via reaction and complex formation with variable amounts of NO, which results in detoxification of this gas. Here, we report the crystal structure of ScNsrR complexed with an hmpA1 gene operator fragment and compare it with those previously reported for [2Fe-2S]-RsrR/rsrR and apo-IscR/hyA complexes. Important structural differences reside in the variation of the DNA minor and major groove widths. In addition, different DNA curvatures and different interactions with the protein sensors are observed. We also report studies of NsrR binding to four hmpA1 variants, which indicate that flexibility in the central region is not a key binding determinant. Our study explores the promotor binding specificities of three closely related transcriptional regulators. The crystal structure of the iron-sulfur protein NsrR from Streptomyces coelicolor bound to a gene operator fragment is reported and compared with other structures, giving insight into the structural determinants of DNA recognition by the NO sensor.
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Affiliation(s)
- Roman Rohac
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France
| | - Jason C Crack
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Eve de Rosny
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France
| | - Océane Gigarel
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Juan C Fontecilla-Camps
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France
| | - Anne Volbeda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, Metalloproteins Unit, F-38000, Grenoble, France.
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32
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Balcão VM, Basu A, Cieza B, Rossi FN, Pereira C, Vila MM, Setubal JC, Ha T, da Silva AM. Pseudomonas-tailed lytic phages: genome mechanical analysis and putative correlation with virion morphogenesis yield. Future Microbiol 2022; 17:1009-1026. [PMID: 35880493 DOI: 10.2217/fmb-2021-0293] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To unveil a putative correlation between phage genome flexibility and virion morphogenesis yield. Materials & methods: A deeper analysis of the mechanical properties of three Pseudomonas aeruginosa lytic phage genomes was undertaken, together with full genome cyclizability calculations. Results & conclusion: A putative correlation was established among phage genome flexibility, eclipse timeframe and virion particle morphogenesis yield, with a more flexible phage genome leading to a higher burst size and a more rigid phage genome leading to lower burst sizes. The results obtained are highly relevant to understand the influence of the phage genome plasticity on the virion morphogenesis yield inside the infected bacterial host cells and assumes particular relevance in the actual context of bacterial resistance to antibiotics.
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Affiliation(s)
- Victor M Balcão
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, 18023-000, Brazil.,Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, P-3810-193, Portugal
| | - Aakash Basu
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Basilio Cieza
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Fernando N Rossi
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Carla Pereira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, P-3810-193, Portugal
| | - Marta Mdc Vila
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, 18023-000, Brazil
| | - João C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Taekjip Ha
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, 05508-000, Brazil
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33
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Grzechowiak M, Ruszkowska A, Sliwiak J, Urbanowicz A, Jaskolski M, Ruszkowski M. New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain. Int J Biol Macromol 2022; 213:589-601. [PMID: 35660042 DOI: 10.1016/j.ijbiomac.2022.05.186] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/18/2022] [Accepted: 05/29/2022] [Indexed: 01/28/2023]
Abstract
WRKY transcription factors (TFs) constitute one of the largest families of plant TFs. Based on the organization of domains and motifs, WRKY TFs are divided into three Groups (I-III). The WRKY subgroup IIa includes three representatives in A. thaliana, AtWRKY18, AtWRKY40, and AtWRKY60, that participate in biotic and abiotic stress responses. Here we present crystal structures of the DNA binding domain (DBD) of AtWRKY18 alone and in the complex with a DNA duplex containing the WRKY-recognition sequence, W-box. Subgroup IIa WRKY TFs are known to form homo and heterodimers. Our data suggest that the dimerization interface of the full-length AtWRKY18 involves contacts between the DBD subunits. DNA binding experiments and structural analysis point out novel aspects of DNA recognition by WRKY TFs. In particular, AtWRKY18-DBD preferentially binds an overlapping tandem of W-boxes accompanied by a quasi-W-box motif. The binding of DNA deforms the B-type double helix, which suggests that the DNA fragment must be prone to form a specific structure. This can explain why despite the short W-box consensus, WRKY TFs can precisely control gene expression. Finally, this first experimental structure of a Group II WRKY TF allowed us to compare Group I-III representatives.
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Affiliation(s)
- Marta Grzechowiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Agnieszka Ruszkowska
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Joanna Sliwiak
- Laboratory of Protein Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Anna Urbanowicz
- Laboratory of Protein Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Mariusz Jaskolski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan 61-614, Poland
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.
