1
|
Campbell JS, Pearce JC, Bebes A, Pradhan A, Yuecel R, Brown AJP, Wakefield JG. Characterising phagocytes and measuring phagocytosis from live Galleria mellonella larvae. Virulence 2024; 15:2313413. [PMID: 38357909 PMCID: PMC10877982 DOI: 10.1080/21505594.2024.2313413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Over the last 20 years, the larva of the greater waxmoth, Galleria mellonella, has rapidly increased in popularity as an in vivo mammalian replacement model organism for the study of human pathogens. Experimental readouts of response to infection are most often limited to observing the melanization cascade and quantifying larval death and, whilst transcriptomic and proteomic approaches, and methods to determine microbial load are also used, a more comprehensive toolkit of profiling infection over time could transform the applicability of this model. As an invertebrate, Galleria harbour an innate immune system comprised of both humoral components and a repertoire of innate immune cells - termed haemocytes. Although information on subtypes of haemocytes exists, there are conflicting reports on their exact number and function. Flow cytometry has previously been used to assay Galleria haemocytes, but protocols include both centrifugation and fixation - physical methods which have the potential to affect haemocyte morphology prior to analysis. Here, we present a method for live haemocyte analysis by flow cytometry, revealing that Galleria haemocytes constitute only a single resolvable population, based on relative size or internal complexity. Using fluorescent zymosan particles, we extend our method to show that up to 80% of the Galleria haemocyte population display phagocytic capability. Finally, we demonstrate that the developed assay reliably replicates in vitro data, showing that cell wall β-1,3-glucan masking by Candida albicans subverts phagocytic responses. As such, our method provides a new tool with which to rapidly assess phagocytosis and understand live infection dynamics in Galleria.
Collapse
Affiliation(s)
| | | | - Attila Bebes
- Exeter Centre for Cytomics, Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, UK
| | - Arnab Pradhan
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Raif Yuecel
- Exeter Centre for Cytomics, Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, UK
| | - Alistair J P Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | | |
Collapse
|
2
|
Lee M, Fraaije MW. Equipping Saccharomyces cerevisiae with an Additional Redox Cofactor Allows F 420-Dependent Bioconversions in Yeast. ACS Synth Biol 2024; 13:921-929. [PMID: 38346396 PMCID: PMC10949242 DOI: 10.1021/acssynbio.3c00718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 03/16/2024]
Abstract
Industrial application of the natural deazaflavin cofactor F420 has high potential for the enzymatic synthesis of high value compounds. It can offer an additional range of chemistry to the use of well-explored redox cofactors such as FAD and their respective enzymes. Its limited access through organisms that are rather difficult to grow has urged research on the heterologous production of F420 using more industrially relevant microorganisms such as Escherichia coli. In this study, we demonstrate the possibility of producing this cofactor in a robust and widely used industrial organism, Saccharomyces cerevisiae, by the heterologous expression of the F420 pathway. Through careful selection of involved enzymes and some optimization, we achieved an F420 yield of ∼1.3 μmol/L, which is comparable to the yield of natural F420 producers. Furthermore, we showed the potential use of F420-producing S. cerevisiae for F420-dependent bioconversions by carrying out the whole-cell conversion of tetracycline. As the first demonstration of F420 synthesis and use for bioconversion in a eukaryotic organism, this study contributes to the development of versatile bioconversion platforms.
Collapse
Affiliation(s)
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| |
Collapse
|
3
|
Tsai K, Zhou Z, Yang J, Xu Z, Xu S, Zandi R, Hao N, Chen W, Alber M. Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582376. [PMID: 38464259 PMCID: PMC10925247 DOI: 10.1101/2024.02.29.582376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Understanding the mechanisms of cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short lifespan and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. In this study, by analyzing experimental data it was shown that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional chemical-mechanical model was developed and used to suggest and test hypothesized mechanisms of bud morphogenesis during aging. Experimentally calibrated simulations showed that tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip guided by the polarized Cdc42 signal during the early stage of budding. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage, as observed in experiments, through a reduction on the new cell surface material insertion or an expansion of the polarization site. Thus model simulations suggest the maintenance of new cell surface material insertion or chemical signal polarization could be weakened due to cellular aging in yeast and other cell types.
Collapse
Affiliation(s)
- Kevin Tsai
- Department of Mathematics, University of California, Riverside, CA, United States of America
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
| | - Zhen Zhou
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA, United States of America
| | - Jiadong Yang
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, United States of America
| | - Zhiliang Xu
- Applied and Computational Mathematics and Statistics Department, University of Notre Dame, Notre Dame, IN, United States of America
| | - Shixin Xu
- Duke Kunshan University, Kunshan, Jiangsu, China
| | - Roya Zandi
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
- Department of Physics and Astronomy, University of California, Riverside, CA, United States of America
- Biophysics Graduate Program, University of California, Riverside, CA, United States of America
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA, United States of America
| | - Weitao Chen
- Department of Mathematics, University of California, Riverside, CA, United States of America
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, United States of America
- Biophysics Graduate Program, University of California, Riverside, CA, United States of America
| | - Mark Alber
- Department of Mathematics, University of California, Riverside, CA, United States of America
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
- Department of Bioengineering, University of California, Riverside, CA, United States of America
- Biophysics Graduate Program, University of California, Riverside, CA, United States of America
| |
Collapse
|
4
|
Kalebina TS, Rekstina VV, Pogarskaia EE, Kulakovskaya T. Importance of Non-Covalent Interactions in Yeast Cell Wall Molecular Organization. Int J Mol Sci 2024; 25:2496. [PMID: 38473742 DOI: 10.3390/ijms25052496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
This review covers a group of non-covalently associated molecules, particularly proteins (NCAp), incorporated in the yeast cell wall (CW) with neither disulfide bridges with proteins covalently attached to polysaccharides nor other covalent bonds. Most NCAp, particularly Bgl2, are polysaccharide-remodeling enzymes. Either directly contacting their substrate or appearing as CW lipid-associated molecules, such as in vesicles, they represent the most movable enzymes and may play a central role in CW biogenesis. The absence of the covalent anchoring of NCAp allows them to be there where and when it is necessary. Another group of non-covalently attached to CW molecules are polyphosphates (polyP), the universal regulators of the activity of many enzymes. These anionic polymers are able to form complexes with metal ions and increase the diversity of non-covalent interactions through charged functional groups with both proteins and polysaccharides. The mechanism of regulation of polysaccharide-remodeling enzyme activity in the CW is unknown. We hypothesize that polyP content in the CW is regulated by another NCAp of the CW-acid phosphatase-which, along with post-translational modifications, may thus affect the activity, conformation and compartmentalization of Bgl2 and, possibly, some other polysaccharide-remodeling enzymes.
Collapse
Affiliation(s)
- Tatyana S Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Valentina V Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elizaveta E Pogarskaia
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Tatiana Kulakovskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino 142290, Russia
| |
Collapse
|
5
|
Liu T, Guo Y, Liao Y, Liu J. Mechanism-guided fine-tuned microbiome potentiates anti-tumor immunity in HCC. Front Immunol 2023; 14:1333864. [PMID: 38169837 PMCID: PMC10758498 DOI: 10.3389/fimmu.2023.1333864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Microbiome, including bacteria, fungi, and viruses, plays a crucial role in shaping distal and proximal anti-tumor immunity. Mounting evidence showed that commensal microbiome critically modulates immunophenotyping of hepatocellular carcinoma (HCC), a leading cause of cancer-related death. However, their role in anti-tumor surveillance of HCC is still poorly understood. Herein, we spotlighted growing interests in how the microbiome influences the progression and immunotherapeutic responses of HCC via changing local tumor microenvironment (TME) upon translocating to the sites of HCC through different "cell-type niches". Moreover, we summarized not only the associations but also the deep insight into the mechanisms of how the extrinsic microbiomes interplay with hosts to shape immune surveillance and regulate TME and immunotherapeutic responses. Collectively, we provided a rationale for a mechanism-guided fine-tuned microbiome to be neoadjuvant immunotherapy in the near future.
Collapse
Affiliation(s)
- Tao Liu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ya Guo
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanxia Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jinping Liu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| |
Collapse
|
6
|
Comeau P, Manso A. A Systematic Evaluation of Curcumin Concentrations and Blue Light Parameters towards Antimicrobial Photodynamic Therapy against Cariogenic Microorganisms. Pharmaceutics 2023; 15:2707. [PMID: 38140048 PMCID: PMC10747634 DOI: 10.3390/pharmaceutics15122707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Dental caries is a highly preventable and costly disease. Unfortunately, the current management strategies are inadequate at reducing the incidence and new minimally invasive strategies are needed. In this study, a systematic evaluation of specific light parameters and aqueous curcumin concentrations for antimicrobial photodynamic therapy (aPDT) was conducted. Aqueous solutions of curcumin were first prepared and evaluated for their light absorbance after applying different ~56 mW/cm2 blue light treatments in a continuous application mode. Next, these same light treatments as well as different application modes were applied to the curcumin solutions and the molar absorptivity coefficient, reactive oxygen species (ROS) release, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) for Streptococcus mutans and the MIC and minimum fungicidal concentration (MFC) for Candida albicans were measured. After up to 1 min of light treatment, the molar absorptivity of curcumin when added to culture media was lower than that for water only; however, at higher energy levels, this difference was not apparent. There was a noted dependence on both ROS type and cariogenic microorganism species on the sensitivity to both blue light treatment and application mode. In conclusion, this study provides new information towards improving the agonistic potential of aPDT associated with curcumin against cariogenic microorganisms.
Collapse
Affiliation(s)
- Patricia Comeau
- Department of Oral Health Science, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
- Department of Chemical and Materials Engineering, Concordia University, Montreal, QC H3G 2W1, Canada
| | - Adriana Manso
- Department of Oral Health Science, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
| |
Collapse
|
7
|
Schiavone M, François JM, Zerbib D, Capp JP. Emerging relevance of cell wall components from non-conventional yeasts as functional ingredients for the food and feed industry. Curr Res Food Sci 2023; 7:100603. [PMID: 37840697 PMCID: PMC10568300 DOI: 10.1016/j.crfs.2023.100603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
Non-conventional yeast species, or non-Saccharomyces yeasts, are increasingly recognized for their involvement in fermented foods. Many of them exhibit probiotic characteristics that are mainly due to direct contacts with other cell types through various molecular components of their cell wall. The biochemical composition and/or the molecular structure of the cell wall components are currently considered the primary determinant of their probiotic properties. Here we first present the techniques that are used to extract and analyze the cell wall components of food industry-related non-Saccharomyces yeasts. We then review the current understanding of the cell wall composition and structure of each polysaccharide from these yeasts. Finally, the data exploring the potential beneficial role of their cell wall components, which could be a source of innovative functional ingredients, are discussed. Such research would allow the development of high value-added products and provide the food industry with novel inputs beyond the well-established S. cerevisiae.
