1
|
Tadesse BT, Svetlicic E, Zhao S, Berhane N, Jers C, Solem C, Mijakovic I. Bad to the bone? - Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms. Microbiol Res 2024; 283:127702. [PMID: 38552381 DOI: 10.1016/j.micres.2024.127702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
Enterococci comprise a group of lactic acid bacteria (LAB) with considerable potential to serve as food fermentation microorganisms. Unfortunately, enterococci have received a lot of negative attention, due to the occurrence of pathogenic and multidrug resistant strains. In this study, we used genomics to select safe candidates among the forty-four studied enterococcal isolates. The genomes of the forty-four strains were fully sequenced and assessed for presence of virulence and antibiotic resistance genes. Nineteen isolates belonging to the species Enterococcus lactis, Enterococcus faecium, Enterococcus durans, and Enterococcus thailandicus, were deemed safe from the genome analysis. The presence of secondary metabolite gene clusters for bacteriocins was assessed, and twelve candidates were found to secrete antimicrobial compounds effective against Listeria monocytogenes isolated from cheese and Staphylococcus aureus. Physiological characterization revealed nineteen industrial potentials; all strains grew well at 42 °C and acidified 1.5 hours faster than their mesophilic counterpart Lactococcus lactis, with which they share metabolism and flavor forming ability. We conclude that a large fraction of the examined enterococci were safe and could serve as excellent food fermentation microorganisms with inherent bioprotective abilities.
Collapse
Affiliation(s)
- Belay Tilahun Tadesse
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark; Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Ema Svetlicic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Shuangqing Zhao
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark
| | - Nega Berhane
- Institute of Biotechnology, University of Gondar, Ethiopia
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Christian Solem
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Kgs Lyngby DK-2800, Denmark.
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark; Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| |
Collapse
|
2
|
Balasubramanian S, Køhler JB, Jers C, Jensen PR, Mijakovic I. Exploring the secretome of Corynebacterium glutamicum ATCC 13032. Front Bioeng Biotechnol 2024; 12:1348184. [PMID: 38415189 PMCID: PMC10896948 DOI: 10.3389/fbioe.2024.1348184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/22/2024] [Indexed: 02/29/2024] Open
Abstract
The demand for alternative sources of food proteins is increasing due to the limitations and challenges associated with conventional food production. Advances in biotechnology have enabled the production of proteins using microorganisms, thus prompting the exploration of attractive microbial hosts capable of producing functional proteins in high titers. Corynebacterium glutamicum is widely used in industry for the production of amino acids and has many advantages as a host organism for recombinant protein production. However, its performance in this area is limited by low yields of target proteins and high levels of native protein secretion. Despite representing a challenge for heterologous protein production, the C. glutamicum secretome has not been fully characterized. In this study, state-of-the-art mass spectrometry-based proteomics was used to identify and analyze the proteins secreted by C. glutamicum. Both the wild-type strain and a strain that produced and secreted a recombinant β-lactoglobulin protein were analyzed. A total of 427 proteins were identified in the culture supernatants, with 148 predicted to possess a secretion signal peptide. MS-based proteomics on the secretome enabled a comprehensive characterization and quantification (based on abundance) of the secreted proteins through label-free quantification (LFQ). The top 12 most abundant proteins accounted for almost 80% of the secretome. These are uncharacterized proteins of unknown function, resuscitation promoting factors, protein PS1, Porin B, ABC-type transporter protein and hypothetical membrane protein. The data can be leveraged for protein production by, e.g., utilizing the signal peptides of the most abundant proteins to improve secretion of heterologous proteins. In addition, secretory stress can potentially be alleviated by inactivating non-essential secreted proteins. Here we provide targets by identifying the most abundant, secreted proteins of which majority are of unknown function. The data from this study can thus provide valuable insight for researchers looking to improve protein secretion and optimize C. glutamicum as a host for secretory protein production.
Collapse
Affiliation(s)
- Suvasini Balasubramanian
- Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julie Bonne Køhler
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Ruhdal Jensen
- Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
3
|
Garg A, Jers C, Hwang HJ, Kalantari A, Ventina I, Mijakovic I. Engineering Bacillus subtilis for production of 3-hydroxypropanoic acid. Front Bioeng Biotechnol 2023; 11:1101232. [PMID: 36726744 PMCID: PMC9885095 DOI: 10.3389/fbioe.2023.1101232] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/04/2023] [Indexed: 01/17/2023] Open
Abstract
3-Hydroxypropionic acid (3-HP) is a valuable platform chemical that is used as a precursor for several higher value-added chemical products. There is an increased interest in development of cell factories as a means for the synthesis of 3-HP and various other platform chemicals. For more than a decade, concentrated effort has been invested by the scientific community towards developing bio-based approaches for the production of 3-HP using primarily Escherichia coli and Klebsiella pneumoniae as production hosts. These hosts however might not be optimal for applications in e.g., food industry due primarily to endotoxin production and the pathogenic origin of particularly the K. pneumoniae. We have previously demonstrated that the generally recognized as safe organism Bacillus subtilis can be engineered to produce 3-HP using glycerol, an abundant by-product of the biodiesel industry, as substrate. For commercial exploitation, there is a need to substantially increase the titer. In the present study, we optimized the bioprocess conditions and further engineered the B. subtilis 3-HP production strain. Thereby, using glycerol as substrate, we were able to improve 3-HP production in a 1-L bioreactor to a final titer of 22.9 g/L 3-HP.