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34
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Vanaja A, Yella VR. Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes. ACS OMEGA 2022; 7:5657-5669. [PMID: 35224327 PMCID: PMC8867553 DOI: 10.1021/acsomega.1c04603] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/27/2022] [Indexed: 05/02/2023]
Abstract
The eukaryotic transcription is orchestrated from a chunk of the DNA region stated as the core promoter. Multifarious and punctilious core promoter signals, viz., TATA-box, Inr, BREs, and Pause Button, are associated with a subset of genes and regulate their spatiotemporal expression. However, the core promoter architecture linked with these signals has not been investigated exhaustively for several species. In this study, we attempted to envisage the adaptive binding landscape of the transcription initiation machinery as a function of DNA structure. To this end, we deployed a set of k-mer based DNA structural estimates and regular expression models derived from experiments, molecular dynamic simulations, and theoretical frameworks, and high-throughout promoter data sets retrieved from the eukaryotic promoter database. We categorized protein-coding gene core promoters based on characteristic motifs at precise locations and analyzed the B-DNA structural properties and non-B-DNA structural motifs for 15 different eukaryotic genomes. We observed that Inr, BREd, and no-motif classes display common patterns of DNA sequence and structural environment. TATA-containing, BREu, and Pause Button classes show a deviant behavior with the TATA class displaying varied axial and twisting flexibility while BREu and Pause Button leaned toward G-quadruplex motif enrichment. Intriguingly, DNA meltability and shape signals are conserved irrespective of the presence or absence of distinct core promoter motifs in the majority of species. Altogether, here we delineated the conserved DNA structural signals associated with several promoter classes that may contribute to the chromatin configuration, orchestration of transcription machinery, and DNA duplex melting during the transcription process.
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Affiliation(s)
- Akkinepally Vanaja
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
- KL
College of Pharmacy, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
| | - Venkata Rajesh Yella
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
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35
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Qi Z, Jung C, Bandilla P, Ludwig C, Heron M, Sophie Kiesel A, Museridze M, Philippou‐Massier J, Nikolov M, Renna Max Schnepf A, Unnerstall U, Ceolin S, Mühlig B, Gompel N, Soeding J, Gaul U. Large-scale analysis of Drosophila core promoter function using synthetic promoters. Mol Syst Biol 2022; 18:e9816. [PMID: 35156763 PMCID: PMC8842121 DOI: 10.15252/msb.20209816] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/02/2023] Open
Abstract
The core promoter plays a central role in setting metazoan gene expression levels, but how exactly it "computes" expression remains poorly understood. To dissect its function, we carried out a comprehensive structure-function analysis in Drosophila. First, we performed a genome-wide bioinformatic analysis, providing an improved picture of the sequence motifs architecture. We then measured synthetic promoters' activities of ~3,000 mutational variants with and without an external stimulus (hormonal activation), at large scale and with high accuracy using robotics and a dual luciferase reporter assay. We observed a strong impact on activity of the different types of mutations, including knockout of individual sequence motifs and motif combinations, variations of motif strength, nucleosome positioning, and flanking sequences. A linear combination of the individual motif features largely accounts for the combinatorial effects on core promoter activity. These findings shed new light on the quantitative assessment of gene expression in metazoans.
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Affiliation(s)
- Zhan Qi
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Christophe Jung
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Peter Bandilla
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Claudia Ludwig
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Mark Heron
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Anja Sophie Kiesel
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Mariam Museridze
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Julia Philippou‐Massier
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Miroslav Nikolov
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Alessio Renna Max Schnepf
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Ulrich Unnerstall
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Stefano Ceolin
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Bettina Mühlig
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Nicolas Gompel
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Johannes Soeding
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
- Max Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Ulrike Gaul
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
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36
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Harada LK, Silva EC, Rossi FP, Cieza B, Oliveira TJ, Pereira C, Tomazetto G, Silva BB, Squina FM, Vila MM, Setubal JC, Ha T, da Silva AM, Balcão VM. Characterization and in vitro testing of newly isolated lytic bacteriophages for the biocontrol of Pseudomonas aeruginosa. Future Microbiol 2022; 17:111-141. [PMID: 34989245 DOI: 10.2217/fmb-2021-0027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aim: Two lytic phages were isolated using P. aeruginosa DSM19880 as host and fully characterized. Materials & methods: Phages were characterized physicochemically, biologically and genomically. Results & conclusion: Host range analysis revealed that the phages also infect some multidrug-resistant (MDR) P. aeruginosa clinical isolates. Increasing MOI from 1 to 1000 significantly increased phage efficiency and retarded bacteria regrowth, but phage ph0034 (reduction of 7.5 log CFU/ml) was more effective than phage ph0031 (reduction of 5.1 log CFU/ml) after 24 h. Both phages belong to Myoviridae family. Genome sequencing of phages ph0031 and ph0034 showed that they do not carry toxin, virulence, antibiotic resistance and integrase genes. The results obtained are highly relevant in the actual context of bacterial resistance to antibiotics.