Collapse
Affiliation(s)
- Marion Schiavone
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Lallemand SAS, Blagnac, France
| | - Jean M. François
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Toulouse White Biotechnology (TWB), UMS INRAE/INSA/CNRS, Toulouse, France
| | - Didier Zerbib
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| |
Collapse
|
8
|
Savin N, Erofeev A, Gorelkin P. Analytical Models for Measuring the Mechanical Properties of Yeast. Cells 2023; 12:1946. [PMID: 37566025 PMCID: PMC10417110 DOI: 10.3390/cells12151946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
The mechanical properties of yeast play an important role in many biological processes, such as cell division and growth, maintenance of internal pressure, and biofilm formation. In addition, the mechanical properties of cells can indicate the degree of damage caused by antifungal drugs, as the mechanical parameters of healthy and damaged cells are different. Over the past decades, atomic force microscopy (AFM) and micromanipulation have become the most widely used methods for evaluating the mechanical characteristics of microorganisms. In this case, the reliability of such an estimate depends on the choice of mathematical model. This review presents various analytical models developed in recent years for studying the mechanical properties of both cells and their individual structures. The main provisions of the applied approaches are described along with their limitations and advantages. Attention is paid to the innovative method of low-invasive nanomechanical mapping with scanning ion-conductance microscopy (SICM), which is currently starting to be successfully used in the discovery of novel drugs acting on the yeast cell wall and plasma membrane.
Collapse
Affiliation(s)
- Nikita Savin
- Research Laboratory of Biophysics, National University of Science and Technology MISiS, Moscow 119049, Russia;
| | - Alexander Erofeev
- Research Laboratory of Biophysics, National University of Science and Technology MISiS, Moscow 119049, Russia;
| | | |
Collapse
|
9
|
Awada Z, Nedjar B. On a finite strain modeling of growth in budding yeast. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2023; 39:e3710. [PMID: 37070287 DOI: 10.1002/cnm.3710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/05/2023] [Accepted: 04/02/2023] [Indexed: 06/07/2023]
Abstract
Cell's ability to proliferate constitutes one of the most defining features of life. The proliferation occurs through a succession of events; the cell cycle, whereby the cell grows and divides. In this paper, focus is made on the growth step and we deal specifically with Saccharomyces cerevisiae yeast that reproduces by budding. For this, we develop a theoretical model to predict the growth powered by the turgor pressure. This cell is herein considered as a thin-walled structure with almost axisymmetrical shape. Due to its soft nature, the large deformation range is a priori assumed through a finite growth modeling framework. The used kinematics is based on the multiplicative decomposition of the deformation gradient into an elastically reversible part and a growth part. Constitutive equations are proposed where use is made of hyperelasticity together with a local evolution equation, this latter to describe the way growth takes place. In particular, two essential parameters are involved: a stress-like threshold, and a characteristic time. The developed model is extended to a shell approach as well. In a finite element context, representative numerical simulations examining stress-dependent growth are given and a parametric study is conducted to show the sensitivity with respect to the above mentioned parameters. Finally, a suggestion for natural contractile ring modeling closes this study.
Collapse
Affiliation(s)
- Zeinab Awada
- MAST (MAterial and STructures), EMGCU (Expérimenation en Modélisation pour le Génic Civil et Urdain), Université Gustave Eiffel, Marne-la-Vallée cedex 2, France
| | - Boumediene Nedjar
- MAST (MAterial and STructures), EMGCU (Expérimenation en Modélisation pour le Génic Civil et Urdain), Université Gustave Eiffel, Marne-la-Vallée cedex 2, France
| |
Collapse
|
10
|
Nittala PVK, Hohreiter A, Rosas Linhard E, Dohn R, Mishra S, Konda A, Divan R, Guha S, Basu A. Integration of silicon chip microstructures for in-line microbial cell lysis in soft microfluidics. LAB ON A CHIP 2023; 23:2327-2340. [PMID: 37083052 PMCID: PMC10259373 DOI: 10.1039/d2lc00896c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The paper presents fabrication methodologies that integrate silicon components into soft microfluidic devices to perform microbial cell lysis for biological applications. The integration methodology consists of a silicon chip that is fabricated with microstructure arrays and embedded in a microfluidic device, which is driven by piezoelectric actuation to perform cell lysis by physically breaking microbial cell walls via micromechanical impaction. We present different silicon microarray geometries, their fabrication techniques, integration of said micropatterned silicon impactor chips into microfluidic devices, and device operation and testing on synthetic microbeads and two yeast species (S. cerevisiae and C. albicans) to evaluate their efficacy. The generalized strategy developed for integration of the micropatterned silicon impactor chip into soft microfluidic devices can serve as an important process step for a new class of hybrid silicon-polymeric devices for future cellular processing applications. The proposed integration methodology can be scalable and integrated as an in-line cell lysis tool with existing microfluidics assays.
Collapse
Affiliation(s)
- Pavani Vamsi Krishna Nittala
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
- Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Allison Hohreiter
- Department of Medicine/Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
- Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Emilio Rosas Linhard
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
- Department of Medicine/Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| | - Ryan Dohn
- Department of Medicine/Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| | - Suryakant Mishra
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
- Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Abhiteja Konda
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Ralu Divan
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Supratik Guha
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA
- Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Anindita Basu
- Department of Medicine/Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA.
| |
Collapse
|
11
|
Bao J, Chen Y, Xing Y, Feng C, Hu Q, Li X, Jiang H. Development of a nested PCR assay for specific detection of Metschnikowia bicuspidata infecting Eriocheir sinensis. Front Cell Infect Microbiol 2022; 12:930585. [PMID: 35937694 PMCID: PMC9352885 DOI: 10.3389/fcimb.2022.930585] [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: 04/28/2022] [Accepted: 06/30/2022] [Indexed: 11/15/2022] Open
Abstract
In recent years, the “milky disease” caused by Metschnikowia bicuspidata has seriously affected the Eriocheir sinensis culture industry. Discovering and blocking the transmission route has become the key to controlling this disease. The existing polymerase chain reaction (PCR) detection technology for M. bicuspidata uses the ribosomal DNA (rDNA) sequence, but low sensitivity and specificity lead to frequent false detections. We developed a highly specific and sensitive nested PCR method to detect M. bicuspidata, by targeting the hyphally regulated cell wall protein (HYR) gene. This nested HYR-PCR produced a single clear band, showed no cross-reaction with other pathogens, and was superior to rDNA-PCR in specificity and sensitivity. The sensitivity of nested HYR-PCR (6.10 × 101 copies/μL) was greater than those of the large subunit ribosomal RNA gene (LSU rRNA; 6.03 × 104 copies/μL) and internal transcribed spacer (ITS; 6.74 × 105 copies/μL) PCRs. The nested HYR-PCR also showed a higher positivity rate (71.1%) than those obtained with LSU rRNA (16.7%) and ITS rDNA (24.4%). In conclusion, we developed a new nested HYR-PCR method for the specific and sensitive detection of M. bicuspidata infection. This will help to elucidate the transmission route of M. bicuspidata and to design effective management and control measures for M. bicuspidata disease.
Collapse
Affiliation(s)
- Jie Bao
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ye Chen
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuenan Xing
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chengcheng Feng
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qingbiao Hu
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaodong Li
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hongbo Jiang
- Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Hongbo Jiang,
| |
Collapse
|
12
|
Dissection and enhancement of prebiotic properties of yeast cell wall oligosaccharides through metabolic engineering. Biomaterials 2022; 282:121379. [DOI: 10.1016/j.biomaterials.2022.121379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/09/2021] [Accepted: 01/16/2022] [Indexed: 02/06/2023]
|
13
|
Lee M, Drenth J, Trajkovic M, de Jong RM, Fraaije MW. Introducing an Artificial Deazaflavin Cofactor in Escherichia coli and Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:938-952. [PMID: 35044755 PMCID: PMC8859854 DOI: 10.1021/acssynbio.1c00552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Deazaflavin-dependent
whole-cell conversions in well-studied and
industrially relevant microorganisms such as Escherichia coli and Saccharomyces cerevisiae have high potential
for the biocatalytic production of valuable compounds. The artificial
deazaflavin FOP (FO-5′-phosphate) can functionally substitute
the natural deazaflavin F420 and can be synthesized in
fewer steps, offering a solution to the limited availability of the
latter due to its complex (bio)synthesis. Herein we set out to produce
FOP in vivo as a scalable FOP production method and as a means for
FOP-mediated whole-cell conversions. Heterologous expression of the
riboflavin kinase from Schizosaccharomyces pombe enabled
in vivo phosphorylation of FO, which was supplied by either organic
synthesis ex vivo, or by a coexpressed FO synthase in vivo, producing
FOP in E. coli as well as in S. cerevisiae. Through combined approaches of enzyme engineering as well as optimization
of expression systems and growth media, we further improved the in
vivo FOP production in both organisms. The improved FOP production
yield in E. coli is comparable to the F420 yield of native F420-producing organisms such
as Mycobacterium smegmatis, but the former can be
achieved in a significantly shorter time frame. Our E. coli expression system has an estimated production rate of 0.078 μmol
L–1 h–1 and results in an intracellular
FOP concentration of about 40 μM, which is high enough to support
catalysis. In fact, we demonstrate the successful FOP-mediated whole-cell
conversion of ketoisophorone using E. coli cells.
In S. cerevisiae, in vivo FOP production by SpRFK using supplied FO was improved through media optimization
and enzyme engineering. Through structure-guided enzyme engineering,
a SpRFK variant with 7-fold increased catalytic efficiency
compared to the wild type was discovered. By using this variant in
optimized media conditions, FOP production yield in S. cerevisiae was 20-fold increased compared to the very low initial yield of
0.24 ± 0.04 nmol per g dry biomass. The results show that bacterial
and eukaryotic hosts can be engineered to produce the functional deazaflavin
cofactor mimic FOP.
