1
|
Korhonen PK, Wang T, Young ND, Byrne JJ, Campos TL, Chang BC, Taki AC, Gasser RB. Analysis of Haemonchus embryos at single cell resolution identifies two eukaryotic elongation factors as intervention target candidates. Comput Struct Biotechnol J 2024; 23:1026-1035. [PMID: 38435301 PMCID: PMC10907403 DOI: 10.1016/j.csbj.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024] Open
Abstract
Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism Caenorhabditis elegans - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms. Here, we created the first single cell atlas for an early developmental stage of Haemonchus contortus - a highly pathogenic, C. elegans-related parasitic nematode. We obtained and curated RNA sequence (snRNA-seq) data from single nuclei from embryonating eggs of H. contortus (150,000 droplets), and selected high-quality transcriptomic data for > 14,000 single nuclei for analysis, and identified 19 distinct clusters of cells. Guided by comparative analyses with C. elegans, we were able to reproducibly assign seven cell clusters to body wall muscle, hypodermis, neuronal, intestinal or seam cells, and identified eight genes that were transcribed in all cell clusters/types, three of which were inferred to be essential in H. contortus. Two of these genes (i.e. Hc-eef-1A and Hc-eef1G), coding for eukaryotic elongation factors (called Hc-eEF1A and Hc-eEF1G), were also demonstrated to be transcribed and expressed in all key developmental stages of H. contortus. Together with these findings, sequence- and structure-based comparative analyses indicated the potential of Hc-eEF1A and/or Hc-eEF1G as intervention targets within the protein biosynthesis machinery of H. contortus. Future work will focus on single cell studies of all key developmental stages and tissues of H. contortus, and on evaluating the suitability of the two elongation factor proteins as drug targets in H. contortus and related nematodes, with a view to finding new nematocidal drug candidates.
Collapse
Affiliation(s)
- Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C.H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
2
|
Oh J, Kim S, Kim S, Kim J, Yeom S, Lee JS. An epitope-tagged Swd2 reveals the different requirements of Swd2 concentration in H3K4 methylation and viability. Biochim Biophys Acta Gene Regul Mech 2024; 1867:195009. [PMID: 38331025 DOI: 10.1016/j.bbagrm.2024.195009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/11/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
Swd2/Cps35 is a common component of the COMPASS H3K4 methyltransferase and CPF transcription termination complex in Saccharomyces cerevisiae. The deletion of SWD2 is lethal, which results from transcription termination defects in snoRNA genes. This study isolated a yeast strain that showed significantly reduced protein level of Swd2 following epitope tagging at its N-terminus (9MYC-SWD2). The reduced level of Swd2 in the 9MYC-SWD2 strain was insufficient for the stability of the Set1 H3K4 methyltransferase, H3K4me3 and snoRNA termination, but the level was enough for viability and growth similar to the wildtype strain. In addition, we presented the genes differentially regulated by the essential protein Swd2 under optimal culture conditions for the first time. The expression of genes known to be decreased in the absence of Set1 and H3K4me3, including NAD biosynthetic process genes and histone genes, was decreased in the 9MYC-SWD2 strain, as expected. However, the effects of Swd2 on the ribosome biogenesis (RiBi) genes were opposite to those of Set1, suggesting that the expression of RiBi genes is regulated by more complex relationship between COMPASS and other Swd2-containing complexes. These data suggest that different concentrations of Swd2 are required for its roles in H3K4me3 and viability and that it may be either contributory or contrary to the transcriptional regulation of Set1/H3K4me3, depending on the gene group.
Collapse
Affiliation(s)
- Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seho Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - SangMyung Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jueun Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon-si 24341, Republic of Korea
| | - Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea; Institute of Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea.
| |
Collapse
|
3
|
Jiang T, Li Y, Hong W, Lin M. A robust CRISPR interference gene repression system in Vibrio parahaemolyticus. Arch Microbiol 2023; 206:41. [PMID: 38147133 PMCID: PMC10751265 DOI: 10.1007/s00203-023-03770-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/15/2023] [Accepted: 11/24/2023] [Indexed: 12/27/2023]
Abstract
Vibrio parahaemolyticus is a significant cause of seafood-associated gastroenteritis and pestilence in aquaculture worldwide. Despite extensive research, strategies for protein depletion in this pathogen remain limited. Herein, we constructed a new CRISPR interference (CRISPRi) system for gene repression based on the combination of a shuttle vector pVv3 and the nuclease-null Cas9 variant (dead Cas9, or dCas9) from Streptococcus pyrogens. This CRISPRi is induced by adding both IPTG and arabinose. We showed that gene repression is scalable via the use of multiple sgRNAs. We also demonstrated that this gene repression can be precisely tuned by adjusting the amount of two different inducers and can be reversed by removing the inducers. This system provides a simple approach for selective gene repression on a genome-wide scale in V. parahaemolyticus. Application of this system will dramatically accelerate investigations of this bacterium, including studies of physiology, pathogenesis, and drug target discovery.
Collapse
Affiliation(s)
- Taoyuan Jiang
- Department of Respiratory Medicine, Nan'an Hospital, 330, Ximei Residential District, Xinhua Street, Quanzhou, Fujian Province, China.
| | - Yuhuan Li
- The Second People's Hospital of Three Gorges University, 18, Tiyuchang Road, Yichang, Hubei Province, China
| | - Wencong Hong
- Department of Respiratory Medicine, Nan'an Hospital, 330, Ximei Residential District, Xinhua Street, Quanzhou, Fujian Province, China
| | - Mingyu Lin
- Department of Respiratory Medicine, Nan'an Hospital, 330, Ximei Residential District, Xinhua Street, Quanzhou, Fujian Province, China
| |
Collapse
|
4
|
Ishikawa K, Soejima S, Saitoh S. Genetic knockdown of genes that are obscure, conserved and essential using CRISPR interference methods in the fission yeast S. pombe. J Cell Sci 2023; 136:309000. [PMID: 37162093 DOI: 10.1242/jcs.261186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/01/2023] [Indexed: 05/11/2023] Open
Abstract
Characterizing functions of essential genes is challenging, as perturbing them is generally lethal. Conditional gene perturbation, including use of temperature-sensitive mutants, has been widely utilized to reveal functions of essential genes in the fission yeast Schizosaccharomyces pombe. However, recently we implemented a systematic and less time-consuming knockdown method, CRISPR interference (CRISPRi), in this organism using catalytically inactive Cas9 (dCas9). This technology has been expected to facilitate characterization of essential genes in S. pombe, although this still has not occurred. Here, CRISPRi was harnessed to study uncharacterized essential genes that are evolutionally conserved from yeasts to mammals. Transcription of these genes, which we call conserved essential obscure (ceo) genes, was repressed using conventional dCas9-mediated CRISPRi and by implementing technologies that enhance repression efficiency or alleviate limitations on small guide RNA (sgRNA) design. These CRISPRi methods successfully reduced transcription of target genes and allowed us to characterize resulting phenotypes. Knockdown of ceo genes inhibited cell proliferation and altered cellular morphology. Thus, dCas9-based CRISPRi methods utilized in this study enhanced accessibility of genetic analyses targeting essential genes in S. pombe.
Collapse
Affiliation(s)
- Ken Ishikawa
- Department of Cell Biology, Institute of Life Science, Kurume University, Asahi-machi 67, Kurume, Fukuoka 830-0011, Japan
| | - Saeko Soejima
- Department of Cell Biology, Institute of Life Science, Kurume University, Asahi-machi 67, Kurume, Fukuoka 830-0011, Japan
| | - Shigeaki Saitoh
- Department of Cell Biology, Institute of Life Science, Kurume University, Asahi-machi 67, Kurume, Fukuoka 830-0011, Japan
| |
Collapse
|
5
|
Shi H, Wu C, Bai T, Chen J, Li Y, Wu H. Identify essential genes based on clustering based synthetic minority oversampling technique. Comput Biol Med 2023; 153:106523. [PMID: 36652869 DOI: 10.1016/j.compbiomed.2022.106523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/13/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Prediction of essential genes in a life organism is one of the central tasks in synthetic biology. Computational predictors are desired because experimental data is often unavailable. Recently, some sequence-based predictors have been constructed to identify essential genes. However, their predictive performance should be further improved. One key problem is how to effectively extract the sequence-based features, which are able to discriminate the essential genes. Another problem is the imbalanced training set. The amount of essential genes in human cell lines is lower than that of non-essential genes. Therefore, predictors trained with such imbalanced training set tend to identify an unseen sequence as a non-essential gene. Here, a new over-sampling strategy was proposed called Clustering based Synthetic Minority Oversampling Technique (CSMOTE) to overcome the imbalanced data issue. Combining CSMOTE with the Z curve, the global features, and Support Vector Machines, a new protocol called iEsGene-CSMOTE was proposed to identify essential genes. The rigorous jackknife cross validation results indicated that iEsGene-CSMOTE is better than the other competing methods. The proposed method outperformed λ-interval Z curve by 35.48% and 11.25% in terms of Sn and BACC, respectively.
