Authors: Tomoya Baba, Takeshi Ara, Miki Hasegawa...

We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

Topics: Escherichia coli; Gene Deletion; Internet; Mutation; Organisms, Genetically Modified

PubMed: 16738554
DOI: 10.1038/msb4100050

Authors: Byoung-Mo Koo, George Kritikos, Jeremiah D Farelli...

A systems-level understanding of Gram-positive bacteria is important from both an environmental and health perspective and is most easily obtained when high-quality, validated genomic resources are available. To this end, we constructed two ordered, barcoded, erythromycin-resistance- and kanamycin-resistance-marked single-gene deletion libraries of the Gram-positive model organism, Bacillus subtilis. The libraries comprise 3,968 and 3,970 genes, respectively, and overlap in all but four genes. Using these libraries, we update the set of essential genes known for this organism, provide a comprehensive compendium of B. subtilis auxotrophic genes, and identify genes required for utilizing specific carbon and nitrogen sources, as well as those required for growth at low temperature. We report the identification of enzymes catalyzing several missing steps in amino acid biosynthesis. Finally, we describe a suite of high-throughput phenotyping methodologies and apply them to provide a genome-wide analysis of competence and sporulation. Altogether, we provide versatile resources for studying gene function and pathway and network architecture in Gram-positive bacteria.

Topics: Amino Acids; Bacillus subtilis; Gene Deletion; Gene Library; Genomic Library; Genomics; High-Throughput Screening Assays; Sequence Deletion; Spores, Bacterial

PubMed: 28189581
DOI: 10.1016/j.cels.2016.12.013

Authors: Jin Liu, Lihong Pan, Wenxuan Hong...

Regulatory T cells (Tregs) are critically involved in neovascularization, an important compensatory mechanism in peripheral artery disease. The contribution of G protein coupled receptor 174 (GPR174), which is a regulator of Treg function and development, in neovascularization remains elusive. Here, we show that genetic deletion of GPR174 in Tregs potentiated blood flow recovery in mice after hindlimb ischemia. GPR174 deficiency upregulates amphiregulin (AREG) expression in Tregs, thereby enhancing endothelial cell functions and reducing pro-inflammatory macrophage polarization and endothelial cell apoptosis. Mechanically, GPR174 regulates AREG expression by inhibiting the nuclear accumulation of early growth response protein 1 (EGR1) via Gαs/cAMP/PKA signal pathway activation. Collectively, these findings demonstrate that GPR174 negatively regulates angiogenesis and vascular remodeling in response to ischemic injury and that GPR174 may be a potential molecular target for therapeutic interventions of ischemic vascular diseases.

Topics: Mice; Animals; Gene Deletion; Ischemia; Receptors, G-Protein-Coupled

PubMed: 36473866
DOI: 10.1038/s41467-022-35159-8

Review

Authors: Jeffrey Statland, Rabi Tawil

Facioscapulohumeral muscular dystrophy (FSHD) is a common type of adult muscular dystrophy and is divided into types 1 and 2 based on genetic mutation. Clinically, both FSHD types often show asymmetric and progressive muscle weakness affecting initially the face, shoulder, and arms followed by the distal then proximal lower extremities. Approximately 95% of patients, termed FSHD1, have a deletion of a key number of repetitive elements on chromosome 4q35. The remaining 5%, termed FSHD2, have no deletion on chromosome 4q35. Nevertheless, both types share a common downstream mechanism, making it possible for future disease-directed therapies to be effective for both FSHD types.

Topics: Gene Deletion; Humans; Muscular Dystrophy, Facioscapulohumeral

PubMed: 25037087
DOI: 10.1016/j.ncl.2014.04.003

Authors: José I Rojas Echenique, Sergey Kryazhimskiy, Alex N Nguyen Ba...

