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Calvanese M, D’Angelo C, Tutino ML, Lauro C. Whole-Cell Biosensor for Iron Monitoring as a Potential Tool for Safeguarding Biodiversity in Polar Marine Environments. Mar Drugs 2024; 22:299. [PMID: 39057408 PMCID: PMC11277574 DOI: 10.3390/md22070299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Iron is a key micronutrient essential for various essential biological processes. As a consequence, alteration in iron concentration in seawater can deeply influence marine biodiversity. In polar marine environments, where environmental conditions are characterized by low temperatures, the role of iron becomes particularly significant. While iron limitation can negatively influence primary production and nutrient cycling, excessive iron concentrations can lead to harmful algal blooms and oxygen depletion. Furthermore, the growth of certain phytoplankton species can be increased in high-iron-content environments, resulting in altered balance in the marine food web and reduced biodiversity. Although many chemical/physical methods are established for inorganic iron quantification, the determination of the bio-available iron in seawater samples is more suitably carried out using marine microorganisms as biosensors. Despite existing challenges, whole-cell biosensors offer other advantages, such as real-time detection, cost-effectiveness, and ease of manipulation, making them promising tools for monitoring environmental iron levels in polar marine ecosystems. In this review, we discuss fundamental biosensor designs and assemblies, arranging host features, transcription factors, reporter proteins, and detection methods. The progress in the genetic manipulation of iron-responsive regulatory and reporter modules is also addressed to the optimization of the biosensor performance, focusing on the improvement of sensitivity and specificity.
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Affiliation(s)
- Marzia Calvanese
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy; (M.C.); (C.D.); (M.L.T.)
- Istituto Nazionale Biostrutture e Biosistemi (I.N.B.B), Viale Medaglie D’Oro 305, 00136 Roma, Italy
| | - Caterina D’Angelo
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy; (M.C.); (C.D.); (M.L.T.)
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy; (M.C.); (C.D.); (M.L.T.)
- Istituto Nazionale Biostrutture e Biosistemi (I.N.B.B), Viale Medaglie D’Oro 305, 00136 Roma, Italy
| | - Concetta Lauro
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy; (M.C.); (C.D.); (M.L.T.)
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Wang C, Yang J, Xu Z, Lv L, Chen S, Hong M, Liu JH. Promoter regulatory mode evolution enhances the high multidrug resistance of tmexCD1-toprJ1. mBio 2024; 15:e0021824. [PMID: 38564664 PMCID: PMC11077950 DOI: 10.1128/mbio.00218-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Antibiotic resistance could rapidly emerge from acquiring the mobile antibiotic resistance genes, which are commonly evolved from an intrinsic gene. The emergence of the plasmid-borne mobilized efflux pump gene cluster tmexCD1-toprJ1 renders the last-resort antibiotic tigecycline ineffective, although its evolutionary mechanism remains unclear. In this study, we investigate the regulatory mechanisms of the progenitor NfxB-MexCD-OprJ, a chromosomally encoded operon that does not mediate antibiotic resistance in the wild-type version, and its homologs, TNfxB1-TMexCD1-TOprJ1 mediating high-level tigecycline resistance, and TNfxB3-TMexCD3-TOprJ1. Mechanistic studies demonstrated that in nfxB-mexCD-oprJ, MexCD expression was under a weaker promoter, PmexC and inhibited by a strong repressor NfxB. For tmexCD1-toprJ1, TMexCD1 was highly expressed owing to the presence of a strong promoter, PtmexC1, and an inactive suppressor, TNfxB1, with a T39R mutation that rendered it unable to bind to promoter DNA. In tnfxB3-tmexCD3-toprJ1b, TMexCD3 expression was intermediate because of the local regulator TNfxB3, which binds to two inverted repeat sequences of PtmexC. Additionally, TNfxB3 exhibited lower protein expression and weaker DNA binding affinity than its ancestor NfxB, together with their promoter activities difference explaining the different expression levels of tmexCD-toprJ homologs. Distinct fitness burdens on these homologs-carrying bacteria were observed due to the corresponding expression level, which might be associated with their global prevalence. In summary, our data depict the mechanisms underlying the evolution and dissemination of an important mobile antibiotic resistance gene from an intrinsic chromosomal gene.IMPORTANCEAs antibiotic resistance seriously challenges global health, tigecycline is one of the few effective drugs in the pipeline against infections caused by multidrug-resistant pathogens. Our previous work identified a novel tigecycline resistance efflux pump gene cluster tmexCD1-toprJ1 in animals and humans, together with its various variants, a rising clinical concern. Herein, this study focused on how the local regulation modes of tmexCD1-toprJ1 evolved to a highly expressed efflux pump. Through comparative analysis between three tnfxB-tmexCD-toprJ homologs and their progenitor nfxB-mexCD-oprJ, modes, we demonstrated the evolutionary dynamics from a chromosomal silent gene to an active state. We found the de-repression of the local regulator and an increase of the promoter activity work together to promote a high production of drug efflux machines and enhance multidrug resistance. Our findings revealed that TMexCD1-TOprJ1 adopts a distinct evolutionary path to achieve higher multidrug resistance, urgently needing tight surveillance.
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Affiliation(s)
- Chengzhen Wang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Jun Yang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Luchao Lv
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Mei Hong
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China
| | - Jian-Hua Liu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, Guangzhou, Guangdong, China
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3
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Tan Z, Tezuka T, Ohnishi Y. Identification of a putative cell wall-hydrolyzing amidase involved in sporangiospore maturation in Actinoplanes missouriensis. J Bacteriol 2024; 206:e0045623. [PMID: 38426722 PMCID: PMC10955841 DOI: 10.1128/jb.00456-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Actinoplanes missouriensis is a filamentous bacterium that differentiates into terminal sporangia, each containing a few hundred spores. Previously, we reported that a cell wall-hydrolyzing N-acetylglucosaminidase, GsmA, is required for the maturation process of sporangiospores in A. missouriensis; sporangia of the gsmA null mutant (ΔgsmA) strain released chains of 2-20 spores under sporangium dehiscence-inducing conditions. In this study, we identified and characterized a putative cell wall hydrolase (AsmA) that is also involved in sporangiospore maturation. AsmA was predicted to have a signal peptide for the general secretion pathway and an N-acetylmuramoyl-l-alanine amidase domain. The transcript level of asmA increased during the early stages of sporangium formation. The asmA null mutant (ΔasmA) strain showed phenotypes similar to those of the wild-type strain, but sporangia of the ΔgsmAΔasmA double mutant released longer spore chains than those from the ΔgsmA sporangia. Furthermore, a weak interaction between AsmA and GsmA was detected in a bacterial two-hybrid assay using Escherichia coli as the host. Based on these results, we propose that AsmA is an enzyme that hydrolyzes peptidoglycan at septum-forming sites to separate adjacent spores during sporangiospore maturation in cooperation with GsmA in A. missouriensis.IMPORTANCEActinoplanes missouriensis produces sporangiospores as dormant cells. The spores inside the sporangia are assumed to be formed from prespores generated by the compartmentalization of intrasporangium hyphae via septation. Previously, we identified GsmA as a cell wall hydrolase responsible for the separation of adjacent spores inside sporangia. However, we predicted that an additional cell wall hydrolase(s) is inevitably involved in the maturation process of sporangiospores because the sporangia of the gsmA null mutant strain released not only tandemly connected spore chains (2-20 spores) but also single spores. In this study, we successfully identified a putative cell wall hydrolase (AsmA) that is involved in sporangiospore maturation in A. missouriensis.
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Affiliation(s)
- Zhuwen Tan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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Huang S, Suo NJ, Henderson TR, Macgregor RB, Henderson JT. Cellular transfection using rapid decrease in hydrostatic pressure. Sci Rep 2024; 14:4631. [PMID: 38409237 PMCID: PMC10897145 DOI: 10.1038/s41598-024-54463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Of all methods exercised in modern molecular biology, modification of cellular properties through the introduction or removal of nucleic acids is one of the most fundamental. As such, several methods have arisen to promote this process; these include the condensation of nucleic acids with calcium, polyethylenimine or modified lipids, electroporation, viral production, biolistics, and microinjection. An ideal transfection method would be (1) low cost, (2) exhibit high levels of biological safety, (3) offer improved efficacy over existing methods, (4) lack requirements for ongoing consumables, (5) work efficiently at any scale, (6) work efficiently on cells that are difficult to transfect by other methods, and (7) be capable of utilizing the widest array of existing genetic resources to facilitate its utility in research, biotechnical and clinical settings. To address such issues, we describe here Pressure-jump-poration (PJP), a method using rapid depressurization to transfect even difficult to modify primary cell types such as embryonic stem cells. The results demonstrate that PJP can be used to introduce an array of genetic modifiers in a safe, sterile manner. Finally, PJP-induced transfection in primary versus transformed cells reveals a surprising dichotomy between these classes which may provide further insight into the process of cellular transformation.
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Affiliation(s)
- Shudi Huang
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Nan Ji Suo
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Tyler R Henderson
- Department of Medical Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Jeffrey T Henderson
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON, M5S 3M2, Canada.
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N MPA, Jeon H, Wang X, Lim HM. Reporter Gene-Based qRT-PCR Assay for Rho-Dependent Termination In Vivo. Cells 2023; 12:2596. [PMID: 37998331 PMCID: PMC10670590 DOI: 10.3390/cells12222596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
In bacteria, the Rho protein mediates Rho-dependent termination (RDT) by identifying a non-specific cytosine-rich Rho utilization site on the newly synthesized RNA. As a result of RDT, downstream RNA transcription is reduced. Due to the bias in reverse transcription and PCR amplification, we could not identify the RDT site by directly measuring the amount of mRNA upstream and downstream of RDT sites. To overcome this difficulty, we employed a 77 bp reporter gene argX, (coding tRNAarg) from Brevibacterium albidum, and we transcriptionally fused it to the sequences to be assayed. We constructed a series of plasmids by combining a segment of the galactose (gal) operon sequences, both with and without the RDT regions at the ends of cistrons (galE, galT, and galM) upstream of argX. The RNA polymerase will transcribe the gal operon sequence and argX unless it encounters the RDT encoded by the inserted sequence. Since the quantitative real-time PCR (qRT-PCR) method detects the steady state following mRNA synthesis and degradation, we observed that tRNAarg is degraded at the same rate in these transcriptional fusion plasmids. Therefore, the amount of tRNAarg can directly reflect the mRNA synthesis. Using this approach, we were able to effectively assay the RDTs and Rho-independent termination (RIT) in the gal operon by quantifying the relative amount of tRNAarg using qRT-PCR analyses. The resultant RDT% for galET, galTK, and at the end of galM were 36, 26, and 63, individually. The resultant RIT% at the end of the gal operon is 33%. Our findings demonstrate that combining tRNAarg with qRT-PCR can directly measure RIT, RDT, or any other signal that attenuates transcription efficiencies in vivo, making it a useful tool for gene expression research.