Collapse
Affiliation(s)
- Hua Shi
- School of Opto-electronic and Communication Engineering, Xiamen University of Technology, Xiamen, China.
| | - Chenjin Wu
- School of Opto-electronic and Communication Engineering, Xiamen University of Technology, Xiamen, China.
| | - Tao Bai
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China; School of Mathematics & Computer Science, Yanan University, Shanxi, 716000, China.
| | - Jiahai Chen
- Xiamen Sankuai Online Technology Co., Ltd, Xiamen, China.
| | - Yan Li
- School of Opto-electronic and Communication Engineering, Xiamen University of Technology, Xiamen, China.
| | - Hao Wu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| |
Collapse
|
6
|
Conway TP, Moye-Rowley WS. Conditional Protein Depletion in the Analysis of Antifungal Drug Resistance in Candida glabrata. Methods Mol Biol 2023; 2658:191-200. [PMID: 37024703 DOI: 10.1007/978-1-0716-3155-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
This chapter illustrates a method to generate Candida glabrata conditional depletion mutants for SNF2, an ATPase subunit of the SWI/SNF chromatin remodeling complex with potential roles in the response to azole drugs. The strategy employed utilizes a plant-specific proteolysis pathway which allows for the rapid degradation of a target protein in the presence of the phytohormone, auxin. The steps taken to generate strains expressing the auxin-inducible plant F-box protein, Tir1, and in which the auxin-binding target, IAA17, is C-terminally fused to Snf2 are described. This acute depletion strategy is suitable for studying the effects of the loss of growth-critical proteins. The rapid depletion afforded by the auxin-induced degradation avoids the potential complications of a null allele causing a severe growth defect and allows a more rapid assessment of the consequences of reduced levels of a protein of interest.
Collapse
Affiliation(s)
- Thomas P Conway
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
7
|
Mukul Das M, Sarkar K. Evaluation of machine learning classifiers for predicting essential genes in Mycobacterium tuberculosis strains. Bioinformation 2022; 18:1126-1130. [PMID: 37701504 PMCID: PMC10492903 DOI: 10.6026/973206300181126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/31/2022] [Indexed: 09/14/2023] Open
Abstract
Accurate investigation and prediction of essential genes from bacterial genome is very important as it might be explored in effective targets for antimicrobial drugs and understanding biological mechanism of a cell. A subset of key features data obtained from 14 genome sequence-based features of 20 strains of Mycobacterium tuberculosis bacteria whose essential gene information was downloaded from ePath and NCBI database for mapping and matching essential genes by using a genome extraction program. The selection of key features was performed by using Genetic Algorithm. For each of three classifiers, 80%, 10% and 10% of subset key features were used for training, validation and testing, respectively. Experimental results (10-f-cv) illustrated that DNN (proposed), DT, and SVM achieved AUC of 0.98, 0.88 and 0.82, respectively. DNN (proposed) outperformed DT and SVM. The higher prediction accuracy of classifiers was observed because of using only key features which also justified better generalizability of classifiers and efficiency of key features related to gene essentiality. Besides, DNN (proposed) also showed best prediction performance while compared with other predictors used in previous studies. The genome extraction program was developed for mapping and matching of essential genes between ePath and NCBI database.
Collapse
Affiliation(s)
- Monish Mukul Das
- Department of Computer Science and Engineering, University of Kalyani, Kalyani, Nadia - 741235
| | - Keka Sarkar
- Department of Microbiology, University of Kalyani, Kalyani, Nadia - 741235
| |
Collapse
|
8
|
Guan M, Ji W, Xu Y, Yan L, Chen D, Li S, Zhang X. Molecular fingerprints of polar narcotic chemicals based on heterozygous essential gene knockout library in Saccharomyces cerevisiae. Chemosphere 2022; 308:136343. [PMID: 36087727 DOI: 10.1016/j.chemosphere.2022.136343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Cytotoxicity of non-polar narcotic chemicals can be predicted by quantitative structure activity relationship (QSAR) models, but the polar narcotic chemicals' actual cytotoxicity exceeds the predicted values by their chemical structures. This discrepancy indicates that the molecular mechanism by which polar narcotic chemicals exert their toxicity is unclear. Taking advantage of Saccharomyces cerevisiae (yeast) functional genome-wide heterozygous essential gene knockout mutants, we here have identified the specific molecular fingerprints of two main chemical structure groups (phenols and anilines) of polar narcotic chemicals (dichlorophen (DCP), 4-chlorophenol (4-CP), 2, 4, 6-trichlorophenol (TCP), 3, 4-dichloroaniline (DCA) and N-methylaniline (NMA)) and one non-polar narcotic chemical 2, 2, 2-trichloroethanol (TCE). Especially, we identify 33, 57, 54, 46, 59 and 53 responsive strains through exposure to TCE, DCP, 4-CP, TCP, DCA and NMA with three test concentrations, respectively, revealing that these polar narcotic chemicals have more responsive strains than the non-polar narcotic chemical. Remarkably, we find that the molecular fingerprints of polar narcotic chemicals in different chemical structure groups are obviously varied, particularly phenols and anilines have their own specific molecular fingerprints. Interestingly, our results demonstrate that the molecular toxicity mechanisms of anilines are associated with DNA replication, but phenols are related with pathway of RNA degradation. Additionally, we find that the two knockout strains (SME1 and DIS3) and the three knockout strains (TSC11, RSP5 and HSF1) can specifically respond to exposure to phenols and anilines, respectively. Thus, they may be served as potential biomarkers to distinguish phenols from anilines. Collectively, our works demonstrate that the functional genomic platform of yeast essential gene mutants can not only act as an effective tool to identify key specific molecular fingerprints for polar narcotic chemicals, but also help to understand the molecular mechanisms of polar narcotic chemicals.
Collapse
Affiliation(s)
- Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China.
| | - Wenya Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Yue Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China
| | - Lu Yan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, China
| | - Dong Chen
- Jiangsu Provincial Academy of Environmental Science, 176 North Jiangdong Rd., Nanjing, Jiangsu, 210036, China
| | - Shengjie Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, Jiangsu, 210023, China; School of Food Science, Nanjing Xiaozhuang University, Jiangsu, Nanjing, 211171, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, China.
| |
Collapse
|
9
|
Oz N, Vayndorf EM, Tsuchiya M, McLean S, Turcios-Hernandez L, Pitt JN, Blue BW, Muir M, Kiflezghi MG, Tyshkovskiy A, Mendenhall A, Kaeberlein M, Kaya A. Evidence that conserved essential genes are enriched for pro-longevity factors. GeroScience 2022; 44:1995-2006. [PMID: 35695982 PMCID: PMC9616985 DOI: 10.1007/s11357-022-00604-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/03/2022] [Indexed: 02/02/2023] Open
Abstract
At the cellular level, many aspects of aging are conserved across species. This has been demonstrated by numerous studies in simple model organisms like Saccharomyces cerevisiae, Caenorhabdits elegans, and Drosophila melanogaster. Because most genetic screens examine loss of function mutations or decreased expression of genes through reverse genetics, essential genes have often been overlooked as potential modulators of the aging process. By taking the approach of increasing the expression level of a subset of conserved essential genes, we found that 21% of these genes resulted in increased replicative lifespan in S. cerevisiae. This is greater than the ~ 3.5% of genes found to affect lifespan upon deletion, suggesting that activation of essential genes may have a relatively disproportionate effect on increasing lifespan. The results of our experiments demonstrate that essential gene overexpression is a rich, relatively unexplored means of increasing eukaryotic lifespan.
Collapse
Affiliation(s)
- Naci Oz
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Elena M Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Mitsuhiro Tsuchiya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Samantha McLean
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | - Jason N Pitt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin W Blue
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael Muir
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael G Kiflezghi
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander Mendenhall
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA.
| |
Collapse
|
10
|
Boldrin F, Manganelli R. Repressible Promoter System to Study Essential Genes in Mycobacteria. Methods Mol Biol 2022; 2377:317-332. [PMID: 34709624 DOI: 10.1007/978-1-0716-1720-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Inducible gene expression systems represent powerful tools for studying essential gene function and for validation of drug targets in bacteria. Even if several regulated promoters have been characterized, only a few of them have been successfully used in Mycobacteria. Here we describe a successful mycobacterial gene regulation system based on the presence of two chromosomally encoded repressors: Pip and TetR, and a tunable promoter (Pptr) that allows a tight regulation of gene expression.
Collapse
Affiliation(s)
- Francesca Boldrin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | |
Collapse
|
11
|
Abstract
Cyanobacteria, a group of diverse bacteria capable of oxygenic photosynthesis, are excellent models for investigating many important cellular processes, such as photosynthesis, nitrogen fixation, and prokaryotic cell differentiation. They also have great potential to become the next-generation cell factories for sustainable biosynthesis of valuable products. However, genetic manipulation in cyanobacteria is not as convenient as in other model bacteria. Particularly, handling essential genes in cyanobacteria has been difficult due to the lack of appropriate tools, limiting our understanding of many important cellular functions encoded by them. We recently develop a CRISPR-based method for constructing the conditional mutants of cyanobacterial essential genes by engineering the ribosome binding site to a theophylline-responsive riboswitch. Here, we provide the details of this method. The principle of this method could be used to construct conditional mutants in a wide range of bacterial species.