Collapse
Affiliation(s)
- Misun Lee
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Jeroen Drenth
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Milos Trajkovic
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - René M. de Jong
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| |
Collapse
|
14
|
Satala D, Gonzalez-Gonzalez M, Smolarz M, Surowiec M, Kulig K, Wronowska E, Zawrotniak M, Kozik A, Rapala-Kozik M, Karkowska-Kuleta J. The Role of Candida albicans Virulence Factors in the Formation of Multispecies Biofilms With Bacterial Periodontal Pathogens. Front Cell Infect Microbiol 2022; 11:765942. [PMID: 35071033 PMCID: PMC8766842 DOI: 10.3389/fcimb.2021.765942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/06/2021] [Indexed: 12/23/2022] Open
Abstract
Periodontal disease depends on the presence of different microorganisms in the oral cavity that during the colonization of periodontal tissues form a multispecies biofilm community, thus allowing them to survive under adverse conditions or facilitate further colonization of host tissues. Not only numerous bacterial species participate in the development of biofilm complex structure but also fungi, especially Candida albicans, that often commensally inhabits the oral cavity. C. albicans employs an extensive armory of various virulence factors supporting its coexistence with bacteria resulting in successful host colonization and propagation of infection. In this article, we highlight various aspects of individual fungal virulence factors that may facilitate the collaboration with the associated bacterial representatives of the early colonizers of the oral cavity, the bridging species, and the late colonizers directly involved in the development of periodontitis, including the “red complex” species. In particular, we discuss the involvement of candidal cell surface proteins—typical fungal adhesins as well as originally cytosolic “moonlighting” proteins that perform a new function on the cell surface and are also present within the biofilm structures. Another group of virulence factors considered includes secreted aspartic proteases (Sap) and other secreted hydrolytic enzymes. The specific structure of the candidal cell wall, dynamically changing during morphological transitions of the fungus that favor the biofilm formation, is equally important and discussed. The non-protein biofilm-composing factors also show dynamic variability upon the contact with bacteria, and their biosynthesis processes could be involved in the stability of mixed biofilms. Biofilm-associated changes in the microbe communication system using different quorum sensing molecules of both fungal and bacterial cells are also emphasized in this review. All discussed virulence factors involved in the formation of mixed biofilm pose new challenges and influence the successful design of new diagnostic methods and the application of appropriate therapies in periodontal diseases.
Collapse
Affiliation(s)
- Dorota Satala
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Miriam Gonzalez-Gonzalez
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland.,Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University in Krakow, Krakow, Poland
| | - Magdalena Smolarz
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Magdalena Surowiec
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Kamila Kulig
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Ewelina Wronowska
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Marcin Zawrotniak
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Andrzej Kozik
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Maria Rapala-Kozik
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| | - Justyna Karkowska-Kuleta
- Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Krakow, Poland
| |
Collapse
|
15
|
Dohn R, Xie B, Back R, Selewa A, Eckart H, Rao RP, Basu A. mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans. Vaccines (Basel) 2021; 10:vaccines10010030. [PMID: 35062691 PMCID: PMC8779198 DOI: 10.3390/vaccines10010030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Advances in high-throughput single-cell RNA sequencing (scRNA-seq) have been limited by technical challenges such as tough cell walls and low RNA quantity that prevent transcriptomic profiling of microbial species at throughput. We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is demonstrated on two yeast species, Saccharomyces cerevisiae, a popular model organism, and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA levels between them. As a proof of concept, we quantified expression differences in heat shock S. cerevisiae using mDrop-seq. We detected differential activation of stress response genes within a seemingly homogenous population of S. cerevisiae under heat shock. We also applied mDrop-seq to C. albicans cells, a polymorphic and clinically relevant species of yeast with a thicker cell wall compared to S. cerevisiae. Single-cell transcriptomes in 39,705 C. albicans cells were characterized using mDrop-seq under different conditions, including exposure to fluconazole, a common anti-fungal drug. We noted differential regulation in stress response and drug target pathways between C. albicans cells, changes in cell cycle patterns and marked increases in histone activity when treated with fluconazole. We demonstrate mDrop-seq to be an affordable and scalable technique that can quantify the variability in gene expression in different yeast species. We hope that mDrop-seq will lead to a better understanding of genetic variation in pathogens in response to stimuli and find immediate applications in investigating drug resistance, infection outcome and developing new drugs and treatment strategies.
Collapse
Affiliation(s)
- Ryan Dohn
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (B.X.); (R.B.); (A.S.); (H.E.); (A.B.)
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
- Correspondence:
| | - Bingqing Xie
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (B.X.); (R.B.); (A.S.); (H.E.); (A.B.)
| | - Rebecca Back
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (B.X.); (R.B.); (A.S.); (H.E.); (A.B.)
| | - Alan Selewa
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (B.X.); (R.B.); (A.S.); (H.E.); (A.B.)
- Biophysical Sciences Graduate Program, University of Chicago, Chicago, IL 60637, USA
| | - Heather Eckart
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (B.X.); (R.B.); (A.S.); (H.E.); (A.B.)
| | - Reeta Prusty Rao
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
| | - Anindita Basu
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; (B.X.); (R.B.); (A.S.); (H.E.); (A.B.)
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
- Biophysical Sciences Graduate Program, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
16
|
Butelmann T, Priks H, Parent Z, Johnston TG, Tamm T, Nelson A, Lahtvee PJ, Kumar R. Metabolism Control in 3D-Printed Living Materials Improves Fermentation. ACS APPLIED BIO MATERIALS 2021; 4:7195-7203. [PMID: 35006951 DOI: 10.1021/acsabm.1c00754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The three-dimensional (3D) printing of cell-containing polymeric hydrogels creates living materials (LMs), offering a platform for developing innovative technologies in areas like biosensors and biomanufacturing. The polymer material properties of cross-linkable F127-bis-urethane methacrylate (F127-BUM) allow reproducible 3D printing and stability in physiological conditions, making it suitable for fabricating LMs. Though F127-BUM-based LMs permit diffusion of solute molecules like glucose and ethanol, it remains unknown whether these are permissible for oxygen, essential for respiration. To determine oxygen permissibility, we quantified dissolved oxygen consumption by the budding yeast-laden F127-BUM-based LMs. Moreover, we obtained data on cell-retaining LMs, which allowed a direct comparison between LMs and suspension cultures. We further developed a highly reliable method to isolate cells from LMs for flow cytometry analysis, cell viability evaluation, and the purification of macromolecules. We found oxygen consumption heavily impaired inside LMs, indicating that yeast metabolism relies primarily on fermentation instead of respiration. Applying this finding to brewing, we observed a higher (3.7%) ethanol production using LMs than the traditional brewing process, indicating improved fermentation. Our study concludes that the present F127-BUM-based LMs are useful for microaerobic processes but developing aerobic bioprocesses will require further research.
Collapse
Affiliation(s)
- Tobias Butelmann
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia.,Institute for Macromolecular Chemistry, University of Freiburg, 79104 Freiburg, Germany
| | - Hans Priks
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Zoel Parent
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Trevor G Johnston
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Tarmo Tamm
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Alshakim Nelson
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Petri-Jaan Lahtvee
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rahul Kumar
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia.,Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| |
Collapse
|
17
|
Evaluating β-1,3-glucan synthesis inhibition using emulsion formation as an indicator. J Microbiol Methods 2021; 190:106327. [PMID: 34517039 DOI: 10.1016/j.mimet.2021.106327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 11/20/2022]
Abstract
INTRODUCTION The cell wall β-1,3-glucan of fungal pathogen Candida albicans is an attractive antifungal target. β-1,3-Glucan is the skeletal structure in the cell wall and the major scaffold for cell wall proteins. In previous studies using Saccharomyces cerevisiae, strong emulsification was detected by mixing cell wall proteins with oil. To date, there have been no reports of applying an emulsification phenomenon to assessing β-1,3-glucan synthesis inhibition. OBJECTIVE The aim of this study was to clarify that emulsification is useful as an indicator for evaluating β-1,3-glucan synthesis inhibition in C. albicans. METHODS At first, whether cell wall proteins released from cells by β-1,3-glucanase treatment worked as an effective emulsifier in C. albicans was examined. Next, whether emulsification occurred even in the culture supernatant brought about by treating with bioactive compounds, including β-1,3-glucan synthesis inhibitors, under osmotic protection was investigated. In addition, the release of cell wall proteins into the culture medium by treating with those compounds was examined. Finally, a simpler evaluation method using emulsion formation was examined for application to screening of inhibitors. RESULTS Emulsification occurred by cell wall proteins obtained by treating with β-1,3-glucanase in C. albicans. In addition, cell wall proteins were released into the culture medium by treating with β-1,3-glucan synthesis inhibitors, resulting in emulsification. However, such phenomena were not observed in the case of other bioactive compounds. Furthermore, emulsification could be detected in the culture broth obtained by static culture on a small scale. CONCLUSIONS The obtained results strongly implied that emulsification results from decreased β-1,3-glucan levels in the cell wall. As emulsification can be simply evaluated by mixing the culture broth with oil, in the future application to the initial assessment and screening of β-1,3-glucan synthesis inhibitors is expected.
Collapse
|
18
|
Banavar SP, Trogdon M, Drawert B, Yi TM, Petzold LR, Campàs O. Coordinating cell polarization and morphogenesis through mechanical feedback. PLoS Comput Biol 2021; 17:e1007971. [PMID: 33507956 PMCID: PMC7872284 DOI: 10.1371/journal.pcbi.1007971] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 02/09/2021] [Accepted: 12/21/2020] [Indexed: 12/30/2022] Open
Abstract
Many cellular processes require cell polarization to be maintained as the cell changes shape, grows or moves. Without feedback mechanisms relaying information about cell shape to the polarity molecular machinery, the coordination between cell polarization and morphogenesis, movement or growth would not be possible. Here we theoretically and computationally study the role of a genetically-encoded mechanical feedback (in the Cell Wall Integrity pathway) as a potential coordination mechanism between cell morphogenesis and polarity during budding yeast mating projection growth. We developed a coarse-grained continuum description of the coupled dynamics of cell polarization and morphogenesis as well as 3D stochastic simulations of the molecular polarization machinery in the evolving cell shape. Both theoretical approaches show that in the absence of mechanical feedback (or in the presence of weak feedback), cell polarity cannot be maintained at the projection tip during growth, with the polarization cap wandering off the projection tip, arresting morphogenesis. In contrast, for mechanical feedback strengths above a threshold, cells can robustly maintain cell polarization at the tip and simultaneously sustain mating projection growth. These results indicate that the mechanical feedback encoded in the Cell Wall Integrity pathway can provide important positional information to the molecular machinery in the cell, thereby enabling the coordination of cell polarization and morphogenesis.