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Affiliation(s)
- Liliam K Harada
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Erica C Silva
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Fernando Pn Rossi
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Basilio Cieza
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Thais J Oliveira
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Carla Pereira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Geizecler Tomazetto
- Department of Engineering, Biological & Chemical Engineering Section (BCE), Aarhus University, Aarhus, Denmark
| | - Bianca B Silva
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Fabio M Squina
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Marta Mdc Vila
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - João C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Taekjip Ha
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Victor M Balcão
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil.,Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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37
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Prusty S, Sarkar R, Chakraborty A, Roy S. Correlation in Domain Fluctuations Navigates Target Search of a Viral Peptide along RNA. J Phys Chem B 2021; 125:12678-12689. [PMID: 34756044 DOI: 10.1021/acs.jpcb.1c07699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological macromolecules often exhibit correlations in fluctuations involving distinct domains. This study decodes their functional implications in RNA-protein recognition and target-specific binding. The target search of a peptide along RNA in a viral TAR-Tat complex is closely monitored using atomistic simulations, steered molecular dynamics simulations, free energy calculations, and a machine-learning-based clustering technique. An anticorrelated domain fluctuation is identified between the tetraloop and the bulge region in the apo form of TAR RNA that sets a hierarchy in the domain-specific fluctuations at each binding event and that directs the succeeding binding footsteps. Thus, at each binding footstep, the dynamic partner selects an RNA location for binding where it senses a higher fluctuation, which is conventionally reduced upon binding. This event stimulates an alternate domain fluctuation, which then dictates sequential binding footstep/s and thus the search progresses. Our cross-correlation maps show that the fluctuations relay from one domain to another specific domain until the anticorrelation between those interdomain fluctuations sustains. Artificial attenuation of that hierarchical domain fluctuation inhibits specific RNA binding. The binding is completed with the arrival of a few long-lived water molecules that mediate slightly distant RNA-protein sites and finally stabilize the overall complex. The study underscores the functional importance of naturally designed fluctuating RNA motifs (bulge, tetraloop) and their interplay in dictating the directionality of the search in a highly dynamic environment.
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Affiliation(s)
- Sangram Prusty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Campus Road, Mohanpur, West Bengal 741246, India
| | - Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Campus Road, Mohanpur, West Bengal 741246, India
| | - Amrita Chakraborty
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Campus Road, Mohanpur, West Bengal 741246, India
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Campus Road, Mohanpur, West Bengal 741246, India
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38
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Sarkar S, Dey U, Khohliwe TB, Yella VR, Kumar A. Analysis of nucleoid-associated protein-binding regions reveals DNA structural features influencing genome organization in Mycobacterium tuberculosis. FEBS Lett 2021; 595:2504-2521. [PMID: 34387867 DOI: 10.1002/1873-3468.14178] [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: 06/11/2021] [Revised: 08/01/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022]
Abstract
Nucleoid-associated proteins (NAPs) maintain bacterial nucleoid configuration through their architectural properties of DNA bending, wrapping, and bridging. However, the contribution of DNA structural alterations to DNA-NAP recognition at the genomic scale remains unresolved. Present work dissects the DNA sequence, shape and altered structural preferences at a genomic scale for six NAPs in Mycobacterium tuberculosis. Results suggest narrower minor groove width (MGW) and higher DNA rigidity are marked for the binding sites of EspR and Lsr2, while mIHF, MtHU and NapM have heterogeneous DNA structural predilections. In contrast, WhiB4-DNA-binding sites were characterized by wider MGW, highly deformable and less curved DNA. This work provides systematic insight into NAP-mediated genome organization as a function of DNA structural features.