Collapse
Affiliation(s)
- Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China.
| | - Tian-Cai Niu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Gui-Ming Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| |
Collapse
|
12
|
Abstract
Genetic balancer systems, which allow effective capture and maintenance of lethal mutations stably, play an important role in identifying essential genes. Whole-genome sequencing (WGS) followed by bioinformatics analysis, combined with genetic mapping data analysis, allows for an efficient and economical means of identifying genomic mutations in essential genes. Using this approach, we successfully identified 104 essential genes on ChrI, ChrIII, and ChrV in C. elegans. In this report, we described a protocol that sequences the genome of prebalanced Caenorhabditis elegans (C. elegans) strains to carry lethal mutations and identifies candidate causal mutations and candidate essential genes using a robust bioinformatics procedure.
Collapse
Affiliation(s)
- Shicheng Yu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Bioland Laboratory, Guangzhou, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Chaoran Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | | |
Collapse
|
13
|
Falchi FA. Analyzing the Function of Essential Genes by Plasmid Shuffling. Methods Mol Biol 2022; 2548:37-49. [PMID: 36151490 DOI: 10.1007/978-1-0716-2581-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Investigations on gene essentiality have important implications in several fields of basic and applied research. A variety of strategies have been developed over the years to identify essential genes. Here, we describe an implemented plasmid shuffling method useful to assess the essentiality of overlapped genes under very stringent conditions. A host strain harboring the chromosomal deletion of the genes of interest is complemented by a thermosensitive plasmid carrying the copy of gene 1, gene 2, and rpsL allele, conferring streptomycin sensitivity to an otherwise resistant strain. A compatible plasmid harboring a different selectable marker and the copy of gene 2 only is transformed into the host strain, resulting in the coexistence of two plasmids. These cells are grown at high temperatures in a medium containing streptomycin. Under such conditions, viable cells are expected to contain only the incoming plasmid and to carry suppressor mutation(s) that bypass the loss of the essential gene 1. The system may thus represent a valuable tool to identify interactions between essential proteins and cell pathways.
Collapse
|
14
|
Aouida M, Ramotar D. A Screening Method to Identify Essential Yeast Genes for Responses Towards Spermine. Methods Mol Biol 2022; 2377:363-9. [PMID: 34709627 DOI: 10.1007/978-1-0716-1720-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We exploited the yeast DAmP mutant collection to identify essential genes that play a role in polyamine resistance. Herein, we described in details the methodology to obtain these genes. This approach is applicable for screening many nontoxic and toxic drugs.
Collapse
|
15
|
Veeranagouda Y, Wexler HM. The Application of Transposon Insertion Sequencing in Identifying Essential Genes in B. fragilis. Methods Mol Biol 2022; 2377:303-15. [PMID: 34709623 DOI: 10.1007/978-1-0716-1720-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Essential genes are those that are indispensable for the survival of organism under specific growth conditions. Investigating essential genes in pathogenic bacteria not only helps to understand vital biological networks but also provides novel targets for drug development. Availability of genetic engineering tools and high-throughput sequencing methods has enabled essential genes identification in many pathogenic gram-positive and gram-negative bacteria. Bacteroides fragilis is one of the major bacteria specific of human gastrointestinal microbiota. When B. fragilis moves out of its niche, it turns into deadly pathogen. Here, we describe detailed method for the essential gene identification in B. fragilis. Generated transposon mutant pool can be used for other applications such as identification of genes responsible for drug resistance in B. fragilis.
Collapse
|
16
|
Luo Z, Wang J, Zhu Y, Sun X, He C, Cai M, Ma J, Wang Y, Han S. SPOP promotes CDCA5 degradation to regulate prostate cancer progression via the AKT pathway. Neoplasia 2021; 23:1037-1047. [PMID: 34509929 PMCID: PMC8435818 DOI: 10.1016/j.neo.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/21/2021] [Accepted: 08/11/2021] [Indexed: 12/02/2022] Open
Abstract
The E3 ubiquitin ligase adaptor Speckle-type POZ protein (SPOP) plays an important tumour suppressor role in prostate cancers (PCa), with mutation rate up to 15%. However, how SPOP mutations regulate prostate tumorigenesis remains elusive. Here, we report the identification of cell division cycle associated 5 (CDCA5) as a SPOP substrate. We found that SPOP interacts with CDCA5 and promotes its polyubiquitin degradation in a degron-dependent manner. This effect was greatly impaired by introducing PCa associated SPOP mutations. Importantly, we found that CDCA5 was essential for PCa cells to survive and proliferate. CDCA5 depletion in PCa cells led to cessation of proliferation, G2M arrest, severe sister chromatid aggregation disturbance, and apoptosis. we also found that CDCA5 knockdown decreased the protein expression of p-GSK3β, increased the activity of caspase-3, caspase-9, and the Bax/Bcl-2 ratio. Besides, we confirmed that CDCA5 interrupted cancer cell behavior via the AKT pathway. In contrast, silencing SPOP or overexpressing CDCA5 increased cell proliferation. Consistently, depleting SPOP along with CDCA5, or overexpressing CDCA5 along with SPOP also caused the growth of cells repressed. Consistent with the functional role of CDCA5, the mRNA and protein levels of CDCA5 were significantly increased in PCa, compared to normal tissues, and its high expression was associated with more severe lymph node metastasis, higher Gleason score, and poorer prognosis. Together, our data showed that SPOP plays a crucial role in inhibiting tumorigenesis and partly achieved this by promoting the degradation of oncoprotein CDCA5.
Collapse
Affiliation(s)
- Zhenzhen Luo
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jing Wang
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yue Zhu
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xiao Sun
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chenchen He
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mengjiao Cai
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jinlu Ma
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | - Suxia Han
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
| |
Collapse
|
17
|
Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
Collapse
Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
18
|
Simons M. Synthetic biology as a technoscience: The case of minimal genomes and essential genes. Stud Hist Philos Sci 2021; 85:127-136. [PMID: 33966767 DOI: 10.1016/j.shpsa.2020.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 06/12/2023]
Abstract
This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific organisms towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience.
Collapse
Affiliation(s)
- Massimiliano Simons
- Ghent University, Department of Philosophy and Moral Sciences, Blandijnberg 2, BE-9000, Ghent, Belgium.
| |
Collapse
|
19
|
Fan L, Xiao W. Study Essential Gene Functions by Plasmid Shuffling. Methods Mol Biol 2020; 2196:53-62. [PMID: 32889712 DOI: 10.1007/978-1-0716-0868-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
An essential gene is defined as a gene that cannot be completely removed from the genome. Investigation of an essential gene function is limited because its deletion strain cannot be readily created. Here we describe a protocol called plasmid shuffling that can be conveniently employed in yeast to study essential gene functions. The essential gene is first cloned into a YCp-based plasmid with URA3 as a selectable marker and then transformed into host cells. The transformed cells can then be used to delete the chromosomal copy of the essential gene. The gene is then cloned into another YCp-based plasmid with a different selectable marker, and the gene sequence can be altered in vitro. Plasmids carrying the mutated gene sequences are transformed into the above cells, resulting in carrying two plasmids. These cells are grown in medium containing 5-FOA that selects ura3 cells. The 5-FOA-resistant cells are expected to only carry the plasmid containing the mutated essential gene, whose functions can be assessed.
Collapse
Affiliation(s)
- Li Fan
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.,College of Life Sciences, Capital Normal University, Beijing, China
| | - Wei Xiao
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada. .,College of Life Sciences, Capital Normal University, Beijing, China.
| |
Collapse
|
20
|
Jasti N, Sebagh D, Riaz M, Wang X, Koripella B, Palanisamy V, Mohammad N, Chen Q, Friedrich M. Towards reconstructing the dipteran demise of an ancient essential gene: E3 ubiquitin ligase Murine double minute. Dev Genes Evol 2020; 230:279-294. [PMID: 32623522 DOI: 10.1007/s00427-020-00663-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Genome studies have uncovered many examples of essential gene loss, raising the question of how ancient genes transition from essentiality to dispensability. We explored this process for the deeply conserved E3 ubiquitin ligase Murine double minute (Mdm), which is lacking in Drosophila despite the conservation of its main regulatory target, the cellular stress response gene p53. Conducting gene expression and knockdown experiments in the red flour beetle Tribolium castaneum, we found evidence that Mdm has remained essential in insects where it is present. Using bioinformatics approaches, we confirm the absence of the Mdm gene family in Drosophila, mapping its loss to the stem lineage of schizophoran Diptera and Pipunculidae (big-headed flies), about 95-85 million years ago. Intriguingly, this gene loss event was preceded by the de novo origin of the gene Companion of reaper (Corp), a novel p53 regulatory factor that is characterized by functional similarities to vertebrate Mdm2 despite lacking E3 ubiquitin ligase protein domains. Speaking against a 1:1 compensatory gene gain/loss scenario, however, we found that hoverflies (Syrphidae) and pointed-wing flies (Lonchopteridae) possess both Mdm and Corp. This implies that the two p53 regulators have been coexisting for ~ 150 million years in select dipteran clades and for at least 50 million years in the lineage to Schizophora and Pipunculidae. Given these extensive time spans of Mdm/Corp coexistence, we speculate that the loss of Mdm in the lineage to Drosophila involved further acquisitions of compensatory gene activities besides the emergence of Corp. Combined with the previously noted reduction of an ancestral P53 contact domain in the Mdm homologs of crustaceans and insects, we conclude that the loss of the ancient Mdm gene family in flies was the outcome of incremental functional regression over long macroevolutionary time scales.