Collapse
Affiliation(s)
- Abhroop Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Hee Jin Hwang
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden,Department of Molecular Science and Technology, Ajou University, World cup-ro, Yeongtong-gu, Suwon-si, South Korea
| | - Aida Kalantari
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ildze Ventina
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden,*Correspondence: Ivan Mijakovic,
| |
Collapse
|
4
|
Svetlicic E, Jaén-Luchoro D, Klobucar RS, Jers C, Kazazic S, Franjevic D, Klobucar G, Shelton BG, Mijakovic I. Genomic characterization and assessment of pathogenic potential of Legionella spp. isolates from environmental monitoring. Front Microbiol 2023; 13:1091964. [PMID: 36713227 PMCID: PMC9879626 DOI: 10.3389/fmicb.2022.1091964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Several species in the genus Legionella are known to cause an acute pneumonia when the aerosols containing the bacteria from man-made water systems are inhaled. The disease is usually caused by Legionella pneumophila, but other species have been implicated in the infection. The disease is frequently manifested as an outbreak, which means several people are affected when exposed to the common source of Legionella contamination. Therefor environmental surveillance which includes isolation and identification of Legionella is performed routinely. However, usually no molecular or genome-based methods are employed in further characterization of the isolates during routine environmental monitoring. During several years of such monitoring, isolates from different geographical locations were collected and 39 of them were sequenced by hybrid de novo approach utilizing short and long sequencing reads. In addition, the isolates were typed by standard culture and MALDI-TOF method. The sequencing reads were assembled and annotated to produce high-quality genomes. By employing discriminatory genome typing, four potential new species in the Legionella genus were identified, which are yet to be biochemically and morphologically characterized. Moreover, functional annotations concerning virulence and antimicrobial resistance were performed on the sequenced genomes. The study contributes to the knowledge on little-known non-pneumophila species present in man-made water systems and establishes support for future genetic relatedness studies as well as understanding of their pathogenic potential.
Collapse
Affiliation(s)
- Ema Svetlicic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases (Sahlgrenska Academy) at the University of Gothenburg, Gothenburg, Sweden
| | | | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark
| | - Snjezana Kazazic
- Laboratory for Mass Spectrometry and Functional Proteomics, Ruder Boskovic Institute, Zagreb, Croatia
| | - Damjan Franjevic
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Goran Klobucar
- Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Kongens Lyngby, Denmark,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden,*Correspondence: Ivan Mijakovic,
| |
Collapse
|
5
|
Helalat SH, Jers C, Bebahani M, Mohabatkar H, Mijakovic I. Metabolic engineering of Deinococcus radiodurans for pinene production from glycerol. Microb Cell Fact 2021; 20:187. [PMID: 34565367 PMCID: PMC8474958 DOI: 10.1186/s12934-021-01674-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The objective of this work was to engineer Deinococcus radiodurans R1 as a microbial cell factory for the production of pinene, a monoterpene molecule prominently used for the production of fragrances, pharmaceutical products, and jet engine biofuels. Our objective was to produce pinene from glycerol, an abundant by-product of various industries. RESULTS To enable pinene production in D. radiodurans, we expressed the pinene synthase from Abies grandis, the geranyl pyrophosphate (GPP) synthase from Escherichia coli, and overexpressed the native 1-deoxy-D-xylulose 5-phosphate synthase. Further, we disrupted the deinoxanthin pathway competing for the substrate GPP by either inactivating the gene dr0862, encoding phytoene synthase, or substituting the native GPP synthase with that of E. coli. These manipulations resulted in a D. radiodurans strain capable of producing 3.2 ± 0.2 mg/L pinene in a minimal medium supplemented with glycerol, with a yield of 0.13 ± 0.04 mg/g glycerol in shake flask cultures. Additionally, our results indicated a higher tolerance of D. radiodurans towards pinene as compared to E. coli. CONCLUSIONS In this study, we successfully engineered the extremophile bacterium D. radiodurans to produce pinene. This is the first study demonstrating the use of D. radiodurans as a cell factory for the production of terpenoid molecules. Besides, its high resistance to pinene makes D. radiodurans a suitable host for further engineering efforts to increase pinene titer as well as a candidate for the production of the other terpenoid molecules.