Screens for epistatic interactions have long been used to characterize functional relationships corresponding to protein complexes, metabolic pathways, and other functional modules. Although epistasis between adaptive mutations is also common in laboratory evolution experiments, the functional basis for these interactions is less well characterized. Here, we quantify the extent to which gene function (as determined by a genome-wide screen for epistasis among deletion mutants) influences the rate and genetic basis of compensatory adaptation in a set of 37 gene deletion mutants nested within 16 functional modules. We find that functional module has predictive power: mutants with deletions in the same module tend to adapt more similarly, on average, than those with deletions in different modules. At the same time, initial fitness also plays a role: independent of the specific functional modules involved, adaptive mutations tend to be systematically more beneficial in less-fit genetic backgrounds, consistent with a general pattern of diminishing returns epistasis. We measured epistatic interactions between initial gene deletion mutations and the mutations that accumulate during compensatory adaptation and found a general trend towards positive epistasis (i.e. mutations tend to be more beneficial in the background in which they arose). In two functional modules, epistatic interactions between the initial gene deletions and the mutations in their descendant lines caused evolutionary entrenchment, indicating an intimate functional relationship. Our results suggest that genotypes with similar epistatic interactions with gene deletion mutations will also have similar epistatic interactions with adaptive mutations, meaning that genome scale maps of epistasis between gene deletion mutations can be predictive of evolutionary dynamics.

Topics: Adaptation, Physiological; Computer Simulation; Epistasis, Genetic; Evolution, Molecular; Gene Deletion; Genes, Fungal; Genetic Fitness; Metabolic Networks and Pathways; Models, Genetic; Mutation; Saccharomyces cerevisiae

PubMed: 30768593
DOI: 10.1371/journal.pgen.1007958

Authors: Michael N Teng, Asuncion Mejias, Octavio Ramilo...

Topics: Atazanavir Sulfate; Case-Control Studies; Child; Child, Preschool; Darunavir; Gene Deletion; HIV; HIV Infections; Humans; Myocardial Infarction; Respiratory Syncytial Virus Infections; Respiratory Syncytial Viruses

PubMed: 31758179
DOI: 10.1093/infdis/jiz604

Authors: Peilin Ruan, Xin Feng, Anchun Cheng...

Duck plague caused by duck plague virus (DPV) is a highly contagious disease that can cause serious morbidity and death in waterfowl such as ducks and geese, and bring huge economic losses to the duck industry. In this study, on the basis of the duck plague virus gC gene deletion strain CHv-ΔgC, based on the duck plague virus bacterial artificial chromosome (BAC) platform in our laboratory, the gE gene was knocked out using the traceless deletion technology to obtain gC/gE double gene deletion candidate vaccine strain CHv-ΔgC/gE. The double gene deletion strain (CHv-ΔgC/gE) constructed in this study has greatly weakened virulence, no pathogenicity to ducks, and stable genetic characteristics and . Ducks immunized with CHv-ΔgC/gE can produce neutralizing antibodies and ELISA antibody levels comparable to those of commercial duck plague attenuated vaccine immunization, and can resist 100 LD CHv challenge of ducks, with good immune protection effect. It has the potential to be further developed into duck plague gC/gE double gene deletion, marked attenuated vaccine.

Topics: Animals; Ducks; Gene Deletion; Herpesviridae Infections; Mardivirus; Vaccines, Attenuated

PubMed: 36059553
DOI: 10.3389/fimmu.2022.963009

Review

Authors: Elliott Rees, George Kirov

Copy number variants (CNVs) at specific loci have been identified as important risk factors for several neuropsychiatric disorders, such as schizophrenia, autism spectrum disorder, intellectual disability (ID) and depression. These CNVs are individually rare (<0.5% frequency), have high effect sizes, and show pleiotropic effects for multiple neuropsychiatric disorders, which implies a shared aetiology. Neuropsychiatric CNVs are also associated with cognitive impairment and other medical morbidities, such as heart defects and obesity. As most neuropsychiatric CNVs are multigenic, it has been challenging to map their effects onto specific biological processes, although gene-set analyses have implicated genes related to the synapse and chromatin regulation. However, future whole-genome sequencing studies have potential for identifying novel single-gene CNV associations, which could provide insights into the pathophysiology underlying neuropsychiatric disorders.