Collapse
Affiliation(s)
- Naveen Jasti
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.,Institute for Protein Design, Washington University, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - Dylan Sebagh
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Mohammed Riaz
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Xin Wang
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Bharat Koripella
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Vasanth Palanisamy
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Nabeel Mohammad
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Qing Chen
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA. .,Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI, 48201, USA.
| |
Collapse
|
21
|
Su Y, Xu Y, Li Q, Yuan G, Zheng D. The essential genome of Ralstonia solanacearum. Microbiol Res 2020; 238:126500. [PMID: 32502949 DOI: 10.1016/j.micres.2020.126500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 01/13/2023]
Abstract
Ralstonia solanacearum is a scientifically/economically important plant pathogenic bacterium. The plant disease caused by R. solanacearum causes huge economic losses, and efficient control measures for the disease remain limited. To gain a better system-level understanding of R. solanacearum, we generated a near-saturated transposon insertion library of R. solanacearum GMI1000 with approximately 240,000 individual insertion mutants. Transposon sequencing (Tn-seq) allowed the mapping of 70.44%-80.96% of all potential insertion sites of the mariner C9 transposase in the genome of R. solanacearum and the identification of 465 genes essential for the growth of R. solanacearum in rich medium. Functional and comparative analyses of essential genes revealed that many basic physiological and biochemical processes such as transcription differ between R. solanacearum and other bacteria. A comparative analysis of essential genes also suggested that 34 genes might be essential only for Ralstonia group bacteria, whereas another 16 essential genes are unique to Ralstonia, providing high-priority candidate targets for developing R. solanacearum-specific drugs.
Collapse
Affiliation(s)
- Yaxing Su
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China
| | - Yanan Xu
- Pharmaceutical College, Guangxi Medical University, Nanning 530021, PR China
| | - Qiqin Li
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China
| | - Gaoqing Yuan
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China
| | - Dehong Zheng
- National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, PR China.
| |
Collapse
|
22
|
Rico AB, Olson AT, Wiebe MS. Generation of Vaccinia Virus Gene Deletion Mutants Using Complementing Cell Lines. Methods Mol Biol 2019; 2023:93-108. [PMID: 31240672 DOI: 10.1007/978-1-4939-9593-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This protocol describes how to couple two techniques, the generation of complementing cells lines and production of viral deletion mutants, to rapidly construct novel tools for poxvirus analysis. Specifically, the production and utilization of a complementing cell line expressing a poxvirus gene of interest are critical for the generation of poxvirus mutants in which essential genes are disrupted. Complementing cells are also valuable for the characterization of vaccinia genes in the absence of infection. Here, we detail the process of isolating vaccinia virus deletion mutants. Deletion mutant generation involves homologous recombination between replicating viral DNA and transfected DNA followed by selection and screening on a complementing cell line that provides the deleted gene in trans. Finally, deletion is confirmed by polymerase chain reaction, sequencing, and functional assays if available.
Collapse
|
23
|
Perenthaler E, Nikoncuk A, Yousefi S, Berdowski WM, Alsagob M, Capo I, van der Linde HC, van den Berg P, Jacobs EH, Putar D, Ghazvini M, Aronica E, van IJcken WFJ, de Valk WG, Medici-van den Herik E, van Slegtenhorst M, Brick L, Kozenko M, Kohler JN, Bernstein JA, Monaghan KG, Begtrup A, Torene R, Al Futaisi A, Al Murshedi F, Mani R, Al Azri F, Kamsteeg EJ, Mojarrad M, Eslahi A, Khazaei Z, Darmiyan FM, Doosti M, Karimiani EG, Vandrovcova J, Zafar F, Rana N, Kandaswamy KK, Hertecant J, Bauer P, AlMuhaizea MA, Salih MA, Aldosary M, Almass R, Al-Quait L, Qubbaj W, Coskun S, Alahmadi KO, Hamad MHA, Alwadaee S, Awartani K, Dababo AM, Almohanna F, Colak D, Dehghani M, Mehrjardi MYV, Gunel M, Ercan-Sencicek AG, Passi GR, Cheema HA, Efthymiou S, Houlden H, Bertoli-Avella AM, Brooks AS, Retterer K, Maroofian R, Kaya N, van Ham TJ, Barakat TS. Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases. Acta Neuropathol 2020; 139:415-442. [PMID: 31820119 PMCID: PMC7035241 DOI: 10.1007/s00401-019-02109-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022]
Abstract
Developmental and/or epileptic encephalopathies (DEEs) are a group of devastating genetic disorders, resulting in early-onset, therapy-resistant seizures and developmental delay. Here we report on 22 individuals from 15 families presenting with a severe form of intractable epilepsy, severe developmental delay, progressive microcephaly, visual disturbance and similar minor dysmorphisms. Whole exome sequencing identified a recurrent, homozygous variant (chr2:64083454A > G) in the essential UDP-glucose pyrophosphorylase (UGP2) gene in all probands. This rare variant results in a tolerable Met12Val missense change of the longer UGP2 protein isoform but causes a disruption of the start codon of the shorter isoform, which is predominant in brain. We show that the absence of the shorter isoform leads to a reduction of functional UGP2 enzyme in neural stem cells, leading to altered glycogen metabolism, upregulated unfolded protein response and premature neuronal differentiation, as modeled during pluripotent stem cell differentiation in vitro. In contrast, the complete lack of all UGP2 isoforms leads to differentiation defects in multiple lineages in human cells. Reduced expression of Ugp2a/Ugp2b in vivo in zebrafish mimics visual disturbance and mutant animals show a behavioral phenotype. Our study identifies a recurrent start codon mutation in UGP2 as a cause of a novel autosomal recessive DEE syndrome. Importantly, it also shows that isoform-specific start-loss mutations causing expression loss of a tissue-relevant isoform of an essential protein can cause a genetic disease, even when an organism-wide protein absence is incompatible with life. We provide additional examples where a similar disease mechanism applies.
Collapse
Affiliation(s)
- Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Anita Nikoncuk
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Soheil Yousefi
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Woutje M Berdowski
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Maysoon Alsagob
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Ivan Capo
- Department for Histology and Embryology, Faculty of Medicine Novi Sad, University of Novi Sad, Novi Sad, Serbia
| | - Herma C van der Linde
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Paul van den Berg
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Edwin H Jacobs
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Darija Putar
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Mehrnaz Ghazvini
- iPS Cell Core Facility, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Wilfred F J van IJcken
- Center for Biomics, Department of Cell Biology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Walter G de Valk
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | | | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Lauren Brick
- Division of Genetics, McMaster Children's Hospital, Hamilton, ON, L8S 4J9, Canada
| | - Mariya Kozenko
- Division of Genetics, McMaster Children's Hospital, Hamilton, ON, L8S 4J9, Canada
| | - Jennefer N Kohler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94035, USA
| | - Jonathan A Bernstein
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94035, USA
| | | | | | | | - Amna Al Futaisi
- Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Fathiya Al Murshedi
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Renjith Mani
- Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Faisal Al Azri
- Department of Radiology and Molecular Imaging, Sultan Qaboos University Hospital, Muscat, Oman
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Genetic Center of Khorasan Razavi, Mashhad, Iran
| | - Atieh Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | | | - Mohammad Doosti
- Department Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
- Innovative Medical Research Center, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Jana Vandrovcova
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Faisal Zafar
- Department of Paediatric Neurology, Children's Hospital and Institute of Child Health, Multan, 60000, Pakistan
| | - Nuzhat Rana
- Department of Paediatric Neurology, Children's Hospital and Institute of Child Health, Multan, 60000, Pakistan
| | | | - Jozef Hertecant
- Department of Pediatrics, Tawam Hospital, and College of Medicine and Health Sciences, UAE University, Al-Ain, UAE
| | | | - Mohammed A AlMuhaizea
- Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Mustafa A Salih
- Neurology Division, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, 11461, Kingdom of Saudi Arabia
| | - Mazhor Aldosary
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Rawan Almass
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Laila Al-Quait
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Wafa Qubbaj
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Serdar Coskun
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Khaled O Alahmadi
- Radiology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Muddathir H A Hamad
- Neurology Division, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, 11461, Kingdom of Saudi Arabia
| | - Salem Alwadaee
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Khalid Awartani
- Obstetrics/Gynecology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Anas M Dababo
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Futwan Almohanna
- Department of Cell Biology, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Murat Gunel
- Department of Neurosurgery, Program On Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - A Gulhan Ercan-Sencicek
- Department of Neurosurgery, Program On Neurogenetics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Masonic Medical Research Institute, Utica, NY, USA
| | - Gouri Rao Passi
- Department of Pediatrics, Pediatric Neurology Clinic, Choithram Hospital and Research Centre, Indore, Madhya Pradesh, India
| | - Huma Arshad Cheema
- Pediatric Gastroenterology Department, Children's Hospital and Institute of Child Health, Lahore, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | | | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | | | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
| |
Collapse
|
24
|
Yang S, Cao X, Yu W, Li S, Zhou YJ. Efficient targeted mutation of genomic essential genes in yeast Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:3037-3047. [PMID: 32043190 DOI: 10.1007/s00253-020-10405-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/13/2020] [Accepted: 01/23/2020] [Indexed: 02/06/2023]
Abstract
Targeted gene mutation by allelic replacement is important for functional genomic analysis and metabolic engineering. However, it is challenging in mutating the essential genes with the traditional method by using a selection marker, since the first step of essential gene knockout will result in a lethal phenotype. Here, we developed a two-end selection marker (Two-ESM) method for site-directed mutation of essential genes in Saccharomyces cerevisiae with the aid of the CRISPR/Cas9 system. With this method, single and double mutations of the essential gene ERG20 (encoding farnesyl diphosphate synthase) in S. cerevisiae were successfully constructed with high efficiencies of 100%. In addition, the Two-ESM method significantly improved the mutation efficiency and simplified the genetic manipulation procedure compared with traditional methods. The genome integration and mutation efficiencies were further improved by dynamic regulation of mutant gene expression and optimization of the integration modules. This Two-ESM method will facilitate the construction of genomic mutations of essential genes for functional genomic analysis and metabolic flux regulation in yeasts. KEY POINTS: • A Two-ESM strategy achieves mutations of essential genes with high efficiency of 100%. • The optimized three-module method improves the integration efficiency by more than three times. • This method will facilitate the functional genomic analysis and metabolic flux regulation.