Collapse
Affiliation(s)
- Seyed Hossein Helalat
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mandana Bebahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
6
|
Sultan A, Jers C, Ganief TA, Shi L, Senissar M, Køhler JB, Macek B, Mijakovic I. Phosphoproteome Study of Escherichia coli Devoid of Ser/Thr Kinase YeaG During the Metabolic Shift From Glucose to Malate. Front Microbiol 2021; 12:657562. [PMID: 33889145 PMCID: PMC8055822 DOI: 10.3389/fmicb.2021.657562] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding phosphorylation-mediated regulation of metabolic enzymes, pathways, and cell phenotypes under metabolic shifts represents a major challenge. The kinases associated with most phosphorylation sites and the link between phosphorylation and enzyme activity remain unknown. In this study, we performed stable isotope labeling by amino acids in cell culture (SILAC)-based proteome and phosphoproteome analysis of Escherichia coli ΔyeaG, a strain lacking a poorly characterized serine/threonine kinase YeaG, to decipher kinase-substrate interactions and the effects on metabolic phenotype during shifts from glucose to malate. The starting point of our analysis was the identification of physiological conditions under which ΔyeaG exhibits a clear phenotype. By metabolic profiling, we discovered that ΔyeaG strain has a significantly shorter lag phase than the wild type during metabolic shift from glucose to malate. Under those conditions, our SILAC analysis revealed several proteins that were differentially phosphorylated in the ΔyeaG strain. By focusing on metabolic enzymes potentially involved in central carbon metabolism, we narrowed down our search for putative YeaG substrates and identified isocitrate lyase AceA as the direct substrate of YeaG. YeaG was capable of phosphorylating AceA in vitro only in the presence of malate, suggesting that this phosphorylation event is indeed relevant for glucose to malate shift. There is currently not enough evidence to firmly establish the exact mechanism of this newly observed regulatory phenomenon. However, our study clearly exemplifies the usefulness of SILAC-based approaches in identifying proteins kinase substrates, when applied in physiological conditions relevant for the activity of the protein kinase in question.
Collapse
Affiliation(s)
- Abida Sultan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tariq A Ganief
- Quantitative Proteomics and Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Meriem Senissar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julie Bonne Køhler
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Boris Macek
- Quantitative Proteomics and Proteome Center Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
7
|
Shi L, Derouiche A, Pandit S, Rahimi S, Kalantari A, Futo M, Ravikumar V, Jers C, Mokkapati VRSS, Vlahoviček K, Mijakovic I. Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation. Mol Biol Evol 2021; 37:1667-1678. [PMID: 32061128 PMCID: PMC7426031 DOI: 10.1093/molbev/msaa035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of presently uncharacterized genes (y-genes). We individually inactivated a representative sample of uncharacterized genes that arose during the same evolutionary periods as the known sporulation genes and tested the resulting strains for sporulation phenotypes. Sporulation was significantly affected in 16 out of 37 (43%) tested strains. In addition to expanding the knowledge base on B. subtilis sporulation, our findings suggest that evolutionary age could be used to help with genome mining.
Collapse
Affiliation(s)
- Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Santosh Pandit
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Shadi Rahimi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Aida Kalantari
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Venkata R S S Mokkapati
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Kristian Vlahoviček
- Bioinformatics group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia.,School of Bioscience, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
8
|
Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020; 594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation regulates a large variety of biological processes in all living cells. In pathogenic bacteria, the study of serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation has shed light on the course of infectious diseases, from adherence to host cells to pathogen virulence, replication, and persistence. Mass spectrometry (MS)-based phosphoproteomics has provided global maps of Ser/Thr/Tyr phosphosites in bacterial pathogens. Despite recent developments, a quantitative and dynamic view of phosphorylation events that occur during bacterial pathogenesis is currently lacking. Temporal, spatial, and subpopulation resolution of phosphorylation data is required to identify key regulatory nodes underlying bacterial pathogenesis. Herein, we discuss how technological improvements in sample handling, MS instrumentation, data processing, and machine learning should improve bacterial phosphoproteomic datasets and the information extracted from them. Such information is expected to significantly extend the current knowledge of Ser/Thr/Tyr phosphorylation in pathogenic bacteria and should ultimately contribute to the design of novel strategies to combat bacterial infections.