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Affiliation(s)
- Monford Paul Abishek N
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Heungjin Jeon
- Infection Control Convergence Research Center, Chungnam National University College of Medicine, Daejeon 34134, Republic of Korea;
| | - Xun Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Heon M. Lim
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea;
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Wang B, Zhao X, Fu T, Chen X, Guo X, Li X, Yang F. Glucose Starvation Stimulates the Promoting Strength of a Novel Evolved Suc2 Promoter. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13838-13847. [PMID: 37669532 DOI: 10.1021/acs.jafc.3c03699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Promoters are essential for designing Saccharomyces cerevisiae cell factories. Identifying novel promoters tuned to produce specific metabolites under increasingly diverse industrial stresses is required to improve the economic feasibility of whole fermentation processes. In this study, a positively evolved Suc2 promoter (SUC 2p) with promoter activity stronger than that of the wild-type Suc2 promoter (SUC 2wtp) was obtained. Quantitative real-time PCR, fluorescence analysis, Western blotting, and a β-galactosidase activity assay revealed that SUC 2p is a medium-strength promoter compared with eight reported promoters at a medium glucose concentration (2% (w/v)). Different glucose concentrations modulated the strength of SUC 2p. Low glucose concentrations (0.05 and 0.5% (w/v)) enhanced the promoter strength of SUC 2p dramatically, with promoter activity higher than that of reported strong promoters. Glucose starvation resulted in the formation of a new Msn2/4 binding site on SUC 2p. Our work should facilitate the development of promoters with novel fine-tuning properties and the construction of S. cerevisiae cell factories suitable for the industrial production of essential chemicals under glucose-deprived conditions.
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Affiliation(s)
- Biying Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoya Zhao
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Tong Fu
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoyu Guo
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
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Maruyama R, Sugiyama T. ER Stress Decreases Gene Expression Of Transmembrane Protein 117 Via Activation of PKR-like ER Kinase. Cell Biochem Biophys 2023; 81:459-468. [PMID: 37421592 DOI: 10.1007/s12013-023-01150-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2023] [Indexed: 07/10/2023]
Abstract
Stress response is an inherent mechanism in the endoplasmic reticulum (ER). The inducers of ER cause a specific cascade of reactions, leading to gene expression. Transmembrane protein 117 (TMEM117) is in the ER and plasma membrane. In our previous study, TMEM117 protein expression was found to be decreased by an ER stress inducer. However, the mechanism underlying this decrease in TMEM117 protein expression remains unclear. This study aimed to elucidate the mechanism underlying the decrease in TMEM117 protein expression during ER stress and identify the unfolded protein response (UPR) pathway related to decreased TMEM117 protein expression. We showed that the gene expression levels of TMEM117 were decreased by ER stress inducers and were regulated by PKR-like ER kinase (PERK), indicating that TMEM117 protein expression was regulated by the signaling pathway. Surprisingly, gene knockdown of activating transcription factor 4 (ATF4) downstream of PERK did not affect the gene expression of TMEM117. These results suggest that TMEM117 protein expression during ER stress is transcriptionally regulated by PERK but not by ATF4. TMEM117 has a potential to be a new therapeutic target against ER stress-related diseases.
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Affiliation(s)
- Ryuto Maruyama
- Graduate School of Bionics, Tokyo University of Technology, 1401-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan.
- Department of Life Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan.
| | - Tomoyasu Sugiyama
- Graduate School of Bionics, Tokyo University of Technology, 1401-1 Katakura-machi, Hachioji, Tokyo, 192-0982, Japan
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Banovetz JT, Manimaran S, Schelske B, Anand RK. Parallel Dielectrophoretic Capture, Isolation, and Electrical Lysis of Individual Breast Cancer Cells to Assess Variability in Enzymatic Activity. Anal Chem 2023; 95:7880-7887. [PMID: 37172139 PMCID: PMC10578154 DOI: 10.1021/acs.analchem.3c00078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Tumor cell heterogeneity drives disease progression and response to therapy, and therefore, there is a need for single-cell analysis methods. In this paper, we present an integrated, scalable method to analyze enzymatic activity in many individual cancer cells at once. The reported method uses dielectrophoresis (DEP) to selectively capture tumor cells at wireless electrodes aligned to an overlying array of cell-sized micropockets. Following hydrodynamic transfer of the captured cells into microfluidic chambers, the chambers are fluidically isolated and sealed with a hydrophobic ionic liquid, which possesses sufficient conductivity to allow for subsequent electrical lysis of the cells to access their contents for enzymatic assay. The wireless electrodes have an interlocking spiral design that ensures successful electrical lysis regardless of the location of the cell within the chamber. Here, breast cancer cells are assessed for β-galactosidase through its activation of a fluorogenic substrate. A key point is that the fluorogenic assay solution was optimized to allow for dielectrophoretic cell capture, thereby obviating the need for a solution exchange step. Our approach has several distinct advantages including a high rate of single-cell capture, a capture efficiency that is independent of the dimensions of the reaction chambers, no need for mechanical closure of reaction volumes, and no observed cross-talk. In this study, first, the steps of cell capture, transfer, and lysis are established on this platform in the presence of the optimized assay solution. We then quantify the increase in fluorescence intensity obtained over the duration of the enzymatic assay of individual cells. Finally, this method is applied to the analysis of β-galactosidase activity in 258 individual MDA-MB-231 breast cancer cells, revealing heterogeneity in expression of this enzyme in this cell line. We expect that the adaptability of this method will allow for expanded studies of single-cell enzymatic expression and activity. This will in turn open avenues of research into cancer cell heterogeneity in metabolism, invasiveness, and drug response. The ability to study these features of cancer at the single-cell level raises the possibility for treatment plans tailored to target the specific combinations of cell subpopulations present in tumors. Furthermore, we expect that this method can be adapted to uses outside of cancer research, such as studies of neuron metabolism, pathogenesis in bacteria, and stem cell development.
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Affiliation(s)
- Joseph T. Banovetz
- Department of Chemistry, Iowa State University, 2415 Osborn Drive, Ames, IA 50011-1021, USA
| | - Sivani Manimaran
- Department of Chemistry, Iowa State University, 2415 Osborn Drive, Ames, IA 50011-1021, USA
| | - Benjamin Schelske
- Department of Chemistry, Iowa State University, 2415 Osborn Drive, Ames, IA 50011-1021, USA
| | - Robbyn K. Anand
- Department of Chemistry, Iowa State University, 2415 Osborn Drive, Ames, IA 50011-1021, USA
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10
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Le D, Akiyama T, Weiss D, Kim M. Dissociation kinetics of small-molecule inhibitors in Escherichia coli is coupled to physiological state of cells. Commun Biol 2023; 6:223. [PMID: 36841892 PMCID: PMC9968327 DOI: 10.1038/s42003-023-04604-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Bioactive small-molecule inhibitors represent a treasure chest for future drugs. In vitro high-throughput screening is a common approach to identify the small-molecule inhibitors that bind tightly to purified targets. Here, we investigate the inhibitor-target binding/unbinding kinetics in E. coli cells using a benzimidazole-derivative DNA inhibitor as a model system. We find that its unbinding rate is not constant but depends on cell growth rate. This dependence is mediated by the cellular activity, forming a feedback loop with the inhibitor's activity. In accordance with this feedback, we find cell-to-cell heterogeneity in inhibitor-target interaction, leading to co-existence of two distinct subpopulations: actively growing cells that dissociate the inhibitors from the targets and non-growing cells that do not. We find similar heterogeneity for other clinical DNA inhibitors. Our studies reveal a mechanism that couples inhibitor-target kinetics to cell physiology and demonstrate the significant effect of this coupling on drug efficacy.
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Affiliation(s)
- Dai Le
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Tatsuya Akiyama
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - David Weiss
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA, 30322, USA.
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA.
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA.
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11
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Shao Y, Yin C, Lv F, Jiang S, Wu S, Han Y, Xue W, Ma Y, Zheng J, Zhan Y, Ke X, Lu W, Lin M, Shang L, Yan Y. The Sigma Factor AlgU Regulates Exopolysaccharide Production and Nitrogen-Fixing Biofilm Formation by Directly Activating the Transcription of pslA in Pseudomonas stutzeri A1501. Genes (Basel) 2022; 13:genes13050867. [PMID: 35627252 PMCID: PMC9141998 DOI: 10.3390/genes13050867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas stutzeri A1501, a plant-associated diazotrophic bacterium, prefers to conform to a nitrogen-fixing biofilm state under nitrogen-deficient conditions. The extracytoplasmic function (ECF) sigma factor AlgU is reported to play key roles in exopolysaccharide (EPS) production and biofilm formation in the Pseudomonas genus; however, the function of AlgU in P. stutzeri A1501 is still unclear. In this work, we mainly investigated the role of algU in EPS production, biofilm formation and nitrogenase activity in A1501. The algU mutant ΔalgU showed a dramatic decrease both in the EPS production and the biofilm formation capabilities. In addition, the biofilm-based nitrogenase activity was reduced by 81.4% in the ΔalgU mutant. The transcriptional level of pslA, a key Psl-like (a major EPS in A1501) synthesis-related gene, was almost completely inhibited in the algU mutant and was upregulated by 2.8-fold in the algU-overexpressing strain. A predicted AlgU-binding site was identified in the promoter region of pslA. The DNase I footprinting assays indicated that AlgU could directly bind to the pslA promoter, and β-galactosidase activity analysis further revealed mutations of the AlgU-binding boxes drastically reduced the transcriptional activity of the pslA promoter; moreover, we also demonstrated that AlgU was positively regulated by RpoN at the transcriptional level and negatively regulated by the RNA-binding protein RsmA at the posttranscriptional level. Taken together, these data suggest that AlgU promotes EPS production and nitrogen-fixing biofilm formation by directly activating the transcription of pslA, and the expression of AlgU is controlled by RpoN and RsmA at different regulatory levels.
