1
|
Koul D, Chander D, Manhas RS, Hossain MM, Dar MJ, Chaubey A. Purification, functional characterization and enhanced production of serratiopeptidase from Serratia marcescens MES-4: An endophyte isolated from Morus rubra. J Biotechnol 2024; 387:58-68. [PMID: 38582407 DOI: 10.1016/j.jbiotec.2024.04.002] [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: 11/25/2023] [Revised: 03/23/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Serratiopeptidase, a proteolytic enzyme serves as an important anti-inflammatory and analgesic medication. Present study reports the production and purification of extracellular serratiopeptidase from an endophyte, Serratia marcescens MES-4, isolated from Morus rubra. Purification of the enzyme by Ion exchange chromatography led to the specific activity of 13,030 U/mg protein of serratiopeptidase, showcasing about 3.1 fold enhanced activity. The catalytic domain of the purified serratiopeptidase, composed of Zn coordinated with three histidine residues (His 209, His 213, and His 219), along with glutamate (Glu 210) and tyrosine (Tyr 249). The molecular mass, as determined by SDS-PAGE was ∼51 kDa. The purified serratiopeptidase displayed optimal activity at pH 9.0, temperature 50°C. Kinetic studies revealed Vmax and Km values of 33,333 U/mL and 1.66 mg/mL, respectively. Further, optimized conditions for the production of serratiopeptidase by Taguchi design led to the productivity of 87 U/mL/h with 87.9 fold enhanced production as compared to the previous conditions.
Collapse
Affiliation(s)
- Diksha Koul
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India
| | - Devtulya Chander
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India
| | - Ravi S Manhas
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Md Mehedi Hossain
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India
| | - Mohd Jamal Dar
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India
| | - Asha Chaubey
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India; Academy of Scientific and Innovative Research, CSIR- Human Resource Development Centre, Campus Ghaziabad, Ghaziabad 201002, India.
| |
Collapse
|
2
|
Sun XM, Xue Z, Sun ML, Zhang Y, Zhang YZ, Fu HH, Zhang YQ, Wang P. Characterization of a Novel Alginate Lyase with Two Alginate Lyase Domains from the Marine Bacterium Vibrio sp. C42. Mar Drugs 2022; 20:md20120746. [PMID: 36547893 PMCID: PMC9781882 DOI: 10.3390/md20120746] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Alginate is abundant in the cell walls of brown algae. Alginate lyases can degrade alginate, and thus play an important role in the marine carbon cycle and industrial production. Currently, most reported alginate lyases contain only one functional alginate lyase domain. AlyC8 is a putative alginate lyase with two alginate lyase domains (CD1 and CD2) from the marine alginate-degrading strain Vibrio sp. C42. To characterize AlyC8 and its two catalytic domains, AlyC8 and its two catalytic domain-deleted mutants, AlyC8-CD1 and AlyC8-CD2, were expressed in Escherichia coli. All three proteins have noticeable activity toward sodium alginate and exhibit optimal activities at pH 8.0-9.0 and at 30-40 °C, demonstrating that both CD1 and CD2 are functional. However, CD1 and CD2 showed opposite substrate specificity. The differences in substrate specificity and degradation products of alginate between the mutants and AlyC8 demonstrate that CD1 and CD2 can act synergistically to enable AlyC8 to degrade various alginate substrates into smaller oligomeric products. Moreover, kinetic analysis indicated that AlyC8-CD1 plays a major role in the degradation of alginate by AlyC8. These results demonstrate that AlyC8 is a novel alginate lyase with two functional catalytic domains that are synergistic in alginate degradation, which is helpful for a better understanding of alginate lyases and alginate degradation.
Collapse
Affiliation(s)
- Xiao-Meng Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Center, Shandong University, Qingdao 266237, China
- Life Science College, Shandong Normal University, Jinan 250014, China
| | - Zhao Xue
- Life Science College, Shandong Normal University, Jinan 250014, China
| | - Mei-Ling Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Yi Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Hui-Hui Fu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Yu-Qiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Center, Shandong University, Qingdao 266237, China
- Correspondence: (Y.-Q.Z.); (P.W.)
| | - Peng Wang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
- Correspondence: (Y.-Q.Z.); (P.W.)
| |
Collapse
|
3
|
Wang D, Li Y, Han L, Yin C, Fu Y, Zhang Q, Zhao X, Li G, Han F, Yu W. Biochemical Properties of a New Polysaccharide Lyase Family 25 Ulvan Lyase TsUly25B from Marine Bacterium Thalassomonas sp. LD5. Mar Drugs 2022; 20:md20030168. [PMID: 35323467 PMCID: PMC8955879 DOI: 10.3390/md20030168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/21/2023] Open
Abstract
Marine macroalgae, contributing much to the bioeconomy, have inspired tremendous attention as sustainable raw materials. Ulvan, as one of the main structural components of green algae cell walls, can be degraded by ulvan lyase through the β-elimination mechanism to obtain oligosaccharides exhibiting several good physiological activities. Only a few ulvan lyases have been characterized until now. This thesis explores the properties of a new polysaccharide lyase family 25 ulvan lyase TsUly25B from the marine bacterium Thalassomonas sp. LD5. Its protein molecular weight was 54.54 KDa, and it was most active under the conditions of 60 °C and pH 9.0. The Km and kcat values were 1.01 ± 0.05 mg/mL and 10.52 ± 0.28 s−1, respectively. TsUly25B was salt-tolerant and NaCl can significantly improve its thermal stability. Over 80% of activity can be preserved after being incubated at 30 °C for two days when the concentration of NaCl in the solution is above 1 M, while 60% can be preserved after incubation at 40 °C for 10 h with 2 M NaCl. TsUly25B adopted an endolytic manner to degrade ulvan polysaccharides, and the main end-products were unsaturated ulvan disaccharides and tetrasaccharides. In conclusion, our research enriches the ulvan lyase library and advances the utilization of ulvan lyases in further fundamental research as well as ulvan oligosaccharides production.
Collapse
Affiliation(s)
- Danni Wang
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
| | - Yujiao Li
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
| | - Lu Han
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
| | - Chengying Yin
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
| | - Yongqing Fu
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
| | - Qi Zhang
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
| | - Xia Zhao
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
| | - Guoyun Li
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
| | - Feng Han
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
- Correspondence: (F.H.); (W.Y.); Tel.: +86-532-82032067 (F.H.); +86-532-82031680 (W.Y.)
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (D.W.); (Y.L.); (L.H.); (C.Y.); (Y.F.); (Q.Z.); (X.Z.); (G.L.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, 5 Yushan Road, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Department of Science & Technology of Shandong Province, 5 Yushan Road, Qingdao 266003, China
- Correspondence: (F.H.); (W.Y.); Tel.: +86-532-82032067 (F.H.); +86-532-82031680 (W.Y.)
| |
Collapse
|
4
|
Hussain MS, Vashist A, Kumar M, Taneja NK, Gautam US, Dwivedi S, Tyagi JS, Gupta RK. Anti-mycobacterial activity of heat and pH stable high molecular weight protein(s) secreted by a bacterial laboratory contaminant. Microb Cell Fact 2022; 21:15. [PMID: 35093096 PMCID: PMC8799974 DOI: 10.1186/s12934-022-01743-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/13/2021] [Accepted: 01/13/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Tuberculosis currently stands as the second leading cause of deaths worldwide due to single infectious agent after Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The current challenges of drug resistance in tuberculosis highlight an urgent need to develop newer anti-mycobacterial compounds. In the present study, we report the serendipitous discovery of a bacterial laboratory contaminant (LC-1) exhibiting a zone of growth inhibition on an agar plate seeded with Mycobacterium tuberculosis. RESULTS We utilized microbiological, biochemical and biophysical approaches to characterize LC-1 and anti-mycobacterial compound(s) in its secretome. Based on 16S rRNA sequencing and BIOLOG analysis, LC-1 was identified as Staphylococcus hominis, a human bacterial commensal. Anti-mycobacterial activity was initially found in 30 kDa retentate that was obtained by ultrafiltration of culture filtrate (CF). SDS-PAGE analysis of peak fractions obtained by size exclusion chromatography of 30 kDa retentate confirmed the presence of high molecular weight (≥ 30 kDa) proteins. Peak fraction-1 (F-1) exhibited inhibitory activity against M. bovis BCG, but not against M. smegmatis, E. coli and S. aureus. The active fraction F-1 was inactivated by treatment with Proteinase K and α-chymotrypsin. However, it retained its anti-mycobacterial activity over a wide range of heat and pH treatment. The anti-mycobacterial activity of F-1 was found to be maintained even after a long storage (~12 months) at - 20 °C. Mass spectrometry analysis revealed that the identified peptide masses do not match with any previously known bacteriocins. CONCLUSIONS The present study highlights the anti-mycobacterial activity of high molecular weight protein(s) present in culture filtrate of LC-1, which may be tested further to target M. tuberculosis. The heat and pH stability of these proteins add to their characteristics as therapeutic proteins and may contribute to their long shelf life. LC-1 being a human commensal can be tested in future for its potential as a probiotic to treat tuberculosis.
Collapse
Affiliation(s)
- Md Sajid Hussain
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201306, India
- School of Vocational Studies and Applied Sciences, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201306, India
| | - Atul Vashist
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, 110029, India.
- Department of Infection & Immunology, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India.
| | - Mahadevan Kumar
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, 110029, India
- Department of Microbiology, Bharati Vidyapeeth University, Medical College, Pune, 411043, India
| | - Neetu Kumra Taneja
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, 110029, India
- Department of Basic and Applied Sciences, NIFTEM, Sonipat, Haryana, 131028, India
| | - Uma Shankar Gautam
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, 110029, India
- School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Seema Dwivedi
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201306, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Rajesh Kumar Gupta
- School of Vocational Studies and Applied Sciences, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201306, India.
| |
Collapse
|
5
|
Dumina M, Zhgun A, Pokrovskaya M, Aleksandrova S, Zhdanov D, Sokolov N, El’darov M. Highly Active Thermophilic L-Asparaginase from Melioribacter roseus Represents a Novel Large Group of Type II Bacterial L-Asparaginases from Chlorobi-Ignavibacteriae-Bacteroidetes Clade. Int J Mol Sci 2021; 22:13632. [PMID: 34948436 PMCID: PMC8709496 DOI: 10.3390/ijms222413632] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023] Open
Abstract
L-asparaginase (L-ASNase) is a biotechnologically relevant enzyme for the pharmaceutical, biosensor and food industries. Efforts to discover new promising L-ASNases for different fields of biotechnology have turned this group of enzymes into a growing family with amazing diversity. Here, we report that thermophile Melioribacter roseus from Ignavibacteriae of the Bacteroidetes/Chlorobi group possesses two L-ASNases-bacterial type II (MrAII) and plant-type (MrAIII). The current study is focused on a novel L-ASNase MrAII that was expressed in Escherichia coli, purified and characterized. The enzyme is optimally active at 70 °C and pH 9.3, with a high L-asparaginase activity of 1530 U/mg and L-glutaminase activity ~19% of the activity compared with L-asparagine. The kinetic parameters KM and Vmax for the enzyme were 1.4 mM and 5573 µM/min, respectively. The change in MrAII activity was not significant in the presence of 10 mM Ni2+, Mg2+ or EDTA, but increased with the addition of Cu2+ and Ca2+ by 56% and 77%, respectively, and was completely inhibited by Zn2+, Fe3+ or urea solutions 2-8 M. MrAII displays differential cytotoxic activity: cancer cell lines K562, Jurkat, LnCap, and SCOV-3 were more sensitive to MrAII treatment, compared with normal cells. MrAII represents the first described enzyme of a large group of uncharacterized counterparts from the Chlorobi-Ignavibacteriae-Bacteroidetes clade.