Collapse
Affiliation(s)
- Julie Bonne Køhler
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mériem Senissar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
9
|
Jers C, Kalantari A, Garg A, Mijakovic I. Production of 3-Hydroxypropanoic Acid From Glycerol by Metabolically Engineered Bacteria. Front Bioeng Biotechnol 2019; 7:124. [PMID: 31179279 PMCID: PMC6542942 DOI: 10.3389/fbioe.2019.00124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
Abstract
3-hydroxypropanoic acid (3-HP) is a valuable platform chemical with a high demand in the global market. 3-HP can be produced from various renewable resources. It is used as a precursor in industrial production of a number of chemicals, such as acrylic acid and its many derivatives. In its polymerized form, 3-HP can be used in bioplastic production. Several microbes naturally possess the biosynthetic pathways for production of 3-HP, and a number of these pathways have been introduced in some widely used cell factories, such as Escherichia coli and Saccharomyces cerevisiae. Latest advances in the field of metabolic engineering and synthetic biology have led to more efficient methods for bio-production of 3-HP. These include new approaches for introducing heterologous pathways, precise control of gene expression, rational enzyme engineering, redirecting the carbon flux based on in silico predictions using genome scale metabolic models, as well as optimizing fermentation conditions. Despite the fact that the production of 3-HP has been extensively explored in established industrially relevant cell factories, the current production processes have not yet reached the levels required for industrial exploitation. In this review, we explore the state of the art in 3-HP bio-production, comparing the yields and titers achieved in different microbial cell factories and we discuss possible methodologies that could make the final step toward industrially relevant cell factories.
Collapse
Affiliation(s)
- Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Aida Kalantari
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Abhroop Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
10
|
Jers C, Ravikumar V, Lezyk M, Sultan A, Sjöling Å, Wai SN, Mijakovic I. The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators. Front Cell Infect Microbiol 2018; 7:537. [PMID: 29376036 PMCID: PMC5768985 DOI: 10.3389/fcimb.2017.00537] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/26/2017] [Indexed: 01/16/2023] Open
Abstract
Protein lysine acetylation is recognized as an important reversible post translational modification in all domains of life. While its primary roles appear to reside in metabolic processes, lysine acetylation has also been implicated in regulating pathogenesis in bacteria. Several global lysine acetylome analyses have been carried out in various bacteria, but thus far there have been no reports of lysine acetylation taking place in the important human pathogen Vibrio cholerae. In this study, we analyzed the lysine acetylproteome of the human pathogen V. cholerae V52. By applying a combination of immuno-enrichment of acetylated peptides and high resolution mass spectrometry, we identified 3,402 acetylation sites on 1,240 proteins. Of the acetylated proteins, more than half were acetylated on two or more sites. As reported for other bacteria, we observed that many of the acetylated proteins were involved in metabolic and cellular processes and there was an over-representation of acetylated proteins involved in protein synthesis. Of interest, we demonstrated that many global transcription factors such as CRP, H-NS, IHF, Lrp and RpoN as well as transcription factors AphB, TcpP, and PhoB involved in direct regulation of virulence in V. cholerae were acetylated. In conclusion, this is the first global protein lysine acetylome analysis of V. cholerae and should constitute a valuable resource for in-depth studies of the impact of lysine acetylation in pathogenesis and other cellular processes.
Collapse
Affiliation(s)
- Carsten Jers
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Vaishnavi Ravikumar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mateusz Lezyk
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Abida Sultan
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sun N Wai
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
11
|
Stancik IA, Šestak MS, Ji B, Axelson-Fisk M, Franjevic D, Jers C, Domazet-Lošo T, Mijakovic I. Serine/Threonine Protein Kinases from Bacteria, Archaea and Eukarya Share a Common Evolutionary Origin Deeply Rooted in the Tree of Life. J Mol Biol 2017; 430:27-32. [PMID: 29138003 DOI: 10.1016/j.jmb.2017.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 11/04/2017] [Accepted: 11/05/2017] [Indexed: 11/26/2022]
Abstract
The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988 (Science, 241, 42-52). It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim. Our comprehensive phylostratigraphic analysis suggests that Hanks-type kinases present in eukarya, bacteria and archaea all share a common evolutionary origin in the lineage leading to the last universal common ancestor (LUCA). We found no evidence to suggest substantial horizontal transfer of genes encoding Hanks-type kinases from eukarya to bacteria. Moreover, our systematic structural comparison suggests that bacterial Hanks-type kinases resemble their eukaryal counterparts very closely, while their structures appear to be dissimilar from other kinase families of bacterial origin. This indicates that a convergent evolution scenario, by which bacterial kinases could have evolved a kinase domain similar to that of eukaryal Hanks-type kinases, is not very likely. Overall, our results strongly support a monophyletic origin of all Hanks-type kinases, and we therefore propose that this term should be adopted as a universal name for this protein family.