Collapse
Affiliation(s)
- Shan Yang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Cao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Shengying Li
- Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, Shandong, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| |
Collapse
|
25
|
Lu JB, Lou YH, Li LC, Zhang XY, Luo XM, Zhang CX. Egf-like gene is essential for cuticle metabolism in the brown planthopper. J Insect Physiol 2019; 116:90-99. [PMID: 31063731 DOI: 10.1016/j.jinsphys.2019.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Using the mass spectrometry analysis of cuticle casts of brown planthopper (BPH, Nilaparvata lugens) and transcriptome analysis of BPH tissues, we identified a gigantic gene (50,922 bp, 16,973 aa) tentatively called Nlegf-like. Multiple transcripts were found. Nlegf-like encodes an integral membrane protein of 16,973 amino acid residues with 260 EGF-like repeats and 16 Ca2+-binding EGF repeats type (cbEGFs) in the extracellular portion. Nlegf-like was highly expressed in the integument and tended to peak at the middle stage or late stage of each nymph instar. Phylogenetic analysis showed this gene is conserved in many other insects. Different double-stranded RNA-mediated RNA interference targeting eight different regions of the Nlegf-like gene resulted in abnormal cuticle formation or molting and lethal phenotypes. Transmission electron microscopy revealed that the newly formed endocuticle was significantly thinner for RNAi-treated BPHs with phenotype of contracted abdomen, or the old cuticle could not be digested sufficiently for those with phenotype of slender body shape or died with molting difficulty when compared with the control group. We suggest that the Nlegf-like is crucial for metabolism of the cuticle in BPH molting.
Collapse
Affiliation(s)
- Jia-Bao Lu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Yi-Han Lou
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Ling-Chen Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Ya Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Xu-Mei Luo
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Chuan-Xi Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
26
|
Wang B, Wang Z, Wang D, Zhang B, Ong SG, Li M, Yu W, Wang Y. krCRISPR: an easy and efficient strategy for generating conditional knockout of essential genes in cells. J Biol Eng 2019; 13:35. [PMID: 31049076 PMCID: PMC6480908 DOI: 10.1186/s13036-019-0150-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/15/2019] [Indexed: 02/06/2023] Open
Abstract
Background CRISPR/Cas9 system is a powerful tool for knocking out genes in cells. However, genes essential for cell survival cannot be directly knocked out. Traditionally, generation of conditional knockout cells requires multiple steps. Results In this study, we developed an easy and efficient strategy to generate conditional knockout cells by using double episomal vectors – one which expresses gRNA and Cas9 nuclease, and the other expresses an inducible rescue gene. Using this system which we named “krCRISPR” (knockout-rescue CRISPR), we showed that essential genes, HDAC3 and DNMT1, can be efficiently knocked out. When cells reach a desired confluency, the exogenous rescue genes can be silenced by the addition of doxycycline. Furthermore, the krCRISPR system enabled us to study the effects of the essential gene mutations on cells. We showed that the P507L mutation in DNMT1 led to downregulation of global DNA methylation in cells, indicating that it is a disease-causing mutation. Conclusions The krCRISPR system offers an easy and efficient platform that facilitates the study of essential genes’ function. Electronic supplementary material The online version of this article (10.1186/s13036-019-0150-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Bei Wang
- 1MOE Key Laboratory of Contemporary Anthropology at School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| | - Zishi Wang
- 1MOE Key Laboratory of Contemporary Anthropology at School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| | - Daqi Wang
- 1MOE Key Laboratory of Contemporary Anthropology at School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| | - Baolong Zhang
- 2Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508 China
| | - Sang-Ging Ong
- 3Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612 USA.,4Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL 60612 USA
| | - Mingqing Li
- 5The Key Lab of Reproduction Regulation of NPFPC in SIPPR, Institute of Reproduction & Development in Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200011 China
| | - Wenqiang Yu
- 2Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508 China
| | - Yongming Wang
- 1MOE Key Laboratory of Contemporary Anthropology at School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| |
Collapse
|
27
|
Najah S, Saulnier C, Pernodet JL, Bury-Moné S. Design of a generic CRISPR-Cas9 approach using the same sgRNA to perform gene editing at distinct loci. BMC Biotechnol 2019; 19:18. [PMID: 30894153 PMCID: PMC6425556 DOI: 10.1186/s12896-019-0509-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CRISPR/Cas (clustered regularly interspaced short palindromic repeat and CRISPR-associated nucleases) based technologies have revolutionized genome engineering. While their use for prokaryotic genome editing is expanding, some limitations remain such as possible off-target effects and design constraints. These are compounded when performing systematic genome editing at distinct loci or when targeting repeated sequences (e.g. multicopy genes or mobile genetic elements). To overcome these limitations, we designed an approach using the same sgRNA and CRISPR-Cas9 system to independently perform gene editing at different loci. RESULTS We developed a two-step procedure based on the introduction by homologous recombination of 'bait' DNA at the vicinity of a gene copy of interest before inducing CRISPR-Cas9 activity. The introduction of a genetic tool encoding a CRISPR-Cas9 complex targeting this 'bait' DNA induces a double strand break near the copy of interest. Its repair by homologous recombination can lead either to reversion or gene copy-specific editing. The relative frequencies of these events are linked to the impact of gene editing on cell fitness. In our study, we used this technology to successfully delete the native copies of two xenogeneic silencers lsr2 paralogs in Streptomyces ambofaciens. We observed that one of these paralogs is a candidate-essential gene since its native locus can be deleted only in the presence of an extra copy. CONCLUSION By targeting 'bait' DNA, we designed a 'generic' CRISPR-Cas9 toolkit that can be used to edit different loci. The differential action of this CRISPR-Cas9 system is exclusively based on the specific recombination between regions surrounding the gene copy of interest. This approach is suitable to edit multicopy genes. One such particular example corresponds to the mutagenesis of candidate-essential genes that requires the presence of an extra copy of the gene before gene disruption. This opens new insights to explore gene essentiality in bacteria and to limit off-target effects during systematic CRISPR-Cas9 based approaches.