Collapse
Affiliation(s)
- Maria Dumina
- Group of Fungal Genetic Engineering, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 117312 Moscow, Russia;
| | - Alexander Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 117312 Moscow, Russia;
| | - Marina Pokrovskaya
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (M.P.); (S.A.); (D.Z.); (N.S.)
| | - Svetlana Aleksandrova
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (M.P.); (S.A.); (D.Z.); (N.S.)
| | - Dmitry Zhdanov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (M.P.); (S.A.); (D.Z.); (N.S.)
| | - Nikolay Sokolov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (M.P.); (S.A.); (D.Z.); (N.S.)
| | - Michael El’darov
- Group of Fungal Genetic Engineering, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 117312 Moscow, Russia;
| |
Collapse
|
6
|
Song X, Zhang L, Hui X, Sun X, Yang J, Wang J, Wu H, Wang X, Zheng Z, Che F, Wang G. Selenium-containing protein from selenium-enriched Spirulina platensis antagonizes oxygen glucose deprivation-induced neurotoxicity by inhibiting ROS-mediated oxidative damage through regulating MPTP opening. Pharm Biol 2021; 59:629-638. [PMID: 34062090 PMCID: PMC8172226 DOI: 10.1080/13880209.2021.1928715] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
CONTEXT Selenium-containing protein from selenium-enriched Spirulina platensis (Se-SP) (syn. Arthrospira platensis [Microcoleaceae]) showed novel antioxidant activity. However, the protective effect of Se-SP against oxygen glucose deprivation (OGD)-induced neural apoptosis has not been reported yet. OBJECTIVE To verify whether Se-SP can inhibit OGD-induced neural apoptosis and explore the underlying mechanism. MATERIALS AND METHODS Primary hippocampal neurons were separated from Sprague-Dawley (SD) rats. 95% N2 + 5% CO2 were employed to establish OGD model. Neurons were treated with 5 and 10 µg/mL Se-SP under OGD condition for 6 h. Neurons without treatment were the control group. Neural viability and apoptosis were detected by MTT, immunofluorescence and western blotting methods. RESULTS Se-SP significantly improved neuronal viability (from 57.2% to 94.5%) and inhibited apoptosis in OGD-treated primary neurons (from 45.6% to 6.3%), followed by improved neuronal morphology and caspases activation. Se-SP co-treatment also effectively suppressed OGD-induced DNA damage by inhibiting ROS accumulation in neurons (from 225.6% to 106.3%). Additionally, mitochondrial dysfunction was also markedly improved by Se-SP co-treatment via balancing Bcl-2 family expression. Moreover, inhibition of mitochondrial permeability transition pore (MPTP) by CsA (an MPTP inhibitor) dramatically attenuated OGD-induced ROS generation (from 100% to 56.2%), oxidative damage, mitochondrial membrane potential (MPP) loss (from 7.5% to 44.3%), and eventually reversed the neuronal toxicity and apoptosis (from 57.4% to 79.6%). DISCUSSION AND CONCLUSIONS Se-SP showed enhanced potential to inhibit OGD-induced neurotoxicity and apoptosis by inhibiting ROS-mediated oxidative damage through regulating MPTP opening, indicating that selenium-containing protein showed broad application in the chemoprevention and chemotherapy against human ischaemic brain injury.
Collapse
Affiliation(s)
- Xiaojie Song
- Department of Neurology, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Neurology, Linyi People’s Hospital, Linyi, China
| | - Lijun Zhang
- Department of Neurology, Linyi People’s Hospital, Linyi, China
| | - Xin Hui
- Department of Neurology, Linyi People’s Hospital, Linyi, China
| | - Xiangfu Sun
- Department of Internal Medicine, Taian Traffic Hospital, Taian, China
| | - Juntao Yang
- Department of Internal Medicine, Taian Traffic Hospital, Taian, China
| | - Jinlei Wang
- Department of Internal Medicine, Taian Traffic Hospital, Taian, China
| | - Hualian Wu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB-CAS), Guangdong Key Laboratory of Marine Materia Medica (LMMM-GD), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xianjun Wang
- Department of Neurology, Linyi People’s Hospital, Linyi, China
| | - Zuncheng Zheng
- Department of Rehabilitation, Taian City Central Hospital, Taian, ChinaShandong
| | - Fengyuan Che
- Department of Neurology, Linyi People’s Hospital, Linyi, China
| | - Guojun Wang
- Department of Neurosurgery, Taian City Central Hospital, Taian, China
| |
Collapse
|
7
|
Ai Y, Wang B, Xiao S, Luo S, Wang Y. Tryptophan Side-Chain Oxidase Enzyme Suppresses Hepatocellular Carcinoma Growth through Degradation of Tryptophan. Int J Mol Sci 2021; 22:ijms222212428. [PMID: 34830310 PMCID: PMC8623686 DOI: 10.3390/ijms222212428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023] Open
Abstract
Tryptophan metabolism plays a role in the occurrence and development of hepatocellular carcinoma cells. By degrading certain amino acids, tumor growth can be limited while maintaining the body’s normal nutritional requirements. Tryptophan side-chain oxidase (TSO) enzyme can degrade tryptophan, and its inhibitory effect on hepatocellular carcinoma cells is worthy of further study. To investigate the degradation effect on tryptophan, TSO was isolated and purified from qq Pseudomonas. The reaction products were identified with high performance liquid chromatography (HPLC) and high-performance liquid chromatography tandem mass spectrometry (HPLC-MS). De novo sequencing provided the complete amino acid sequence of TSO. The results of CCK-8, colony formation, transwell, and qPCR confirmed that TSO had inhibitory effects on the proliferation and migration of HCCLM3 (human hepatocarcinoma cell line) and HepG2 cells. The results of flow cytometry confirmed its apoptotic activity. In animal experiments, we found that the tumor-suppressive effect was better in the oncotherapy group than the intraperitoneal injection group. The results of immunohistochemistry also suggested that TSO could inhibit proliferation and promote apoptosis. In conclusion, a specific enzyme that can degrade tryptophan and inhibit the growth of hepatoma cells was authenticated, and its basic information was obtained by extraction/purification and amino acid sequencing.
Collapse
Affiliation(s)
| | | | | | | | - Yefu Wang
- Correspondence: ; Tel.: +86-13907185508
| |
Collapse
|
8
|
Pham TH, Rao S, Cheng TC, Wang PC, Chen SC. The moonlighting protein fructose 1,6-bisphosphate aldolase as a potential vaccine candidate against Photobacterium damselae subsp. piscicida in Asian sea bass (Lates calcarifer). Dev Comp Immunol 2021; 124:104187. [PMID: 34186149 DOI: 10.1016/j.dci.2021.104187] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Vaccination is the most effective, safe, and environmentally friendly method to prevent the outbreak of Photobacterium damselae subsp. piscicida (Phdp), a dangerous pathogen in aquaculture worldwide. Here, recombinant proteins of catalase, superoxide dismutase, isocitrate dehydrogenase, fructose 1,6-bisphosphate aldolase (Fba), and a mixture of all four proteins were investigated for their immunoprotective effects against photobacteriosis in Asian sea bass (Lates calcarifer). After immunization, experimental fish showed an increase in specific antibody levels and lysozyme activities, especially the Fba group. After a lethal challenge with Phdp strain AOD105021, the Fba group achieved the highest relative percentage of survival rate (70.21%) and a significantly lower bacterial load in the spleens than other groups 3 days after infection. The results suggest that Fba is a good candidate for subunit vaccine development against photobacteriosis in fish.
Collapse
Affiliation(s)
- Trung Hieu Pham
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan.
| | - Shreesha Rao
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan.
| | - Ta-Chih Cheng
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan; Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan.
| | - Pei-Chi Wang
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan; Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan; Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan; Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan.
| | - Shih-Chu Chen
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan; Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan; Research Centre for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan; Research Centre for Fish Vaccine and Diseases, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan; Southern Taiwan Fish Diseases Research Centre, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan.
| |
Collapse
|
9
|
Gautom T, Dheeman D, Levy C, Butterfield T, Alvarez Gonzalez G, Le Roy P, Caiger L, Fisher K, Johannissen L, Dixon N. Structural basis of terephthalate recognition by solute binding protein TphC. Nat Commun 2021; 12:6244. [PMID: 34716322 PMCID: PMC8556258 DOI: 10.1038/s41467-021-26508-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/06/2021] [Indexed: 11/08/2022] Open
Abstract
Biological degradation of Polyethylene terephthalate (PET) plastic and assimilation of the corresponding monomers ethylene glycol and terephthalate (TPA) into central metabolism offers an attractive route for bio-based molecular recycling and bioremediation applications. A key step is the cellular uptake of the non-permeable TPA into bacterial cells which has been shown to be dependent upon the presence of the key tphC gene. However, little is known from a biochemical and structural perspective about the encoded solute binding protein, TphC. Here, we report the biochemical and structural characterisation of TphC in both open and TPA-bound closed conformations. This analysis demonstrates the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA and closely related analogues. Further phylogenetic and genomic context analysis of the tph genes reveals homologous operons as a genetic resource for future biotechnological and metabolic engineering efforts towards circular plastic bio-economy solutions.
Collapse
Affiliation(s)
- Trishnamoni Gautom
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
- Department of Biotechnology, Gauhati University, Guwahati, Assam, India
- Royal School of Bio-Sciences, Royal Global University, Guwahati, Assam, India
| | - Dharmendra Dheeman
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Colin Levy
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Thomas Butterfield
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Guadalupe Alvarez Gonzalez
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Philip Le Roy
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Lewis Caiger
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Karl Fisher
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Linus Johannissen
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB) and Department of Chemistry, The University of Manchester, Manchester, UK.
| |
Collapse
|
10
|
Zorigt T, Furuta Y, Simbotwe M, Ochi A, Tsujinouchi M, Shawa M, Shimizu T, Isoda N, Enkhtuya J, Higashi H. Development of ELISA based on Bacillus anthracis capsule biosynthesis protein CapA for naturally acquired antibodies against anthrax. PLoS One 2021; 16:e0258317. [PMID: 34634075 PMCID: PMC8504768 DOI: 10.1371/journal.pone.0258317] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/18/2021] [Accepted: 09/23/2021] [Indexed: 11/30/2022] Open
Abstract
Anthrax is a zoonotic disease caused by the gram-positive spore-forming bacterium Bacillus anthracis. Detecting naturally acquired antibodies against anthrax sublethal exposure in animals is essential for anthrax surveillance and effective control measures. Serological assays based on protective antigen (PA) of B. anthracis are mainly used for anthrax surveillance and vaccine evaluation. Although the assay is reliable, it is challenging to distinguish the naturally acquired antibodies from vaccine-induced immunity in animals because PA is cross-reactive to both antibodies. Although additional data on the vaccination history of animals could bypass this problem, such data are not readily accessible in many cases. In this study, we established a new enzyme-linked immunosorbent assay (ELISA) specific to antibodies against capsule biosynthesis protein CapA antigen of B. anthracis, which is non-cross-reactive to vaccine-induced antibodies in horses. Using in silico analyses, we screened coding sequences encoded on pXO2 plasmid, which is absent in the veterinary vaccine strain Sterne 34F2 but present in virulent strains of B. anthracis. Among the 8 selected antigen candidates, capsule biosynthesis protein CapA (GBAA_RS28240) and peptide ABC transporter substrate-binding protein (GBAA_RS28340) were detected by antibodies in infected horse sera. Of these, CapA has not yet been identified as immunoreactive in other studies to the best of our knowledge. Considering the protein solubility and specificity of B. anthracis, we prepared the C-terminus region of CapA, named CapA322, and developed CapA322-ELISA based on a horse model. Comparative analysis of the CapA322-ELISA and PAD1-ELISA (ELISA uses domain one of the PA) showed that CapA322-ELISA could detect anti-CapA antibodies in sera from infected horses but was non-reactive to sera from vaccinated horses. The CapA322-ELISA could contribute to the anthrax surveillance in endemic areas, and two immunoreactive proteins identified in this study could be additives to the improvement of current or future vaccine development.
Collapse
Affiliation(s)
- Tuvshinzaya Zorigt
- Division of Infection and Immunity, International Institute for Zoonosis Control (Former Research Center for Zoonosis Control), Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshikazu Furuta
- Division of Infection and Immunity, International Institute for Zoonosis Control (Former Research Center for Zoonosis Control), Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Manyando Simbotwe
- Division of Infection and Immunity, International Institute for Zoonosis Control (Former Research Center for Zoonosis Control), Hokkaido University, Sapporo, Japan
| | - Akihiro Ochi
- Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Mai Tsujinouchi
- Division of Infection and Immunity, International Institute for Zoonosis Control (Former Research Center for Zoonosis Control), Hokkaido University, Sapporo, Japan
| | - Misheck Shawa
- Division of Infection and Immunity, International Institute for Zoonosis Control (Former Research Center for Zoonosis Control), Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Tomoko Shimizu
- Division of Infection and Immunity, International Institute for Zoonosis Control (Former Research Center for Zoonosis Control), Hokkaido University, Sapporo, Japan
| | - Norikazu Isoda
- Laboratory of Microbiology, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | | | - Hideaki Higashi
- Division of Infection and Immunity, International Institute for Zoonosis Control (Former Research Center for Zoonosis Control), Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- * E-mail:
| |
Collapse
|
11
|
Semache N, Benamia F, Kerouaz B, Belhaj IS, Bounour S, Belghith H, Gargouri A, Ladjama A, Djeghaba Z. Artificial Neural Networks and Response Surface Methodology Approach for Optimization of an Eco-Friendly and Detergent-Stable Lipase Production from Actinomadura Keratinilytica Strain Cpt29. Acta Chim Slov 2021; 68:575-586. [PMID: 34897543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
This work mainly focused on the production of an efficient, economical, and eco-friendly lipase (AKL29) from Actinomadura keratinilytica strain Cpt29 isolated from poultry compost in north east of Algeria, for use in detergent industries. AKL29 shows a significant lipase activity (45 U/mL) towards hydrolyzed triacylglycerols, indicating that it is a true lipase. For maximum lipase production the modeling and optimization of potential culture parameters such as incubation temperature, cultivation time, and Tween 80 (v/v) were built using RSM and ANN approaches. The results show that both the two models provided good quality predictions, yet the ANN showed a clear superiority over RSM for both data fitting and estimation capabilities. A 4.1-fold increase in lipase production was recorded under the following optimal condition: incubation temperature (37.9 °C), cultivation time (111 h), and Tween 80 (3.27%, v/v). Furthermore, the partially purified lipase showed good stability, high compatibility, and significant wash performance with various commercial laundry detergents, making this novel lipase a promising potential candidate for detergent industries.