Collapse
Affiliation(s)
- Ivan Andreas Stancik
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Lyngby, Denmark
| | - Martin Sebastijan Šestak
- Laboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Marina Axelson-Fisk
- Department of Mathematical Sciences, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Damjan Franjevic
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Lyngby, Denmark
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, HR-10002 Zagreb, Croatia; Catholic University of Croatia, Ilica 242, HR-10000 Zagreb, Croatia
| | - Ivan Mijakovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Lyngby, Denmark.
| |
Collapse
|
12
|
Nyffenegger C, Nordvang RT, Jers C, Meyer AS, Mikkelsen JD. Design of Trypanosoma rangeli sialidase mutants with improved trans-sialidase activity. PLoS One 2017; 12:e0171585. [PMID: 28158299 PMCID: PMC5291517 DOI: 10.1371/journal.pone.0171585] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/23/2017] [Indexed: 11/30/2022] Open
Abstract
A sialidase (EC 3.2.1.18) from the non-pathogenic Trypanosoma rangeli, TrSA, has been shown to exert trans-sialidase activity after mutation of five specific amino acids in the active site (M96V, A98P, S120Y, G249Y, Q284P) to form the so-called TrSA5mut enzyme. By computational and hypothesis driven approaches additional mutations enhancing the trans-sialidase activity have been suggested. In the present work, we made a systematic combination of these mutations leading to seven new variants of the T. rangeli sialidase, having 6–16 targeted amino acid mutations. The resulting enzyme variants were analyzed via kinetics for their ability to carry out trans-sialidase reaction using CGMP and D-lactose as substrates. The sialidase variants with 15 and 16 mutations, respectively, exhibited significantly improved trans-sialidase activity for D-lactose sialylation. Our results corroborate, that computational studies of trans-glycosylation can be a valuable input in the design of novel trans-glycosidases, but also highlight the importance of experimental validation in order to assess the performance. In conclusion, two of the seven mutants displayed a dramatic switch in specificity from hydrolysis towards trans-sialylation and constitute the most potent trans-sialidase mutants of TrSA described in literature to date.
Collapse
Affiliation(s)
- Christian Nyffenegger
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rune Thorbjørn Nordvang
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carsten Jers
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
- * E-mail:
| | - Anne S. Meyer
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jørn Dalgaard Mikkelsen
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
13
|
Ravikumar V, Jers C, Mijakovic I. Elucidating Host-Pathogen Interactions Based on Post-Translational Modifications Using Proteomics Approaches. Front Microbiol 2015; 6:1313. [PMID: 26635773 PMCID: PMC4653285 DOI: 10.3389/fmicb.2015.01312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes with the capability to survive in the host tissue and efficiently subvert its innate immune responses can cause various health hazards. There is an inherent need to understand microbial infection patterns and mechanisms in order to develop efficient therapeutics. Microbial pathogens display host specificity through a complex network of molecular interactions that aid their survival and propagation. Co-infection states further lead to complications by increasing the microbial burden and risk factors. Quantitative proteomics based approaches and post-translational modification analysis can be efficiently applied to gain an insight into the molecular mechanisms involved. The measurement of the proteome and post-translationally modified proteome dynamics using mass spectrometry, results in a wide array of information, such as significant changes in protein expression, protein abundance, the modification status, the site occupancy level, interactors, functional significance of key players, potential drug targets, etc. This mini review discusses the potential of proteomics to investigate the involvement of post-translational modifications in bacterial pathogenesis and host-pathogen interactions.
Collapse
Affiliation(s)
- Vaishnavi Ravikumar
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology , Gothenburg, Sweden
| | - Carsten Jers
- Department of Systems Biology, Technical University of Denmark , Lyngby, Denmark
| | - Ivan Mijakovic
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology , Gothenburg, Sweden ; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Hørsholm, Denmark
| |
Collapse
|
14
|
Li H, Rasmussen MI, Larsen MR, Guo Y, Jers C, Palmisano G, Mikkelsen JD, Kirpekar F. AutomatedN-glycan profiling of a mutantTrypanosoma rangelisialidase expressed inPichia pastoris, using tandem mass spectrometry and bioinformatics. Glycobiology 2015; 25:1350-61. [DOI: 10.1093/glycob/cwv063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/07/2015] [Indexed: 12/23/2022] Open
|
15
|
Jers C, Guo Y, Kepp K, Mikkelsen J. Mutants of Micromonospora viridifaciens sialidase have highly variable activities on natural and non-natural substrates. Protein Eng Des Sel 2015; 28:37-44. [DOI: 10.1093/protein/gzu054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
16
|
Zeuner B, Jers C, Mikkelsen JD, Meyer AS. Methods for improving enzymatic trans-glycosylation for synthesis of human milk oligosaccharide biomimetics. J Agric Food Chem 2014; 62:9615-31. [PMID: 25208138 DOI: 10.1021/jf502619p] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Recently, significant progress has been made within enzymatic synthesis of biomimetic, functional glycans, including, for example, human milk oligosaccharides. These compounds are mainly composed of N-acetylglucosamine, fucose, sialic acid, galactose, and glucose, and their controlled enzymatic synthesis is a novel field of research in advanced food ingredient chemistry, involving the use of rare enzymes, which have until now mainly been studied for their biochemical significance, not for targeted biosynthesis applications. For the enzymatic synthesis of biofunctional glycans reaction parameter optimization to promote "reverse" catalysis with glycosidases is currently preferred over the use of glycosyl transferases. Numerous methods exist for minimizing the undesirable glycosidase-catalyzed hydrolysis and for improving the trans-glycosylation yields. This review provides an overview of the approaches and data available concerning optimization of enzymatic trans-glycosylation for novel synthesis of complex bioactive carbohydrates using sialidases, α-l-fucosidases, and β-galactosidases as examples. The use of an adequately high acceptor/donor ratio, reaction time control, continuous product removal, enzyme recycling, and/or the use of cosolvents may significantly improve trans-glycosylation and biocatalytic productivity of the enzymatic reactions. Protein engineering is also a promising technique for obtaining high trans-glycosylation yields, and proof-of-concept for reversing sialidase activity to trans-sialidase action has been established. However, the protein engineering route currently requires significant research efforts in each case because the structure-function relationship of the enzymes is presently poorly understood.