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Affiliation(s)
- Yahui Shao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Changyan Yin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Fanyang Lv
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Shanshan Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Shaoyu Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yueyue Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Wei Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yiyuan Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Juan Zheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yuhua Zhan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Xiubin Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Liguo Shang
- School of Basic Medicine, GuangXi University of Chinese Medicine, Nanning 530200, China
- Correspondence: (L.S.); (Y.Y.)
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
- Correspondence: (L.S.); (Y.Y.)
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12
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Fan G, Song W, Guan Z, Zhang W, Lu X. Some novel features of strong promoters discovered in Cytophaga hutchinsonii. Appl Microbiol Biotechnol 2022; 106:2529-2540. [PMID: 35318522 DOI: 10.1007/s00253-022-11869-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022]
Abstract
Cytophaga hutchinsonii is an important Gram-negative bacterium belonging to the Bacteroides phylum that can efficiently degrade cellulose. But the promoter that mediates the initiation of gene transcription has been unknown for a long time. In this study, we determined the transcription start site (TSS) of C. hutchinsonii by 5' rapid amplification of cDNA ends (5'RACE). The promoter structure was first identified as TAAT and TATTG which are located -5 and -31 bp upstream of TSS, respectively. The function of -5 and -31 regions and the spacer length of the promoter Pchu_1284 were explored by site directed ligase-independent mutagenesis (SLIM). The results showed that the promoter activities were sharply decreased when the TTG motif was mutated into guanine (G) or cytosine (C). Interestingly, we found that the strong promoter was accompanied with many TTTG motifs which could enhance the promoter activities within certain copies. These characteristics were different from other promoters of Bacteriodes species. Furthermore, we carried out genome scanning analysis for C. hutchinsonii and another Bacteroides species by Perl6.0. The results indicated that the promoter structure of C. hutchinsonii possessed more unique features than other species. Also, the screened inducible promoter Pchu_2268 was used to overexpress protein CHU_2196 with a molecular weight of 120 kDa in C. hutchinsonii. The present study enriched the promoter structure of Bacteroidetes species and also provided a novel method for the highly expressed large protein (cellulase) in vivo, which was helpful to elucidate the unique cellulose degradation mechanism of C. hutchinsonii.Key points• The conserved structure of strong promoter of C. hutchinsonii was elucidated.• Two novel regulation motifs of TTTG and AATTATG in the promoter were discovered.• A new method for induced expression of cellulase in vivo was established.• Helpful for explained the unique cellulose degradation mechanism of C. hutchinsonii.
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Affiliation(s)
- Guoqing Fan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Wenxia Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Zhiwei Guan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China.,School of Life Science, Qilu Normal University, Jinan, 250200, China
| | - Weican Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266200, China.
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13
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Mustafa F, Liebich S, Andreescu S. Nanoparticle-based amplification for sensitive detection of β-galactosidase activity in fruits. Anal Chim Acta 2021; 1186:339129. [PMID: 34756270 DOI: 10.1016/j.aca.2021.339129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/28/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
Development of fast and sensitive assays for enzyme activity detection has received a great deal of attention because of the wide spread applications in measurements of numerous clinical, food and environmental processes. Herein, a novel amplification approach to enhance the sensitivity of colorimetric assays for detection of β-galactosidase (β-Gal) activity is proposed. β-Gal detection is important in biomedical applications and in food industry, where it is associated with the ripening process of fruits. The method is based on the use of multivalent cerium oxide nanoparticles (CeNPs) which catalyze the oxidation of 4-aminophenol (4-AP) produced in the hydrolysis process of the 4-aminophenyl-β-d-galactopyranoside substrate (4-APG) by β-Gal, thus enhancing detection sensitivity of β-Gal in the visible range. The developed assay is highly sensitive and easy to use. Using the optimized procedure, a limit of detection of 0.06 mU/mL was obtained with a linearity range up to 2.0 mU/mL. The feasibility of the method was demonstrated for detection of β-Gal activity in fruits and the results were compared with the conventional assay, providing over a 30-fold amplification as compared to a commercially available β-Gal protocol. The advantage of the presented assay is its biocatalytic event amplified by a secondary reaction, which enables much more sensitive detection of the enzymatic product. The sensing platform can be applied broadly to a variety of applications that rely on β-Gal activity measurements.
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Affiliation(s)
- Fatima Mustafa
- Department of Chemistry and Biomolecular Science, Clarkson University, USA
| | - Steve Liebich
- Department of Chemistry and Biomolecular Science, Clarkson University, USA
| | - Silvana Andreescu
- Department of Chemistry and Biomolecular Science, Clarkson University, USA.
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14
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Wall DA, Tarrant SP, Wang C, Mills KV, Lennon CW. Intein Inhibitors as Novel Antimicrobials: Protein Splicing in Human Pathogens, Screening Methods, and Off-Target Considerations. Front Mol Biosci 2021; 8:752824. [PMID: 34692773 PMCID: PMC8529194 DOI: 10.3389/fmolb.2021.752824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 01/20/2023] Open
Abstract
Protein splicing is a post-translational process by which an intervening polypeptide, or intein, catalyzes its own removal from the flanking polypeptides, or exteins, concomitant with extein ligation. Although inteins are highly abundant in the microbial world, including within several human pathogens, they are absent in the genomes of metazoans. As protein splicing is required to permit function of essential proteins within pathogens, inteins represent attractive antimicrobial targets. Here we review key proteins interrupted by inteins in pathogenic mycobacteria and fungi, exciting discoveries that provide proof of concept that intein activity can be inhibited and that this inhibition has an effect on the host organism's fitness, and bioanalytical methods that have been used to screen for intein activity. We also consider potential off-target inhibition of hedgehog signaling, given the similarity in structure and function of inteins and hedgehog autoprocessing domains.
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Affiliation(s)
- Diana A Wall
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Seanan P Tarrant
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States.,Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Christopher W Lennon
- Department of Biological Sciences, Murray State University, Murray, KY, United States
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15
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Kim SI, Kim E, Yoon H. σ S-Mediated Stress Response Induced by Outer Membrane Perturbation Dampens Virulence in Salmonella enterica serovar Typhimurium. Front Microbiol 2021; 12:750940. [PMID: 34659184 PMCID: PMC8516096 DOI: 10.3389/fmicb.2021.750940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 08/30/2021] [Indexed: 12/13/2022] Open
Abstract
Salmonella alters cellular processes as a strategy to improve its intracellular fitness during host infection. Alternative σ factors are known to rewire cellular transcriptional regulation in response to environmental stressors. σs factor encoded by the rpoS gene is a key regulator required for eliciting the general stress response in many proteobacteria. In this study, Salmonella Typhimurium deprived of an outer membrane protein YcfR was attenuated in intracellular survival and exhibited downregulation in Salmonella pathogenicity island-2 (SPI-2) genes. This decreased SPI-2 expression caused by the outer membrane perturbation was abolished in the absence of rpoS. Interestingly, regardless of the defects in the outer membrane integrity, RpoS overproduction decreased transcription from the common promoter of ssrA and ssrB, which encode a two-component regulatory system for SPI-2. RpoS was found to compete with RpoD for binding to the PssrA region, and its binding activity with RNA polymerase (RNAP) to form Eσs holoenzyme was stimulated by the small regulatory protein Crl. This study demonstrates that Salmonella undergoing RpoS-associated stress responses due to impaired envelope integrity may reciprocally downregulate the expression of SPI-2 genes to reduce its virulence.
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Affiliation(s)
- Seul I Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Eunsuk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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16
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Hahm KM, Park SH, Oh SW, Kim JH, Yeom HS, Lee HJ, Yang S, Cho JY, Park JO, Lee J. Aspergillus oryzae-Fermented Wheat Peptone Enhances the Potential of Proliferation and Hydration of Human Keratinocytes through Activation of p44/42 MAPK. Molecules 2021; 26:molecules26196074. [PMID: 34641617 PMCID: PMC8512833 DOI: 10.3390/molecules26196074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/25/2021] [Accepted: 10/05/2021] [Indexed: 01/10/2023] Open
Abstract
Identifying materials contributing to skin hydration, essential for normal skin homeostasis, has recently gained increased research interest. In this study, we investigated the potential benefits and mechanisms of action of Aspergillus oryzae-fermented wheat peptone (AFWP) on the proliferation and hydration of human skin keratinocytes, through in vitro experiments using HaCaT cell lines. The findings revealed that compared to unfermented wheat peptone, AFWP exhibited an improved amino acid composition, significantly (p < 0.05) higher DPPH scavenging capability and cell proliferation activity, and reduced lipopolysaccharide-induced NO production in RAW 264.7 cells. Furthermore, we separated AFWP into eleven fractions, each ≤2 kDa; of these, fraction 4 (AFW4) demonstrated the highest efficacy in the cell proliferation assay and was found to be the key component responsible for the cell proliferation potential and antioxidant properties of AFWP. Additionally, AFW4 increased the expression of genes encoding natural moisturizing factors, including filaggrin, transglutaminase-1, and hyaluronic acid synthase 1–3. Furthermore, AFW4 activated p44/42 MAPK, but not JNK and p38 MAPK, whereas PD98059, a p44/42 MAPK inhibitor, attenuated the beneficial effects of AFW4 on the skin, suggesting that the effects of AFW4 are mediated via p44/42 MAPK activation. Finally, in clinical studies, AFW4 treatment resulted in increased skin hydration and reduced trans-epidermal water loss compared with a placebo group. Collectively, these data provide evidence that AFW4 could be used as a potential therapeutic agent to improve skin barrier damage induced by external stresses.
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Affiliation(s)
- Kyung Man Hahm
- Molecular Dermatology Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon City 16419, Gyunggi Do, Korea; (K.M.H.); (S.W.O.); (S.Y.)