Collapse
|
12
|
Silchenko AS, Rasin AB, Zueva AO, Kusaykin MI, Zvyagintseva TN, Rubtsov NK, Ermakova SP. Discovery of a fucoidan endo-4O-sulfatase: Regioselective 4O-desulfation of fucoidans and its effect on anticancer activity in vitro. Carbohydr Polym 2021; 271:118449. [PMID: 34364583 DOI: 10.1016/j.carbpol.2021.118449] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 03/23/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022]
Abstract
Fucoidans are a class of sulfated fucose-containing bioactive polysaccharides produced by brown algae. The biological effects exhibited by fucoidans are thought to be related to their sulfation. However, the lack of methods for sulfation control does not allow for a reliable conclusion about the influence of the position of certain sulfate groups on the observed biological effects. We identified the gene encoding the endo-acting fucoidan sulfatase swf5 in the marine bacterium Wenyingzhuangia fucanilytica CZ1127T. This is the first report on the sequence of fucoidan endo-sulfatase. Sulfatase SWF5 belongs to the subfamily S1_22 of the family S1. SWF5 was shown to remove 4O-sulfation in fucoidans composed from the alternating α-(1→3)- and α-(1→4)-linked residues of sulfated L-fucose but not from fucoidans with the α-(1→3)-linked backbone. The endo-sulfatase was used to selectively prepare 4O-desulfated fucoidan derivatives. It was shown that the 4O-desulfated fucoidans inhibit colony formation of DLD-1 and MCF-7 cells less effectively than unmodified fucoidans. Presumably, 4O-sulfation makes a significant contribution to the anticancer activity of fucoidans.
Collapse
Affiliation(s)
- A S Silchenko
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia.
| | - A B Rasin
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia
| | - A O Zueva
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia
| | - M I Kusaykin
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia
| | - T N Zvyagintseva
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia
| | - N K Rubtsov
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia
| | - S P Ermakova
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia.
| |
Collapse
|
13
|
Liu J, Tassinari M, Souza DP, Naskar S, Noel JK, Bohuszewicz O, Buck M, Williams TA, Baum B, Low HH. Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. Cell 2021; 184:3660-3673.e18. [PMID: 34166615 PMCID: PMC8281802 DOI: 10.1016/j.cell.2021.05.041] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/24/2020] [Accepted: 05/25/2021] [Indexed: 12/31/2022]
Abstract
Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life.
Collapse
Affiliation(s)
- Jiwei Liu
- Department of Infectious Disease, Imperial College, London, UK
| | | | - Diorge P Souza
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Souvik Naskar
- Department of Infectious Disease, Imperial College, London, UK
| | - Jeffrey K Noel
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Martin Buck
- Department of Life Sciences, Imperial College, London, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Buzz Baum
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK; Institute for the Physics of Living Systems, University College London, London, UK.
| | - Harry H Low
- Department of Infectious Disease, Imperial College, London, UK.
| |
Collapse
|
14
|
Gurunathan R, Huang B, Ponnusamy VK, Hwang JS, Dahms HU. Novel recombinant keratin degrading subtilisin like serine alkaline protease from Bacillus cereus isolated from marine hydrothermal vent crabs. Sci Rep 2021; 11:12007. [PMID: 34099743 PMCID: PMC8185006 DOI: 10.1038/s41598-021-90375-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/20/2021] [Indexed: 11/25/2022] Open
Abstract
Microbial secondary metabolites from extreme environments like hydrothermal vents are a promising source for industrial applications. In our study the protease gene from Bacillus cereus obtained from shallow marine hydrothermal vents in the East China Sea was cloned, expressed and purified. The protein sequence of 38 kDa protease SLSP-k was retrieved from mass spectrometry and identified as a subtilisin serine proteinase. The novel SLSP-k is a monomeric protein with 38 amino acid signal peptides being active over wide pH (7-11) and temperature (40-80 °C) ranges, with maximal hydrolytic activities at pH 10 and at 50 °C temperature. The hydrolytic activity is stimulated by Ca2+, Co2+, Mn2+, and DTT. It is inhibited by Fe2+, Cd2+, Cu2+, EDTA, and PMSF. The SLSP-k is stable in anionic, non-anionic detergents, and solvents. The ability to degrade keratin in chicken feather and hair indicates that this enzyme is suitable for the degradation of poultry waste without the loss of nutritionally essential amino acids which otherwise are lost in hydrothermal processing. Therefore, the proteinase is efficient in environmental friendly bioconversion of animal waste into fertilizers or value added products such as secondary animal feedstuffs.
Collapse
Affiliation(s)
- Revathi Gurunathan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
| | - Bin Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
- Regenerative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
| | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan.
- Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung, 20224, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan.
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan.
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan.
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan.
| |
Collapse
|
15
|
Meng J, Wang YY, Hao YP, Zhang SB, Ding CH, You YZ. Coating function and stabilizing effects of surface layer protein from Lactobacillus acidophilus ATCC 4356 on liposomes. Int J Biol Macromol 2021; 183:457-462. [PMID: 33933546 DOI: 10.1016/j.ijbiomac.2021.04.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/07/2021] [Accepted: 04/22/2021] [Indexed: 11/30/2022]
Abstract
Surface layer proteins (SLPs) are crystalline arrays in the outermost layer of cell envelope in many archaea and bacteria. SLPs subunits have the ability to reassemble on the surface of lipid layers. In this work, the SLP from Lactobacillus acidophilus ATCC 4356 was extracted and reassembled on the surface of positively charged liposomes composed of dipalmitoyl phosphatidylcholine, cholesterol and octadecylamine. Zeta potentials and particle size were determined to describe the adsorption process of SLP on liposomes. The liposomes completely coated with SLP were observed by transmission electron microscope. To investigate the stabilizing effects of SLP on liposomes, carboxyfluorescein (CF) was encapsulated and its leakage was determined as an evaluation index. The results showed that the L. acidophilus ATCC 4356 SLP significantly (P < 0.05) increased the stability of the liposomes in the course of thermal challenge. Furthermore, SLP was able to reduce the aggregation of liposomes in serum. Storage stability of liposomes was performed at 25 °C, 4 °C and -20 °C for 90 days. And the SLP-coated liposomes released less CF than the control liposomes during storage at the three evaluated temperatures. Our findings extended the application field of Lactobacillus SLPs and introduced a novel nanocarrier system with good chemical stability.
Collapse
Affiliation(s)
- Jun Meng
- College of Food Science and Engineering, Henan University of Technology, 100 Lianhua Road, Zhengzhou, Henan Province 450001, China.
| | - Yan-Yang Wang
- College of Food Science and Engineering, Henan University of Technology, 100 Lianhua Road, Zhengzhou, Henan Province 450001, China
| | - Yun-Peng Hao
- College of Food Science and Technology, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, Henan Province 450002, China
| | - Shao-Bing Zhang
- College of Food Science and Engineering, Henan University of Technology, 100 Lianhua Road, Zhengzhou, Henan Province 450001, China
| | - Chang-He Ding
- College of Food Science and Engineering, Henan University of Technology, 100 Lianhua Road, Zhengzhou, Henan Province 450001, China
| | - Yan-Zhi You
- College of Food Science and Engineering, Henan University of Technology, 100 Lianhua Road, Zhengzhou, Henan Province 450001, China
| |
Collapse
|
16
|
Du YE, Bae ES, Lim Y, Cho JC, Nam SJ, Shin J, Lee SK, Nam SI, Oh DC. Svalbamides A and B, Pyrrolidinone-Bearing Lipodipeptides from Arctic Paenibacillus sp. Mar Drugs 2021; 19:229. [PMID: 33920625 PMCID: PMC8073366 DOI: 10.3390/md19040229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 11/23/2022] Open
Abstract
Two new secondary metabolites, svalbamides A (1) and B (2), were isolated from a culture extract of Paenibacillus sp. SVB7 that was isolated from surface sediment from a core (HH17-1085) taken in the Svalbard archipelago in the Arctic Ocean. The combinational analysis of HR-MS and NMR spectroscopic data revealed the structures of 1 and 2 as being lipopeptides bearing 3-amino-2-pyrrolidinone, d-valine, and 3-hydroxy-8-methyldecanoic acid. The absolute configurations of the amino acid residues in svalbamides A and B were determined using the advanced Marfey's method, in which the hydrolysates of 1 and 2 were derivatized with l- and d- forms of 1-fluoro-2,4-dinitrophenyl-5-alanine amide (FDAA). The absolute configurations of 1 and 2 were completely assigned by deducing the stereochemistry of 3-hydroxy-8-methyldecanoic acid based on DP4 calculations. Svalbamides A and B induced quinone reductase activity in Hepa1c1c7 murine hepatoma cells, indicating that they represent chemotypes with a potential for functioning as chemopreventive agents.
Collapse
Affiliation(s)
- Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (Y.E.D.); (E.S.B.); (J.S.); (S.K.L.)
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (Y.E.D.); (E.S.B.); (J.S.); (S.K.L.)
| | - Yeonjung Lim
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (Y.L.); (J.-C.C.)
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Korea; (Y.L.); (J.-C.C.)
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Korea;
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (Y.E.D.); (E.S.B.); (J.S.); (S.K.L.)
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (Y.E.D.); (E.S.B.); (J.S.); (S.K.L.)
| | - Seung-Il Nam
- Korea Polar Research Institute, Incheon 21990, Korea;
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (Y.E.D.); (E.S.B.); (J.S.); (S.K.L.)
| |
Collapse
|
17
|
Sun X, Hill P, Liu J, Qian J, Ma Y, Zhou S. Marine-Source Quorum Quenching Enzyme YtnP to Improve Hygiene Quality in Dental Units. Mar Drugs 2021; 19:md19040225. [PMID: 33923695 PMCID: PMC8073825 DOI: 10.3390/md19040225] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/02/2022] Open
Abstract
Biofilm in dental unit water lines may pose a health risk to patients and dental practitioners. An AdiC-like quorum quenching enzyme, YtnP, was cloned from a deep-sea probiotic Bacillus velezensis, and heterologously expressed in E. coli to examine the application on the improvement of hygiene problems caused by biofilm infection of Pseudomonas aeruginosa in dental units. Pseudomonas bacteria were isolated from dental chair units and used to grow static biofilms in the laboratory. A water filter system was designed to test the antifouling activity of YtnP in Laboratory, to simulate the biofilm contamination on water filter in dental unit water lines. The results demonstrated that the enzyme of YtnP was able to degrade the N-acyl homoserine lactones, significantly inhibited the EPS generation, biofilm formation, and virulence factors production (pyocyanin and rhamnolipid) of P. aeruginosa, and was efficient on the antifouling against P. aeruginosa. The findings in this study indicated the possibility of YtnP as novel disinfectant reagent for hygiene treatment in dental units.
Collapse
Affiliation(s)
- Xiaohui Sun
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (J.Q.); (Y.M.); (S.Z.)