Collapse
Affiliation(s)
- Birgitte Zeuner
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark , Building 229, DK-2800 Kgs. Lyngby, Denmark
| | | | | | | |
Collapse
|
17
|
Kobir A, Poncet S, Bidnenko V, Delumeau O, Jers C, Zouhir S, Grenha R, Nessler S, Noirot P, Mijakovic I. Phosphorylation ofBacillus subtilisgene regulator AbrB modulates its DNA-binding properties. Mol Microbiol 2014; 92:1129-41. [DOI: 10.1111/mmi.12617] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2014] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | | | - Carsten Jers
- INRA; UMR-1319 Micalis; F-78350 Jouy-en-Josas France
| | - Samira Zouhir
- Laboratoire d'Enzymologie et Biochimie Structurales; UPR3082 CNRS; 91198 Gif sur Yvette France
| | - Rosa Grenha
- Laboratoire d'Enzymologie et Biochimie Structurales; UPR3082 CNRS; 91198 Gif sur Yvette France
| | - Sylvie Nessler
- Laboratoire d'Enzymologie et Biochimie Structurales; UPR3082 CNRS; 91198 Gif sur Yvette France
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire; UMR8619 CNRS; Université Paris-Sud 11; 91405 Orsay France
| | | | - Ivan Mijakovic
- INRA; UMR-1319 Micalis; F-78350 Jouy-en-Josas France
- Chalmers University of Technology, Systems and Synthetic Biology; Department of Chemical and Biological Engineering; 41296 Gothenburg Sweden
| |
Collapse
|
18
|
Michalak M, Larsen DM, Jers C, Almeida JR, Willer M, Li H, Kirpekar F, Kjærulff L, Gotfredsen CH, Nordvang RT, Meyer AS, Mikkelsen JD. Biocatalytic production of 3′-sialyllactose by use of a modified sialidase with superior trans-sialidase activity. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.10.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
19
|
Jers C, Soufi B, Grangeasse C, Deutscher J, Mijakovic I. Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks. Expert Rev Proteomics 2014; 5:619-27. [DOI: 10.1586/14789450.5.4.619] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
20
|
Ravikumar V, Shi L, Krug K, Derouiche A, Jers C, Cousin C, Kobir A, Mijakovic I, Macek B. Quantitative phosphoproteome analysis of Bacillus subtilis reveals novel substrates of the kinase PrkC and phosphatase PrpC. Mol Cell Proteomics 2014; 13:1965-78. [PMID: 24390483 DOI: 10.1074/mcp.m113.035949] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Reversible protein phosphorylation on serine, threonine, and tyrosine (Ser/Thr/Tyr) residues plays a critical role in regulation of vital processes in the cell. Despite of considerable progress in our understanding of the role of this modification in bacterial physiology, the dynamics of protein phosphorylation during bacterial growth has rarely been systematically addressed. In addition, little is known about in vivo substrates of bacterial Ser/Thr/Tyr kinases and phosphatases. An excellent candidate to study these questions is the Gram-positive bacterium Bacillus subtilis, one of the most intensively investigated bacterial model organism with both research and industrial applications. Here we employed gel-free phosphoproteomics combined with SILAC labeling and high resolution mass spectrometry to study the proteome and phosphoproteome dynamics during the batch growth of B. subtilis. We measured the dynamics of 1666 proteins and 64 phosphorylation sites in five distinct phases of growth. Enzymes of the central carbon metabolism and components of the translation machinery appear to be highly phosphorylated in the stationary phase, coinciding with stronger expression of Ser/Thr kinases. We further used the SILAC workflow to identify novel putative substrates of the Ser/Thr kinase PrkC and the phosphatase PrpC during stationary phase. The overall number of putative substrates was low, pointing to a high kinase and phosphatase specificity. One of the phosphorylation sites affected by both, PrkC and PrpC, was the Ser281 on the oxidoreductase YkwC. We showed that PrkC phosphorylates and PrpC dephosphorylates YkwC in vitro and that phosphorylation at Ser281 abolishes the oxidoreductase activity of YkwC in vitro and in vivo. Our results present the most detailed phosphoproteomic analysis of B. subtilis growth to date and provide the first global in vivo screen of PrkC and PrpC substrates.