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Affiliation(s)
- Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | - Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | | | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, India
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39
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Shao J, Yan Y, Ding D, Wang D, He Y, Pan Y, Yan W, Kharbanda A, Li H, Huang H. Destruction of DNA-Binding Proteins by Programmable Oligonucleotide PROTAC (O'PROTAC): Effective Targeting of LEF1 and ERG. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102555. [PMID: 34397171 PMCID: PMC8529430 DOI: 10.1002/advs.202102555] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/30/2021] [Indexed: 05/03/2023]
Abstract
DNA-binding proteins, including transcription factors (TFs), play essential roles in various cellular processes and pathogenesis of diseases, deeming to be potential therapeutic targets. However, these proteins are generally considered undruggable as they lack an enzymatic catalytic site or a ligand-binding pocket. Proteolysis-targeting chimera (PROTAC) technology has been developed by engineering a bifunctional molecule chimera to bring a protein of interest (POI) to the proximity of an E3 ubiquitin ligase, thus inducing the ubiquitination of POI and further degradation through the proteasome pathway. Here, the development of oligonucleotide-based PROTAC (O'PROTACs), a class of noncanonical PROTACs in which a TF-recognizing double-stranded oligonucleotide is incorporated as a binding moiety of POI is reported. It is demonstrated that O'PROTACs of lymphoid enhancer-binding factor 1 (LEF1) and ETS-related gene (ERG), two highly cancer-related transcription factors, successfully promote degradation of these proteins, impede their transcriptional activity, and inhibit cancer cell growth in vitro and in vivo. The programmable nature of O'PROTACs indicates that this approach is also applicable to destruct other TFs. O'PROTACs not only can serve as a research tool but also can be harnessed as a therapeutic arsenal to target DNA binding proteins for effective treatment of diseases such as cancer.
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Affiliation(s)
- Jingwei Shao
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - Yuqian Yan
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Donglin Ding
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Dejie Wang
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Yundong He
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Yunqian Pan
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
| | - Wei Yan
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - Anupreet Kharbanda
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - Hong‐yu Li
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Arkansas for Medical SciencesLittle RockAR72205USA
| | - Haojie Huang
- Department of Biochemistry and Molecular BiologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
- Department of UrologyMayo Clinic College of Medicine and ScienceRochesterMN55905USA
- Mayo Clinic Cancer CenterMayo Clinic College of Medicine and ScienceRochesterMN55905USA
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40
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Dohnalová H, Lankaš F. Deciphering the mechanical properties of
B‐DNA
duplex. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
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41
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Hörberg J, Moreau K, Tamás MJ, Reymer A. Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors. Nucleic Acids Res 2021; 49:9280-9293. [PMID: 34387667 PMCID: PMC8450079 DOI: 10.1093/nar/gkab691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022] Open
Abstract
Activator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA-binding sites, our ability to predict new binding sites and explain how the proteins achieve different gene expression levels remains limited. Here we address the role of sequence-specific DNA flexibility for stability and specific binding of AP-1 factors, using microsecond-long molecular dynamics simulations. As a model system, we employ yeast AP-1 factor Yap1 binding to three different response elements from two genetic environments. Our data show that Yap1 actively exploits the sequence-specific flexibility of DNA within the response element to form stable protein–DNA complexes. The stability also depends on the four to six flanking nucleotides, adjacent to the response elements. The flanking sequences modulate the conformational adaptability of the response element, making it more shape-efficient to form specific contacts with the protein. Bioinformatics analysis of differential expression of the studied genes supports our conclusions: the stability of Yap1–DNA complexes, modulated by the flanking environment, influences the gene expression levels. Our results provide new insights into mechanisms of protein–DNA recognition and the biological regulation of gene expression levels in eukaryotes.