- Natural Products Laboratory, Daebong LS Co., Ltd., Incheon 21697, Korea; (J.H.K.); (H.S.Y.); (H.J.L.)
| | - See-Hyoung Park
- Department of Bio and Chemical Engineering, Hongik University, Sejong City 30016, Korea;
| | - Sae Woong Oh
- Molecular Dermatology Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon City 16419, Gyunggi Do, Korea; (K.M.H.); (S.W.O.); (S.Y.)
| | - Ji Hye Kim
- Natural Products Laboratory, Daebong LS Co., Ltd., Incheon 21697, Korea; (J.H.K.); (H.S.Y.); (H.J.L.)
| | - Hyun Sook Yeom
- Natural Products Laboratory, Daebong LS Co., Ltd., Incheon 21697, Korea; (J.H.K.); (H.S.Y.); (H.J.L.)
| | - Hye Ja Lee
- Natural Products Laboratory, Daebong LS Co., Ltd., Incheon 21697, Korea; (J.H.K.); (H.S.Y.); (H.J.L.)
| | - Seoyeon Yang
- Molecular Dermatology Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon City 16419, Gyunggi Do, Korea; (K.M.H.); (S.W.O.); (S.Y.)
| | - Jae Youl Cho
- Molecular Immunology Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon City 16419, Gyunggi Do, Korea
- Correspondence: (J.Y.C.); (J.O.P.); (J.L.); Tel.: +82-31-290-7861 (J.L.)
| | - Jin Oh Park
- Natural Products Laboratory, Daebong LS Co., Ltd., Incheon 21697, Korea; (J.H.K.); (H.S.Y.); (H.J.L.)
- Correspondence: (J.Y.C.); (J.O.P.); (J.L.); Tel.: +82-31-290-7861 (J.L.)
| | - Jongsung Lee
- Molecular Dermatology Laboratory, Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon City 16419, Gyunggi Do, Korea; (K.M.H.); (S.W.O.); (S.Y.)
- Correspondence: (J.Y.C.); (J.O.P.); (J.L.); Tel.: +82-31-290-7861 (J.L.)
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17
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Interaction between the type 4 pili machinery and a diguanylate cyclase fine-tune c-di-GMP levels during early biofilm formation. Proc Natl Acad Sci U S A 2021; 118:2105566118. [PMID: 34168081 DOI: 10.1073/pnas.2105566118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To initiate biofilm formation, it is critical for bacteria to sense a surface and respond precisely to activate downstream components of the biofilm program. Type 4 pili (T4P) and increasing levels of c-di-GMP have been shown to be important for surface sensing and biofilm formation, respectively; however, mechanisms important in modulating the levels of this dinucleotide molecule to define a precise output response are unknown. Here, using macroscopic bulk assays and single-cell tracking analyses of Pseudomonas aeruginosa, we uncover a role of the T4P alignment complex protein, PilO, in modulating the activity of the diguanylate cyclase (DGC) SadC. Two-hybrid and bimolecular fluorescence complementation assays, combined with genetic studies, are consistent with a model whereby PilO interacts with SadC and that the PilO-SadC interaction inhibits SadC's activity, resulting in decreased biofilm formation and increased motility. Using single-cell tracking, we monitor both the mean c-di-GMP and the variance of this dinucleotide in individual cells. Mutations that increase PilO-SadC interaction modestly, but significantly, decrease both the average and variance in c-di-GMP levels on a cell-by-cell basis, while mutants that disrupt PilO-SadC interaction increase the mean and variance of c-di-GMP levels. This work is consistent with a model wherein P. aeruginosa uses a component of the T4P scaffold to fine-tune the levels of this dinucleotide signal during surface commitment. Finally, given our previous findings linking SadC to the flagellar machinery, we propose that this DGC acts as a bridge to integrate T4P and flagellar-derived input signals during initial surface engagement.
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18
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Hashiguchi Y, Tezuka T, Mouri Y, Konishi K, Fujita A, Hirata A, Ohnishi Y. Regulation of Sporangium Formation, Spore Dormancy, and Sporangium Dehiscence by a Hybrid Sensor Histidine Kinase in Actinoplanes missouriensis: Relationship with the Global Transcriptional Regulator TcrA. J Bacteriol 2020; 202:e00228-20. [PMID: 32839172 PMCID: PMC7549356 DOI: 10.1128/jb.00228-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/17/2020] [Indexed: 11/20/2022] Open
Abstract
The rare actinomycete Actinoplanes missouriensis forms terminal sporangia containing a few hundred flagellated spores. In response to water, the sporangia open and release the spores into external environments. The orphan response regulator TcrA functions as a global transcriptional activator during sporangium formation and dehiscence. Here, we report the characterization of an orphan hybrid histidine kinase, HhkA. Sporangia of an hhkA deletion mutant contained many distorted or ectopically germinated spores and scarcely opened to release the spores under sporangium dehiscence-inducing conditions. These phenotypic changes are quite similar to those observed in a tcrA deletion mutant. Comparative RNA sequencing analysis showed that genes controlled by HhkA mostly overlap TcrA-regulated genes. The direct interaction between HhkA and TcrA was suggested by a bacterial two-hybrid assay, but this was not conclusive. The phosphorylation of TcrA using acetyl phosphate as a phosphate donor markedly enhanced its affinity for the TcrA box sequences in the electrophoretic mobility shift assay. Taking these observations together with other results, we proposed that HhkA and TcrA compose a cognate two-component regulatory system, which controls the transcription of the genes involved in many aspects of morphological development, including sporangium formation, spore dormancy, and sporangium dehiscence in A. missouriensisIMPORTANCEActinoplanes missouriensis goes through complex morphological differentiation, including formation of flagellated spore-containing sporangia, sporangium dehiscence, swimming of zoospores, and germination of zoospores to filamentous growth. Although the orphan response regulator TcrA globally activates many genes required for sporangium formation, spore dormancy, and sporangium dehiscence, its partner histidine kinase remained unknown. Here, we analyzed the function of an orphan hybrid histidine kinase, HhkA, and proposed that HhkA constitutes a cognate two-component regulatory system with TcrA. That HhkA and TcrA homologues are highly conserved among the genus Actinoplanes and several closely related rare actinomycetes indicates that this possible two-component regulatory system is employed for complex morphological development in sporangium- and/or zoospore-forming rare actinomycetes.
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Affiliation(s)
- Yuichiro Hashiguchi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Mouri
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kenji Konishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Azusa Fujita
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Aiko Hirata
- Bioimaging Center, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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19
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Duan J, Zhao Y, Li H, Habernig L, Gordon MD, Miao X, Engström Y, Büttner S. Bab2 Functions as an Ecdysone-Responsive Transcriptional Repressor during Drosophila Development. Cell Rep 2020; 32:107972. [PMID: 32726635 DOI: 10.1016/j.celrep.2020.107972] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/30/2020] [Accepted: 07/08/2020] [Indexed: 12/01/2022] Open
Abstract
Drosophila development is governed by distinct ecdysone steroid pulses that initiate spatially and temporally defined gene expression programs. The translation of these signals into tissue-specific responses is crucial for metamorphosis, but the mechanisms that confer specificity to systemic ecdysone pulses are far from understood. Here, we identify Bric-à-brac 2 (Bab2) as an ecdysone-responsive transcriptional repressor that controls temporal gene expression during larval to pupal transition. Bab2 is necessary to terminate Salivary gland secretion (Sgs) gene expression, while premature Bab2 expression blocks Sgs genes and causes precocious salivary gland histolysis. The timely expression of bab2 is controlled by the ecdysone-responsive transcription factor Broad, and manipulation of EcR/USP/Broad signaling induces inappropriate Bab2 expression and termination of Sgs gene expression. Bab2 directly binds to Sgs loci in vitro and represses all Sgs genes in vivo. Our work characterizes Bab2 as a temporal regulator of somatic gene expression in response to systemic ecdysone signaling.
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Affiliation(s)
- Jianli Duan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yunpo Zhao
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China; Department of Zoology, Life Science Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
| | - Haichao Li
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Michael D Gordon
- Department of Zoology, Life Science Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Xuexia Miao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ylva Engström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden; Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria.
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20
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Billot R, Plener L, Jacquet P, Elias M, Chabrière E, Daudé D. Engineering acyl-homoserine lactone-interfering enzymes toward bacterial control. J Biol Chem 2020; 295:12993-13007. [PMID: 32690609 DOI: 10.1074/jbc.rev120.013531] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/17/2020] [Indexed: 12/20/2022] Open
Abstract
Enzymes able to degrade or modify acyl-homoserine lactones (AHLs) have drawn considerable interest for their ability to interfere with the bacterial communication process referred to as quorum sensing. Many proteobacteria use AHL to coordinate virulence and biofilm formation in a cell density-dependent manner; thus, AHL-interfering enzymes constitute new promising antimicrobial candidates. Among these, lactonases and acylases have been particularly studied. These enzymes have been isolated from various bacterial, archaeal, or eukaryotic organisms and have been evaluated for their ability to control several pathogens. Engineering studies on these enzymes were carried out and successfully modulated their capacity to interact with specific AHL, increase their catalytic activity and stability, or enhance their biotechnological potential. In this review, special attention is paid to the screening, engineering, and applications of AHL-modifying enzymes. Prospects and future opportunities are also discussed with a view to developing potent candidates for bacterial control.
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Affiliation(s)
- Raphaël Billot
- Gene&GreenTK, Marseille, France; IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | | | | | - Mikael Elias
- Molecular Biology and Biophysics and Biotechnology Institute, Department of Biochemistry, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric Chabrière
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France.
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21
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Bacterial alginate regulators and phage homologs repress CRISPR-Cas immunity. Nat Microbiol 2020; 5:679-687. [PMID: 32203410 PMCID: PMC7190418 DOI: 10.1038/s41564-020-0691-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 02/12/2020] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas systems are adaptive immune systems that protect bacteria from bacteriophage (phage) infection1. To provide immunity, RNA-guided protein surveillance complexes recognize foreign nucleic acids, triggering their destruction by Cas nucleases2. While the essential requirements for immune activity are well understood, the physiological cues that regulate CRISPR-Cas expression are not. Here, a forward genetic screen identifies a two-component system (KinB/AlgB), previously characterized in regulating Pseudomonas aeruginosa alginate biosynthesis3,4, as a regulator of the expression and activity of the P. aeruginosa Type I-F CRISPR-Cas system. Downstream of KinB/AlgB, activators of alginate production AlgU (a σE orthologue) and AlgR, repress CRISPR-Cas activity during planktonic and surface-associated growth5. AmrZ, another alginate regulator6, is triggered to repress CRISPR-Cas immunity during surface-association. Pseudomonas phages and plasmids have taken advantage of this regulatory scheme, and carry hijacked homologs of AmrZ that repress CRISPR-Cas expression and activity. This suggests that while CRISPR-Cas regulation may be important to limit self-toxicity, endogenous repressive pathways represent a vulnerability for parasite manipulation.