Topics: DNA Copy Number Variations; Gene Deletion; Gene Duplication; Genetic Predisposition to Disease; Genome-Wide Association Study; Humans; Mental Disorders; Whole Genome Sequencing

PubMed: 33752146
DOI: 10.1016/j.gde.2021.02.014

Systematic review of the status of pfhrp2 and pfhrp3 gene deletion, approaches and methods used for its estimation and reporting in Plasmodium falciparum populations in Africa: review of published studies 2010-2019.

Authors: Bosco B Agaba, Adoke Yeka, Sam Nsobya...

BACKGROUND

Malaria rapid diagnostic tests based on histidine-rich protein-2 have played a vital role in improving malaria case management and surveillance particularly in Africa, where Plasmodium falciparum is predominant. However, their usefulness has been threatened by the emergence of gene deletion on P. falciparum histidine rich protein 2 (pfhrp2) and P. falciparum histidine rich protein 3 (pfhrp3). Use of standard and recommended methods is key for accurate investigation, confirmation and reporting of pfhrp2 and pfhrp3 gene deletion.

METHODS

A systematic review was conducted to assess the status, methods and approaches that have been used for investigation, confirmation and reporting of pfhrp2 and pfhrp3 gene deletion in Africa. An online search was done using PubMed and MEDLINE Google Scholar for all articles published in English on pfhrp2/3 gene deletion in Africa. Relevant articles that met the inclusion criteria were summarized and assessed based on the protocol recommended by the World Health Organization for confirmation and reporting of pfhrp2/3 gene deletion.

RESULTS

The search identified a total of 18 articles out of which 14 (77.7%) fulfilled the criteria for inclusion and were retained for review. The articles were distributed across 12 countries where the pfhrp2 and pfhrp3 gene deletion studies were conducted and reported. The level of pfhrp2/3 gene deletion across selected studies in Africa ranged from the highest 62% to the lowest 0.4%. There was wide variation in methods and approaches including study designs, size and sampling and whether both pfhrp2 and pfhrp3 double deletions or pfhrp2 single deletion were investigated, with a wide variation in laboratory methods.

CONCLUSION

Based on the review, there is evidence of the presence of pfhrp2/3 gene-deleted P. falciparum parasites in Africa. The approaches and methods used for investigation, confirmation and reporting of pfhrp2/3 deleted parasites have varied between studies and across countries. Countries that are considering plans to investigate, confirm and report pfhrp2/3 deletion should use recommended standard and harmonized methods to prevent unnecessary recommendations for costly switch of RDTs in Africa.

Topics: Africa; Antigens, Protozoan; Diagnostic Tests, Routine; Gene Deletion; Malaria, Falciparum; Plasmodium falciparum; Protozoan Proteins

PubMed: 31694718
DOI: 10.1186/s12936-019-2987-4

Authors: Steffen Porwollik, Carlos A Santiviago, Pui Cheng...

We constructed two collections of targeted single gene deletion (SGD) mutants and two collections of targeted multi-gene deletion (MGD) mutants in Salmonella enterica sv Typhimurium 14028s. The SGD mutant collections contain (1), 3517 mutants in which a single gene is replaced by a cassette containing a kanamycin resistance (KanR) gene oriented in the sense direction (SGD-K), and (2), 3376 mutants with a chloramphenicol resistance gene (CamR) oriented in the antisense direction (SGD-C). A combined total of 3773 individual genes were deleted across these SGD collections. The MGD collections contain mutants bearing deletions of contiguous regions of three or more genes and include (3), 198 mutants spanning 2543 genes replaced by a KanR cassette (MGD-K), and (4), 251 mutants spanning 2799 genes replaced by a CamR cassette (MGD-C). Overall, 3476 genes were deleted in at least one MGD collection. The collections with different antibiotic markers permit construction of all viable combinations of mutants in the same background. Together, the libraries allow hierarchical screening of MGDs for different phenotypic followed by screening of SGDs within the target MGD regions. The mutants of these collections are stored at BEI Resources (www.beiresources.org) and publicly available.

Topics: Chloramphenicol Resistance; Gene Deletion; Gene Library; Genes, Bacterial; Kanamycin Resistance; Mutagenesis, Site-Directed; Mutation; Salmonella typhimurium; Sequence Deletion

PubMed: 25007190
DOI: 10.1371/journal.pone.0099820