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Affiliation(s)
- Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Kevin Moreau
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Anna Reymer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
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42
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Symphony of the DNA flexibility and sequence environment orchestrates p53 binding to its responsive elements. Gene 2021; 803:145892. [PMID: 34375633 DOI: 10.1016/j.gene.2021.145892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 08/05/2021] [Indexed: 11/23/2022]
Abstract
The p53 tumor suppressor protein maintains the genome fidelity and integrity by modulating several cellular activities. It regulates these events by interacting with a heterogeneous set of response elements (REs) of regulatory genes in the background of chromatin configuration. At the p53-RE interface, both the base readout and torsional-flexibility of DNA account for high-affinity binding. However, DNA structure is an entanglement of a multitude of physicochemical features, both local and global structure should be considered for dealing with DNA-protein interactions. The goal of current research work is to conceptualize and abstract basic principles of p53-RE binding affinity as a function of structural alterations in DNA such as bending, twisting, and stretching flexibility and shape. For this purpose, we have exploited high throughput in-vitro relative affinity information of responsive elements and genome binding events of p53 from HT-Selex and ChIP-Seq experiments respectively. Our results confirm the role of torsional flexibility in p53 binding, and further, we reveal that DNA axial bending, stretching stiffness, propeller twist, and wedge angles are intimately linked to p53 binding affinity when compared to homeodomain, bZIP, and bHLH proteins. Besides, a similar DNA structural environment is observed in the distal sequences encompassing the actual binding sites of p53 cistrome genes. Additionally, we revealed that p53 cistrome target genes have unique promoter architecture, and the DNA flexibility of genomic sequences around REs in cancer and normal cell types display major differences. Altogether, our work provides a keynote on DNA structural features of REs that shape up the in-vitro and in-vivo high-affinity binding of the p53 transcription factor.
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43
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Ge W, Meier M, Roth C, Söding J. Bayesian Markov models improve the prediction of binding motifs beyond first order. NAR Genom Bioinform 2021; 3:lqab026. [PMID: 33928244 PMCID: PMC8057495 DOI: 10.1093/nargab/lqab026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/11/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific DNA motifs. Accurate models for predicting binding affinities are crucial for quantitatively understanding of transcriptional regulation. Motifs are commonly described by position weight matrices, which assume that each position contributes independently to the binding energy. Models that can learn dependencies between positions, for instance, induced by DNA structure preferences, have yielded markedly improved predictions for most TFs on in vivo data. However, they are more prone to overfit the data and to learn patterns merely correlated with rather than directly involved in TF binding. We present an improved, faster version of our Bayesian Markov model software, BaMMmotif2. We tested it with state-of-the-art motif discovery tools on a large collection of ChIP-seq and HT-SELEX datasets. BaMMmotif2 models of fifth-order achieved a median false-discovery-rate-averaged recall 13.6% and 12.2% higher than the next best tool on 427 ChIP-seq datasets and 164 HT-SELEX datasets, respectively, while being 8 to 1000 times faster. BaMMmotif2 models showed no signs of overtraining in cross-cell line and cross-platform tests, with similar improvements on the next-best tool. These results demonstrate that dependencies beyond first order clearly improve binding models for most TFs.
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Affiliation(s)
- Wanwan Ge
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Markus Meier
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Roth
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Johannes Söding
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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44
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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45
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Runthala A. Probabilistic divergence of a template-based modelling methodology from the ideal protocol. J Mol Model 2021; 27:25. [PMID: 33411019 DOI: 10.1007/s00894-020-04640-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022]
Abstract
Protein structural information is essential for the detailed mapping of a functional protein network. For a higher modelling accuracy and quicker implementation, template-based algorithms have been extensively deployed and redefined. The methods only assess the predicted structure against its native state/template and do not estimate the accuracy for each modelling step. A divergence measure is therefore postulated to estimate the modelling accuracy against its theoretical optimal benchmark. By freezing the domain boundaries, the divergence measures are predicted for the most crucial steps of a modelling algorithm. To precisely refine the score using weighting constants, big data analysis could further be deployed.
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Affiliation(s)
- Ashish Runthala
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh, 522502, India.
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46
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Prabhakant A, Panigrahi A, Krishnan M. Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding. J Chem Inf Model 2020; 60:6366-6376. [PMID: 33108170 DOI: 10.1021/acs.jcim.0c00617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CAP, which entails repositioning of DNA recognition helices (F-helices) in the DBD to dock favorably to the target DNA. Despite considerable progress, much remains to be understood about the mechanistic details of DNA recognition by CAP and about the map of allosteric pathways involved in CAP-mediated gene transcription. The present study uses molecular dynamics and umbrella sampling simulations to investigate the mechanism of cAMP- and DNA-induced changes in the conformation and energetics of F-helices observed during the allosteric regulation of CAP by cAMP and the subsequent binding to the DNA promoter region. Using novel collective variables, the free energy profiles associated with the orientation and dynamics of F-helices in the unliganded, cAMP-bound, and cAMP-DNA-bound states of CAP are calculated and compared. The binding-induced alterations in the resultant free energy profiles reveal important flexibility constraints imposed on DBD upon cAMP and DNA binding. A comprehensive analysis of residue-wise interaction maps reveals potential allosteric pathways between CBD and DBD that facilitate the allosteric transduction of regulatory signals in CAP. The revelation that the predicted allosteric pathways crisscross the intersubunit interface offers important clues on the microscopic origin of the intersubunit cooperativity and dimer stability of CAP.