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22
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Sjodt M, Rohs PDA, Gilman MSA, Erlandson SC, Zheng S, Green AG, Brock KP, Taguchi A, Kahne D, Walker S, Marks DS, Rudner DZ, Bernhardt TG, Kruse AC. Structural coordination of polymerization and crosslinking by a SEDS-bPBP peptidoglycan synthase complex. Nat Microbiol 2020; 5:813-820. [PMID: 32152588 PMCID: PMC7540724 DOI: 10.1038/s41564-020-0687-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/11/2020] [Indexed: 11/09/2022]
Abstract
The Shape, Elongation, Division, and Sporulation (“SEDS”) proteins are a highly conserved family of transmembrane glycosyltransferases that work in concert with class B penicillin binding proteins (bPBPs) to build the bacterial peptidoglycan cell wall1–6. How these proteins coordinate polymerization of new glycan strands with their crosslinking to the existing peptidoglycan meshwork remains unclear. Here, we report the crystal structure of the prototypical SEDS protein RodA from Thermus thermophilus in complex with its cognate bPBP at 3.3 Å resolution. The structure reveals a 1:1 stoichiometric complex with two extensive interaction interfaces between the proteins: one in the membrane plane and the other at the extracytoplasmic surface. When in complex with a bPBP, RodA shows a ~10 Å shift of transmembrane helix 7 that exposes a large membrane-accessible cavity. Negative-stain electron microscopy reveals that the complex can adopt a variety of different conformations. These data define the bPBP pedestal domain as the key allosteric activator of RodA both in vitro and in vivo, explaining how a SEDS:bPBP complex can coordinate its dual enzymatic activities of peptidoglycan polymerization and crosslinking to build the cell wall.
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Affiliation(s)
- Megan Sjodt
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Patricia D A Rohs
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah C Erlandson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sanduo Zheng
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Anna G Green
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kelly P Brock
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Atsushi Taguchi
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - David Z Rudner
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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23
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Protein Aggregation is Associated with Acinetobacter baumannii Desiccation Tolerance. Microorganisms 2020; 8:microorganisms8030343. [PMID: 32121206 PMCID: PMC7142981 DOI: 10.3390/microorganisms8030343] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/23/2022] Open
Abstract
Desiccation tolerance has been implicated as an important characteristic that potentiates the spread of the bacterial pathogen Acinetobacter baumannii on dry surfaces. Here we explore several factors influencing desiccation survival of A. baumannii. At the macroscale level, we find that desiccation tolerance is influenced by cell density and growth phase. A transcriptome analysis indicates that desiccation represents a unique state for A. baumannii compared to commonly studied growth phases and strongly influences pathways responsible for proteostasis. Remarkably, we find that an increase in total cellular protein aggregates, which is often considered deleterious, correlates positively with the ability of A. baumannii to survive desiccation. We show that inducing protein aggregate formation prior to desiccation increases survival and, importantly, that proteins incorporated into cellular aggregates can retain activity. Our results suggest that protein aggregates may promote desiccation tolerance in A. baumannii through preserving and protecting proteins from damage during desiccation until rehydration occurs.
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24
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Min KB, Yoon SS. Transcriptome analysis reveals that the RNA polymerase-binding protein DksA1 has pleiotropic functions in Pseudomonas aeruginosa. J Biol Chem 2020; 295:3851-3864. [PMID: 32047111 DOI: 10.1074/jbc.ra119.011692] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/09/2020] [Indexed: 12/20/2022] Open
Abstract
The stringent response (SR) is a highly conserved stress response in bacteria. It is composed of two factors, (i) a nucleotide alarmone, guanosine tetra- and pentaphosphate ((p)ppGpp), and (ii) an RNA polymerase-binding protein, DksA, that regulates various phenotypes, including bacterial virulence. The clinically significant opportunistic bacterial pathogen Pseudomonas aeruginosa possesses two genes, dksA1 and dksA2, that encode DksA proteins. It remains elusive, however, which of these two genes plays a more important role in SR regulation. In this work, we compared genome-wide, RNA-Seq-based transcriptome profiles of ΔdksA1, ΔdksA2, and ΔdksA1ΔdksA2 mutants to globally assess the effects of these gene deletions on transcript levels coupled with phenotypic analyses. The ΔdksA1 mutant exhibited substantial defects in a wide range of phenotypes, including quorum sensing (QS), anaerobiosis, and motility, whereas the ΔdksA2 mutant exhibited no significant phenotypic changes, suggesting that the dksA2 gene may not have an essential function in P. aeruginosa under the conditions used here. Of note, the ΔdksA1 mutants displayed substantially increased transcription of genes involved in polyamine biosynthesis, and we also detected increased polyamine levels in these mutants. Because SAM is a shared precursor for the production of both QS autoinducers and polyamines, these findings suggest that DksA1 deficiency skews the flow of SAM toward polyamine production rather than to QS signaling. Together, our results indicate that DksA1, but not DksA2, controls many important phenotypes in P. aeruginosa We conclude that DksA1 may represent a potential target whose inhibition may help manage recalcitrant P. aeruginosa infections.
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Affiliation(s)
- Kyung Bae Min
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea .,Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea.,Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
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25
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Coomer CA, Carlon-Andres I, Iliopoulou M, Dustin ML, Compeer EB, Compton AA, Padilla-Parra S. Single-cell glycolytic activity regulates membrane tension and HIV-1 fusion. PLoS Pathog 2020; 16:e1008359. [PMID: 32084246 PMCID: PMC7055913 DOI: 10.1371/journal.ppat.1008359] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 03/04/2020] [Accepted: 01/27/2020] [Indexed: 12/21/2022] Open
Abstract
There has been resurgence in determining the role of host metabolism in viral infection yet deciphering how the metabolic state of single cells affects viral entry and fusion remains unknown. Here, we have developed a novel assay multiplexing genetically-encoded biosensors with single virus tracking (SVT) to evaluate the influence of global metabolic processes on the success rate of virus entry in single cells. We found that cells with a lower ATP:ADP ratio prior to virus addition were less permissive to virus fusion and infection. These results indicated a relationship between host metabolic state and the likelihood for virus-cell fusion to occur. SVT revealed that HIV-1 virions were arrested at hemifusion in glycolytically-inactive cells. Interestingly, cells acutely treated with glycolysis inhibitor 2-deoxyglucose (2-DG) become resistant to virus infection and also display less surface membrane cholesterol. Addition of cholesterol in these in glycolytically-inactive cells rescued the virus entry block at hemifusion and enabled completion of HIV-1 fusion. Further investigation with FRET-based membrane tension and membrane order reporters revealed a link between host cell glycolytic activity and host membrane order and tension. Indeed, cells treated with 2-DG possessed lower plasma membrane lipid order and higher tension values, respectively. Our novel imaging approach that combines lifetime imaging (FLIM) and SVT revealed not only changes in plasma membrane tension at the point of viral fusion, but also that HIV is less likely to enter cells at areas of higher membrane tension. We therefore have identified a connection between host cell glycolytic activity and membrane tension that influences HIV-1 fusion in real-time at the single-virus fusion level in live cells.
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Affiliation(s)
- Charles A. Coomer
- Cellular Imaging Group, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, United States of America
- University of Kentucky, College of Medicine, Lexington, Kentucky, United States of America
- Division of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, United Kingdom
| | - Irene Carlon-Andres
- Cellular Imaging Group, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
- Division of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, United Kingdom
| | - Maro Iliopoulou
- Cellular Imaging Group, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Michael L. Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Ewoud B. Compeer
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Alex A. Compton
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Sergi Padilla-Parra
- Cellular Imaging Group, Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom
- Division of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, United Kingdom
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26
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An Autocrine Wnt5a Loop Promotes NF-κB Pathway Activation and Cytokine/Chemokine Secretion in Melanoma. Cells 2019; 8:cells8091060. [PMID: 31510045 PMCID: PMC6770184 DOI: 10.3390/cells8091060] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/29/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022] Open
Abstract
Wnt5a signaling has been implicated in the progression of cancer by regulating multiple cellular processes, largely migration and invasion, epithelial-mesenchymal transition (EMT), and metastasis. Since Wnt5a signaling has also been involved in inflammatory processes in infectious and inflammatory diseases, we addressed the role of Wnt5a in regulating NF-κB, a pivotal mediator of inflammatory responses, in the context of cancer. The treatment of melanoma cells with Wnt5a induced phosphorylation of the NF-κB subunit p65 as well as IKK phosphorylation and IκB degradation. By using cDNA overexpression, RNA interference, and dominant negative mutants we determined that ROR1, Dvl2, and Akt (from the Wnt5a pathway) and TRAF2 and RIP (from the NF-κB pathway) are required for the Wnt5a/NF-κB crosstalk. Wnt5a also induced p65 nuclear translocation and increased NF-κB activity as evidenced by reporter assays and a NF-κB-specific upregulation of RelB, Bcl-2, and Cyclin D1. Further, stimulation of melanoma cells with Wnt5a increased the secretion of cytokines and chemokines, including IL-6, IL-8, IL-11, and IL-6 soluble receptor, MCP-1, and TNF soluble receptor I. The inhibition of endogenous Wnt5a demonstrated that an autocrine Wnt5a loop is a major regulator of the NF-κB pathway in melanoma. Taken together, these results indicate that Wnt5a activates the NF-κB pathway and has an immunomodulatory effect on melanoma through the secretion of cytokines and chemokines.