- Correspondence: (X.S.); (P.H.); Tel.: +86-595-616-2305 (X.S.)
| | - Philip Hill
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughbrough LE12 5RD, UK
- Correspondence: (X.S.); (P.H.); Tel.: +86-595-616-2305 (X.S.)
| | - Jia Liu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (J.Q.); (Y.M.); (S.Z.)
| | - Jing Qian
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (J.Q.); (Y.M.); (S.Z.)
| | - Yuting Ma
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (J.Q.); (Y.M.); (S.Z.)
| | - Shufeng Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (J.Q.); (Y.M.); (S.Z.)
| |
Collapse
|
18
|
Pang Y, Yang J, Chen X, Jia Y, Li T, Jin J, Liu H, Jiang L, Hao Y, Zhang H, Xie Y. An Antifungal Chitosanase from Bacillus subtilis SH21. Molecules 2021; 26:molecules26071863. [PMID: 33806149 PMCID: PMC8036696 DOI: 10.3390/molecules26071863] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
Bacillus subtilis SH21 was observed to produce an antifungal protein that inhibited the growth of F. solani. To purify this protein, ammonium sulfate precipitation, gel filtration chromatography, and ion-exchange chromatography were used. The purity of the purified product was 91.33% according to high-performance liquid chromatography results. Sodium dodecyl sulfate–polyacrylamide gel electrophoresis and liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis revealed that the molecular weight of the protein is 30.72 kDa. The results of the LC–MS/MS analysis and a subsequent sequence-database search indicated that this protein was a chitosanase, and thus, we named it chitosanase SH21. Scanning and transmission electron microscopy revealed that chitosanase SH21 appeared to inhibit the growth of F. solani by causing hyphal ablation, distortion, or abnormalities, and cell-wall depression. The minimum inhibitory concentration of chitosanase SH21 against F. solani was 68 µg/mL. Subsequently, the corresponding gene was cloned and sequenced, and sequence analysis indicated an open reading frame of 831 bp. The predicted secondary structure indicated that chitosanase SH21 has a typical a-helix from the glycoside hydrolase (GH) 46 family. The tertiary structure shared 40% similarity with that of Streptomyces sp. N174. This study provides a theoretical basis for a topical cream against fungal infections in agriculture and a selection marker on fungi.
Collapse
Affiliation(s)
- Yuanxiang Pang
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
| | - Jianjun Yang
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
| | - Xinyue Chen
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
| | - Yu Jia
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
| | - Tong Li
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
| | - Junhua Jin
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
| | - Hui Liu
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
| | - Linshu Jiang
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
| | - Yanling Hao
- Key Laboratory of Functional Dairy Science of Beijing and Chinese Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China;
| | - Hongxing Zhang
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
- Correspondence: (H.Z.); (Y.X.)
| | - Yuanhong Xie
- Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticides, Beijing Laboratory for Food Quality and Safety, Beijing Engineering Laboratory of Probiotics Key Technology Development, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, Food Science and Engineering College, Beijing University of Agriculture, Beijing 102206, China; (Y.P.); (J.Y.); (X.C.); (Y.J.); (T.L.); (J.J.); (H.L.); (L.J.)
- Correspondence: (H.Z.); (Y.X.)
| |
Collapse
|
19
|
Chen GE, Adams NBP, Jackson PJ, Dickman MJ, Hunter CN. How the O 2-dependent Mg-protoporphyrin monomethyl ester cyclase forms the fifth ring of chlorophylls. Nat Plants 2021; 7:365-375. [PMID: 33731920 PMCID: PMC7610348 DOI: 10.1038/s41477-021-00876-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/08/2021] [Indexed: 05/19/2023]
Abstract
Mg-protoporphyrin IX monomethyl ester (MgPME) cyclase catalyses the formation of the isocyclic ring, producing protochlorophyllide a and contributing substantially to the absorption properties of chlorophylls and bacteriochlorophylls. The O2-dependent cyclase is found in both oxygenic phototrophs and some purple bacteria. We overproduced the simplest form of the cyclase, AcsF, from Rubrivivax gelatinosus, in Escherichia coli. In biochemical assays the di-iron cluster within AcsF is reduced by ferredoxin furnished by NADPH and ferredoxin:NADP+ reductase, or by direct coupling to Photosystem I photochemistry, linking cyclase to the photosynthetic electron transport chain. Kinetic analyses yielded a turnover number of 0.9 min-1, a Michaelis-Menten constant of 7.0 µM for MgPME and a dissociation constant for MgPME of 0.16 µM. Mass spectrometry identified 131-hydroxy-MgPME and 131-keto-MgPME as cyclase reaction intermediates, revealing the steps that form the isocyclic ring and completing the work originated by Sam Granick in 1950.
Collapse
Affiliation(s)
- Guangyu E Chen
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Nathan B P Adams
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Philip J Jackson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
| |
Collapse
|
20
|
Mäkinen JJ, Shin Y, Vieras E, Virta P, Metsä-Ketelä M, Murakami KS, Belogurov GA. The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases. Nat Commun 2021; 12:796. [PMID: 33542236 PMCID: PMC7862312 DOI: 10.1038/s41467-021-21005-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/24/2020] [Accepted: 01/06/2021] [Indexed: 01/18/2023] Open
Abstract
RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2'dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2'OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2'dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here, we show that a conserved Arg residue uses a two-pronged strategy to select against 2'dNTPs in multi-subunit RNAPs. The conserved Arg interacts with the 2'OH group to promote NTP binding, but selectively inhibits incorporation of 2'dNTPs by interacting with their 3'OH group to favor the catalytically-inert 2'-endo conformation of the deoxyribose moiety. This deformative action is an elegant example of an active selection against a substrate that is a substructure of the correct substrate. Our findings provide important insights into the evolutionary origins of biopolymers and the design of selective inhibitors of viral RNAPs.
Collapse
Affiliation(s)
- Janne J Mäkinen
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Yeonoh Shin
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Eeva Vieras
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, Finland
| | | | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | | |
Collapse
|
21
|
Rodarte JV, Abendroth J, Edwards TE, Lorimer DD, Staker BL, Zhang S, Myler PJ, McLaughlin KJ. Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis. Acta Crystallogr F Struct Biol Commun 2021; 77:54-60. [PMID: 33620038 PMCID: PMC7900926 DOI: 10.1107/s2053230x21001497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022] Open
Abstract
Rickettsia felis, a Gram-negative bacterium that causes spotted fever, is of increasing interest as an emerging human pathogen. R. felis and several other Rickettsia strains are classed as National Institute of Allergy and Infectious Diseases priority pathogens. In recent years, R. felis has been shown to be adaptable to a wide range of hosts, and many fevers of unknown origin are now being attributed to this infectious agent. Here, the structure of acetoacetyl-CoA reductase from R. felis is reported at a resolution of 2.0 Å. While R. felis acetoacetyl-CoA reductase shares less than 50% sequence identity with its closest homologs, it adopts a fold common to other short-chain dehydrogenase/reductase (SDR) family members, such as the fatty-acid synthesis II enzyme FabG from the prominent pathogens Staphylococcus aureus and Bacillus anthracis. Continued characterization of the Rickettsia proteome may prove to be an effective means of finding new avenues of treatment through comparative structural studies.
Collapse
Affiliation(s)
- Justas V. Rodarte
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, New York, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Sunny Zhang
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, New York, USA
| |
Collapse
|
22
|
Koteshwara A, Philip NV, Aranjani JM, Hariharapura RC, Volety Mallikarjuna S. A set of simple methods for detection and extraction of laminarinase. Sci Rep 2021; 11:2489. [PMID: 33510321 PMCID: PMC7844030 DOI: 10.1038/s41598-021-81807-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/04/2020] [Indexed: 11/08/2022] Open
Abstract
A carefully designed ammonium sulfate precipitation will simplify extraction of proteins and is considered to be a gold standard among various precipitation methods. Therefore, optimization of ammonium sulfate precipitation can be an important functional step in protein purification. The presence of high amounts of ammonium sulphate precludes direct detection of many enzymatically active proteins including reducing sugar assays (e.g. Nelson-Somogyi, Reissig and 3,5-dinitrosalicylic acid methods) for assessing carbohydrases (e.g. laminarinase (β (1-3)-glucanohydrolase), cellulases and chitinases). In this study, a simple method was developed using laminarin infused agarose plate for the direct analysis of the ammonium sulphate precipitates from Streptomyces rimosus AFM-1. The developed method is simple and convenient that can give accurate results even in presence of ammonium sulfate in the crude precipitates. Laminarin is a translucent substrate requiring the use of a stain to visualize the zones of hydrolysis in a plate assay. A very low-cost and locally available fluorescent optical fabric brightener Tinopal CBS-X has been used as a stain to detect the zones of hydrolysis. We also report simple methods to prepare colloidal chitin and cell free supernatant in this manuscript.
Collapse
Affiliation(s)
- Ananthamurthy Koteshwara
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Nancy V Philip
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Jesil Mathew Aranjani
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Raghu Chandrashekhar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Subrahmanyam Volety Mallikarjuna
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India.
| |
Collapse
|
23
|
Lu Q, Okanda T, Yang Y, Khalifa HO, Haque A, Takemura H, Matsumoto T. High-Speed Quenching Probe-Polymerase Chain Reaction Assay for the Rapid Detection of Carbapenemase-Producing Gene Using GENECUBE: A Fully Automatic Gene Analyzer. Mol Diagn Ther 2021; 25:231-238. [PMID: 33453050 DOI: 10.1007/s40291-020-00511-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND The prevalence of carbapenemase-producing organisms (CPOs) globally poses a public health threat; however, detecting carbapenemases is a challenge because of their variety. METHODS GENECUBE, a fully automated gene analyzer, detects a target gene in a short time and simultaneously detects its single nucleotide polymorphism. We used this property to develop for the first time a rapid assay for detecting CPOs from cultured bacteria using GENECUBE. The original primer-probe sets were used to detect blaKPC, blaIMP, blaVIM, blaNDM, and blaOXA-48-like from 149 CPOs (nine types) and 61 non-CPOs. RESULTS The sensitivity, specificity, and positive and negative predictions of the GENECUBE assay were 100%. This assay detected carbapenemase single-producers and carbapenemase co-producers with 100% accuracy. The time required for detects of four types of carbapenemase at one run was about 30 min, but it took about 1 h to detect all five types. In addition, this assay performed the rapid detection and classification of blaOXA-48, blaOXA-181, blaOXA-232, and blaOXA-244 simultaneously. CONCLUSIONS The GENECUBE assay is a promising tool for controlling the spread of CPOs and helping to select accurate and rapid antibiotic therapies.
Collapse
Affiliation(s)
- Qi Lu
- Department of Infectious Diseases, International University of Health and Welfare, Narita, Japan
- Department of Neonatology, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Takashi Okanda
- Department of Infectious Diseases, International University of Health and Welfare, Narita, Japan.
- Department of Microbiology, St. Marianna University School of Medicine, Kawasaki, Japan.
| | - Yu Yang
- Department of Infectious Diseases, International University of Health and Welfare, Narita, Japan
| | - Hazim O Khalifa
- Department of Infectious Diseases, International University of Health and Welfare, Narita, Japan
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - Anwarul Haque
- Department of Infectious Diseases, International University of Health and Welfare, Narita, Japan
| | - Hiromu Takemura
- Department of Microbiology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Tetsuya Matsumoto
- Department of Infectious Diseases, International University of Health and Welfare, Narita, Japan
| |
Collapse
|
24
|
Marcos-Fernández R, Ruiz L, Blanco-Míguez A, Margolles A, Sánchez B. Precision modification of the human gut microbiota targeting surface-associated proteins. Sci Rep 2021; 11:1270. [PMID: 33446697 PMCID: PMC7809461 DOI: 10.1038/s41598-020-80187-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
This work describes a new procedure that allows the targeted modification of the human gut microbiota by using antibodies raised against bacterial surface-associated proteins specific to the microorganism of interest. To this end, a polyclonal antibody recognising the surface-associated protein Surface Layer Protein A of Lactobacillus acidophilus DSM20079T was developed. By conjugating this antibody with fluorescent probes and magnetic particles, we were able to specifically identify this bacterium both in a synthetic, and in real gut microbiotas by means of a flow cytometry approach. Further, we demonstrated the applicability of this antibody to deplete complex human gut microbiotas from L. acidophilus in a single step. L. acidophilus was found to interact with other bacteria both in synthetic and in real microbiotas, as reflected by its concomitant depletion together with other species. Further optimization of the procedure including a trypsin step enabled to achieve the selective and complete isolation of this species. Depleting a single species from a gut microbiota, using antibodies recognizing specific cell surface elements of the target organism, will open up novel ways to tackle research on the specific immunomodulatory and metabolic contributions of a bacterium of interest in the context of a complex human gut microbiota, including the investigation into therapeutic applications by adding/depleting a key bacterium. This represents the first work in which an antibody/flow-cytometry based application enabled the targeted edition of human gut microbiotas, and represents the basis for the design of precision microbiome-based therapies.