Collapse
Affiliation(s)
- Samhita P. Banavar
- Department of Physics, University of California, University of California, Santa Barbara, California, United States of America
- California NanoSystems Institute, University of California, Santa Barbara, California, United States of America
| | - Michael Trogdon
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
| | - Brian Drawert
- Department of Computer Science, University of North Carolina, Asheville, North Carolina, United States of America
| | - Tau-Mu Yi
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, California, United States of America
| | - Linda R. Petzold
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
- Center for Bioengineering, University of California, Santa Barbara, California, United States of America
| | - Otger Campàs
- California NanoSystems Institute, University of California, Santa Barbara, California, United States of America
- Department of Mechanical Engineering, University of California, Santa Barbara, California, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, California, United States of America
- Center for Bioengineering, University of California, Santa Barbara, California, United States of America
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| |
Collapse
|
19
|
Lenardon MD, Sood P, Dorfmueller HC, Brown AJ, Gow NA. Scalar nanostructure of the Candida albicans cell wall; a molecular, cellular and ultrastructural analysis and interpretation. Cell Surf 2020; 6:100047. [PMID: 33294751 PMCID: PMC7691183 DOI: 10.1016/j.tcsw.2020.100047] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/16/2022] Open
Abstract
Despite the importance of fungal cell walls as the principle determinant of fungal morphology and the defining element determining fungal interactions with other cells, few scalar models have been developed that reconcile chemical and microscopic attributes of its structure. The cell wall of the fungal pathogen Candida albicans is comprised of an amorphous inner skeletal layer of β(1,3)- and β(1,6)-glucan and chitin and an outer fibrillar layer thought to be dominated by highly mannosylated cell wall proteins. The architecture of these two layers can be resolved at the electron microscopy level, but the visualised structure of the wall has not yet been defined precisely in chemical terms. We have therefore examined the precise structure, location and molecular sizes of the cell wall components using transmission electron microscopy and tomography and tested predictions of the cell wall models using mutants and agents that perturb the normal cell wall structure. We demonstrate that the fibrils are comprised of a frond of N-linked outer chain mannans linked to a basal layer of GPI-proteins concentrated in the mid-wall region and that the non-elastic chitin microfibrils are cantilevered with sufficient lengths of non-fibrillar chitin and/or β-glucan to enable the chitin-glucan cage to flex, e.g. during morphogenesis and osmotic swelling. We present the first three-dimensional nano-scalar model of the C. albicans cell wall which can be used to test hypotheses relating to the structure-function relationships that underpin the pathobiology of this fungal pathogen.
Collapse
Key Words
- 2D, two dimensions
- 2°, secondary
- 3D, three dimensions
- 3°, tertiary
- 6xHis, hexahistidine tag
- AFM, atomic force microscopy
- BSA, bovine serum albumin
- CWPs, cell wall proteins
- Cell wall proteins
- ChBD, chitin binding domain
- Chitin
- EndoH, endoglycosidase H
- Fc-dectin-1, soluble chimeric form of dectin-1
- Fungal cell wall ultrastructure
- GPI, glycosylphosphatidylinositol
- HPF/FS, high pressure freezing/freeze substitution
- HuCκ, human kappa light chain
- N-mannan
- NMR, nuclear magnetic resonance
- OD600, optical density at 600 nm
- PAMPs, pathogen associated molecular patterns
- PBS, phosphate buffered saline
- PRRs, pattern recognition receptors
- SEM, scanning electron microscopy
- TEM, transmission electron microscopy
- WGA, wheat germ agglutinin
- rpm, revolutions per minute
- scAb, single chain antibody
- β-glucan
Collapse
Affiliation(s)
- Megan D. Lenardon
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Prashant Sood
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Helge C. Dorfmueller
- Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Alistair J.P. Brown
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Neil A.R. Gow
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| |
Collapse
|
20
|
Tsai K, Britton S, Nematbakhsh A, Zandi R, Chen W, Alber M. Role of combined cell membrane and wall mechanical properties regulated by polarity signals in cell budding. Phys Biol 2020; 17:065011. [PMID: 33085651 DOI: 10.1088/1478-3975/abb208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Budding yeast, Saccharomyces cerevisiae, serves as a prime biological model to study mechanisms underlying asymmetric growth. Previous studies have shown that prior to bud emergence, polarization of a conserved small GTPase Cdc42 must be established on the cell membrane of a budding yeast. Additionally, such polarization contributes to the delivery of cell wall remodeling enzymes and hydrolase from cytosol through the membrane, to change the mechanical properties of the cell wall. This leads to the hypothesis that Cdc42 and its associated proteins at least indirectly regulate cell surface mechanical properties. However, how the surface mechanical properties in the emerging bud are changed and whether such change is important are not well understood. To test several hypothesised mechanisms, a novel three-dimensional coarse-grained particle-based model has been developed which describes inhomogeneous mechanical properties of the cell surface. Model simulations predict alternation of the levels of stretching and bending stiffness of the cell surface in the bud region by the polarized Cdc42 signals is essential for initiating bud formation. Model simulations also suggest that bud shape depends strongly on the distribution of the polarized signaling molecules while the neck width of the emerging bud is strongly impacted by the mechanical properties of the chitin and septin rings. Moreover, the temporal change of the bud mechanical properties is shown to affect the symmetry of the bud shape. The 3D model of asymmetric cell growth can also be used for studying viral budding and other vegetative reproduction processes performed via budding, as well as detailed studies of cell growth.
Collapse
Affiliation(s)
- Kevin Tsai
- Department of Mathematics, University of California, Riverside, CA, United States of America. Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, United States of America
| | | | | | | | | | | |
Collapse
|
21
|
Suthers PF, Dinh HV, Fatma Z, Shen Y, Chan SHJ, Rabinowitz JD, Zhao H, Maranas CD. Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. Metab Eng Commun 2020; 11:e00148. [PMID: 33134082 PMCID: PMC7586132 DOI: 10.1016/j.mec.2020.e00148] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/08/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022] Open
Abstract
Many platform chemicals can be produced from renewable biomass by microorganisms, with organic acids making up a large fraction. Intolerance to the resulting low pH growth conditions, however, remains a challenge for the industrial production of organic acids by microorganisms. Issatchenkia orientalis SD108 is a promising host for industrial production because it is tolerant to acidic conditions as low as pH 2.0. With the goal to systematically assess the metabolic capabilities of this non-model yeast, we developed a genome-scale metabolic model for I. orientalis SD108 spanning 850 genes, 1826 reactions, and 1702 metabolites. In order to improve the model’s quantitative predictions, organism-specific macromolecular composition and ATP maintenance requirements were determined experimentally and implemented. We examined its network topology, including essential genes and flux coupling analysis and drew comparisons with the Yeast 8.3 model for Saccharomyces cerevisiae. We explored the carbon substrate utilization and examined the organism’s production potential for the industrially-relevant succinic acid, making use of the OptKnock framework to identify gene knockouts which couple production of the targeted chemical to biomass production. The genome-scale metabolic model iIsor850 is a data-supported curated model which can inform genetic interventions for overproduction. Genome-scale metabolic model iIsor850 describes metabolism of I. orientalis SD108. Customized biomass reaction highlights differences with S. cerevisiae. Chemostat data elucidate growth-associated ATP maintenance. Substrate utilization and CRISPR/Cas9 gene knockout phenotypes validate model. Model pinpoints candidate gene deletions coupling succinic acid production to growth.
Collapse
Affiliation(s)
- Patrick F Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hoang V Dinh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yihui Shen
- Department of Chemistry, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Siu Hung Joshua Chan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champagne, Urbana, IL, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
22
|
Hunsaker EW, McAuliffe KJ, Franz KJ. Fluconazole analogues with metal-binding motifs impact metal-dependent processes and demonstrate antifungal activity in Candida albicans. J Biol Inorg Chem 2020; 25:729-745. [PMID: 32542530 PMCID: PMC7415656 DOI: 10.1007/s00775-020-01796-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/25/2020] [Indexed: 12/28/2022]
Abstract
Azole antifungals are an important class of antifungal drugs due to their low cost, ability to be administered orally, and broad-spectrum activity. However, their widespread and long-term use have given rise to adaptation mechanisms that render these compounds less effective against common fungal pathogens, including Candida albicans. New antifungals are desperately needed as drug-resistant strains become more prevalent. We recently showed that copper supplementation potentiates the activity of the azole antifungal fluconazole against the opportunistic fungal pathogen C. albicans. Here, we report eight new azole analogues derived from fluconazole in which one triazole group has been replaced with a metal-binding group, a strategy designed to enhance potentiation of azole antifungal activity by copper. The bioactivity of all eight compounds was tested and compared to that of fluconazole. Three of the analogues showed activity against C. albicans and two had lower levels of trailing growth. One compound, Flu-TSCZ, was found to impact the levels, speciation, and bioavailability of cellular metals.
Collapse
Affiliation(s)
- Elizabeth W Hunsaker
- Department of Chemistry, French Family Science Center, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Katherine J McAuliffe
- Department of Chemistry, French Family Science Center, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Katherine J Franz
- Department of Chemistry, French Family Science Center, Duke University, 124 Science Drive, Durham, NC, 27708, USA.
| |
Collapse
|
23
|
Lawrence CL, Okoh AO, Vishwapathi V, McKenna ST, Critchley ME, Smith RB. N-alkylated linear heptamethine polyenes as potent non-azole leads against Candida albicans fungal infections. Bioorg Chem 2020; 102:104070. [PMID: 32682157 DOI: 10.1016/j.bioorg.2020.104070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023]
Abstract
In this study, eighteen heptamethine dyes were synthesised and their antifungal activities were evaluated against three clinically relevant yeast species.. The eighteen dyes were placed within classes based on their core subunit i.e. 2,3,3-trimethylindolenine (5a-f), 1,1,2-trimethyl-1H-benzo[e]indole (6a-f), or 2-methylbenzothiazole (7a-f). The results presented herein imply that the three families of cyanine dyes, in particular compounds 5a-f, show high potential as selective scaffolds to treat C. albicans infections. This opens up the opportunity for further optimisation and investigation of this class compounds for potential antifungal treatment.
Collapse
Affiliation(s)
- Clare L Lawrence
- UCLan Research Centre for Drug Design and Development, School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK.
| | - Adeyi Okoh Okoh
- UCLan Research Centre for Smart Materials, University of Central Lancashire, Preston PR1 2HE, UK
| | - Vinod Vishwapathi
- UCLan Research Centre for Smart Materials, University of Central Lancashire, Preston PR1 2HE, UK
| | - Sean T McKenna
- UCLan Research Centre for Smart Materials, University of Central Lancashire, Preston PR1 2HE, UK
| | - Megan E Critchley
- UCLan Research Centre for Smart Materials, University of Central Lancashire, Preston PR1 2HE, UK
| | - Robert B Smith
- UCLan Research Centre for Smart Materials, University of Central Lancashire, Preston PR1 2HE, UK.
| |
Collapse
|
24
|
Hunsaker EW, Franz KJ. Candida albicans reprioritizes metal handling during fluconazole stress. Metallomics 2020; 11:2020-2032. [PMID: 31709426 DOI: 10.1039/c9mt00228f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Maintenance of metal homeostasis is critical to cell survival due to the multitude of cellular processes that depend on one or more metal cofactors. Here, we show that the opportunistic fungal pathogen Candida albicans extensively remodels its metal homeostasis networks to respond to treatment with the antifungal drug fluconazole. Disruption of the ergosterol biosynthetic pathway by fluconazole requires C. albicans adaptation, including increased Cu import and storage, increased retention of Fe, Mn, and Zn, altered utilization of Cu- and Mn-dependent enzymes, mobilization of Fe stores, and increased production of the heme prosthetic group utilized by the enzyme target of fluconazole. The findings offer a new perspective for thinking about fungal response to drug stress that pushes cells out of their metal homeostatic zones, leading them to enact metal-associated adaptation mechanisms to restore homeostasis to survive.