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27
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Szatkowska R, Garcia-Albornoz M, Roszkowska K, Holman SW, Furmanek E, Hubbard SJ, Beynon RJ, Adamczyk M. Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1. Biochem J 2019; 476:1053-1082. [PMID: 30885983 PMCID: PMC6448137 DOI: 10.1042/bcj20180701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 02/07/2023]
Abstract
Protein biosynthesis is energetically costly, is tightly regulated and is coupled to stress conditions including glucose deprivation. RNA polymerase III (RNAP III)-driven transcription of tDNA genes for production of tRNAs is a key element in efficient protein biosynthesis. Here we present an analysis of the effects of altered RNAP III activity on the Saccharomyces cerevisiae proteome and metabolism under glucose-rich conditions. We show for the first time that RNAP III is tightly coupled to the glycolytic system at the molecular systems level. Decreased RNAP III activity or the absence of the RNAP III negative regulator, Maf1 elicit broad changes in the abundance profiles of enzymes engaged in fundamental metabolism in S. cerevisiae In a mutant compromised in RNAP III activity, there is a repartitioning towards amino acids synthesis de novo at the expense of glycolytic throughput. Conversely, cells lacking Maf1 protein have greater potential for glycolytic flux.
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Affiliation(s)
- Roza Szatkowska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Manuel Garcia-Albornoz
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, U.K
| | - Katarzyna Roszkowska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, U.K
| | - Emil Furmanek
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Simon J Hubbard
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, U.K
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, U.K
| | - Malgorzata Adamczyk
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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28
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Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP. Jungle Express is a versatile repressor system for tight transcriptional control. Nat Commun 2018; 9:3617. [PMID: 30190458 PMCID: PMC6127294 DOI: 10.1038/s41467-018-05857-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 07/30/2018] [Indexed: 11/09/2022] Open
Abstract
Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of 'Jungle Express', an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 µM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale.
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Affiliation(s)
- Thomas L Ruegg
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Institute of Botany, University of Basel, 4001, Basel, Switzerland
| | - Jose H Pereira
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joseph C Chen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - Andy DeGiovanni
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Pavel Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Giovani P Tomaleri
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Michael P Thelen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
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29
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Cao H, Villatoro-Hernandez J, Weme RDO, Frenzel E, Kuipers OP. Boosting heterologous protein production yield by adjusting global nitrogen and carbon metabolic regulatory networks in Bacillus subtilis. Metab Eng 2018; 49:143-152. [DOI: 10.1016/j.ymben.2018.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/23/2018] [Accepted: 08/06/2018] [Indexed: 01/19/2023]
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30
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Shao L, Chen Z, Soutto M, Zhu S, Lu H, Romero-Gallo J, Peek R, Zhang S, El-Rifai W. Helicobacter pylori-induced miR-135b-5p promotes cisplatin resistance in gastric cancer. FASEB J 2018; 33:264-274. [PMID: 29985646 DOI: 10.1096/fj.201701456rr] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Helicobacter pylori infection is a major risk factor for the development of gastric cancer. Aberrant expression of microRNAs is strongly implicated in gastric tumorigenesis; however, their contribution in response to H. pylori infection has not been fully elucidated. In this study, we evaluated the expression of miR-135b-5p and its role in gastric cancer. We describe the overexpression of miR-135b-5p in human gastric cancer tissue samples compared with normal tissue samples. Furthermore, we found that miR-135b-5p is also up-regulated in gastric tumors from the trefoil factor 1-knockout mouse model. Infection with H. pylori induced the expression of miR-135b-5p in the in vitro and in vivo models. miR-135b-5p induction was mediated by NF-κB. Treatment of gastric cancer cells with TNF-α induced miR-135b-5p in a NF-κB-dependent manner. Mechanistically, we found that miR-135b-5p targets Krüppel-like factor 4 (KLF4) and binds to its 3' UTR, leading to reduced KLF4 expression. Functionally, high levels of miR-135b-5p suppress apoptosis and induce cisplatin resistance. Our results uncovered a mechanistic link between H. pylori infection and miR-135b-5p-KLF4, suggesting that targeting miR-135b-5p could be a potential therapeutic approach to circumvent resistance to cisplatin.-Shao, L., Chen, Z., Soutto, M., Zhu, S., Lu, H., Romero-Gallo, J., Peek, R., Zhang, S., El-Rifai, W. Helicobacter pylori-induced miR-135b-5p promotes cisplatin resistance in gastric cancer.
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Affiliation(s)
- Linlin Shao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Department of Veterans Affairs, Miami Healthcare System, Miami, Florida, USA
| | - Zheng Chen
- Department of Veterans Affairs, Miami Healthcare System, Miami, Florida, USA.,Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA; and
| | - Mohammed Soutto
- Department of Veterans Affairs, Miami Healthcare System, Miami, Florida, USA
| | - Shoumin Zhu
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA; and
| | - Heng Lu
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA; and
| | - Judith Romero-Gallo
- Division of Gastroenterology, Hematology, and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard Peek
- Division of Gastroenterology, Hematology, and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wael El-Rifai
- Department of Veterans Affairs, Miami Healthcare System, Miami, Florida, USA.,Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA; and
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31
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Wang H, Shi C, Xie Q, Wang Y, Liu S, Li C, He C, Tao J. Genome-Wide Analysis of β-Galactosidases in Xanthomonas campestris pv. campestris 8004. Front Microbiol 2018; 9:957. [PMID: 29867862 PMCID: PMC5958218 DOI: 10.3389/fmicb.2018.00957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/24/2018] [Indexed: 11/29/2022] Open
Abstract
Bacterial β-galactosidase is involved in lactose metabolism and acts as a prevalent reporter enzyme used in studying the activities of prokaryotic and eukaryotic promoters. Xanthomonas campestris pv. campestris (Xcc) is the pathogen of black rot disease in crucifers. β-Galactosidase activity can be detected in Xcc culture, which makes Escherichia coli LacZ unable to be used as a reporter enzyme in Xcc. To systemically understand the β-galactosidase in Xcc and construct a β-galactosidase -deficient strain for promoter activity analysis using LacZ as a reporter, we here analyzed the putative β-galactosidases in Xcc 8004. As glycosyl hydrolase (GH) family 2 (GH2) and 35 (GH35) family enzymes were reported to have beta-galactosidase activities, we studied all of them encoded by Xcc 8004. When expressed in E. coli, only two of the enzymes, XC1214 and XC2985, were found to have β-galactosidase activity. When deleted from the Xcc 8004 genome, only the XC1214 mutant had no β-galactosidase activity, and other GH2 and GH35 gene deletions resulted in no significant reduction in β-galactosidase activity. Therefore, XC1214 is the main β-galactosidase in Xcc 8004. Notably, we have constructed a β-galactosidase-free strain that can be employed in gene traps using LacZ as a reporter in Xcc. The results reported herein should facilitate the development of high-capacity screening assays that utilize the LacZ reporter system in Xcc.
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Affiliation(s)
- Huiqi Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Haikou, China.,Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chenyi Shi
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Qingbiao Xie
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Haikou, China.,Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yaxin Wang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shiyao Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Haikou, China.,Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chunxia Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Haikou, China.,Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Haikou, China.,Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Jun Tao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Haikou, China.,Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
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32
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Stiegler SC, Rübbelke M, Korotkov VS, Weiwad M, John C, Fischer G, Sieber SA, Sattler M, Buchner J. A chemical compound inhibiting the Aha1-Hsp90 chaperone complex. J Biol Chem 2017; 292:17073-17083. [PMID: 28851842 PMCID: PMC5641884 DOI: 10.1074/jbc.m117.797829] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/20/2017] [Indexed: 11/06/2022] Open
Abstract
The eukaryotic Hsp90 chaperone machinery comprises many co-chaperones and regulates the conformation of hundreds of cytosolic client proteins. Therefore, it is not surprising that the Hsp90 machinery has become an attractive therapeutic target for diseases such as cancer. The compounds used so far to target this machinery affect the entire Hsp90 system. However, it would be desirable to achieve a more selective targeting of Hsp90-co-chaperone complexes. To test this concept, in this-proof-of-principle study, we screened for modulators of the interaction between Hsp90 and its co-chaperone Aha1, which accelerates the ATPase activity of Hsp90. A FRET-based assay that monitored Aha1 binding to Hsp90 enabled identification of several chemical compounds modulating the effect of Aha1 on Hsp90 activity. We found that one of these inhibitors can abrogate the Aha1-induced ATPase stimulation of Hsp90 without significantly affecting Hsp90 ATPase activity in the absence of Aha1. NMR spectroscopy revealed that this inhibitory compound binds the N-terminal domain of Hsp90 close to its ATP-binding site and overlapping with a transient Aha1-interaction site. We also noted that this inhibitor does not dissociate the Aha1-Hsp90 complex but prevents the specific interaction with the N-terminal domain of Hsp90 required for catalysis. In consequence, the inhibitor affected the activation and processing of Hsp90-Aha1-dependent client proteins in vivo We conclude that it is possible to abrogate a specific co-chaperone function of Hsp90 without inhibiting the entire Hsp90 machinery. This concept may also hold true for other co-chaperones of Hsp90.