Collapse
Affiliation(s)
- Raquel Marcos-Fernández
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Aitor Blanco-Míguez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| |
Collapse
|
25
|
Sahin-Tóth J, Kovács E, Tóthpál A, Juhász J, Forró B, Bányai K, Havril K, Horváth A, Ghidán Á, Dobay O. Whole genome sequencing of coagulase positive staphylococci from a dog-and-owner screening survey. PLoS One 2021; 16:e0245351. [PMID: 33428679 PMCID: PMC7799803 DOI: 10.1371/journal.pone.0245351] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 10/07/2020] [Accepted: 12/28/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Staphylococcus aureus and S. pseudintermedius are the two most common coagulase positive staphylococci (CPS). S. aureus is more prevalent among humans, whereas S. pseudintermedius is more commonly isolated from dogs, however, both can cause various community and hospital acquired diseases in humans. METHODS In the current study we screened 102 dogs and 84 owners in Hungary. We tested the antibiotic susceptibility of the strains and in order to get a better picture of the clonal relationship of the strains, we used pulsed-field gel electrophoresis. In addition, three pairs of isolates with identical PFGE patterns were whole genome sequenced, MLST and spa types were established. RESULTS Carriage rate of S. aureus was 23.8% in humans and 4.9% in dogs and two cases of co-carriage were found among dogs and owners. S. pseudintermedius carriage rate was 2.4% and 34.3%, respectively, with only one co-carriage. The isolates were generally rather susceptible to the tested antibiotics, but high tetracycline resistance of S. pseudintermedius strains was noted. The co-carried isolates shared almost the same resistance genes (including tet(K), bla(Z), norA, mepR, lmrS, fosB) and virulence gene pattern. Apart from the common staphylococcal enzymes and cytotoxins, we found enterotoxins and exfoliative toxins as well. The two S. aureus pairs belonged to ST45-t630, ST45-t671 and ST15-t084, ST15-t084, respectively. The co-carried S. pseudintermedius isolates shared the same housekeeping gene alleles determining a novel sequence type ST1685. CONCLUSIONS Based on the genomic data, dog-owner co-carried strains displayed only insignificant differences therefore provided evidence for potential human-to-dog and dog-to-human transmission.
Collapse
Affiliation(s)
- Judit Sahin-Tóth
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Eszter Kovács
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Adrienn Tóthpál
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - János Juhász
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Barbara Forró
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Kata Havril
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Andrea Horváth
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Ágoston Ghidán
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Orsolya Dobay
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
- * E-mail:
| |
Collapse
|
26
|
Vigouroux A, Meyer T, Naretto A, Legrand P, Aumont-Nicaise M, Di Cicco A, Renoud S, Doré J, Lévy D, Vial L, Lavire C, Moréra S. Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum. Nucleic Acids Res 2021; 49:529-546. [PMID: 33313837 PMCID: PMC7797058 DOI: 10.1093/nar/gkaa1181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/05/2020] [Revised: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
A species-specific region, denoted SpG8-1b allowing hydroxycinnamic acids (HCAs) degradation is important for the transition between the two lifestyles (rhizospheric versus pathogenic) of the plant pathogen Agrobacterium fabrum. Indeed, HCAs can be either used as trophic resources and/or as induced-virulence molecules. The SpG8-1b region is regulated by two transcriptional regulators, namely, HcaR (Atu1422) and Atu1419. In contrast to HcaR, Atu1419 remains so far uncharacterized. The high-resolution crystal structures of two fortuitous citrate complexes, two DNA complexes and the apoform revealed that the tetrameric Atu1419 transcriptional regulator belongs to the VanR group of Pfam PF07729 subfamily of the large GntR superfamily. Until now, GntR regulators were described as dimers. Here, we showed that Atu1419 represses three genes of the HCAs catabolic pathway. We characterized both the effector and DNA binding sites and identified key nucleotides in the target palindrome. From promoter activity measurement using defective gene mutants, structural analysis and gel-shift assays, we propose N5,N10-methylenetetrahydrofolate as the effector molecule, which is not a direct product/substrate of the HCA degradation pathway. The Zn2+ ion present in the effector domain has both a structural and regulatory role. Overall, our work shed light on the allosteric mechanism of transcription employed by this GntR repressor.
Collapse
Affiliation(s)
- Armelle Vigouroux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Thibault Meyer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Anaïs Naretto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette, France
| | - Magali Aumont-Nicaise
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Aurélie Di Cicco
- Sorbonne Université, Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 26 rue d’Ulm, 75005 Paris, France
| | - Sébastien Renoud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Jeanne Doré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Daniel Lévy
- Sorbonne Université, Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 26 rue d’Ulm, 75005 Paris, France
| | - Ludovic Vial
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Céline Lavire
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Solange Moréra
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|
27
|
Abstract
Classical and culture-based methods for the identification and characterization of the biochemical properties of microorganisms are slow and labor-intensive. Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) has been used for the analysis of bacterial pathogen strain-specific diagnostic peptides allowing the characterization of bacterial strains.Here, we describe the analysis of tryptic digestion peptides by LC-ESI-MS/MS to search for specific biomarkers useful for the rapid identification of, on the one hand, the bacterial species and, on the other hand, the physiological and biochemical characteristics such as the expression of virulence factors, including toxins, immune-modulatory factors, and exoenzymes.
Collapse
Affiliation(s)
- Ana G Abril
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Ignacio Ortea
- Institute Maimónides of Biomedica Investigation of Córdoba, Córdoba, Spain
| | - Jorge Barros-Velázquez
- Departamento de Química Analítica, Nutrición y Bromatología, Area de Tecnología de los Alimentos, Facultad de Veterinaria, Campus Lugo, 27002, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Tomás G Villa
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Campus Sur 15782, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Pilar Calo-Mata
- Departamento de Química Analítica, Nutrición y Bromatología, Area de Tecnología de los Alimentos, Facultad de Veterinaria, Campus Lugo, 27002, Universidad de Santiago de Compostela, A Coruña, Spain.
| |
Collapse
|
28
|
Nilvebrant J, Åstrand M, Hober S. An Orthogonal Fusion Tag for Efficient Protein Purification. Methods Mol Biol 2021; 2178:159-166. [PMID: 33128750 DOI: 10.1007/978-1-0716-0775-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this chapter, we present an efficient method for stringent protein purification facilitated by a dual affinity tag referred to as ABDz1, which is based on a 5 kDa albumin-binding domain from Streptococcal Protein G. The small fusion tag enables an orthogonal affinity purification approach based on two successive and highly specific affinity purification steps. This approach is enabled by native binding of ABDz1 to human serum albumin and engineered binding to Staphylococcal Protein A, respectively. The ABDz1-tag can be fused to either terminus of a protein of interest and the purification steps can be carried out using standard laboratory equipment.
Collapse
Affiliation(s)
- Johan Nilvebrant
- Division of Protein Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH/AlbaNova University Center, Stockholm, Sweden
| | - Mikael Åstrand
- Division of Protein Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH/AlbaNova University Center, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry Biotechnology and Health (CBH), AlbaNova University Center, Stockholm, Sweden.
| |
Collapse
|
29
|
Abstract
OmpA-like proteins located in the outer bacterial membrane are potential virulence factors from the major periodontal pathogens Porphyromonas gingivalis and Tannerella forsythia. Our previous studies have shown that OmpA-like proteins are glycosylated by O-linked N-acetylglucosamine (O-GlcNAc) and are strongly reactive to wheat germ agglutinin (WGA) lectin, which shows sugar specificity to GlcNAc. Utilizing this property, we have developed a separation method for OmpA-like proteins by affinity chromatography using WGA lectin-agarose. The purity of enriched native OmpA-like proteins were confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Coomassie Brilliant Blue (CBB) staining. More importantly, the purified OmpA-like proteins formed a unique trimeric structure keeping their bioactivity intact. In this chapter, we describe a detailed procedure to separate OmpA-like proteins, which may be used to further progress the biological studies of OmpA-like proteins.
Collapse
Affiliation(s)
- Yukitaka Murakami
- Department of Dental Basic Education (Biology), Asahi University School of Dentistry, Mizuho, Gifu, Japan.
| | - Keiji Nagano
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Ishikari-Tobetsu, Hokkaido, Japan
| | - Yoshiaki Hasegawa
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nisshin, Aichi, Japan
| |
Collapse
|
30
|
Torres-Corral Y, Santos Y. Development of a real-time PCR assay for detection and quantification of Streptococcus iniae using the lactate permease gene. J Fish Dis 2021; 44:53-61. [PMID: 32959452 DOI: 10.1111/jfd.13267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
The aim of this study is the development and evaluation of a rapid and accurate quantitative PCR (qPCR)-based protocol for detection of zoonotic pathogen Streptococcus iniae in bacterial cultures and tissues of diseased fish. For this purpose, the lactate permease-encoding (lldY) gene was selected as a target for the design of S. iniae-specific primers based on comparative genomic analysis using 45 sequences retrieved from NCBI genome database. Specificity and applicability of these primers were tested using 115 bacterial strains and fish tissues infected with S. iniae. Sensitivity, reproducibility and efficiency of qPCR assay were also determined. The developed qPCR assay showed 100% specificity with pure bacterial cultures or DNA extracted from S. iniae or tissues of fish infected with the bacterium. The method has high sensitivity with a detection limit of 1.12 × 101 amplicon copies per assay (equivalent to 2 × 10-9 ng/µl) using bacterial DNA and of 1.44 × 101 gene copies in tissues of fish infected with S. iniae. In conclusion, this qPCR protocol provides an accurate and sensitive alternative for the identification of S. iniae and its detection on fish tissues that can be implemented as a routine tool in microbiological laboratories.
Collapse
Affiliation(s)
- Yolanda Torres-Corral
- Departamento de Microbiología y Parasitología, Instituto de Análisis Químico y Biológico (IAQBUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ysabel Santos
- Departamento de Microbiología y Parasitología, Instituto de Análisis Químico y Biológico (IAQBUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| |
Collapse
|
31
|
Bartlett SL, Diel DG, Wang L, Zec S, Laverack M, Martins M, Caserta LC, Killian ML, Terio K, Olmstead C, Delaney MA, Stokol T, Ivančić M, Jenkins-Moore M, Ingerman K, Teegan T, McCann C, Thomas P, McAloose D, Sykes JM, Calle PP. SARS-COV-2 INFECTION AND LONGITUDINAL FECAL SCREENING IN MALAYAN TIGERS ( PANTHERA TIGRIS JACKSONI), AMUR TIGERS ( PANTHERA TIGRIS ALTAICA ), AND AFRICAN LIONS ( PANTHERA LEO KRUGERI) AT THE BRONX ZOO, NEW YORK, USA. J Zoo Wildl Med 2021; 51:733-744. [PMID: 33480553 DOI: 10.1638/2020-0171] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged as the cause of a global pandemic in 2019-2020. In March 2020, New York City became the epicenter in the United States for the pandemic. On 27 March 2020, a Malayan tiger (Panthera tigris jacksoni) at the Bronx Zoo in New York City developed a cough and wheezing with subsequent inappetence. Over the next week, an additional Malayan tiger and two Amur tigers (Panthera tigris altaica) in the same building and three lions (Panthera leo krugeri) in a separate building also became ill. The index case was anesthetized for diagnostic workup. Physical examination and bloodwork results were unremarkable. Thoracic radiography and ultrasonography revealed a bronchial pattern with peribronchial cuffing and mild lung consolidation with alveolar-interstitial syndrome, respectively. SARS-CoV-2 RNA was identified by real-time, reverse transcriptase PCR (rRT-PCR) on oropharyngeal and nasal swabs and tracheal wash fluid. Cytologic examination of tracheal wash fluid revealed necrosis, and viral RNA was detected in necrotic cells by in situ hybridization, confirming virus-associated tissue damage. SARS-CoV-2 was isolated from the tracheal wash fluid of the index case, as well as the feces from one Amur tiger and one lion. Fecal viral RNA shedding was confirmed in all seven clinical cases and an asymptomatic Amur tiger. Respiratory signs abated within 1-5 days for most animals, although they persisted intermittently for 16 days in the index case. Fecal RNA shedding persisted for as long as 35 days beyond cessation of respiratory signs. This case series describes the clinical presentation, diagnostic evaluation, and management of tigers and lions infected with SARS-CoV-2 and describes the duration of viral RNA fecal shedding in these cases. This report documents the first known natural transmission of SARS-CoV-2 from humans to nondomestic felids.