Collapse
Affiliation(s)
- Elizabeth W Hunsaker
- Department of Chemistry, Duke University, French Family Science Center, 124 Science Drive, Durham, North Carolina 27708, USA.
| | | |
Collapse
|
25
|
Sheppard S, Dikicioglu D. Dynamic modelling of the killing mechanism of action by virus-infected yeasts. J R Soc Interface 2020; 16:20190064. [PMID: 30890050 DOI: 10.1098/rsif.2019.0064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Killer yeasts are microorganisms, which can produce and secrete proteinaceous toxins, a characteristic gained via infection by a virus. These toxins are able to kill sensitive cells of the same or a related species. From a biotechnological perspective, killer yeasts are beneficial due to their antifungal/antimicrobial activity, but also regarded as problematic for large-scale fermentation processes, whereby those yeasts would kill starter cultures species and lead to stuck fermentations. Here, we propose a mechanistic model of the toxin-binding kinetics pertaining to the killer population coupled with the toxin-induced death kinetics of the sensitive population to study toxic action. The dynamic model captured the transient toxic activity starting from the introduction of killer cells into the culture at the time of inoculation through to induced cell death. The kinetics of K1/K2 activity via its primary pathway of toxicity was 5.5 times faster than its activity at low concentration inducing the apoptotic pathway in sensitive cells. Conversely, we showed that the primary pathway for K28 was approximately three times slower than its equivalent apoptotic pathway, indicating the particular relevance of K28 in biotechnological applications where the toxin concentration is rarely above those limits to trigger the primary pathway of killer activity.
Collapse
Affiliation(s)
- Sean Sheppard
- 1 St John's College , St John's Street, Cambridge , UK
| | - Duygu Dikicioglu
- 2 Department of Chemical Engineering and Biotechnology, University of Cambridge , Cambridge , UK
| |
Collapse
|
26
|
de Sá NP, Pôssa AP, Perez P, Ferreira JMS, Fonseca NC, Lino CI, Cruz LB, de Oliveira RB, Rosa CA, Borelli BM, Mylonakis E, Fuchs BB, Johann S. Antifungal Activity Directed Toward the Cell Wall by 2-Cyclohexylidenhydrazo- 4-Phenyl-Thiazole Against Candida albicans. Infect Disord Drug Targets 2020; 19:428-438. [PMID: 29852876 DOI: 10.2174/1871526518666180531101605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/10/2018] [Accepted: 05/28/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND The increasing incidence of invasive forms of candidiasis and resistance to antifungal therapy leads us to seek new and more effective antifungal compounds. OBJECTIVE To investigate the antifungal activity and toxicity as well as to evaluate the potential targets of 2- cyclohexylidenhydrazo-4-phenyl-thiazole (CPT) in Candida albicans. METHODS The antifungal activity of CPT against the survival of C. albicans was investigated in Caenorhabditis elegans. Additionally, we determined the effect of CPT on the inhibition of C. albicans adhesion capacity to buccal epithelial cells (BECs), the toxicity of CPT in mammalian cells, and the potential targets of CPT in C. albicans. RESULTS CPT exhibited a minimum inhibitory concentration (MIC) value of 0.4-1.9 µg/mL. Furthermore, CPT at high concentrations (>60 x MIC) showed no or low toxicity in HepG2 cells and <1% haemolysis in human erythrocytes. In addition, CPT decreased the adhesion capacity of yeasts to the BECs and prolonged the survival of C. elegans infected with C. albicans. Analysis of CPT-treated cells showed that their cell wall was thinner than that of untreated cells, especially the glucan layer. We found that there was a significantly lower quantity of 1,3-β-D-glucan present in CPT-treated cells than that in untreated cells. Assays performed on several mutant strains showed that the MIC value of CPT was high for its antifungal activity on yeasts with defective 1,3-β-glucan synthase. CONCLUSION In conclusion, CPT appears to target the cell wall of C. albicans, exhibits low toxicity in mammalian cells, and prolongs the survival of C. elegans infected with C. albicans.
Collapse
Affiliation(s)
- Nívea P de Sá
- Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Antonio Carlos, 6627, Pampulha - CEP 31270-901, Belo Horizonte - MG, Brazil
| | - Ana P Pôssa
- Laboratorio de Microbiologia, Campus Centro- Oeste Dona Lindu, Universidade Federal de Sao Joao del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Pilar Perez
- Instituto de Biologia Fundamental y Genomica CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Jaqueline M S Ferreira
- Laboratorio de Microbiologia, Campus Centro- Oeste Dona Lindu, Universidade Federal de Sao Joao del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Nayara C Fonseca
- Departamento de Produtos Farmaceuticos, Faculdade de Farmacia, Universidade Federal de Minas Gerais, Belo Horizonte - MG, Brazil
| | - Cleudiomar I Lino
- Departamento de Produtos Farmaceuticos, Faculdade de Farmacia, Universidade Federal de Minas Gerais, Belo Horizonte - MG, Brazil
| | - Lana B Cruz
- Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Antonio Carlos, 6627, Pampulha - CEP 31270-901, Belo Horizonte - MG, Brazil
| | - Renata B de Oliveira
- Departamento de Produtos Farmaceuticos, Faculdade de Farmacia, Universidade Federal de Minas Gerais, Belo Horizonte - MG, Brazil
| | - Carlos A Rosa
- Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Antonio Carlos, 6627, Pampulha - CEP 31270-901, Belo Horizonte - MG, Brazil
| | - Beatriz M Borelli
- Departamento de Microbiologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Antonio Carlos, 6627, Pampulha - CEP 31270-901, Belo Horizonte - MG, Brazil
| | - Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School, and Brown University, Providence, RI, United States
| | - Beth B Fuchs
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School, and Brown University, Providence, RI, United States
| | - Susana Johann
- Instituto de Biologia Fundamental y Genomica CSIC, Universidad de Salamanca, Salamanca, Spain
| |
Collapse
|
27
|
Moran KD, Lew DJ. How Diffusion Impacts Cortical Protein Distribution in Yeasts. Cells 2020; 9:cells9051113. [PMID: 32365827 PMCID: PMC7291136 DOI: 10.3390/cells9051113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
Proteins associated with the yeast plasma membrane often accumulate asymmetrically within the plane of the membrane. Asymmetric accumulation is thought to underlie diverse processes, including polarized growth, stress sensing, and aging. Here, we review our evolving understanding of how cells achieve asymmetric distributions of membrane proteins despite the anticipated dissipative effects of diffusion, and highlight recent findings suggesting that differential diffusion is exploited to create, rather than dissipate, asymmetry. We also highlight open questions about diffusion in yeast plasma membranes that remain unsolved.
Collapse
|
28
|
A Theoretical Framework for Evolutionary Cell Biology. J Mol Biol 2020; 432:1861-1879. [PMID: 32087200 DOI: 10.1016/j.jmb.2020.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/20/2020] [Accepted: 02/04/2020] [Indexed: 11/24/2022]
Abstract
One of the last uncharted territories in evolutionary biology concerns the link with cell biology. Because all phenotypes ultimately derive from events at the cellular level, this connection is essential to building a mechanism-based theory of evolution. Given the impressive developments in cell biological methodologies at the structural and functional levels, the potential for rapid progress is great. The primary challenge for theory development is the establishment of a quantitative framework that transcends species boundaries. Two approaches to the problem are presented here: establishing the long-term steady-state distribution of mean phenotypes under specific regimes of mutation, selection, and drift and evaluating the energetic costs of cellular structures and functions. Although not meant to be the final word, these theoretical platforms harbor potential for generating insight into a diversity of unsolved problems, ranging from genome structure to cellular architecture to aspects of motility in organisms across the Tree of Life.
Collapse
|
29
|
Absolute Quantification of the Central Carbon Metabolome in Eight Commonly Applied Prokaryotic and Eukaryotic Model Systems. Metabolites 2020; 10:metabo10020074. [PMID: 32093075 PMCID: PMC7073941 DOI: 10.3390/metabo10020074] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 02/07/2023] Open
Abstract
Absolute quantification of intracellular metabolite pools is a prerequisite for modeling and in-depth biological interpretation of metabolomics data. It is the final step of an elaborate metabolomics workflow, with challenges associated with all steps—from sampling to quantifying the physicochemically diverse metabolite pool. Chromatographic separation combined with mass spectrometric (MS) detection is the superior platform for high coverage, selective, and sensitive detection of metabolites. Herein, we apply our quantitative MS-metabolomics workflow to measure and present the central carbon metabolome of a panel of commonly applied biological model systems. The workflow includes three chromatographic methods combined with isotope dilution tandem mass spectrometry to allow for absolute quantification of 68 metabolites of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and the amino acid and (deoxy) nucleoside pools. The biological model systems; Bacillus subtilis, Saccharomyces cerevisiae, two microalgal species, and four human cell lines were all cultured in commonly applied culture media and sampled in exponential growth phase. Both literature and databases are scarce with comprehensive metabolite datasets, and existing entries range over several orders of magnitude. The workflow and metabolite panel presented herein can be employed to expand the list of reference metabolomes, as encouraged by the metabolomics community, in a continued effort to develop and refine high-quality quantitative metabolomics workflows.
Collapse
|
30
|
Cottier F, Hall RA. Face/Off: The Interchangeable Side of Candida Albicans. Front Cell Infect Microbiol 2020; 9:471. [PMID: 32047726 PMCID: PMC6997470 DOI: 10.3389/fcimb.2019.00471] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
Due to limited mobility, fungi, like most unicellular organisms, have evolved mechanisms to adapt to sudden chemical and/or physical variation in their environment. Candida albicans is recognized as a model organism to study eukaryotic responses to environmental changes, as this human commensal yeast but also opportunistic pathogen responds to numerous environmental cues through switching morphologies from yeast to hyphae growth. This mechanism is largely controlled by two major pathways: cAMP-PKA and MAPK, but each environmental signal is sensed by specific sensors. However, morphological switching is not the only response C. albicans exerts in response to environmental cues. Recently, fungal cell wall remodeling in response to host-derived environmental cues has been identified as a way for C. albicans to manipulate the innate immune system. The fungal cell wall is composed of a chitin skeleton linked to a network of β-glucan, which anchors proteins and mannans to the fungal cell surface. As localized on the cell surface, these molecules drive interactions with the environment and other cells, particularly with host immune cells. C. albicans is recognized by immune cells such as neutrophils and macrophages via pathogen recognition receptors (PRRs) that bind different components of the cell wall. While β-glucan and mannan are proinflammatory molecules, chitin can induce anti-inflammatory responses. Interestingly, C. albicans is able to regulate the exposure of these pathogen-associated molecular patterns (PAMPs) according to environmental cues resulting in a modulation of the host immune response. This review describes the mechanisms involved in C. albicans response to environmental changes and their effect on immune recognition.