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Affiliation(s)
- Sandrine C Stiegler
- From the Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | - Martin Rübbelke
- From the Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
- the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Vadim S Korotkov
- From the Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | - Matthias Weiwad
- the Max Planck Research Unit for Enzymology of Protein Folding, 06120 Halle/Saale, Germany, and
| | - Christine John
- From the Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | - Gunter Fischer
- the Max Planck Research Unit for Enzymology of Protein Folding, 06120 Halle/Saale, Germany, and
| | - Stephan A Sieber
- From the Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
| | - Michael Sattler
- From the Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, D-85747 Garching, Germany
- the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Buchner
- From the Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, D-85747 Garching, Germany,
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33
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Rasoulianboroujeni M, Kupgan G, Moghadam F, Tahriri M, Boughdachi A, Khoshkenar P, Ambrose J, Kiaie N, Vashaee D, Ramsey J, Tayebi L. Development of a DNA-liposome complex for gene delivery applications. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 75:191-197. [DOI: 10.1016/j.msec.2017.02.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/17/2016] [Accepted: 02/06/2017] [Indexed: 01/22/2023]
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Hossain M, Stillman B. Opposing roles for DNA replication initiator proteins ORC1 and CDC6 in control of Cyclin E gene transcription. eLife 2016; 5. [PMID: 27458800 PMCID: PMC4987141 DOI: 10.7554/elife.12785] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
Newly born cells either continue to proliferate or exit the cell division cycle. This decision involves delaying expression of Cyclin E that promotes DNA replication. ORC1, the Origin Recognition Complex (ORC) large subunit, is inherited into newly born cells after it binds to condensing chromosomes during the preceding mitosis. We demonstrate that ORC1 represses Cyclin E gene (CCNE1) transcription, an E2F1 activated gene that is also repressed by the Retinoblastoma (RB) protein. ORC1 binds to RB, the histone methyltransferase SUV39H1 and to its repressive histone H3K9me3 mark. ORC1 cooperates with SUV39H1 and RB protein to repress E2F1-dependent CCNE1 transcription. In contrast, the ORC1-related replication protein CDC6 binds Cyclin E-CDK2 kinase and in a feedback loop removes RB from ORC1, thereby hyper-activating CCNE1 transcription. The opposing effects of ORC1 and CDC6 in controlling the level of Cyclin E ensures genome stability and a mechanism for linking directly DNA replication and cell division commitment. DOI:http://dx.doi.org/10.7554/eLife.12785.001 Living cells must replicate their DNA before they divide so that the newly formed cells can each receive an identical copy of the genetic material. Before DNA replication can begin, a number of proteins must come together to form so-called pre-replicative complexes at many locations along the DNA molecules. These protein complexes then serve as landing pads for many other DNA replication proteins. One component of the pre-replicative complex, a protein called ORC1, helps to recruit another protein called CDC6 that in turn acts with Cyclin E to promote the replication of the DNA. Cyclin E is a protein that is only expressed when cells commit to divide. Previous research has shown that a lack of ORC1 causes the levels of Cyclin E to rise in human cells, but it was not understood how cells regulate the levels of Cyclin E. Now, Hossain and Stillman show that the ORC1 protein switches off the gene that encodes Cyclin E early on in newly born cells, and therefore prevents the Cyclin E protein from being produced. The experiments show that ORC1 does this by binding near one end of the gene for Cyclin E and interacting with two other proteins to inactivate the gene. Thus, ORC1 establishes a period when Cyclin E is absent from a newly formed cell. This essentially gives the cell time to ‘decide’ (based on external cues and its own signaling) whether it will divide again or enter into a non-dividing state. When a cell does decide to divide, the levels of CDC6 rise. CDC6 is another component of the pre-replicative complex and Hossain and Stillman find that CDC6 works to counteract the effects of ORC1 and reactivate the gene for Cyclin E. This activity leads to a dramatic increase in the production of Cyclin E, which in turn allows the cells to commit to another round of DNA replication and division. The opposing effects of ORC1 and CDC6 control the levels of Cyclin E and provide a link between DNA replication and a cell’s decision to divide. Further work is now needed to see whether ORC1 inactivates other genes in addition to the one that encodes Cyclin E. DOI:http://dx.doi.org/10.7554/eLife.12785.002
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Affiliation(s)
- Manzar Hossain
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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35
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Ushijima B, Videau P, Poscablo D, Stengel JW, Beurmann S, Burger AH, Aeby GS, Callahan SM. Mutation of the toxR or mshA genes from Vibrio coralliilyticus strain OCN014 reduces infection of the coral Acropora cytherea. Environ Microbiol 2016; 18:4055-4067. [PMID: 27348808 DOI: 10.1111/1462-2920.13428] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/19/2016] [Indexed: 01/09/2023]
Abstract
Thermal stress increases the incidence of coral disease, which is predicted to become more common with climate change, even on pristine reefs such as those surrounding Palmyra Atoll in the Northern Line Islands that experience minimal anthropogenic stress. Here we describe a strain of Vibrio coralliilyticus, OCN014, which was isolated from Acropora cytherea during an outbreak of Acropora white syndrome (AWS), a tissue loss disease that infected 25% of the A. cytherea population at Palmyra Atoll in 2009. OCN014 recreated signs of disease in experimentally infected corals in a temperature-dependent manner. Genes in OCN014 with expression levels positively correlated with temperature were identified using a transposon-mediated genetic screen. Mutant strains harbouring transposon insertions in two such genes, toxR (a toxin regulator) and mshA (the 11th gene of the 16-gene mannose-sensitive hemagglutinin (MSHA) type IV pilus operon), had reduced infectivity of A. cytherea. Deletion of toxR and the MSHA operon in a second strain of V. coralliilyticus, OCN008, that induces acute Montipora white syndrome in a temperature-independent manner had similarly reduced virulence. This work provides a link between temperature-dependent expression of virulence factors in a pathogen and infection of its coral host.
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Affiliation(s)
- Blake Ushijima
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.,Hawai'i Institute of Marine Biology, Kāne'ohe, HI, 96744, USA
| | - Patrick Videau
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97331, USA
| | - Donna Poscablo
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.,Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - John W Stengel
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Silvia Beurmann
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.,Hawai'i Institute of Marine Biology, Kāne'ohe, HI, 96744, USA
| | - Andrew H Burger
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.,Hawai'i Institute of Marine Biology, Kāne'ohe, HI, 96744, USA
| | - Greta S Aeby
- Hawai'i Institute of Marine Biology, Kāne'ohe, HI, 96744, USA
| | - Sean M Callahan
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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36
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Soutto M, Romero-Gallo J, Krishna U, Piazuelo MB, Washington MK, Belkhiri A, Peek RM, El-Rifai W. Loss of TFF1 promotes Helicobacter pylori-induced β-catenin activation and gastric tumorigenesis. Oncotarget 2016; 6:17911-22. [PMID: 25980439 PMCID: PMC4627225 DOI: 10.18632/oncotarget.3772] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/14/2015] [Indexed: 12/14/2022] Open
Abstract
Using in vitro and in vivo models, we investigated the role of TFF1 in suppressing H. pylori-mediated activation of oncogenic β-catenin in gastric tumorigenesis. A reconstitution of TFF1 expression in gastric cancer cells decreased H. pylori-induced β-catenin nuclear translocation, as compared to control (p < 0.001). These cells exhibited significantly lower β-catenin transcriptional activity, measured by pTopFlash reporter, and induction of its target genes (CCND1 and c-MYC), as compared to control. Because of the role of AKT in regulating β-catenin, we performed Western blot analysis and demonstrated that TFF1 reconstitution abrogates H. pylori-induced p-AKT (Ser473), p-β-catenin (Ser552), c-MYC, and CCND1 protein levels. For in vivo validation, we utilized the Tff1-KO gastric neoplasm mouse model. Following infection with PMSS1 H. pylori strain, we detected an increase in the nuclear staining for β-catenin and Ki-67 with a significant induction in the levels of Ccnd1 and c-Myc in the stomach of the Tff1-KO, as compared to Tff1-WT mice (p < 0.05). Only 10% of uninfected Tff1-KO mice, as opposed to one-third of H. pylori-infected Tff1-KO mice, developed invasive adenocarcinoma (p = 0.03). These findings suggest that loss of TFF1 could be a critical step in promoting the H. pylori-mediated oncogenic activation of β-catenin and gastric tumorigenesis.
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Affiliation(s)
- Mohammed Soutto
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA.,Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Judith Romero-Gallo
- Division of Gastroenterology, Hepatology, & Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Uma Krishna
- Division of Gastroenterology, Hepatology, & Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Blanca Piazuelo
- Division of Gastroenterology, Hepatology, & Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Kay Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Abbes Belkhiri
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard M Peek
- Division of Gastroenterology, Hepatology, & Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Wael El-Rifai
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA.,Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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37
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Xu H, Wang Y, Lu J, Zhang B, Zhang Z, Si L, Wu L, Yao T, Zhang C, Xiao S, Zhang L, Xia Q, Zhou D. Re-exploration of the Codon Context Effect on Amber Codon-Guided Incorporation of Noncanonical Amino Acids in Escherichia coli by the Blue-White Screening Assay. Chembiochem 2016; 17:1250-6. [PMID: 27028123 DOI: 10.1002/cbic.201600117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/06/2022]
Abstract
The effect of codon context on amber codon-guided incorporation of noncanonical amino acids (NAAs) has been previously examined by antibiotic selection. Here, we re-explored this effect by screening a library in which three nucleotides upstream and downstream of the amber codon were randomised, and inserted within the lacZ-α gene. Thousands of clones were obtained and distinguished by the depth of blue colour upon exposure to X-gal. Large-scale sequencing revealed remarkable preferences in nucleotides downstream of the amber codon, and moderate preferences for upstream nucleotides. Nucleotide preference was quantified by a dual-luciferase assay, which verified that the optimum context for NAA incorporation, AATTAGACT, was applicable to different proteins. Our work provides a general guide for engineering amber codons into genes of interest in bacteria.
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Affiliation(s)
- Huan Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Yan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Jiaqi Lu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Bo Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Ziwei Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Longlong Si
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Ling Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Tianzhuo Yao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Chuanling Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Sulong Xiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China.
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing, 100191, China.
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38
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AK-1, a SIRT2 inhibitor, destabilizes HIF-1α and diminishes its transcriptional activity during hypoxia. Cancer Lett 2016; 373:138-145. [DOI: 10.1016/j.canlet.2016.01.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 02/07/2023]
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39
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Soutto M, Chen Z, Saleh MA, Katsha A, Zhu S, Zaika A, Belkhiri A, El-Rifai W. TFF1 activates p53 through down-regulation of miR-504 in gastric cancer. Oncotarget 2015; 5:5663-73. [PMID: 25015107 PMCID: PMC4170596 DOI: 10.18632/oncotarget.2156] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The expression of TFF1 is frequently down-regulated in human gastric cancer whereas its knockout leads to the development of gastric adenomas and carcinomas in mouse models. The molecular mechanisms underlying the TFF1 tumor suppressor functions remain unclear. In this study, we demonstrate, using colony formation assay and Annexin V staining, that reconstitution of TFF1 expression in gastric cancer cell models suppresses cell growth and promotes cell death. Furthermore, using a tumor xenograft mouse model of gastric cancer, we demonstrated that reconstitution of TFF1 suppresses tumor growth in vivo. The results from PG13-luciferase reporter assay and Western blot analysis indicated that TFF1 promotes the expression and transcription activity of the p53 protein. Further analysis using cycloheximide-based protein assay and quantitative real-time PCR data suggested that TFF1 does not interfere with p53 mRNA levels or protein stability. Alternatively, we found that the reconstitution of TFF1 down-regulates miR-504, a negative regulator of p53. Western blot analysis data demonstrated that miR-504 abrogates TFF1-induced p53 protein expression and activity. In conclusion, the in vitro and in vivo data demonstrate, for the first time, a novel mechanism by which the tumor suppressor functions of TFF1 involve activation of p53 through down-regulation of miR-504.