Collapse
Affiliation(s)
- Soumaya Najah
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Corinne Saulnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Stéphanie Bury-Moné
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-Sur-Yvette, France
| |
Collapse
|
28
|
Uddin R, Zahra NUA, Azam SS. Identification of glucosyl-3-phosphoglycerate phosphatase as a novel drug target against resistant strain of Mycobacterium tuberculosis (XDR1219) by using comparative metabolic pathway approach. Comput Biol Chem 2019; 79:91-102. [PMID: 30743161 DOI: 10.1016/j.compbiolchem.2019.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/13/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
Abstract
Tuberculosis (TB) is a major global health challenge. It has been afflicting human for thousands of years and is still severely affecting a huge population. The etiological agent of the disease is Mycobacterium tuberculosis (MTB) that survives in the human host in latent, dormant, and non-replicative state by evading the immune system. It is one of the leading causes of infection related death worldwide. The situation is exacerbated by the massive increase in the resistant strains such as multi-drug resistant TB (MDR-TB) and extensive drug-resistant TB (XDR-TB). The resistance is as severe that it resulted in failure of the current chemotherapy regimens (i.e. anti-tubercular drugs). It is therefore imperative to discover the new anti-tuberculosis drug targets and their potential inhibitors. Current study has made the use of in silico approaches to perform the comparative metabolic pathway analysis of the MTBXDR1219 with the host i.e. H. sapiens. We identified several metabolic pathways which are unique to pathogen only. By performing subtractive genomic analysis 05 proteins as potential drug target are retrieved. This study suggested that the identified proteins are essential for the bacterial survival and non-homolog to the host proteins. Furthermore, we selected glucosyl-3-phosoglycerate phosphatase (GpgP, EC 5.4.2.1) out of the 05 proteins for molecular docking analysis and virtual screening. The protein is involved in the biosynthesis of methylglucose lipopolysaccharides (MGLPs) which regulate the biosynthesis of mycolic acid. Mycolic acid is the building block of the unique cell wall of the MTB which is responsible for the resistance and pathogenicity. A relatively larger library consisting of 10,431 compounds was screened using AutoDock Vina to predict the binding modes and to rank the potential inhibitors. No potent inhibitor against MTB GpgP has been reported yet, therefore ranking of compounds is performed by making a comparison with the substrate i.e. glucosyl-3-phosphoglycerate. The obtained results provide the understanding of underlying mechanism of interactions of ligands with protein. Follow up study will include the study of the Protein-Protein Interactions (PPIs), and to propose the potential inhibitors against them.
Collapse
Affiliation(s)
- Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan.
| | - Noor-Ul-Ain Zahra
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
29
|
Kurata T, Nakanishi S, Hashimoto M, Taoka M, Isobe T, Kato JI. Subunit Composition of Ribosome in the yqgF Mutant Is Deficient in pre-16S rRNA Processing of Escherichia coli. J Mol Microbiol Biotechnol 2018; 28:179-182. [PMID: 30566952 DOI: 10.1159/000494494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/15/2018] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli 16S, 23S, and 5S ribosomal RNAs (rRNAs) are transcribed as a single primary transcript, which is subsequently processed into mature rRNAs by several RNases. Three RNases (RNase III, RNase E, and RNase G) were reported to function in processing the 5'-leader of precursor 16S rRNA (pre-16S rRNA). Previously, we showed that a novel essential YqgF is involved in that processing. Here we investigated the ribosome subunits of the yqgFts mutant by LC-MS/MS. The mutant ribosome had decreased copy numbers of ribosome protein S1, suggesting that the yqgF gene enables incorporation of ribosomal protein S1 into ribosome by processing of the 5'-end of pre-16S rRNA. The ribosome protein S1 is essential for translation in E. coli; therefore, our results suggest that YqgF converts the inactive form of newly synthesized ribosome into the active form at the final step of ribosome assembly.
Collapse
Affiliation(s)
- Tatsuaki Kurata
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Shinobu Nakanishi
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Masayuki Hashimoto
- Institute of Molecular Medicine, Medical College, National Cheng-Kung University, Tainan City, Taiwan.,Infectious Disease and Signal Transduction Center, Medical College, National Cheng-Kung University, Tainan City, Taiwan
| | - Masato Taoka
- Department of Chemistry, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Jun-Ichi Kato
- Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan,
| |
Collapse
|
30
|
Yu S, Zheng C, Zhou F, Baillie DL, Rose AM, Deng Z, Chu JSC. Genomic identification and functional analysis of essential genes in Caenorhabditis elegans. BMC Genomics 2018; 19:871. [PMID: 30514206 PMCID: PMC6278001 DOI: 10.1186/s12864-018-5251-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 11/14/2018] [Indexed: 11/27/2022] Open
Abstract
Background Essential genes are required for an organism’s viability and their functions can vary greatly, spreading across many pathways. Due to the importance of essential genes, large scale efforts have been undertaken to identify the complete set of essential genes and to understand their function. Studies of genome architecture and organization have found that genes are not randomly disturbed in the genome. Results Using combined genetic mapping, Illumina sequencing, and bioinformatics analyses, we successfully identified 44 essential genes with 130 lethal mutations in genomic regions of C. elegans of around 7.3 Mb from Chromosome I (left). Of the 44 essential genes, six of which were genes not characterized previously by mutant alleles, let-633/let-638 (B0261.1), let-128 (C53H9.2), let-511 (W09C3.4), let-162 (Y47G6A.18), let-510 (Y47G6A.19), and let-131 (Y71G12B.6). Examine essential genes with Hi-C data shows that essential genes tend to cluster within TAD units rather near TAD boundaries. We have also shown that essential genes in the left half of chromosome I in C. elegans function in enzyme and nucleic acid binding activities during fundamental processes, such as DNA replication, transcription, and translation. From protein-protein interaction networks, essential genes exhibit more protein connectivity than non-essential genes in the genome. Also, many of the essential genes show strong expression in embryos or early larvae stages, indicating that they are important to early development. Conclusions Our results confirmed that this work provided a more comprehensive picture of the essential gene and their functional characterization. These genetic resources will offer important tools for further heath and disease research. Electronic supplementary material The online version of this article (10.1186/s12864-018-5251-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shicheng Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China. .,Wuhan Frasergen Bioinformatics, Wuhan East Lake High-tech Zone, Wuhan, 430075, China.
| | - Chaoran Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fan Zhou
- Wuhan Frasergen Bioinformatics, Wuhan East Lake High-tech Zone, Wuhan, 430075, China
| | - David L Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Ann M Rose
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | | |
Collapse
|
31
|
Yin H, Kassner M. In Vitro High-Throughput RNAi Screening to Accelerate the Process of Target Identification and Drug Development. Methods Mol Biol 2016; 1470:137-49. [PMID: 27581290 DOI: 10.1007/978-1-4939-6337-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
High-throughput RNA interference (HT-RNAi) is a powerful tool that can be used to knock down gene expression in order to identify novel genes and pathways involved in many cellular processes. It is a systematic, yet unbiased, approach to identify essential or synthetic lethal genes that promote cell survival in diseased cells as well as genes that confer resistance or sensitivity to drug treatment. This information serves as a foundation for enhancing current treatments for cancer and other diseases by identifying new drug targets, uncovering potential combination therapies, and helping clinicians match patients with the most effective treatment based on genetic information. Here, we describe the method of performing an in vitro HT-RNAi screen using chemically synthesized siRNA.
Collapse
|
32
|
Zhao L, Anderson MT, Wu W, T Mobley HL, Bachman MA. TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. BMC Bioinformatics 2017; 18:326. [PMID: 28683752 PMCID: PMC5500955 DOI: 10.1186/s12859-017-1745-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/26/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Tn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data is that multiple mutants in a gene provides independent evidence to prioritize that gene as being essential. The existing methods do not account for this feature or rely on a high-density transposon library. Moreover, these methods are unable to accommodate complex designs. RESULTS The method proposed here is specifically designed for the analysis of Tn-Seq data. It utilizes two steps to estimate the conditional essentiality for each gene in the genome. First, it collects evidence of conditional essentiality for each insertion by comparing read counts of that insertion between conditions. Second, it combines insertion-level evidence for the corresponding gene. It deals with data from both low- and high-density transposon libraries and accommodates complex designs. Moreover, it is very fast to implement. The performance of the proposed method was tested on simulated data and experimental Tn-Seq data from Serratia marcescens transposon mutant library used to identify genes that contribute to fitness in a murine model of infection. CONCLUSION We describe a new, efficient method for identifying conditionally essential genes in Tn-Seq experiments with high detection sensitivity and specificity. It is implemented as TnseqDiff function in R package Tnseq and can be installed from the Comprehensive R Archive Network, CRAN.
Collapse
Affiliation(s)
- Lili Zhao
- Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, USA.
| | - Mark T Anderson
- Department of Microbiology and Immunology, School of medicine, University of Michigan, Ann Arbor, USA
| | - Weisheng Wu
- BRCF Bioinformatics Core, University of Michigan, Ann Arbor, USA
| | - Harry L T Mobley
- Department of Microbiology and Immunology, School of medicine, University of Michigan, Ann Arbor, USA
| | - Michael A Bachman
- Department of Pathology, School of medicine, University of Michigan, Ann Arbor, USA
| |
Collapse
|
33
|
Zhang YJ, Chen G, Lin H, Wang P, Kuang B, Liu J, Chen S. Development of a regulatable expression system for the functional study of Vibrio vulnificus essential genes. Antonie Van Leeuwenhoek 2017; 110:607-614. [PMID: 28044234 DOI: 10.1007/s10482-016-0827-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/24/2016] [Indexed: 11/28/2022]
Abstract
We developed a regulatable gene expression system for Vibrio vulnificus, which contains a lacIq-pTrc cassette. Monomeric red fluorescence protein (mRFP) was used as a reporter to test this system. The results showed that this system tightly controlled the expression of mRFP without leaky expression and was suitable for the controlled expression of genes encoding recombinant proteins in V. vulnificus. To demonstrate the utility of this system, a dominant negative form of V. vulnificus VVMO6_RS04990, a homolog of Escherichia coli LolD that is essential in lipoprotein transport and membrane biogenesis, was inducibly expressed. Expression of the dominant negative LolD homolog, which has a mutation in the ATPase domain, resulted in a growth defect in V. vulnificus cells and impaired cell envelope stability. This result suggests that the V. vulnificus LolD homolog plays a role in cell envelope biogenesis. This tight and titratable expression system will therefore be a valuable tool for the study of essential genes in V. vulnificus.