Collapse
Affiliation(s)
- Fabien Cottier
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Rebecca A Hall
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom.,Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| |
Collapse
|
31
|
Seyedjavadi SS, Khani S, Eslamifar A, Ajdary S, Goudarzi M, Halabian R, Akbari R, Zare-Zardini H, Imani Fooladi AA, Amani J, Razzaghi-Abyaneh M. The Antifungal Peptide MCh-AMP1 Derived From Matricaria chamomilla Inhibits Candida albicans Growth via Inducing ROS Generation and Altering Fungal Cell Membrane Permeability. Front Microbiol 2020; 10:3150. [PMID: 32038583 PMCID: PMC6985553 DOI: 10.3389/fmicb.2019.03150] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 12/29/2019] [Indexed: 01/22/2023] Open
Abstract
The rise of antifungal drug resistance in Candida species responsible for life threatening candidiasis is considered as an increasing challenge for the public health. MCh-AMP1 has previously been reported as a natural peptide from Matricaria chamomilla L. flowers with broad-spectrum antifungal activity against human pathogenic molds and yeasts. In the current study, the mode of action of synthetic MCh-AMP1 was investigated against Candida albicans, the major etiologic agent of life-threatening nosocomial candidiasis at cellular and molecular levels. Candida albicans ATCC 10231 was cultured in presence of various concentrations of MCh-AMP1 (16-64 μg/mL) and its mode of action was investigated using plasma membrane permeabilization assays, reactive oxygen species (ROS) induction, potassium ion leakage and ultrastructural analyses by electron microscopy. MCh-AMP1 showed fungicidal activity against Candida albicans at the concentrations of 32 and 64 μg/mL. The peptide increased fungal cell membrane permeability as evidenced by elevating of PI uptake and induced potassium leakage from the yeast cells. ROS production was induced by the peptide inside the fungal cells to a maximum of 64.8% at the concentration of 64 μg/mL. Scanning electron microscopy observations showed cell deformation as shrinkage and folding of treated yeast cells. Transmission electron microscopy showed detachment of plasma membrane from the cell wall, cell depletion and massive destruction of intracellular organelles and cell membrane of the fungal cells. Our results demonstrated that MCh-AMP1 caused Candida albicans cell death via increasing cell membrane permeability and inducing ROS production. Therefore, MCh-AMP1 could be considered as a promising therapeutic agent to combat Candida albicans infections.
Collapse
Affiliation(s)
| | - Soghra Khani
- Department of Mycology, Pasteur Institute of Iran, Tehran, Iran
| | - Ali Eslamifar
- Department of Clinical Research, Pasteur Institute of Iran, Tehran, Iran
| | - Soheila Ajdary
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Raheleh Halabian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Akbari
- Department of Microbiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Hadi Zare-Zardini
- Hematology and Oncology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | |
Collapse
|
32
|
|
33
|
Dinh HV, Suthers PF, Chan SHJ, Shen Y, Xiao T, Deewan A, Jagtap SS, Zhao H, Rao CV, Rabinowitz JD, Maranas CD. A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. Metab Eng Commun 2019; 9:e00101. [PMID: 31720216 PMCID: PMC6838544 DOI: 10.1016/j.mec.2019.e00101] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/21/2022] Open
Abstract
Rhodosporidium toruloides is a red, basidiomycetes yeast that can accumulate a large amount of lipids and produce carotenoids. To better assess this non-model yeast's metabolic capabilities, we reconstructed a genome-scale model of R. toruloides IFO0880's metabolic network (iRhto1108) accounting for 2204 reactions, 1985 metabolites and 1108 genes. In this work, we integrated and supplemented the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organism's metabolic capabilities. Predictions of genotype-phenotype relations were improved through manual curation of gene-protein-reaction rules for 543 reactions leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specificity of 53.8%). Organism-specific macromolecular composition and ATP maintenance requirements were experimentally measured for two separate growth conditions: (i) carbon and (ii) nitrogen limitations. Overall, iRhto1108 reproduced R. toruloides's utilization capabilities for 18 alternate substrates, matched measured wild-type growth yield, and recapitulated the viability of 772 out of 819 deletion mutants. As a demonstration to the model's fidelity in guiding engineering interventions, the OptForce procedure was applied on iRhto1108 for triacylglycerol overproduction. Suggested interventions recapitulated many of the previous successful implementations of genetic modifications and put forth a few new ones.
Collapse
Affiliation(s)
- Hoang V. Dinh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, 306 Chemical and Biomedical Engineering Building, PA, 16802-4400, USA
| | - Patrick F. Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, 306 Chemical and Biomedical Engineering Building, PA, 16802-4400, USA
| | - Siu Hung Joshua Chan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, 306 Chemical and Biomedical Engineering Building, PA, 16802-4400, USA
| | - Yihui Shen
- Department of Chemistry, Princeton University, 285 Frick Laboratory, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Tianxia Xiao
- Department of Chemistry, Princeton University, 285 Frick Laboratory, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Anshu Deewan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champagne, 114 Roger Adams Laboratory MC 712, Urbana, IL, 61801, USA
| | - Sujit S. Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champagne, 114 Roger Adams Laboratory MC 712, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champagne, 114 Roger Adams Laboratory MC 712, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher V. Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champagne, 114 Roger Adams Laboratory MC 712, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, 285 Frick Laboratory, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, 306 Chemical and Biomedical Engineering Building, PA, 16802-4400, USA
| |
Collapse
|
34
|
Ortiz-Rivero E, Prorok K, Skowickł M, Lu D, Bednarkiewicz A, Jaque D, Haro-González P. Single-Cell Biodetection by Upconverting Microspinners. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1904154. [PMID: 31583832 DOI: 10.1002/smll.201904154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/13/2019] [Indexed: 06/10/2023]
Abstract
Near-infrared-light-mediated optical tweezing of individual upconverting particles has enabled all-optical single-cell studies, such as intracellular thermal sensing and minimally invasive cytoplasm investigations. Furthermore, the intrinsic optical birefringence of upconverting particles renders them light-driven luminescent spinners with a yet unexplored potential in biomedicine. In this work, the use of upconverting spinners is showcased for the accurate and specific detection of single-cell and single-bacteria attachment events, through real-time monitoring of the spinners rotation velocity of the spinner. The physical mechanisms linking single-attachment to the angular deceleration of upconverting spinners are discussed in detail. Concomitantly, the upconversion emission generated by the spinner is harnessed for simultaneous thermal sensing and thermal control during the attachment event. Results here included demonstrate the potential of upconverting particles for the development of fast, high-sensitivity, and cost-effective systems for single-cell biodetection.
Collapse
Affiliation(s)
- Elisa Ortiz-Rivero
- Fluorescence Imaging Group, Departamento de Física de Materiales, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Katarzyna Prorok
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, ul.Okolna 2, 50-422, Wroclaw, Poland
| | - Michal Skowickł
- Łukasiewicz Research Network - Port Polish Center for Technology Development, ul.Stablowicka 147, 54-066, Wrocław, Poland
| | - Dasheng Lu
- Fluorescence Imaging Group, Departamento de Física de Materiales, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Artur Bednarkiewicz
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, ul.Okolna 2, 50-422, Wroclaw, Poland
| | - Daniel Jaque
- Fluorescence Imaging Group, Departamento de Física de Materiales, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Nanobiology Group, Instituto Ramón y Cajal de Investigación, Sanitaria Hospital Ramón y Cajal, Ctra.De Colmenar Viejo, Km. 9100, 28034, Madrid, Spain
| | - Patricia Haro-González
- Fluorescence Imaging Group, Departamento de Física de Materiales, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| |
Collapse
|
35
|
ClTI, a Kunitz trypsin inhibitor purified from Cassia leiandra Benth. seeds, exerts a candidicidal effect on Candida albicans by inducing oxidative stress and necrosis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183032. [DOI: 10.1016/j.bbamem.2019.183032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/11/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023]
|
36
|
Cortés JCG, Curto MÁ, Carvalho VSD, Pérez P, Ribas JC. The fungal cell wall as a target for the development of new antifungal therapies. Biotechnol Adv 2019; 37:107352. [PMID: 30797093 DOI: 10.1016/j.biotechadv.2019.02.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/23/2019] [Accepted: 02/16/2019] [Indexed: 12/17/2022]
Abstract
In the past three decades invasive mycoses have globally emerged as a persistent source of healthcare-associated infections. The cell wall surrounding the fungal cell opposes the turgor pressure that otherwise could produce cell lysis. Thus, the cell wall is essential for maintaining fungal cell shape and integrity. Given that this structure is absent in host mammalian cells, it stands as an important target when developing selective compounds for the treatment of fungal infections. Consequently, treatment with echinocandins, a family of antifungal agents that specifically inhibits the biosynthesis of cell wall (1-3)β-D-glucan, has been established as an alternative and effective antifungal therapy. However, the existence of many pathogenic fungi resistant to single or multiple antifungal families, together with the limited arsenal of available antifungal compounds, critically affects the effectiveness of treatments against these life-threatening infections. Thus, new antifungal therapies are required. Here we review the fungal cell wall and its relevance in biotechnology as a target for the development of new antifungal compounds, disclosing the most promising cell wall inhibitors that are currently in experimental or clinical development for the treatment of some invasive mycoses.
Collapse
Affiliation(s)
- Juan Carlos G Cortés
- Instituto de Biología Funcional y Genómica and Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain.
| | - M-Ángeles Curto
- Instituto de Biología Funcional y Genómica and Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - Vanessa S D Carvalho
- Instituto de Biología Funcional y Genómica and Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - Pilar Pérez
- Instituto de Biología Funcional y Genómica and Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain
| | - Juan Carlos Ribas
- Instituto de Biología Funcional y Genómica and Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, Salamanca, Spain.
| |
Collapse
|
37
|
Abstract
In many yeast and fungi, β-(1,3)-glucan and chitin are essential components of the cell wall, an important structure that surrounds cells and which is responsible for their mechanical protection and necessary for maintaining the cellular shape. In addition, the cell wall is a dynamic structure that needs to be remodelled along with the different phases of the fungal life cycle or in response to extracellular stimuli. Since β-(1,3)-glucan and chitin perform a central structural role in the assembly of the cell wall, it has been postulated that β-(1,3)-glucanases and chitinases should perform an important function in cell wall softening and remodelling. This review focusses on fungal glucanases and chitinases and their role during fungal morphogenesis.