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Affiliation(s)
- Akshay Prabhakant
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhinandan Panigrahi
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
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Long L, Li X, Wei H, Li W. Features of the Influence of a DNA Sequence on Its Adjacent Sequence. ACS OMEGA 2020; 5:23631-23644. [PMID: 32984683 PMCID: PMC7512436 DOI: 10.1021/acsomega.0c02264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
To explore the features of the influence of a DNA sequence (here called sequence A) on its adjacent sequence (here called sequence B), we linked some DNA repeated sequences to the 5'-end of the T7 promoter in the plasmid pET-42a (+) or the 5'- and/or 3'-end(s) of the EcoRI site in some DNA fragments using PCR and other molecular cloning methods. As a result, we found that the efficiency of the T7 promoter and EcoRI could be impacted by some flanking sequences, indicating that sequence B could be impacted by sequence A. The features of such influence include the following: (i) sequence A can directly impact sequence B without changing/modifying the base composition of sequence B or destroying the inherent connection between sequence B and its function-related sequences; (ii) such influence does not need the participation of trans-acting factors or products of sequence A (if any); (iii) such an influence might be undetectable when the activities of trans-acting factors of sequence B are normal but might become detectable when those are lower than the normal one; (iv) such an influence might be enhancive, inhibitory, or unobvious; (v) the influence of sequence A linked to the 5'-end of sequence B might be the same as or opposite to that of sequence A linked to the 3'-end; and (vi) the influences of sequence A linked to different ends of sequence B could enhance or partially offset each other when sequence A is linked to both 5'- and 3'-ends of sequence B. These findings might give us a further understanding of the interaction of two adjacent DNA sequences.
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Affiliation(s)
- Lijuan Long
- Department
of Pediatrics, First Affiliated Hospital
of Guangxi Medical University, #6, Shuangyong Road, Nanning, 530021 Guangxi, China
| | - Xinxin Li
- Department
of Nuclear Medicine, First Affiliated Hospital
of Guangxi Medical University, #6, Shuangyong Road, Nanning, 530021 Guangxi, China
| | - Hailang Wei
- Medical
Scientific Research Center, Guangxi Medical
University, #22, Shuangyong Road, Nanning, 530021 Guangxi, China
| | - Wei Li
- Medical
Scientific Research Center, Guangxi Medical
University, #22, Shuangyong Road, Nanning, 530021 Guangxi, China
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Yella VR, Vanaja A, Kulandaivelu U, Kumar A. Delving into Eukaryotic Origins of Replication Using DNA Structural Features. ACS OMEGA 2020; 5:13601-13611. [PMID: 32566825 PMCID: PMC7301376 DOI: 10.1021/acsomega.0c00441] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/15/2020] [Indexed: 05/18/2023]
Abstract
DNA replication in eukaryotes is an intricate process, which is precisely synchronized by a set of regulatory proteins, and the replication fork emanates from discrete sites on chromatin called origins of replication (Oris). These spots are considered as the gateway to chromosomal replication and are stereotyped by sequence motifs. The cognate sequences are noticeable in a small group of entire origin regions or totally absent across different metazoans. Alternatively, the use of DNA secondary structural features can provide additional information compared to the primary sequence. In this article, we report the trends in DNA sequence-based structural properties of origin sequences in nine eukaryotic systems representing different families of life. Biologically relevant DNA secondary structural properties, namely, stability, propeller twist, flexibility, and minor groove shape were studied in the sequences flanking replication start sites. Results indicate that Oris in yeasts show lower stability, more rigidity, and narrow minor groove preferences compared to genomic sequences surrounding them. Yeast Oris also show preference for A-tracts and the promoter element TATA box in the vicinity of replication start sites. On the contrary, Drosophila melanogaster, humans, and Arabidopsis thaliana do not have such features in their Oris, and instead, they show high preponderance of G-rich sequence motifs such as putative G-quadruplexes or i-motifs and CpG islands. Our extensive study applies the DNA structural feature computation to delve into origins of replication across organisms ranging from yeasts to mammals and including a plant. Insights from this study would be significant in understanding origin architecture and help in designing new algorithms for predicting DNA trans-acting factor recognition events.