Collapse
Affiliation(s)
- Vaishnavi Ravikumar
- From the ‡Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Germany
| | - Lei Shi
- §Micalis UMR 1319, AgroParisTech/Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Karsten Krug
- From the ‡Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Germany
| | - Abderahmane Derouiche
- §Micalis UMR 1319, AgroParisTech/Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Carsten Jers
- §Micalis UMR 1319, AgroParisTech/Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Charlotte Cousin
- §Micalis UMR 1319, AgroParisTech/Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Ahasanul Kobir
- §Micalis UMR 1319, AgroParisTech/Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Ivan Mijakovic
- §Micalis UMR 1319, AgroParisTech/Institut National de la Recherche Agronomique, Jouy en Josas, France; ¶Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Boris Macek
- From the ‡Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Germany;
| |
Collapse
|
21
|
Jers C, Michalak M, Larsen DM, Kepp KP, Li H, Guo Y, Kirpekar F, Meyer AS, Mikkelsen JD. Rational design of a new Trypanosoma rangeli trans-sialidase for efficient sialylation of glycans. PLoS One 2014; 9:e83902. [PMID: 24404142 PMCID: PMC3880268 DOI: 10.1371/journal.pone.0083902] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 11/18/2013] [Indexed: 12/23/2022] Open
Abstract
This paper reports rational engineering of Trypanosoma rangeli sialidase to develop an effective enzyme for a potentially important type of reactivity: production of sialylated prebiotic glycans. The Trypanosoma cruzi trans-sialidase and the homologous T. rangeli sialidase has previously been used to investigate the structural requirements for trans-sialidase activity. We observed that the T. cruzi trans-sialidase has a seven-amino-acid motif (197–203) at the border of the substrate binding cleft. The motif differs substantially in chemical properties and substitution probability from the homologous sialidase, and we hypothesised that this motif is important for trans-sialidase activity. The 197–203 motif is strongly positively charged with a marked change in hydrogen bond donor capacity as compared to the sialidase. To investigate the role of this motif, we expressed and characterised a T. rangeli sialidase mutant, Tr13. Conditions for efficient trans-sialylation were determined, and Tr13's acceptor specificity demonstrated promiscuity with respect to the acceptor molecule enabling sialylation of glycans containing terminal galactose and glucose and even monomers of glucose and fucose. Sialic acid is important in association with human milk oligosaccharides, and Tr13 was shown to sialylate a number of established and potential prebiotics. Initial evaluation of prebiotic potential using pure cultures demonstrated, albeit not selectively, growth of Bifidobacteria. Since the 197–203 motif stands out in the native trans-sialidase, is markedly different from the wild-type sialidase compared to previous mutants, and is shown here to confer efficient and broad trans-sialidase activity, we suggest that this motif can serve as a framework for future optimization of trans-sialylation towards prebiotic production.
Collapse
Affiliation(s)
- Carsten Jers
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Malwina Michalak
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Dorte M. Larsen
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Kasper P. Kepp
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Haiying Li
- Department of Biochemistry and Molecular Biology, Southern University of Denmark, Odense, Denmark
| | - Yao Guo
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, Southern University of Denmark, Odense, Denmark
| | - Anne S. Meyer
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Jørn D. Mikkelsen
- Center for BioProcess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
| |
Collapse
|
22
|
Guo Y, Jers C, Meyer AS, Arnous A, Li H, Kirpekar F, Mikkelsen JD. A Pasteurella multocida sialyltransferase displaying dual trans-sialidase activities for production of 3′-sialyl and 6′-sialyl glycans. J Biotechnol 2014; 170:60-7. [DOI: 10.1016/j.jbiotec.2013.11.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/15/2013] [Accepted: 11/20/2013] [Indexed: 11/26/2022]
|
23
|
Silva IR, Larsen DM, Jers C, Derkx P, Meyer AS, Mikkelsen JD. Enhancing RGI lyase thermostability by targeted single point mutations. Appl Microbiol Biotechnol 2013; 97:9727-35. [DOI: 10.1007/s00253-013-5184-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/07/2013] [Accepted: 08/10/2013] [Indexed: 11/25/2022]
|
24
|
Jers C, Kobir A, Søndergaard EO, Jensen PR, Mijakovic I. Bacillus subtilis two-component system sensory kinase DegS is regulated by serine phosphorylation in its input domain. PLoS One 2011; 6:e14653. [PMID: 21304896 PMCID: PMC3033389 DOI: 10.1371/journal.pone.0014653] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 01/10/2011] [Indexed: 11/18/2022] Open
Abstract
Bacillus subtilis two-component system DegS/U is well known for the complexity of its regulation. The cytosolic sensory kinase DegS does not receive a single predominant input signal like most two-component kinases, instead it integrates a wide array of metabolic inputs that modulate its activity. The phosphorylation state of the response regulator DegU also does not confer a straightforward “on/off” response; it is fine-tuned and at different levels triggers different sub-regulons. Here we describe serine phosphorylation of the DegS sensing domain, which stimulates its kinase activity. We demonstrate that DegS phosphorylation can be carried out by at least two B. subtilis Hanks-type kinases in vitro, and this stimulates the phosphate transfer towards DegU. The consequences of this process were studied in vivo, using phosphomimetic (Ser76Asp) and non-phosphorylatable (Ser76Ala) mutants of DegS. In a number of physiological assays focused on different processes regulated by DegU, DegS S76D phosphomimetic mutant behaved like a strain with intermediate levels of DegU phosphorylation, whereas DegS S76A behaved like a strain with lower levels of DegU phophorylation. These findings suggest a link between DegS phosphorylation at serine 76 and the level of DegU phosphorylation, establishing this post-translational modification as an additional trigger for this two-component system.