Collapse
Affiliation(s)
- César Roncero
- Instituto de Biología Funcional Y Genómica (IBFG), Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain
| | - Carlos R Vázquez de Aldana
- Instituto de Biología Funcional Y Genómica (IBFG), Consejo Superior de Investigaciones Científicas/Universidad de Salamanca, Salamanca, Spain.
| |
Collapse
|
38
|
Impact of Fungal MAPK Pathway Targets on the Cell Wall. J Fungi (Basel) 2018; 4:jof4030093. [PMID: 30096860 PMCID: PMC6162559 DOI: 10.3390/jof4030093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022] Open
Abstract
The fungal cell wall is an extracellular organelle that provides structure and protection to cells. The cell wall also influences the interactions of cells with each other and surfaces. The cell wall can be reorganized in response to changing environmental conditions and different types of stress. Signaling pathways control the remodeling of the cell wall through target proteins that are in many cases not well defined. The Mitogen Activated Protein Kinase pathway that controls filamentous growth in yeast (fMAPK) was required for normal growth in media containing the cell wall perturbing agent Calcofluor White (CFW). A mass spectrometry (MASS-SPEC) approach and analysis of expression profiling data identified cell wall proteins and modifying enzymes whose levels were influenced by the fMAPK pathway. These include Flo11p, Flo10p, Tip1p, Pry2p and the mannosyltransferase, Och1p. Cells lacking Flo11p or Och1p were sensitive to CFW. The identification of cell wall proteins controlled by a MAPK pathway may provide insights into how signaling pathways regulate the cell wall.
Collapse
|
39
|
Trunk K, Peltier J, Liu YC, Dill BD, Walker L, Gow NAR, Stark MJR, Quinn J, Strahl H, Trost M, Coulthurst SJ. The type VI secretion system deploys antifungal effectors against microbial competitors. Nat Microbiol 2018; 3:920-931. [PMID: 30038307 PMCID: PMC6071859 DOI: 10.1038/s41564-018-0191-x] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 06/07/2018] [Indexed: 12/28/2022]
Abstract
Interactions between bacterial and fungal cells shape many polymicrobial communities. Bacteria elaborate diverse strategies to interact and compete with other organisms, including the deployment of protein secretion systems. The type VI secretion system (T6SS) delivers toxic effector proteins into host eukaryotic cells and competitor bacterial cells, but, surprisingly, T6SS-delivered effectors targeting fungal cells have not been reported. Here we show that the 'antibacterial' T6SS of Serratia marcescens can act against fungal cells, including pathogenic Candida species, and identify the previously undescribed effector proteins responsible. These antifungal effectors, Tfe1 and Tfe2, have distinct impacts on the target cell, but both can ultimately cause fungal cell death. 'In competition' proteomics analysis revealed that T6SS-mediated delivery of Tfe2 disrupts nutrient uptake and amino acid metabolism in fungal cells, and leads to the induction of autophagy. Intoxication by Tfe1, in contrast, causes a loss of plasma membrane potential. Our findings extend the repertoire of the T6SS and suggest that antifungal T6SSs represent widespread and important determinants of the outcome of bacterial-fungal interactions.
Collapse
Affiliation(s)
- Katharina Trunk
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Julien Peltier
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Yi-Chia Liu
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Brian D Dill
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Louise Walker
- Aberdeen Fungal Group, Institute of Medical Sciences, MRC Centre for Medical Mycology at the University of Aberdeen, Aberdeen, UK
| | - Neil A R Gow
- Aberdeen Fungal Group, Institute of Medical Sciences, MRC Centre for Medical Mycology at the University of Aberdeen, Aberdeen, UK
| | - Michael J R Stark
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Janet Quinn
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Newcastle University, Newcastle-upon-Tyne, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK.
| | - Sarah J Coulthurst
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
| |
Collapse
|
40
|
Paramasivan K, Rajagopal K, Mutturi S. Studies on Squalene Biosynthesis and the Standardization of Its Extraction Methodology from Saccharomyces cerevisiae. Appl Biochem Biotechnol 2018; 187:691-707. [DOI: 10.1007/s12010-018-2845-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022]
|
41
|
Cell Size Influences the Reproductive Potential and Total Lifespan of the Saccharomyces cerevisiae Yeast as Revealed by the Analysis of Polyploid Strains. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1898421. [PMID: 29743970 PMCID: PMC5883977 DOI: 10.1155/2018/1898421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/04/2017] [Accepted: 01/01/2018] [Indexed: 11/17/2022]
Abstract
The total lifespan of the yeast Saccharomyces cerevisiae may be divided into two phases: the reproductive phase, during which the cell undergoes mitosis cycles to produce successive buds, and the postreproductive phase, which extends from the last division to cell death. These phases may be regulated by a common mechanism or by distinct ones. In this paper, we proposed a more comprehensive approach to reveal the mechanisms that regulate both reproductive potential and total lifespan in cell size context. Our study was based on yeast cells, whose size was determined by increased genome copy number, ranging from haploid to tetraploid. Such experiments enabled us to test the hypertrophy hypothesis, which postulates that excessive size achieved by the cell-the hypertrophy state-is the reason preventing the cell from further proliferation. This hypothesis defines the reproductive potential value as the difference between the maximal size that a cell can reach and the threshold value, which allows a cell to undergo its first cell cycle and the rate of the cell size to increase per generation. Here, we showed that cell size has an important impact on not only the reproductive potential but also the total lifespan of this cell. Moreover, the maximal cell size value, which limits its reproduction capacity, can be regulated by different factors and differs depending on the strain ploidy. The achievement of excessive size by the cell (hypertrophic state) may lead to two distinct phenomena: the cessation of reproduction without "mother" cell death and the cessation of reproduction with cell death by bursting, which has not been shown before.
Collapse
|
42
|
Shahina Z, El-Ganiny AM, Minion J, Whiteway M, Sultana T, Dahms TES. Cinnamomum zeylanicum bark essential oil induces cell wall remodelling and spindle defects in Candida albicans. Fungal Biol Biotechnol 2018; 5:3. [PMID: 29456868 PMCID: PMC5807769 DOI: 10.1186/s40694-018-0046-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/16/2018] [Indexed: 12/01/2022] Open
Abstract
Background Cinnamon (Cinnamomum zeylanicum) bark extract exhibits potent inhibitory activity against Candida albicans but the antifungal mechanisms of this essential oil remain largely unexplored. Results We analyzed the impact of cinnamon bark oil on C. albicans RSY150, and clinical strains isolated from patients with candidemia and candidiasis. The viability of RSY150 was significantly compromised in a dose dependent manner when exposed to cinnamon bark oil, with extensive cell surface remodelling at sub inhibitory levels (62.5 μg/mL). Atomic force microscopy revealed cell surface exfoliation, altered ultrastructure and reduced cell wall integrity for both RSY150 and clinical isolates exposed to cinnamon bark oil. Cell wall damage induced by cinnamon bark oil was confirmed by exposure to stressors and the sensitivity of cell wall mutants involved in cell wall organization, biogenesis, and morphogenesis. The essential oil triggered cell cycle arrest by disrupting beta tubulin distribution, which led to mitotic spindle defects, ultimately compromising the cell membrane and allowing leakage of cellular components. The multiple targets of cinnamon bark oil can be attributed to its components, including cinnamaldehyde (74%), and minor components (< 6%) such as linalool (3.9%), cinamyl acetate (3.8%), α-caryophyllene (5.3%) and limonene (2%). Complete inhibition of the mitotic spindle assembly was observed in C. albicans treated with cinnamaldehyde at MIC (112 μg/mL). Conclusions Since cinnamaldehyde disrupts both the cell wall and tubulin polymerization, it may serve as an effective antifungal, either by chemical modification to improve its specificity and efficacy or in combination with other antifungal drugs. Electronic supplementary material The online version of this article (10.1186/s40694-018-0046-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zinnat Shahina
- 1Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK Canada
| | - Amira M El-Ganiny
- 2Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | | | - Malcolm Whiteway
- 4Centre for Structural and Functional Genomics, Concordia University, Montreal, QC Canada
| | - Taranum Sultana
- 1Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK Canada
| | - Tanya E S Dahms
- 1Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK Canada.,3Regina Qu'Appelle Health Region, Regina, SK Canada
| |
Collapse
|
43
|
Mionić Ebersold M, Petrović M, Fong WK, Bonvin D, Hofmann H, Milošević I. Hexosomes with Undecylenic Acid Efficient against Candida albicans. NANOMATERIALS (BASEL, SWITZERLAND) 2018; 8:E91. [PMID: 29414873 PMCID: PMC5853723 DOI: 10.3390/nano8020091] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/28/2018] [Accepted: 02/01/2018] [Indexed: 11/22/2022]
Abstract
Due to the growing issues with fungal infections, especially with Candida, there is still a need to develop novel anti-Candida materials. One of the known antifungal agents is undecylenic acid (UA), which still cannot be efficiently used due to its oily nature, and thus limited solubility. By taking advantage of the properties of UA, we developed an emulsion with hexagonal phase, i.e., hexosomes, whose structure and morphology was studied by small-angle X-ray scattering and cryo-electron microscopy, respectively. The presence of UA in the hexosome was confirmed by spectroscopy. Moreover, we studied the anti-Candida effect of hexosomes and their cytotoxicity toward human cells. The minimal inhibitory concentration for the 50% and 90% Candida-growth reduction was found at 0.01 and 0.16 wt % hexosomes, respectively (i.e., 2 and 32 pghex/C.a.cell, respectively). The percentage of metabolically active Candida was reduced by 72-96% at hexosome concentrations of 1.0-8.2 pghex/C.a.cell as compared to untreated Candida. Furthermore, at the same concentration range the embedded filamentation test after 24 and 48 h showed the inhibition of both the filamentation and growth of Candida, while the preliminary toxicity test showed that hexosomes were nontoxic for human cells. All these render the here-developed hexosomes with UA efficient and promising anti-Candida agents.