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Affiliation(s)
- Mohammed Soutto
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA. Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Zheng Chen
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mohamed A Saleh
- Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ahmed Katsha
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shoumin Zhu
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexander Zaika
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Abbes Belkhiri
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Wael El-Rifai
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA. Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA. Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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40
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Chua SL, Sivakumar K, Rybtke M, Yuan M, Andersen JB, Nielsen TE, Givskov M, Tolker-Nielsen T, Cao B, Kjelleberg S, Yang L. C-di-GMP regulates Pseudomonas aeruginosa stress response to tellurite during both planktonic and biofilm modes of growth. Sci Rep 2015; 5:10052. [PMID: 25992876 PMCID: PMC4438720 DOI: 10.1038/srep10052] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/20/2015] [Indexed: 11/09/2022] Open
Abstract
Stress response plays an important role on microbial adaptation under hostile environmental conditions. It is generally unclear how the signaling transduction pathway mediates a stress response in planktonic and biofilm modes of microbial communities simultaneously. Here, we showed that metalloid tellurite (TeO3(2-)) exposure induced the intracellular content of the secondary messenger cyclic di-GMP (c-di-GMP) of Pseudomonas aeruginosa. Two diguanylate cyclases (DGCs), SadC and SiaD, were responsible for the increased intracellular content of c-di-GMP. Enhanced c-di-GMP levels by TeO3(2-) further increased P. aeruginosa biofilm formation and resistance to TeO3(2-). P. aeruginosa ΔsadCΔsiaD and PAO1/p(lac)-yhjH mutants with low intracellular c-di-GMP content were more sensitive to TeO3(2-) exposure and had low relative fitness compared to the wild-type PAO1 planktonic and biofilm cultures exposed to TeO3(2-). Our study provided evidence that c-di-GMP level can play an important role in mediating stress response in microbial communities during both planktonic and biofilm modes of growth.
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Affiliation(s)
- Song Lin Chua
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] NUS Graduate School of Integrative Sciences and Engineering, National University of Singapore, Singapore 117543
| | - Krishnakumar Sivakumar
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551
| | - Morten Rybtke
- Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Mingjun Yuan
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Jens Bo Andersen
- Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Thomas E Nielsen
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Michael Givskov
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Bin Cao
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Staffan Kjelleberg
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] Center for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | - Liang Yang
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] School of Biological Sciences, Nanyang Technological University, Singapore 637551
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41
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Ye Y, Sun Z, Guo A, Song LS, Grobe JL, Chen S. Ablation of the GNB3 gene in mice does not affect body weight, metabolism or blood pressure, but causes bradycardia. Cell Signal 2014; 26:2514-20. [PMID: 25093805 DOI: 10.1016/j.cellsig.2014.07.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/26/2014] [Accepted: 07/28/2014] [Indexed: 11/18/2022]
Abstract
G protein β3 (Gβ3) is an isoform of heterotrimeric G protein β subunits involved in transducing G protein coupled receptor (GPCR) signaling. Polymorphisms in Gβ3 (GNB3) are associated with many human disorders (e.g. hypertension, diabetes and obesity) but the role of GNB3 in these pathogeneses remains unclear. Here, Gβ3-null mice (GNB3(-/-)) were characterized to determine how Gβ3 functions to regulate blood pressure, body weight and metabolism. We found Gβ3 expression restricted to limited types of tissues, including the retina, several regions of the brain and heart ventricles. Gβ3-deficient mice were normal as judged by body weight gain by age or by feeding with high-fat diet (HFD); glucose tolerance and insulin sensitivity; baseline blood pressure and angiotensin II infusion-induced hypertension. During tail-cuff blood pressure measurements, however, Gβ3-null mice had slower heart rates (~450 vs ~500 beats/min). This bradycardia was not observed in isolated and perfused Gβ3-null mouse hearts. Moreover, mouse hearts isolated from GNB3(-/-) and controls responded equivalently to muscarinic receptor- and β-adrenergic receptor-stimulated bradycardia and tachycardia, respectively. Since no difference was seen in isolated hearts, Gβ3 is unlikely to be involved directly in the GPCR signaling activity that controls heart pacemaker activity. These results demonstrate that although Gβ3 appears dispensable in mice for the regulation of blood pressure, body weight and metabolic features associated with obesity and diabetes, Gβ3 may regulate heart rate.
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Affiliation(s)
- Yuanchao Ye
- Department of Pharmacology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Zhizeng Sun
- Department of Pharmacology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Ang Guo
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Long-Sheng Song
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Justin L Grobe
- Department of Pharmacology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Songhai Chen
- Department of Pharmacology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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Thirumalai MK, Roy A, Sanikommu S, Arockiaraj J, Pasupuleti M. A simple, robust enzymatic-based high-throughput screening method for antimicrobial peptides discovery against Escherichia coli. J Pept Sci 2014; 20:341-8. [DOI: 10.1002/psc.2619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 01/16/2014] [Accepted: 01/23/2014] [Indexed: 11/11/2022]
Affiliation(s)
| | - Arpita Roy
- SRM Research Institute; SRM University; Chennai Tamil Nadu India
| | - Suma Sanikommu
- Department of Biochemistry; Chaitanya PG College; Kishanpura, Hanamkonda, Warangal 506001 India
| | - Jesu Arockiaraj
- Division of Fisheries Biotechnology & Molecular Biology, Research Department of Biotechnology, Faculty of Science and Humanities; SRM University; Kattankulathur, Chennai 603 203 India
| | - Mukesh Pasupuleti
- Central Drug Research Institute; B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road Lucknow 226031 India
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Xu Z, Gao X, He Y, Ju J, Zhang M, Liu R, Wu Y, Ma C, Ma C, Lin Z, Huang X, Zhao Q. Synergistic effect of SRY and its direct target, WDR5, on Sox9 expression. PLoS One 2012; 7:e34327. [PMID: 22523547 PMCID: PMC3327683 DOI: 10.1371/journal.pone.0034327] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 02/25/2012] [Indexed: 11/18/2022] Open
Abstract
SRY is a sex-determining gene that encodes a transcription factor, which triggers male development in most mammals. The molecular mechanism of SRY action in testis determination is, however, poorly understood. In this study, we demonstrate that WDR5, which encodes a WD-40 repeat protein, is a direct target of SRY. EMSA experiments and ChIP assays showed that SRY could bind to the WDR5 gene promoter directly. Overexpression of SRY in LNCaP cells significantly increased WDR5 expression concurrent with histone H3K4 methylation on the WDR5 promoter. To specifically address whether SRY contributes to WDR5 regulation, we introduced a 4-hydroxy-tamoxifen-inducible SRY allele into LNCaP cells. Conditional SRY expression triggered enrichment of SRY on the WDR5 promoter resulting in induction of WDR5 transcription. We found that WDR5 was self regulating through a positive feedback loop. WDR5 and SRY interacted and were colocalized in cells. In addition, the interaction of WDR5 with SRY resulted in activation of Sox9 while repressing the expression of β-catenin. These results suggest that, in conjunction with SRY, WDR5 plays an important role in sex determination.
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Affiliation(s)
- Zhen Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xinxing Gao
- Model Animal Research Center, Nanjing University, Nanjing, China
| | - Yinghong He
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
- School of Basic Medicine, Dali University, Yunnan, China
| | - Junyi Ju
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Miaomiao Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ronghua Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yupeng Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chunyan Ma
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chi Ma
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhaoyu Lin
- Model Animal Research Center, Nanjing University, Nanjing, China
| | - Xingxu Huang
- Model Animal Research Center, Nanjing University, Nanjing, China
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Molecular Immunology and Cancer Research Center, School of Life Sciences, Nanjing University, Nanjing, China
- * E-mail:
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How to screen non-viral gene delivery systems in vitro? J Control Release 2011; 154:218-32. [PMID: 21600249 DOI: 10.1016/j.jconrel.2011.05.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 03/31/2011] [Accepted: 05/01/2011] [Indexed: 11/21/2022]
Abstract
Screening of new gene delivery candidates regarding transfection efficiency and toxicity is usually performed by reading out transgene expression levels relative to a reference formulation after in vitro transfection. However, over the years and among different laboratories, this screening has been performed in a variety of cell lines, using a variety of conditions and read-out systems, and by comparison to a variety of reference formulations. This makes a direct comparison of results difficult, if not impossible. Reaching a consensus would enable placing new results into context of previous findings and estimate the overall contribution to the improvement of non-viral gene delivery. In this paper we illustrate the sensitivity of transfection outcomes on testing conditions chosen, and propose a screening protocol with the aim of standardization within the field.
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Abstract
When a transient or stable transfection assay is developed for a promoter, a primary objective is to quantify promoter strength. Because transfection efficiency in such assays can be low, promoters are commonly fused to heterologous reporter genes that encode enzymes that can be quantified using highly sensitive assays. The reporter protein's activity or fluorescence within a transfected cell population is approximately proportional to the steady-state mRNA level. In this protocol, cells transfected with an Escherichia coli transposon chloramphenicol acetyltransferase (CAT) reporter plasmid are lysed by repeated cycles of freezing and thawing and cellular debris is removed by centrifugation. The lysate is incubated with [(14)C]chloramphenicol and acetyl-coenzyme A; CAT catalyzes the acetylation of chloramphenicol. The acetylated products and the unmodified reactants are separated from the aqueous solution by organic extraction with ethyl acetate. Acetylation is monitored by autoradiography following thin-layer chromatography (TLC) to separate the acetylated from the unacetylated forms. The percent conversion of [(14)C]chloramphenicol to acetyl-[(14)C]chloramphenicol can be measured by PhosphorImager analysis of the TLC plate, by excising the radioactive spots from the TLC plate and counting in a scintillation counter, or by densitometry analysis of an autoradiograph. The acetylated (14)C-labeled product can also be quantified without TLC by organic extraction and scintillation counting using reagent-grade chemicals.
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