Collapse
Affiliation(s)
- Carsten Jers
- Center for Systems Microbiology, Technical University of Denmark, Lyngby, Denmark
| | - Ahasanul Kobir
- Micalis, AgroParisTech/Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Peter Ruhdal Jensen
- Center for Systems Microbiology, Technical University of Denmark, Lyngby, Denmark
| | - Ivan Mijakovic
- Micalis, AgroParisTech/Institut National de la Recherche Agronomique, Jouy en Josas, France
- * E-mail:
| |
Collapse
|
25
|
|
26
|
Jers C, Pedersen MM, Paspaliari DK, Schütz W, Johnsson C, Soufi B, Macek B, Jensen PR, Mijakovic I. Bacillus subtilis BY-kinase PtkA controls enzyme activity and localization of its protein substrates. Mol Microbiol 2010; 77:287-99. [PMID: 20497499 DOI: 10.1111/j.1365-2958.2010.07227.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus subtilis BY-kinase PtkA was previously shown to phosphorylate, and thereby regulate the activity of two classes of protein substrates: UDP-glucose dehydrogenases and single-stranded DNA-binding proteins. Our recent phosphoproteome study identified nine new tyrosine-phosphorylated proteins in B. subtilis. We found that the majority of these proteins could be phosphorylated by PtkA in vitro. Among these new substrates, single-stranded DNA exonuclease YorK, and aspartate semialdehyde dehydrogenase Asd were activated by PtkA-dependent phosphorylation. Because enzyme activity was not affected in other cases, we used fluorescent protein tags to study the impact of PtkA on localization of these proteins in vivo. For several substrates colocalization with PtkA was observed, and more importantly, the localization pattern of the proteins enolase, YjoA, YnfE, YvyG, Ugd and SsbA was dramatically altered in DeltaptkA background. Our results confirm that PtkA can control enzyme activity of its substrates in some cases, but also reveal a new mode of action for PtkA, namely ensuring correct cellular localization of its targets.
Collapse
Affiliation(s)
- Carsten Jers
- Micalis UMR 1319, AgroParisTech-INRA, Jouy-en-Josas, France
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Miller ML, Soufi B, Jers C, Blom N, Macek B, Mijakovic I. NetPhosBac - A predictor for Ser/Thr phosphorylation sites in bacterial proteins. Proteomics 2009; 9:116-25. [DOI: 10.1002/pmic.200800285] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
28
|
Soufi B, Jers C, Hansen ME, Petranovic D, Mijakovic I. Insights from site-specific phosphoproteomics in bacteria. Biochim Biophys Acta 2007; 1784:186-92. [PMID: 17881301 DOI: 10.1016/j.bbapap.2007.07.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 07/26/2007] [Accepted: 07/30/2007] [Indexed: 10/22/2022]
Abstract
Recent advances in mass spectrometry allowed the charting of bacterial serine/threonine/tyrosine phosphoproteomes with unprecedented accuracy, including the acquisition of a large number of phosphorylation sites. Phosphorylated bacterial proteins are involved in some key housekeeping processes, and their phosphorylation is expected to play an important regulatory role. When coupled to stable isotope labeling by amino acids in cell culture (SILAC), high-resolution mass spectrometry allows the detection of changes in the occupancy of phosphorylation sites in response to various stimuli. This and similar approaches promise to lead bacterial phosphoproteomics into the era of systems biology, where the entire phosphorylation-based regulatory networks will be charted, modelled, and ultimately engineered to obtain desired properties.
Collapse
Affiliation(s)
- Boumediene Soufi
- Center for Microbial Biotechnology, BioCentrum, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | | | | | | | | |
Collapse
|