Collapse
Affiliation(s)
- Marijana Mionić Ebersold
- Powder Technology Laboratory, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Milica Petrović
- Powder Technology Laboratory, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
- Faculty of Medicine, University of Niš, 18000 Niš, Serbia.
| | - Wye-Khay Fong
- Adolphe Merkle Institute, University of Fribourg, 1700 Fribourg, Switzerland.
| | - Debora Bonvin
- Powder Technology Laboratory, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Heinrich Hofmann
- Powder Technology Laboratory, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| | - Irena Milošević
- Powder Technology Laboratory, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
| |
Collapse
|
44
|
Iurciuc (Tincu) CE, Savin A, Atanase LI, Danu M, Martin P, Popa M. Encapsulation of Saccharomyces cerevisiae in hydrogel particles based gellan ionically cross-linked with zinc acetate. POWDER TECHNOL 2018. [DOI: 10.1016/j.powtec.2017.11.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
45
|
Banavar SP, Gomez C, Trogdon M, Petzold LR, Yi TM, Campàs O. Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis. PLoS Comput Biol 2018; 14:e1005940. [PMID: 29346368 PMCID: PMC5790295 DOI: 10.1371/journal.pcbi.1005940] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 01/30/2018] [Accepted: 12/22/2017] [Indexed: 11/18/2022] Open
Abstract
The shaping of individual cells requires a tight coordination of cell mechanics and growth. However, it is unclear how information about the mechanical state of the wall is relayed to the molecular processes building it, thereby enabling the coordination of cell wall expansion and assembly during morphogenesis. Combining theoretical and experimental approaches, we show that a mechanical feedback coordinating cell wall assembly and expansion is essential to sustain mating projection growth in budding yeast (Saccharomyces cerevisiae). Our theoretical results indicate that the mechanical feedback provided by the Cell Wall Integrity pathway, with cell wall stress sensors Wsc1 and Mid2 increasingly activating membrane-localized cell wall synthases Fks1/2 upon faster cell wall expansion, stabilizes mating projection growth without affecting cell shape. Experimental perturbation of the osmotic pressure and cell wall mechanics, as well as compromising the mechanical feedback through genetic deletion of the stress sensors, leads to cellular phenotypes that support the theoretical predictions. Our results indicate that while the existence of mechanical feedback is essential to stabilize mating projection growth, the shape and size of the cell are insensitive to the feedback.
Collapse
Affiliation(s)
- Samhita P. Banavar
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
- California NanoSystems Institute, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Carlos Gomez
- California NanoSystems Institute, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Michael Trogdon
- Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Linda R. Petzold
- Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Center for Bioengineering, University of California, Santa Barbara, Santa Barbara, United States of America
| | - Tau-Mu Yi
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Otger Campàs
- California NanoSystems Institute, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Center for Bioengineering, University of California, Santa Barbara, Santa Barbara, United States of America
| |
Collapse
|
46
|
Mena A, Medina DA, García-Martínez J, Begley V, Singh A, Chávez S, Muñoz-Centeno MC, Pérez-Ortín JE. Asymmetric cell division requires specific mechanisms for adjusting global transcription. Nucleic Acids Res 2017; 45:12401-12412. [PMID: 29069448 PMCID: PMC5716168 DOI: 10.1093/nar/gkx974] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/10/2017] [Indexed: 12/19/2022] Open
Abstract
Most cells divide symmetrically into two approximately identical cells. There are many examples, however, of asymmetric cell division that can generate sibling cell size differences. Whereas physical asymmetric division mechanisms and cell fate consequences have been investigated, the specific problem caused by asymmetric division at the transcription level has not yet been addressed. In symmetrically dividing cells the nascent transcription rate increases in parallel to cell volume to compensate it by keeping the actual mRNA synthesis rate constant. This cannot apply to the yeast Saccharomyces cerevisiae, where this mechanism would provoke a never-ending increasing mRNA synthesis rate in smaller daughter cells. We show here that, contrarily to other eukaryotes with symmetric division, budding yeast keeps the nascent transcription rates of its RNA polymerases constant and increases mRNA stability. This control on RNA pol II-dependent transcription rate is obtained by controlling the cellular concentration of this enzyme.
Collapse
Affiliation(s)
- Adriana Mena
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Universitat de València, Dr. Moliner, 50, Burjassot 46100, Valencia, Spain
| | - Daniel A Medina
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Universitat de València, Dr. Moliner, 50, Burjassot 46100, Valencia, Spain
| | - José García-Martínez
- Departamento de Genética and E.R.I. Biotecmed, Universitat de València, Dr. Moliner, 50, Burjassot 46100, Valencia, Spain
| | - Victoria Begley
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Sevilla, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Sevilla, Spain
| | - Mari C Muñoz-Centeno
- Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, 41013 Sevilla, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Universitat de València, Dr. Moliner, 50, Burjassot 46100, Valencia, Spain
| |
Collapse
|
47
|
Zhao G, Chen Y, Carey L, Futcher B. Cyclin-Dependent Kinase Co-Ordinates Carbohydrate Metabolism and Cell Cycle in S. cerevisiae. Mol Cell 2017; 62:546-57. [PMID: 27203179 DOI: 10.1016/j.molcel.2016.04.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 03/17/2016] [Accepted: 04/21/2016] [Indexed: 01/15/2023]
Abstract
Cyclin-dependent kinases (CDKs) control cell division in eukaryotes by phosphorylating proteins involved in division. But successful proliferation requires co-ordination between division and cellular growth in mass. Previous proteomic studies suggested that metabolic proteins, as well as cell division proteins, could potentially be substrates of cyclin-dependent kinases. Here we focus on two metabolic enzymes of the yeast S. cerevisiae, neutral trehalase (Nth1) and glycogen phosphorylase (Gph1), and show that their activities are likely directly controlled by CDK activity, thus allowing co-ordinate regulation of carbohydrate metabolism with cell division processes. In this case, co-ordinate regulation may optimize the decision to undertake a final cell division as nutrients are being exhausted. Co-regulation of cell division processes and metabolic processes by CDK activity may be a general phenomenon important for co-ordinating the cell cycle with growth.
Collapse
Affiliation(s)
- Gang Zhao
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yuping Chen
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Lucas Carey
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Futcher
- Department of Molecular Genetics & Microbiology, Stony Brook University, Stony Brook, NY 11794, USA.
| |
Collapse
|
48
|
Iurciuc (Tincu) CE, Savin A, Atanase LI, Martin P, Popa M. Physico-chemical characteristics and fermentative activity of the hydrogel particles based on polysaccharides mixture with yeast cells immobilized, obtained by ionotropic gelation. FOOD AND BIOPRODUCTS PROCESSING 2017. [DOI: 10.1016/j.fbp.2017.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
49
|
Escalera-Fanjul X, Campero-Basaldua C, Colón M, González J, Márquez D, González A. Evolutionary Diversification of Alanine Transaminases in Yeast: Catabolic Specialization and Biosynthetic Redundancy. Front Microbiol 2017; 8:1150. [PMID: 28694796 PMCID: PMC5483587 DOI: 10.3389/fmicb.2017.01150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Gene duplication is one of the major evolutionary mechanisms providing raw material for the generation of genes with new or modified functions. The yeast Saccharomyces cerevisiae originated after an allopolyploidization event, which involved mating between two different ancestral yeast species. ScALT1 and ScALT2 codify proteins with 65% identity, which were proposed to be paralogous alanine transaminases. Further analysis of their physiological role showed that while ScALT1 encodes an alanine transaminase which constitutes the main pathway for alanine biosynthesis and the sole pathway for alanine catabolism, ScAlt2 does not display alanine transaminase activity and is not involved in alanine metabolism. Moreover, phylogenetic studies have suggested that ScALT1 and ScALT2 come from each one of the two parental strains which gave rise to the ancestral hybrid. The present work has been aimed to the understanding of the properties of the ancestral type Lacchancea kluyveri LkALT1 and Kluyveromyces lactis KlALT1, alanine transaminases in order to better understand the ScALT1 and ScALT2 evolutionary history. These ancestral -type species were chosen since they harbor ALT1 genes, which are related to ScALT2. Presented results show that, although LkALT1 and KlALT1 constitute ScALT1 orthologous genes, encoding alanine transaminases, both yeasts display LkAlt1 and KlAlt1 independent alanine transaminase activity and additional unidentified alanine biosynthetic and catabolic pathway(s). Furthermore, phenotypic analysis of null mutants uncovered the fact that KlAlt1 and LkAlt1 have an additional role, not related to alanine metabolism but is necessary to achieve wild type growth rate. Our study shows that the ancestral alanine transaminase function has been retained by the ScALT1 encoded enzyme, which has specialized its catabolic character, while losing the alanine independent role observed in the ancestral type enzymes. The fact that ScAlt2 conserves 64% identity with LkAlt1 and 66% with KlAlt1, suggests that ScAlt2 diversified after the ancestral hybrid was formed. ScALT2 functional diversification resulted in loss of both alanine transaminase activity and the additional alanine-independent LkAlt1 function, since ScALT2 did not complement the Lkalt1Δ phenotype. It can be concluded that LkALT1 and KlLALT1 functional role as alanine transaminases was delegated to ScALT1, while ScALT2 lost this role during diversification.
Collapse
Affiliation(s)
| | | | | | | | | | - Alicia González
- Instituto de Fisiología Celular, Departamento de Bioquímica y Biología Estructural, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| |
Collapse
|
50
|
Zatorska E, Gal L, Schmitt J, Bausewein D, Schuldiner M, Strahl S. Cellular Consequences of Diminished Protein O-Mannosyltransferase Activity in Baker's Yeast. Int J Mol Sci 2017; 18:ijms18061226. [PMID: 28598353 PMCID: PMC5486049 DOI: 10.3390/ijms18061226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 01/08/2023] Open
Abstract
O-Mannosylation is a type of protein glycosylation initiated in the endoplasmic reticulum (ER) by the protein O-mannosyltransferase (PMT) family. Despite the vital role of O-mannosylation, its molecular functions and regulation are not fully characterized. To further explore the cellular impact of protein O-mannosylation, we performed a genome-wide screen to identify Saccharomyces cerevisiae mutants with increased sensitivity towards the PMT-specific inhibitor compound R3A-5a. We identified the cell wall and the ER as the cell compartments affected most upon PMT inhibition. Especially mutants with defects in N-glycosylation, biosynthesis of glycosylphosphatidylinositol-anchored proteins and cell wall β-1,6-glucan showed impaired growth when O-mannosylation became limiting. Signaling pathways that counteract cell wall defects and unbalanced ER homeostasis, namely the cell wall integrity pathway and the unfolded protein response, were highly crucial for the cell growth. Moreover, among the most affected mutants, we identified Ost3, one of two homologous subunits of the oligosaccharyltransferase complexes involved in N-glycosylation, suggesting a functional link between the two pathways. Indeed, we identified Pmt2 as a substrate for Ost3 suggesting that the reduced function of Pmt2 in the absence of N-glycosylation promoted sensitivity to the drug. Interestingly, even though S. cerevisiae Pmt1 and Pmt2 proteins are highly similar on the sequence, as well as the structural level and act as a complex, we identified only Pmt2, but not Pmt1, as an Ost3-specific substrate protein.
Collapse
Affiliation(s)
- Ewa Zatorska
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Jaro Schmitt
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Daniela Bausewein
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany.
| |
Collapse
|