Collapse
Affiliation(s)
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | | | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Leonardo Cardia Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Veterinary Services, United States Department of Agriculture, Ames, IA 50010, USA
| | - Karen Terio
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois, Brookfield, IL 60513, USA
| | - Colleen Olmstead
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA
| | - Martha A Delaney
- Zoological Pathology Program, College of Veterinary Medicine, University of Illinois, Brookfield, IL 60513, USA
| | - Tracy Stokol
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Melinda Jenkins-Moore
- National Veterinary Services Laboratories, Veterinary Services, United States Department of Agriculture, Ames, IA 50010, USA
| | | | - Taryn Teegan
- Wildlife Conservation Society, Bronx, NY 10460, USA
| | | | | | | | - John M Sykes
- Wildlife Conservation Society, Bronx, NY 10460, USA
| | - Paul P Calle
- Wildlife Conservation Society, Bronx, NY 10460, USA
| |
Collapse
|
32
|
Kulikova VV, Anufrieva NV, Kotlov MI, Morozova EA, Koval VS, Belyi YF, Revtovich SV, Demidkina TV. O-acetylhomoserine sulfhydrylase from Clostridium novyi. Cloning, expression of the gene and characterization of the enzyme. Protein Expr Purif 2020; 180:105810. [PMID: 33338587 DOI: 10.1016/j.pep.2020.105810] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/19/2022]
Abstract
The gene NT01CX_1210 of pathogenic bacterium Clostridium novyi annotated as encoding O-acetylhomoserine sulfhydrylase was cloned and expressed in Escherichia coli. The gene product having O-acetylhomoserine sulfhydrylase activity was purified to homogeneity. The protein showed molecular mass of approximately 184 kDa for the native form and 46 kDa for the subunit. The enzyme catalyzes the γ-substitution reaction of O-acetylhomoserine with maximum activity at pH 7.5. Analysis of C. novyi genome allowed us to suggest that there is only one way for the synthesis of l-methionine in the bacterium. The data obtained may provide the basis for further study of the role of OAHS in Clostridium bacteria and an ascertainment of its mechanism.
Collapse
Affiliation(s)
- Vitalia V Kulikova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia.
| | - Natalya V Anufrieva
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Mikhail I Kotlov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Elena A Morozova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Vasiliy S Koval
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Yury F Belyi
- Gamaleya National Research Centre of Epidemiology and Microbiology, Ministry of Health of Russian Federation, Gamaleya Street, 18, Moscow, 123098, Russia
| | - Svetlana V Revtovich
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| |
Collapse
|
33
|
Aliaga Goltsman DS, Alexander LM, Devoto AE, Albers JB, Liu J, Butterfield CN, Brown CT, Thomas BC. Novel Type V-A CRISPR Effectors Are Active Nucleases with Expanded Targeting Capabilities. CRISPR J 2020; 3:454-461. [PMID: 33146573 PMCID: PMC7757703 DOI: 10.1089/crispr.2020.0043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Indexed: 12/29/2022] Open
Abstract
Cas12a enzymes are quickly being adopted for use in a variety of genome-editing applications. These programmable nucleases are part of adaptive microbial immune systems, the natural diversity of which has been largely unexplored. Here, we identified novel families of Type V-A CRISPR nucleases through a large-scale analysis of metagenomes collected from a variety of complex environments, and developed representatives of these systems into gene-editing platforms. The nucleases display extensive protein variation and can be programmed by a single-guide RNA with specific motifs. The majority of these enzymes are part of systems recovered from uncultivated organisms, some of which also encode a divergent Type V effector. Biochemical analysis uncovered unexpected protospacer adjacent motif diversity, indicating that these systems will facilitate a variety of genome-engineering applications. The simplicity of guide sequences and activity in human cell lines suggest utility in gene and cell therapies.
Collapse
Affiliation(s)
| | | | | | | | - Jason Liu
- Metagenomi, Inc., Emeryville, California, USA
| | | | | | | |
Collapse
|
34
|
Orlando M, Pucciarelli S, Lotti M. Endolysins from Antarctic Pseudomonas Display Lysozyme Activity at Low Temperature. Mar Drugs 2020; 18:E579. [PMID: 33233712 PMCID: PMC7699920 DOI: 10.3390/md18110579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Organisms specialized to thrive in cold environments (so-called psychrophiles) produce enzymes with the remarkable ability to catalyze chemical reactions at low temperature. Cold activity relies on adaptive changes in the proteins' sequence and structural organization that result in high conformational flexibility. As a consequence of flexibility, several such enzymes are inherently heat sensitive. Cold-active enzymes are of interest for application in a number of bioprocesses, where cold activity coupled with easy thermal inactivation can be of advantage. We describe the biochemical and functional properties of two glycosyl hydrolases (named LYS177 and LYS188) of family 19 (GH19), identified in the genome of an Antarctic marine Pseudomonas. Molecular evolutionary analysis placed them in a group of characterized GH19 endolysins active on lysozyme substrates, such as peptidoglycan. Enzyme activity peaks at about 25-35 °C and 40% residual activity is retained at 5 °C. LYS177 and LYS188 are thermolabile, with Tm of 52 and 45 °C and half-lives of 48 and 12 h at 37 °C, respectively. Bioinformatics analyses suggest that low heat stability may be associated to temperature-driven increases in local flexibility occurring mainly in a specific region of the polypeptide that is predicted to contain hot spots for aggregation.
Collapse
Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, 20126 Milano, Italy;
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, 20126 Milano, Italy;
| |
Collapse
|
35
|
Doan CT, Tran TN, Nguyen VB, Nguyen AD, Wang SL. Utilization of Seafood Processing By-Products for Production of Proteases by Paenibacillus sp. TKU052 and Their Application in Biopeptides' Preparation. Mar Drugs 2020; 18:md18110574. [PMID: 33233577 PMCID: PMC7699763 DOI: 10.3390/md18110574] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Microbial fermentation of by-products is a renewable and efficient technique in the development of a range of useful products. In this study, protease synthesis by Paenibacillus sp. TKU052 was carried out on culture media containing some common seafood processing by-products (SPBPs) as the sole source of carbon and nitrogen (C/N). The most suitable C/N nutrition source for the production of proteases was found to be 3.0% (w/v) demineralized crab shells powder (deCSP) and maximal enzyme activity of 4.41 ± 0.16 U/mL was detected on the third day of the culture. Two proteases (P1 and P2) with a similar molecular weight of 31 kDa were successfully isolated and purified from the 3-day deCSP-containing medium. Both P1 and P2 exhibited the highest activity of gelatin hydrolysis at pH 6 and 60 °C. The gelatin hydrolysates catalyzed by Paenibacillus TKU052 proteases were evaluated for biological activities, including 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, angiotensin-I converting enzyme (ACE) inhibition, and prebiotic activities. The gelatin hydrolysates expressed 31.76–43.95% DPPH radical scavenging activity and 31.58–36.84% ACE inhibitory activity, which was higher than those from gelatin. Gelatin hydrolysates also showed the growth-enhancing effect on Bifidobacterium bifidum BCRC 14615 with an increase to 135.70–147.81%. In short, Paenibacillus sp. TKU052 could be a potential strain to utilize crab shell wastes to produce proteases for bio-active peptides’ preparation.
Collapse
Affiliation(s)
- Chien Thang Doan
- Department of Natural Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (C.T.D.); (T.N.T.)
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan
| | - Thi Ngoc Tran
- Department of Natural Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (C.T.D.); (T.N.T.)
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan
| | - Van Bon Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (V.B.N.); (A.D.N.)
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (V.B.N.); (A.D.N.)
| | - San-Lang Wang
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan
- Life Science Development Center, Tamkang University, New Taipei City 25137, Taiwan
- Correspondence: ; Tel.: +886-2-2621-5656; Fax: +886-2-2620-9924
| |
Collapse
|
36
|
Vuillemin M, Silchenko AS, Cao HTT, Kokoulin MS, Trang VTD, Holck J, Ermakova SP, Meyer AS, Mikkelsen MD. Functional Characterization of a New GH107 Endo-α-(1,4)-Fucoidanase from the Marine Bacterium Formosa haliotis. Mar Drugs 2020; 18:E562. [PMID: 33213084 PMCID: PMC7698502 DOI: 10.3390/md18110562] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 12/27/2022] Open
Abstract
Fucoidans from brown macroalgae are sulfated fucose-rich polysaccharides, that have several beneficial biological activities, including anti-inflammatory and anti-tumor effects. Controlled enzymatic depolymerization of the fucoidan backbone can help produce homogeneous, defined fucoidan products for structure-function research and pharmaceutical uses. However, only a few endo-fucoidanases have been described. This article reports the genome-based discovery, recombinant expression in Escherichia coli, stabilization, and functional characterization of a new bacterial endo-α-(1,4)-fucoidanase, Fhf1, from Formosa haliotis. Fhf1 catalyzes the cleavage of α-(1,4)-glycosidic linkages in fucoidans built of alternating α-(1,3)-/α-(1,4)-linked l-fucopyranosyl sulfated at C2. The native Fhf1 is 1120 amino acids long and belongs to glycoside hydrolase (GH) family 107. Deletion of the signal peptide and a 470 amino acid long C-terminal stretch led to the recombinant expression of a robust, minimized enzyme, Fhf1Δ470 (71 kDa). Fhf1Δ470 has optimal activity at pH 8, 37-40 °C, can tolerate up to 500 mM NaCl, and requires the presence of divalent cations, either Ca2+, Mn2+, Zn2+ or Ni2+, for maximal activity. This new enzyme has the potential to serve the need for controlled enzymatic fucoidan depolymerization to produce bioactive sulfated fucoidan oligomers.
Collapse
Affiliation(s)
- Marlene Vuillemin
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
| | - Artem S. Silchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia; (A.S.S.); (M.S.K); (S.P.E.)
| | - Hang Thi Thuy Cao
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam;
| | - Maxim S. Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia; (A.S.S.); (M.S.K); (S.P.E.)
| | - Vo Thi Dieu Trang
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam;
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
| | - Svetlana P. Ermakova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia; (A.S.S.); (M.S.K); (S.P.E.)
| | - Anne S. Meyer
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
| | - Maria Dalgaard Mikkelsen
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
| |
Collapse
|
37
|
Selezneva AI, Gutka HJ, Wolf NM, Qurratulain F, Movahedzadeh F, Abad-Zapatero C. Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis. Acta Crystallogr F Struct Biol Commun 2020; 76:524-535. [PMID: 33135671 PMCID: PMC7605111 DOI: 10.1107/s2053230x20013370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/05/2020] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of the class II fructose-1,6-bisphosphatase (FBPaseII) from the important pathogen Francisella tularensis is presented at 2.4 Å resolution. Its structural and functional relationships to the closely related phosphatases from Mycobacterium tuberculosis (MtFBPaseII) and Escherichia coli (EcFBPaseII) and to the dual phosphatase from Synechocystis strain 6803 are discussed. FBPaseII from F. tularensis (FtFBPaseII) was crystallized in a monoclinic crystal form (space group P21, unit-cell parameters a = 76.30, b = 100.17, c = 92.02 Å, β = 90.003°) with four chains in the asymmetric unit. Chain A had two coordinated Mg2+ ions in its active center, which is distinct from previous findings, and is presumably deactivated by their presence. The structure revealed an approximate 222 (D2) symmetry homotetramer analogous to that previously described for MtFBPaseII, which is formed by a crystallographic dyad and which differs from the exact tetramer found in EcFBPaseII at a 222 symmetry site in the crystal. Instead, the approximate homotetramer is very similar to that found in the dual phosphatase from Synechocystis, even though no allosteric effector was found in FtFBPase. The amino-acid sequence and folding of the active site of FtFBPaseII result in structural characteristics that are more similar to those of the previously published EcFBPaseII than to those of MtFBPaseII. The kinetic parameters of native FtFBPaseII were found to be in agreement with published studies. Kinetic analyses of the Thr89Ser and Thr89Ala mutations in the active site of the enzyme are consistent with the previously proposed mechanism for other class II bisphosphatases. The Thr89Ala variant enzyme was inactive but the Thr89Ser variant was partially active, with an approximately fourfold lower Km and Vmax than the native enzyme. The structural and functional insights derived from the structure of FtFBPaseII will provide valuable information for the design of specific inhibitors.