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Affiliation(s)
- Venkata Rajesh Yella
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Guntur 522502, Andhra Pradesh, India
| | - Akkinepally Vanaja
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Guntur 522502, Andhra Pradesh, India
- KL
College of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur 522502, Andhra Pradesh, India
| | - Umasankar Kulandaivelu
- KL
College of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur 522502, Andhra Pradesh, India
| | - Aditya Kumar
- Department
of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
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Faltejsková K, Jakubec D, Vondrášek J. Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation. Int J Mol Sci 2020; 21:ijms21113986. [PMID: 32498246 PMCID: PMC7312683 DOI: 10.3390/ijms21113986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/01/2022] Open
Abstract
Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein–DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions with hydrophobic amino acid residues is a universal element of protein–DNA recognition. We provide evidence to support this by associating each DNA minor groove-binding amino acid residue with the local dimensions of the DNA double helix using a novel algorithm. The widened DNA minor grooves are associated with high GC content. However, some AT-rich sequences contacted by hydrophobic amino acids (e.g., phenylalanine) display extreme values of minor groove width as well. For a number of hydrophobic amino acids, distinct secondary structure preferences could be identified for residues interacting with the widened DNA minor groove. These results hold even after discarding the most populous families of minor groove-binding proteins.
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Affiliation(s)
- Kateřina Faltejsková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech Republic;
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague 2, Czech Republic
| | - David Jakubec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech Republic;
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Prague 2, Czech Republic
- Correspondence: (D.J.); (J.V.); Tel.: +420-220183267 (J.V.)
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 166 10 Prague 6, Czech Republic;
- Correspondence: (D.J.); (J.V.); Tel.: +420-220183267 (J.V.)
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Giri M, Maulik A, Singh M. Signatures of Specific DNA Binding by the AT-Rich Interaction Domain of BAF250a. Biochemistry 2019; 59:100-113. [PMID: 31825600 DOI: 10.1021/acs.biochem.9b00852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The AT-rich interaction domain (ARID) containing BAF250a is a subunit of the BAF-A class of SWI/SNF chromatin remodeling complexes. The ARID belongs to a family of conserved DNA binding domains found in several eukaryotic proteins; however, its exact contribution to BAF250a function and the mechanism of its DNA binding are not well understood. Here we have probed the interaction of the BAF250a ARID with three different double-stranded DNA (dsDNA) sequences to understand its DNA binding properties. A comprehensive biophysical and thermodynamic study using nuclear magnetic resonance (NMR) spectroscopy and isothermal titration calorimetry revealed the complex nature of BAF250a ARID-DNA interactions. The thermodynamic signatures of the BAF250a ARID with 12 A-T bp dsDNA (AT-12) are distinct from those of 12 G-C bp dsDNA (GC-12) or 12 bp Dickerson dodecamer DNA (DD-12) sequences. We observed that the binding of the BAF250a ARID with AT-12 DNA is enthalpically driven in a tested temperature range of 5-25 °C. BAF250a ARID/AT-12 DNA interaction exhibited a larger negative calorimetric specific heat change (ΔCp) compared to that of BAF250a ARID/GC-12 DNA or BAF250a ARID/DD-12 DNA interactions. In the presence of salt (NaCl), ARID/AT-12 DNA binding was less perturbed than ARID/GC-12 DNA or ARID/DD-12 DNA binding. Overall, these results show that BAF250a ARID/AT-12 DNA interaction has signatures of "specific" binding. Furthermore, using NMR chemical shift perturbation experiments, we have identified DNA binding residues on the BAF250a ARID and generated a data-driven HADDOCK model of the ARID/DNA complex that was further supported by mutating key lysine residues that were found to be important for DNA binding.
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Affiliation(s)
- Malyasree Giri
- Molecular Biophysics Unit , Indian Institute of Science , Bengaluru 560012 , India
| | - Aditi Maulik
- Molecular Biophysics Unit , Indian Institute of Science , Bengaluru 560012 , India
| | - Mahavir Singh
- Molecular Biophysics Unit , Indian Institute of Science , Bengaluru 560012 , India.,NMR Research Centre , Indian Institute of Science , Bengaluru 560012 , India
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