Collapse
Affiliation(s)
- Yan-Jiao Zhang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, People's Republic of China
| | - Guozhong Chen
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, People's Republic of China
| | - Huiyuan Lin
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, People's Republic of China
| | - Pan Wang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, People's Republic of China
| | - Baozhi Kuang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, People's Republic of China
| | - Jing Liu
- Central Laboratory, Qingdao Agriculture University, Qingdao, 266109, Shandong, People's Republic of China
| | - Shiyong Chen
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, Shandong, People's Republic of China.
- Collaborative Innovation Center for Marine Biomass Fibers, Materials and Textiles of Shandong Province, Qingdao University, Qingdao, 266071, Shandong, People's Republic of China.
| |
Collapse
|
34
|
Ianiri G, Boyce KJ, Idnurm A. Isolation of conditional mutations in genes essential for viability of Cryptococcus neoformans. Curr Genet 2016; 63:519-530. [PMID: 27783209 DOI: 10.1007/s00294-016-0659-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/02/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
Abstract
Discovering the genes underlying fundamental processes that enable cells to live and reproduce is a technical challenge, because loss of gene function in mutants results in organisms that cannot survive. This study describes a forward genetics method to identify essential genes in fungi, based on the propensity for Agrobacterium tumefaciens to insert T-DNA molecules into the promoters or 5' untranslated regions of genes and by placing a conditional promoter within the T-DNA. Insertions of the promoter of the GAL7 gene were made in the human pathogen Cryptococcus neoformans. Nine strains of 960 T-DNA insertional mutants screened grew on media containing galactose, but had impaired growth on media containing glucose, which suppresses expression from GAL7. T-DNA insertions were found in the homologs of IDI1, MRPL37, NOC3, NOP56, PRE3 and RPL17, all of which are essential in ascomycete yeasts Saccharomyces cerevisiae or Schizosaccharomyces pombe. Altering the carbon source in the medium provided a system to identify phenotypes in response to stress agents. The pre3 proteasome subunit mutant was further characterized. The T-DNA insertion and phenotype co-segregate in progeny from a cross, and the growth defect is complemented by the reintroduction of the wild type gene into the insertional mutant. A deletion allele was generated in a diploid strain, this heterozygous strain was sporulated, and analysis of the progeny provided additional genetic evidence that PRE3 is essential. The experimental design is applicable to other fungi and has other forward genetic applications such as to isolate over-expression suppressors or enhance the production of traits of interest.
Collapse
Affiliation(s)
- Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA.,Dipartimento di Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Via F. De Sanctis Snc, 86100, Campobasso, Italy
| | - Kylie J Boyce
- School of BioSciences, BioSciences 2, University of Melbourne, Building 122, Melbourne, VIC, 3010, Australia
| | - Alexander Idnurm
- School of BioSciences, BioSciences 2, University of Melbourne, Building 122, Melbourne, VIC, 3010, Australia.
| |
Collapse
|
35
|
Ward MS, Silva I, Martinez W, Jefferson J, Rahman S, Garcia JM, Kanichar D, Roppiyakuda L, Kosmowska E, Faust MA, Tran KP, Chow F, Buglo E, Zhou F, Groziak MP, Xu HH. Identification of cellular targets of a series of boron heterocycles using TIPA II-A sensitive target identification platform. Bioorg Med Chem 2016; 24:3267-75. [PMID: 27301675 DOI: 10.1016/j.bmc.2016.05.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/23/2016] [Accepted: 05/28/2016] [Indexed: 11/24/2022]
Abstract
One of the hurdles in the discovery of antibiotics is the difficulty of linking antibacterial compounds to their cellular targets. Our laboratory has employed a genome-wide approach of over-expressing essential genes in order to identify cellular targets of antibacterial inhibitors. Our objective in this project was to develop and validate a more sensitive disk diffusion based platform of target identification (Target Identification Platform for Antibacterials version 2; TIPA II) using a collection of cell clones in an Escherichia coli mutant (AS19) host with increased outer membrane permeability. Five known antibiotics/inhibitors and 28 boron heterocycles were tested by TIPA II assay, in conjunction with the original assay TIPA. The TIPA II was more sensitive than TIPA because eight boron heterocycles previously found to be inactive to AG1 cells in TIPA assays exhibited activity to AS19 cells. For 15 boron heterocycles, resistant colonies were observed within the zones of inhibition only on the inducing plates in TIPA II assays. DNA sequencing confirmed that resistant clones harbor plasmids with fabI gene as insert, indicating that these boron heterocycles all target enoyl ACP reductase. Additionally, cell-based assays and dose response curved obtained indicated that for two boron heterocycle inhibitors, the fabI cell clone in AG1 (wild-type) host cells exhibited at least 11 fold more resistance under induced conditions than under non-induced conditions. Moreover, TIPA II also identified cellular targets of known antibacterial inhibitors triclosan, phosphomycin, trimethoprim, diazaborine and thiolactomycin, further validating the utility of the new system.
Collapse
Affiliation(s)
- Matthew S Ward
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Isba Silva
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Walfre Martinez
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Jameka Jefferson
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Shakila Rahman
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Jeanie M Garcia
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Divya Kanichar
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - Lance Roppiyakuda
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - Ewa Kosmowska
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - Michelle A Faust
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - Kim P Tran
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - Felicia Chow
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - Elena Buglo
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - Feimeng Zhou
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Michael P Groziak
- Department of Chemistry and Biochemistry, California State University East Bay, Hayward, CA 94542, USA
| | - H Howard Xu
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA.
| |
Collapse
|
36
|
Marchegiani E, Sidhu Y, Haynes K, Lebrun MH. Conditional gene expression and promoter replacement in Zymoseptoria tritici using fungal nitrate reductase promoters. Fungal Genet Biol 2015; 79:174-9. [PMID: 26092804 DOI: 10.1016/j.fgb.2015.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/23/2015] [Accepted: 04/27/2015] [Indexed: 10/23/2022]
Abstract
Studying essential genes in haploid fungi requires specific tools. Conditional promoter replacement (CPR) is an efficient method for testing gene essentiality. However, this tool requires promoters that can be strongly down-regulated. To this end, we tested the nitrate reductase promoters of Magnaporthe oryzae (pMoNIA1) and Zymoseptoria tritici (pZtNIA1) for their conditional expression in Z. tritici. Expression of EGFP driven by pMoNIA1 or pZtNIA1 was induced on nitrate and down-regulated on glutamate (10-fold less than nitrate). Levels of differential expression were similar for both promoters, demonstrating that the Z. tritici nitrogen regulatory network functions with a heterologous promoter similarly to a native promoter. To establish CPR, the promoter of Z. tritici BGS1, encoding a β-1,3-glucan synthase, was replaced by pZtNIA1 using targeted sequence replacement. Growth of pZtNIA1::BGS1 CPR transformants was strongly reduced in conditions repressing pZtNIA1, while their growth was similar to wild type in conditions inducing pZtNIA1. This differential phenotype demonstrates that BGS1 is important for growth in Z. tritici. In addition, in inducing conditions, pZtNIA1::BGS1 CPR transformants were hyper-sensitive to Calcofluor white, a cell wall disorganizing agent. Nitrate reductase promoters are therefore suitable for conditional promoter replacement in Z. tritici. This tool is a major step toward identifying novel fungicide targets.
Collapse
|
37
|
Vecchietti D, Ferrara S, Rusmini R, Macchi R, Milani M, Bertoni G. Crystal structure of YeaZ from Pseudomonas aeruginosa. Biochem Biophys Res Commun 2016; 470:460-465. [PMID: 26768361 DOI: 10.1016/j.bbrc.2016.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 01/03/2016] [Indexed: 10/22/2022]
Abstract
The Pseudomonas aeruginosa PA3685 locus encodes a conserved protein that shares 49% sequence identity with Escherichia coli YeaZ, which was recently reported as involved in the biosynthesis of threonylcarbamoyl adenosine (t(6)A), a universal modified tRNA nucleoside. Many YeaZ orthologues were reported as "essential for life" among various bacterial species, suggesting a critical role for both these proteins and for the t(6)A biosynthetic pathway. We provide here evidences that PA3685 protein (PaYeaZ) is essential. Additionally, we describe its purification, crystallization, and crystallographic structure. The crystal structure shows that PaYeaZ is composed of two domains one of which is the platform to form protein-protein interaction involved either in homodimeric assembly or in the formation of the multiprotein complex required for the synthesis of t(6)A. These features make the PaYeaZ protein a potential target candidate for the design of novel inhibitors able to hinder the complex formation and expected to abolish the crucial activity of t(6)A synthesis.