Collapse
Affiliation(s)
- Anna I. Selezneva
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Hiten J. Gutka
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Nina M. Wolf
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fnu Qurratulain
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| |
Collapse
|
38
|
Doukyu N, Ishikawa M. Cholesterol oxidase from Rhodococcus erythropolis with high specificity toward β-cholestanol and pytosterols. PLoS One 2020; 15:e0241126. [PMID: 33104755 PMCID: PMC7588053 DOI: 10.1371/journal.pone.0241126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/02/2020] [Accepted: 10/08/2020] [Indexed: 12/05/2022] Open
Abstract
Two genes (choRI and choRII) encoding cholesterol oxidases belonging to the vanillyl-alcohol oxidase (VAO) family were cloned on the basis of putative cholesterol oxidase gene sequences in the genome sequence data of Rhodococcus erythropolis PR4. The genes corresponding to the mature enzymes were cloned in a pET vector and expressed in Escherichia coli. The two cholesterol oxidases produced from the recombinant E. coli were purified to examine their properties. The amino acid sequence of ChoRI showed significant similarity (57%) to that of ChoRII. ChoRII was more stable than ChoRI in terms of pH and thermal stability. The substrate specificities of these enzymes differed distinctively from one another. Interestingly, the activities of ChoRII toward β-cholestanol, β-sitosterol, and stigmasterol were 2.4-, 2.1-, and 1.7-fold higher, respectively, than those of cholesterol. No cholesterol oxidases with high activity toward these sterols have been reported so far. The cholesterol oxidation products from these two enzymes also differed. ChoRI and ChoRII oxidized cholesterol to form cholest-4-en-3-one and 6β-hydroperoxycholest-4-en-3-one, respectively.
Collapse
Affiliation(s)
- Noriyuki Doukyu
- Department of Life Sciences, Toyo University, Itakura-machi, Gunma, Japan
- Graduate School of Life Sciences, Toyo University, Itakura-machi, Gunma, Japan
- Bio-Nano Electronic Research Center, Toyo University, Kawagoe, Saitama, Japan
- * E-mail:
| | - Makoto Ishikawa
- Graduate School of Life Sciences, Toyo University, Itakura-machi, Gunma, Japan
| |
Collapse
|
39
|
Guo X, Sun Q, Xi H, Zhang Y, Guo M, Zhang C, Zhu S, Gu T, Kong W, Wu Y. Expression, purification, and characterization of pneumococcal PsaA-PspA fusion protein. Protein Expr Purif 2020; 178:105782. [PMID: 33122039 DOI: 10.1016/j.pep.2020.105782] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/01/2020] [Accepted: 10/14/2020] [Indexed: 11/30/2022]
Abstract
Streptococcus pneumoniae is a gram-positive bacterial pathogen causing invasive pneumonia, meningitis, otitis media, and bacteremia. Owing to the current pitfalls of polysaccharide and polysaccharide-conjugate vaccines, protein vaccines are considered promising candidates against pneumonia. Pneumococcal surface protein A (PspA) and pneumococcal surface adhesin A (PsaA) are virulence proteins showing good immunogenicity and protective effects against S. pneumoniae strains in mice. In this study, we expressed the fusion protein PsaA-PspA, which consists of PsaA and the N-terminal region of PspA family 1 and 2, in Escherichia coli. We describe a novel and effective method to purify PsaA-PspA using hydroxyapatite and two-step chromatography. After determining the optimal induction conditions and a series of purification steps, we obtained PsaA-PspA fusion protein with over 95% purity at a final yield of 22.44% from the starting cell lysate. The molecular weight of PsaA-PspA was approximately 83.6 kDa and its secondary structure was evaluated by circular dichroism. Immunization with the purified protein induced high levels of IgG antibodies in mice. Collectively, these results demonstrate that our purification method can effectively produce high-purity PsaA-PspA fusion protein with biological activity and chemical integrity, which can be widely applied to the purification of other PspA subclass proteins.
Collapse
Affiliation(s)
- Xiaonan Guo
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Qing Sun
- CSPC Biotechnology Company, Shijiazhuang, China
| | - Hualong Xi
- BCHT Biotechnology Company, Changchun, China
| | - Yue Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Mengze Guo
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Chenxing Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Shidong Zhu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Tiejun Gu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Yongge Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China.
| |
Collapse
|
40
|
Wang G, Zhou Y, Ma K, Zhang F, Ye J, Zhong G, Yang X. Bioconversion of recombinantly produced precursor peptide pqqA into pyrroloquinoline quinone (PQQ) using a cell-free in vitro system. Protein Expr Purif 2020; 178:105777. [PMID: 33069826 DOI: 10.1016/j.pep.2020.105777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/11/2023]
Abstract
Pyrroloquinoline quinone (PQQ) has been recognized as the third class of redox cofactors in addition to the well-known nicotinamides (NAD(P)+) and flavins (FAD, FMN). It plays important physiological roles in various organisms and has strong antioxidant properties. The biosynthetic pathway of PQQ involves a gene cluster composed of 4-7 genes, named pqqA-G, among which pqqA is a key gene for PQQ synthesis, encoding the precursor peptide PqqA. To produce recombinant PqqA in E. coli, fusion tags were used to increase the stability and solubility of the peptide, as well simplify the scale-up of the fermentation process. In this paper, pqqA from Gluconobacter oxydans 621H was expressed in E. coli BL21 (DE3) as a fusion protein with SUMO and purified using a hexahistidine (His6) tag. The SUMO fusion protein and His6 tag were specifically recognized and cleaved by the SUMO specific ULP protease, and immobilized-metal affinity chromatography was used to obtain high-purity precursor peptide PqqA. Expression and purification of target proteins was confirmed by Tricine-SDS-PAGE. Finally, the synthesis of PQQ in a cell-free enzymatic reaction in vitro was confirmed by LC-MS.
Collapse
Affiliation(s)
- Guanglu Wang
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Yifei Zhou
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Ke Ma
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Fan Zhang
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Jianbin Ye
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Guifang Zhong
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China
| | - Xuepeng Yang
- Laboratory of Biotransformation and Biocatalysis, School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450000, People's Republic of China; School of Food and Bioengineering/Collaborative Innovation Center for Production and Safety, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450001, People's Republic of China.
| |
Collapse
|
41
|
Pang Z, Zhang L, Coaker G, Ma W, He SY, Wang N. Citrus CsACD2 Is a Target of Candidatus Liberibacter Asiaticus in Huanglongbing Disease. Plant Physiol 2020; 184:792-805. [PMID: 32759268 PMCID: PMC7536665 DOI: 10.1104/pp.20.00348] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/27/2020] [Indexed: 05/06/2023]
Abstract
Citrus Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (Las), is one of the most destructive citrus diseases worldwide, yet how Las causes HLB is poorly understood. Here we show that a Las-secreted protein, SDE15 (CLIBASIA_04025), suppresses plant immunity and promotes Las multiplication. Transgenic expression of SDE15 in Duncan grapefruit (Citrus × paradisi) suppresses the hypersensitive response induced by Xanthomonas citri ssp. citri (Xcc) and reduces the expression of immunity-related genes. SDE15 also suppresses the hypersensitive response triggered by the Xanthomonas vesicatoria effector protein AvrBsT in Nicotiana benthamiana, suggesting that it may be a broad-spectrum suppressor of plant immunity. SDE15 interacts with the citrus protein CsACD2, a homolog of Arabidopsis (Arabidopsis thaliana) ACCELERATED CELL DEATH 2 (ACD2). SDE15 suppression of plant immunity is dependent on CsACD2, and overexpression of CsACD2 in citrus suppresses plant immunity and promotes Las multiplication, phenocopying overexpression of SDE15. Identification of CsACD2 as a susceptibility target has implications in genome editing for novel plant resistance against devastating HLB.
Collapse
Affiliation(s)
- Zhiqian Pang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida/Institute of Food and Agricultural Sciences, Lake Alfred, Florida 33850
| | - Li Zhang
- MSU-DOE Plant Research Laboratory, Plant Resilient Institute, Michigan State University, East Lansing, Michigan 48824
- Howard Hughes Medical Institute, Michigan State University, East Lansing, Michigan 48824
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, California 95616
| | - Wenbo Ma
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
| | - Sheng-Yang He
- MSU-DOE Plant Research Laboratory, Plant Resilient Institute, Michigan State University, East Lansing, Michigan 48824
- Howard Hughes Medical Institute, Michigan State University, East Lansing, Michigan 48824
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida/Institute of Food and Agricultural Sciences, Lake Alfred, Florida 33850
| |
Collapse
|
42
|
Mushtaq A, Ansari TM, Mustafa G, Shad MA, Cruz-Reyes J, Jamil A. Isolation and characterization of nprB, a novel protease from Streptomyces thermovulgaris. Pak J Pharm Sci 2020; 33:2361-2369. [PMID: 33832913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacterial proteases are of great pharmaceutical importance and have a key role in various biological processes and in life cycle of several pathogens. New technology used for rational protein engineering as well improved delivery options will expand the potential pharmaceutical applications of proteases. The catalytic proteases belong to metalloproteases (EC.3.4.24) that comprise thermo lysine. The metalloproteases and their homologs have many important biotechnological and therapeutic applications. In the present study, a novel protease gene nprB was isolated from a thermophilic bacterium Streptomyces thermovulgaris and bioinformatics analyses were performed. PCR amplification and sequencing of nprB gene indicated an open reading frame of 178 aa (20191.18 Dalton). Based on protein sequence homology as well as conserved motifs and PTF domain the protein is characterized as a thermo lysine-like protease and is a member of M4 family of metalloproteases. Different bioinformatics tools such as ProtParam, SOPMA, signalP4.1 and ProDom from the ExPAsy server were used for structural and functional analyses. A phylogram was also reconstructed to reveal evolutionary relationships of nprB with its various homologs. The provided data will serve as a background to further reveal pharmaceutical and biotechnological importance of this novel protease gene from S. thermovulgaris in future.
Collapse
Affiliation(s)
- Amna Mushtaq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | | | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Amer Jamil
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| |
Collapse
|
43
|
Takahashi H, Dohmae N, Kim KS, Shimuta K, Ohnishi M, Yokoyama S, Yanagisawa T. Genetic incorporation of non-canonical amino acid photocrosslinkers in Neisseria meningitidis: New method provides insights into the physiological function of the function-unknown NMB1345 protein. PLoS One 2020; 15:e0237883. [PMID: 32866169 PMCID: PMC7458321 DOI: 10.1371/journal.pone.0237883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 04/28/2020] [Accepted: 08/04/2020] [Indexed: 02/01/2023] Open
Abstract
Although whole-genome sequencing has provided novel insights into Neisseria meningitidis, many open reading frames have only been annotated as hypothetical proteins with unknown biological functions. Our previous genetic analyses revealed that the hypothetical protein, NMB1345, plays a crucial role in meningococcal infection in human brain microvascular endothelial cells; however, NMB1345 has no homology to any identified protein in databases and its physiological function could not be elucidated using pre-existing methods. Among the many biological technologies to examine transient protein-protein interaction in vivo, one of the developed methods is genetic code expansion with non-canonical amino acids (ncAAs) utilizing a pyrrolysyl-tRNA synthetase/tRNAPyl pair from Methanosarcina species: However, this method has never been applied to assign function-unknown proteins in pathogenic bacteria. In the present study, we developed a new method to genetically incorporate ncAAs-encoded photocrosslinking probes into N. meningitidis by utilizing a pyrrolysyl-tRNA synthetase/tRNAPyl pair and elucidated the biological function(s) of the NMB1345 protein. The results revealed that the NMB1345 protein directly interacts with PilE, a major component of meningococcal pili, and further physicochemical and genetic analyses showed that the interaction between the NMB1345 protein and PilE was important for both functional pilus formation and meningococcal infectious ability in N. meningitidis. The present study using this new methodology for N. meningitidis provides novel insights into meningococcal pathogenesis by assigning the function of a hypothetical protein.
Collapse
Affiliation(s)
- Hideyuki Takahashi
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
- * E-mail:
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ken Shimuta
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
| | - Makoto Ohnishi
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, Yokohama, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| | - Tatsuo Yanagisawa
- RIKEN Structural Biology Laboratory, Yokohama, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| |
Collapse
|
44
|
Fidor A, Grabski M, Gawor J, Gromadka R, Węgrzyn G, Mazur-Marzec H. Nostoc edaphicum CCNP1411 from the Baltic Sea-A New Producer of Nostocyclopeptides. Mar Drugs 2020; 18:E442. [PMID: 32858999 PMCID: PMC7551626 DOI: 10.3390/md18090442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Nostocyclopeptides (Ncps) constitute a small class of nonribosomal peptides, exclusively produced by cyanobacteria of the genus Nostoc. The peptides inhibit the organic anion transporters, OATP1B3 and OATP1B1, and prevent the transport of the toxic microcystins and nodularin into hepatocytes. So far, only three structural analogues, Ncp-A1, Ncp-A2 and Ncp-M1, and their linear forms were identified in Nostoc strains as naturally produced cyanometabolites. In the current work, the whole genome sequence of the new Ncps producer, N. edaphicum CCNP1411 from the Baltic Sea, has been determined. The genome consists of the circular chromosome (7,733,505 bps) and five circular plasmids (from 44.5 kb to 264.8 kb). The nostocyclopeptide biosynthetic gene cluster (located between positions 7,609,981-7,643,289 bps of the chromosome) has been identified and characterized in silico. The LC-MS/MS analyzes of N. edaphicum CCNP1411 cell extracts prepared in aqueous methanol revealed several products of the genes. Besides the known peptides, Ncp-A1 and Ncp-A2, six other compounds putatively characterized as new noctocyclopeptide analogues were detected. This includes Ncp-E1 and E2 and their linear forms (Ncp-E1-L and E2-L), a cyclic Ncp-E3 and a linear Ncp-E4-L. Regardless of the extraction conditions, the cell contents of the linear nostocyclopeptides were found to be higher than the cyclic ones, suggesting a slow rate of the macrocyclization process.
Collapse
Affiliation(s)
- Anna Fidor
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Jan Gawor
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Robert Gromadka
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
| |
Collapse
|
45
|
Rasheed NA, Hussein NR. Characterization of different virulent factors in methicillin-resistant Staphylococcus aureus isolates recovered from Iraqis and Syrian refugees in Duhok city, Iraq. PLoS One 2020; 15:e0237714. [PMID: 32804961 PMCID: PMC7430753 DOI: 10.1371/journal.pone.0237714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 02/06/2020] [Accepted: 07/31/2020] [Indexed: 11/18/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a serious public health problem. There is limited information regarding the genetics of MRSA strains among the native Iraqi and incoming Syrian refugee communities. We aimed to characterize the genotypes and different virulence factors of MRSA in strains isolated from these two communities. Frozen MRSA strains (125) isolated from the native Iraqi and Syrian refugee communities were used in this study. PCR (singleplex and multiplex) and agr typing was used for the genotypic analysis of different virulence genes. We tested for the presence of virulence genes including pvl, arcA, tst, lukE/lukD, hla, hlb, eta, etb and agr. Prevalence of arcA MRSA in the Iraqi community (56.58%) was significantly higher (p = 0.008) than that in the Syrian refugee community (32.66%). Prevalence of lukE-lukD was also significantly higher (p = 0.001) in the Iraqi (82.89%) compared to that in the Syrian refugee community (57.14%). Further, prevalence of hla MRSA in the Iraqi community was (93.4%) and in the Syrian refugee community was (71.4%); (p = 0.0008). No significant differences were observed in the prevalence of pvl, tst, eta, etb and hlb. The most dominant agr types in both Iraqi (76.1% and 10.5%) and Syrian refugee (44.9% and 18.37%) communities were I and III. To sum up, no significant differences were observed between the groups for a majority of virulence factors. This is the first investigation of MRSA genotypes and virulence in both these communities. These results could be useful for further studies that assess the genetic relatedness of strains in the region for epidemiological and monitoring purposes, which would be crucial to limiting the spread of MRSA.
Collapse
Affiliation(s)
- Narin A. Rasheed
- Department of Medical Microbiology, College of Medicine, University of Duhok, Kurdistan Region, Iraq
- Akre Technical Institute, Duhok Polytechnic University, Duhok, Kurdistan Region, Iraq
- * E-mail:
| | - Nawfal R. Hussein
- Department of Medicine, College of Medicine, University of Zakho, Zakho, Kurdistan Region, Iraq
| |
Collapse
|
46
|
Bu G, Parrish S, Gleason PR, Nielsen DR, Nannenga BL. Heterologous expression and purification of the bicarbonate transporter BicA from Synechocystis sp. PCC 6803. Protein Expr Purif 2020; 175:105716. [PMID: 32738437 DOI: 10.1016/j.pep.2020.105716] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/25/2020] [Accepted: 07/22/2020] [Indexed: 11/18/2022]
Abstract
The high-flux/low-affinity cyanobacterial bicarbonate transporter BicA is a member of sulfate permease/solute carrier 26 (SulP/SLC26) family and plays a major role in cyanobacterial inorganic carbon uptake. In order to study this important membrane protein, robust platforms for over-expression and protocols for purification are required. In this work we have optimized the expression and purification of BicA from strain Synechocystis sp. PCC 6803 (BicA6803) in Escherichia coli. It was determined that expression with C43 (DE3) Rosetta2 at 37 °C produced the highest levels of over-expressed BicA6803 relative to other strains screened, and membrane solubilization with n-dodecyl-β-d-maltopyranoside facilitated the purification of high levels of stable and homogenous BicA6803. Using these expression and purification strategies, the final yields of purified BicA were 6.5 ± 1.0 mg per liter of culture.
Collapse
Affiliation(s)
- Guanhong Bu
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Sydney Parrish
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, 85287, USA
| | - Patrick R Gleason
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA; Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85278, USA
| | - David R Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, 85287, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
| |
Collapse
|
47
|
Shah S, Damare S. Cellular response of Brevibacterium casei #NIOSBA88 to arsenic and chromium-a proteomic approach. Braz J Microbiol 2020; 51:1885-1895. [PMID: 32729030 DOI: 10.1007/s42770-020-00353-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/25/2020] [Indexed: 11/25/2022] Open
Abstract
Cellular response against different heavy metal stress differs with the metal. Arsenic and chromium are heavy metals and toxic to living systems. The concentration of these metals in seawater is very low. However, due to their solubility in nature, they actively enter cells via various transport mechanisms and cause damage to the cells. Brevibacterium casei #NIOSBA88, a marine-derived, gram-positive isolate was multi-metal tolerant. Proteomic analysis of this isolate in response to arsenic and chromium resulted in the identification of total 2549 proteins, out of which 880 proteins were found to be commonly expressed at 750 mgL-1 arsenic and 100 mgL-1 chromium and in absence of both the metals. In contrast, 533, 212, and 270 proteins were found to be unique in the absence of any metal, 750 mgL-1 of arsenic and 100 mgL-1 of chromium respectively. Proteins such as antibiotic biosynthesis monooxygenase, ArsR family transcriptional regulator, cytochrome C oxidase subunit II, and thioredoxin reductase were exclusively expressed only in response to arsenic and chromium. Other proteins like superoxide dismutase, lipid hydroperoxide reductase, and thioredoxin-disulfide reductase were found to be upregulated in response to both the metals. Most of the proteins involved in the normal cell functioning were found to be downregulated. Major metabolic functions affected include amino acid metabolism, carbohydrate metabolism, translation, and energy metabolism. Peptide mass fingerprinting of Brevibacterium casei #NIOSBA88 exposed to arsenic and chromium respectively revealed the deleterious effect of these metals on the bacterium and its strategy to overcome the stress.
Collapse
Affiliation(s)
- Shruti Shah
- Biological Oceanography Division, CSIR- National Institute of Oceanography, Dona Paula, Goa, India
| | - Samir Damare
- Biological Oceanography Division, CSIR- National Institute of Oceanography, Dona Paula, Goa, India.
| |
Collapse
|
48
|
Introvigne ML, Taracila MA, Prati F, Caselli E, Bonomo RA. α-Triazolylboronic Acids: A Promising Scaffold for Effective Inhibitors of KPCs. ChemMedChem 2020; 15:1283-1288. [PMID: 32459878 PMCID: PMC8256004 DOI: 10.1002/cmdc.202000126] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/25/2020] [Indexed: 11/07/2022]
Abstract
Boronic acids are known reversible covalent inhibitors of serine β-lactamases. The selectivity and high potency of specific boronates bearing an amide side chain that mimics the β-lactam's amide side chain have been advanced in several studies. Herein, we describe a new class of boronic acids in which the amide group is replaced by a bioisostere triazole. The boronic acids were obtained in a two-step synthesis that relies on the solid and versatile copper-catalyzed azide-alkyne cycloaddition (CuAAC) followed by boronate deprotection. All of the compounds show very good inhibition of the Klebsiella pneumoniae carbapenemase KPC-2, with Ki values ranging from 1 nM to 1 μM, and most of them are able to restore cefepime activity against K. pneumoniae harboring blaKPC-2 . In particular, compound 1 e, bearing a sulfonamide substituted by a thiophene ring, proved to be an excellent KPC-2 inhibitor (Ki =30 nM); it restored cefepime susceptibility in KPC-Kpn cells (MIC=0.5 μg/mL) with values similar to that of vaborbactam (Ki =20 nM, MIC in KPC-Kpn 0.5 μg/mL). Our findings suggest that α-triazolylboronates might represent an effective scaffold for the treatment of KPC-mediated infections.
Collapse
Affiliation(s)
- Maria Luisa Introvigne
- Clinical and Experimental Medicine PhD Programme, University of Modena and Reggio Emilia, via Università 4, 41121, Modena, Italy
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Magdalena A Taracila
- Departments of Medicine
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Robert A Bonomo
- Departments of Medicine
- Pharmacology, Biochemistry and Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University, 2109 Adelbert Rd., Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| |
Collapse
|
49
|
Tran KN, Pham N, Jang SH, Lee C. Purification and characterization of a novel medium-chain ribitol dehydrogenase from a lichen-associated bacterium Sphingomonas sp. PLoS One 2020; 15:e0235718. [PMID: 32639976 PMCID: PMC7343156 DOI: 10.1371/journal.pone.0235718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 04/23/2020] [Accepted: 06/20/2020] [Indexed: 11/27/2022] Open
Abstract
Sugar alcohols (polyols) are abundant carbohydrates in lichen-forming algae and transported to other lichen symbionts, fungi, and bacteria. Particularly, ribitol is an abundant polyol in the lichen Cetraria sp. Polyols have important physiological roles in lichen symbiosis, but polyol utilization in lichen-associated bacteria has been largely unreported. Herein, we purified and characterized a novel ribitol dehydrogenase (RDH) from a Cetraria sp.-associated bacterium Sphingomonas sp. PAMC 26621 grown on a minimal medium containing D-ribitol (the RDH hereafter referred to as SpRDH). SpRDH is present as a trimer in its native form, and the molecular weight of SpRDH was estimated to be 39 kDa by SDS-PAGE and 117 kDa by gel filtration chromatography. SpRDH converted D-ribitol to D-ribulose using NAD+ as a cofactor. As far as we know, SpRDH is the first RDH belonging to the medium-chain dehydrogenase/reductase family. Multiple sequence alignments indicated that the catalytic amino acid residues of SpRDH consist of Cys37, His65, Glu66, and Glu157, whereas those of short-chain RDHs consist of Ser, Tyr, and Lys. Furthermore, unlike other short-chain RDHs, SpRDH did not require divalent metal ions for its catalytic activity. Despite SpRDH originating from a psychrophilic Arctic bacterium, Sphingomonas sp., it had maximum activity at 60°C and exhibited high thermal stability within the 4-50°C range. Further studies on the structure/function relationship and catalytic mechanism of SpRDH will expand our understanding of its role in lichen symbiosis.
Collapse
Affiliation(s)
- Kiet N. Tran
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Nhung Pham
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| |
Collapse
|
50
|
Cheng W, Yan X, Xiao J, Chen Y, Chen M, Jin J, Bai Y, Wang Q, Liao Z, Chen Q. Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12. Sci Rep 2020; 10:10920. [PMID: 32616809 PMCID: PMC7331586 DOI: 10.1038/s41598-020-67921-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 02/02/2020] [Accepted: 06/16/2020] [Indexed: 01/09/2023] Open
Abstract
Alginate-degrading bacteria or alginate lyases can be used to oligomerize alginate. In this study, an alginate-degrading bacterium with high alginolytic activity was successfully screened by using Sargassum fusiforme sludge. When the strain was grown on a plate containing sodium alginate, the transparent ring diameter (D) was 2.2 cm and the ratio (D/d) of transparent ring diameter to colony diameter (d) was 8.8. After 36 h in culture at a temperature of 28 °C shaken at 150 r/min, the enzymatic activity of the fermentation supernatant reached 160 U/mL, and the enzymatic activity of the bacterial precipitate harvested was 2,645 U/mL. The strain was named Cobetia sp. cqz5-12. Its genome is circular in shape, 4,209,007 bp in size, with a 62.36% GC content. It contains 3,498 predicted coding genes, 72 tRNA genes, and 21 rRNA genes. The functional annotations for the coding genes demonstrated that there were 181 coding genes in the genome related to carbohydrate transport and metabolism and 699 coding genes with unknown functions. Three putative coding genes, alg2107, alg2108 and alg2112, related to alginate degradation were identified by analyzing the carbohydrate active enzyme (CAZy) database. Moreover, proteins Alg2107 and Alg2112 were successfully expressed and exhibited alginate lyase activity.
Collapse
Affiliation(s)
- Wenwen Cheng
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Xuanyu Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Jiali Xiao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Yunyun Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Minghui Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Jiayi Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Yu Bai
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Qi Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China
| | - Zhiyong Liao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China.
| | - Qiongzhen Chen
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, People's Republic of China.
| |
Collapse
|