Collapse
Affiliation(s)
- Davide Vecchietti
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Silvia Ferrara
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Ruggero Rusmini
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Raffaella Macchi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| | - Mario Milani
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy; CNR-Istituto di Biofisica, Via Celoria 26, I-20133, Milano, Italy.
| | - Giovanni Bertoni
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133, Milano, Italy
| |
Collapse
|
38
|
Villela AD, Eichler P, Pinto AFM, Rodrigues-Junior V, Yates Iii JR, Bizarro CV, Basso LA, Santos DS. Gene replacement and quantitative mass spectrometry approaches validate guanosine monophosphate synthetase as essential for Mycobacterium tuberculosis growth. Biochem Biophys Rep 2015; 4:277-282. [PMID: 29124214 PMCID: PMC5669397 DOI: 10.1016/j.bbrep.2015.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/05/2015] [Accepted: 10/07/2015] [Indexed: 01/10/2023] Open
Abstract
Guanosine monophosphate synthetase (GMPS), encoded by guaA gene, is a key enzyme for guanine nucleotide biosynthesis in Mycobacterium tuberculosis. The guaA gene from several bacterial pathogens has been shown to be involved in virulence; however, no information about the physiological effect of direct guaA deletion in M. tuberculosis has been described so far. Here, we demonstrated that the guaA gene is essential for M. tuberculosis H37Rv growth. The lethal phenotype of guaA gene disruption was avoided by insertion of a copy of the ortholog gene from Mycobacterium smegmatis, indicating that this GMPS protein is functional in M. tuberculosis. Protein validation of the guaA essentiality observed by PCR was approached by shotgun proteomic analysis. A quantitative method was performed to evaluate protein expression levels, and to check the origin of common and unique peptides from M. tuberculosis and M. smegmatis GMPS proteins. These results validate GMPS as a molecular target for drug design against M. tuberculosis, and GMPS inhibitors might prove to be useful for future development of new drugs to treat human tuberculosis. The guaA gene is essential for M. tuberculosis H37Rv growth. The lethal phenotype of guaA gene disruption was avoided by the ortholog gene from M. smegmatis. Multiplexed LC–MS/MS analysis was performed to validate protein expression levels. The guaA essentiality was confirmed by gene replacement and quantitative mass spectrometry.
Collapse
Affiliation(s)
- Anne Drumond Villela
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690, Hospital São Lucas, 90619-900 Porto Alegre, RS, Brazil
| | - Paula Eichler
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| | - Antonio Frederico Michel Pinto
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| | - Valnês Rodrigues-Junior
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690, Hospital São Lucas, 90619-900 Porto Alegre, RS, Brazil
| | - John R Yates Iii
- Department of Chemical Physiology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Cristiano Valim Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| | - Luiz Augusto Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690, Hospital São Lucas, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| | - Diógenes Santiago Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul - PUCRS, Avenida Ipiranga, 6681, TecnoPUC 92A, 90619-900 Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Prédio 12A, 90619-900 Porto Alegre, RS, Brazil
| |
Collapse
|
39
|
Kamei Y, Tai A, Dakeyama S, Yamamoto K, Inoue Y, Kishimoto Y, Ohara H, Mukai Y. Transcription factor genes essential for cell proliferation and replicative lifespan in budding yeast. Biochem Biophys Res Commun 2015; 463:351-6. [PMID: 26022127 DOI: 10.1016/j.bbrc.2015.05.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 05/17/2015] [Indexed: 11/18/2022]
Abstract
Many of the lifespan-related genes have been identified in eukaryotes ranging from the yeast to human. However, there is limited information available on the longevity genes that are essential for cell proliferation. Here, we investigated whether the essential genes encoding DNA-binding transcription factors modulated the replicative lifespan of Saccharomyces cerevisiae. Heterozygous diploid knockout strains for FHL1, RAP1, REB1, and MCM1 genes showed significantly short lifespan. (1)H-nuclear magnetic resonance analysis indicated a characteristic metabolic profile in the Δfhl1/FHL1 mutant. These results strongly suggest that FHL1 regulates the transcription of lifespan related metabolic genes. Thus, heterozygous knockout strains could be the potential materials for discovering further novel lifespan genes.
Collapse
Affiliation(s)
- Yuka Kamei
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Akiko Tai
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Shota Dakeyama
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Kaori Yamamoto
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Yamato Inoue
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Yoshifumi Kishimoto
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Hiroya Ohara
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Yukio Mukai
- Department of Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan.
| |
Collapse
|
40
|
Yang L, Wang J, Wang H, Lv Y, Zuo Y, Jiang W. Characterization of essential genes by topological properties in the perturbation sensitivity network. Biochem Biophys Res Commun 2014; 448:473-9. [PMID: 24802397 DOI: 10.1016/j.bbrc.2014.04.136] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 04/25/2014] [Indexed: 11/29/2022]
Abstract
Genes that are indispensable for survival are called essential genes. In recent years, the analysis of essential genes has become extremely important for understanding the way a cell functions. With the advent of large-scale gene expression profiling technologies, it is now possible to profile transcriptional changes in the entire genome of Saccharomyces cerevisiae. Notwithstanding the accumulation of gene expression profiling in recent years, only a few studies have used these data to construct the network for S. cerevisiae. In this paper, based on the transcriptional profiling of the S. cerevisiae genome in hundreds of different gene disruptions, the perturbation sensitivity (PS) network is constructed. A scale-free topology with node degree following a power-law distribution is shown in the PS network. Twelve topological properties are used to investigate the characteristics of essential and non-essential genes in the PS network. Most of the properties are found to be statistically discriminative between essential and non-essential genes. In addition, the F-score is used to estimate the essentiality of each property, and the core number demonstrates the highest F-score among all properties.
Collapse
Affiliation(s)
- Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Jizhe Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Huiping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yingli Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yongchun Zuo
- The National Research Center for Animal Transgenic Biotechnology, Inner Mongolia University, Hohhot 010021, PR China.
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, PR China.
| |
Collapse
|
41
|
Moretti-Almeida G, Netto LES, Monteiro G. The essential gene YMR134W from Saccharomyces cerevisiae is important for appropriate mitochondrial iron utilization and the ergosterol biosynthetic pathway. FEBS Lett 2013; 587:3008-13. [PMID: 23892078 DOI: 10.1016/j.febslet.2013.07.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/04/2013] [Accepted: 07/09/2013] [Indexed: 11/28/2022]
Abstract
A thermosensitive strain (YMR134W(ts)) of the essential gene YMR134W presented up to 40% less ergosterol, threefold lower oxygen consumption and impaired growth on respiratory conditions. The iron content in the mitochondrial fraction of YMR134W(ts) cells was considerably low, despite these cells uptake and accumulate more iron from the culture media than wild-type cells. YMR134W(ts) cells were also more susceptible to oxidative stress. The results suggest that Ymr134wp is essential to aerobic growth due to its function in ergosterol biosynthesis, playing a role in maintaining mitochondrial and plasma membrane integrity and consequently impacting the iron homeostasis, respiratory metabolism and antioxidant response.
Collapse
Affiliation(s)
- Gabriel Moretti-Almeida
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo - USP, Brazil.
| | | | | |
Collapse
|
42
|
Saremy S, Boroujeni ME, Bhattacharjee B, Mittal V, Chatterjee J. Identification of potential apicoplast associated therapeutic targets in human and animal pathogen Toxoplasma gondii ME49. Bioinformation 2011; 7:379-83. [PMID: 22347778 PMCID: PMC3280436 DOI: 10.6026/97320630007379] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/08/2011] [Indexed: 11/23/2022] Open
Abstract
Toxoplasma gondii ME49 is an obligatory intracellular apicomplexa parasite that causes toxoplasmosis in humans, domesticated and
wild animals. Waterborne outbreaks of acute toxoplasmosis worldwide reinforce the transmission of Toxoplasma gondii ME49 to
humans through contaminated water and may have a greater epidemiological impact than previously believed. In the quest for
drug and vaccine target identification subtractive genomics involving subtraction between the host and pathogen genome has been
implemented for enlisting essential pathogen specific proteins. Using this approach, our analysis on both human and Toxoplasma
gondii ME49 reveals that out of 7987 protein coding sequences of the pathogen, 950 represent essential non human-homologous
proteins. Subcellular localization prediction & comparative-biochemical pathway analysis of these essential proteins gives a list of
apicoplast-associated proteins having unique pathogen-specific metabolic pathway. These apicoplast-associated enzymes involved
in fatty acid biosynthesis pathway of Toxoplasma gondii ME49, may be used as potential drug targets, as the pathway is vital for the
protozoan's survival. Structure prediction of drug target proteins was done using fold based recognition method. Screening of the
functional inhibitors against these novel targets may result in discovery of novel therapeutic compounds that can be effective
against Toxoplasma gondii ME49.
Collapse
Affiliation(s)
| | | | - Biplab Bhattacharjee
- Department of Biotechnology, PES Institute of Technology, Bangalore, INDIA
- Biplab Bhattacharjee:
| | | | - Jhinuk Chatterjee
- Department of Biotechnology, PES Institute of Technology, Bangalore, INDIA
| |
Collapse
|