1
|
Thøgersen MS, Zervas A, Stougaard P, Ellegaard-Jensen L. Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland. Front Microbiol 2024; 15:1358787. [PMID: 38655082 PMCID: PMC11035741 DOI: 10.3389/fmicb.2024.1358787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.
Collapse
|
2
|
Rasmussen CB, Scavenius C, Thøgersen IB, Harwood SL, Larsen Ø, Bjerga GEK, Stougaard P, Enghild JJ, Thøgersen MS. Characterization of a novel cold-adapted intracellular serine protease from the extremophile Planococcus halocryophilus Or1. Front Microbiol 2023; 14:1121857. [PMID: 36910232 PMCID: PMC9995970 DOI: 10.3389/fmicb.2023.1121857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
The enzymes of microorganisms that live in cold environments must be able to function at ambient temperatures. Cold-adapted enzymes generally have less ordered structures that convey a higher catalytic rate, but at the cost of lower thermodynamic stability. In this study, we characterized P355, a novel intracellular subtilisin protease (ISP) derived from the genome of Planococcus halocryophilus Or1, which is a bacterium metabolically active down to -25°C. P355's stability and activity at varying pH values, temperatures, and salt concentrations, as well as its temperature-dependent kinetics, were determined and compared to an uncharacterized thermophilic ISP (T0099) from Parageobacillus thermoglucosidasius, a previously characterized ISP (T0034) from Planococcus sp. AW02J18, and Subtilisin Carlsberg (SC). The results showed that P355 was the most heat-labile of these enzymes, closely followed by T0034. P355 and T0034 exhibited catalytic constants (k cat ) that were much higher than those of T0099 and SC. Thus, both P355 and T0034 demonstrate the characteristics of the stability-activity trade-off that has been widely observed in cold-adapted proteases.
Collapse
Affiliation(s)
| | | | - Ida B Thøgersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Øivind Larsen
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | | | - Peter Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | |
Collapse
|
3
|
Harvey KL, Jarocki VM, Charles IG, Djordjevic SP. The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis. Front Microbiol 2019; 10:2351. [PMID: 31708880 PMCID: PMC6822514 DOI: 10.3389/fmicb.2019.02351] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/27/2019] [Indexed: 12/25/2022] Open
Abstract
Elongation factor thermal unstable Tu (EF-Tu) is a G protein that catalyzes the binding of aminoacyl-tRNA to the A-site of the ribosome inside living cells. Structural and biochemical studies have described the complex interactions needed to effect canonical function. However, EF-Tu has evolved the capacity to execute diverse functions on the extracellular surface of both eukaryote and prokaryote cells. EF-Tu can traffic to, and is retained on, cell surfaces where can interact with membrane receptors and with extracellular matrix on the surface of plant and animal cells. Our structural studies indicate that short linear motifs (SLiMs) in surface exposed, non-conserved regions of the molecule may play a key role in the moonlighting functions ascribed to this ancient, highly abundant protein. Here we explore the diverse moonlighting functions relating to pathogenesis of EF-Tu in bacteria and examine putative SLiMs on surface-exposed regions of the molecule.
Collapse
Affiliation(s)
- Kate L Harvey
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Veronica M Jarocki
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ian G Charles
- Quadram Institute, Norwich, United Kingdom.,Norwich Medical School, Norwich, United Kingdom
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| |
Collapse
|
4
|
Huang J, Xu Y, Zhang Y, Sun A, Hu Y. Utilization of one novel deep-sea microbial protease sin3406-1 in the preparation of ethyl (S)-3-hydroxybutyrate through kinetic resolution. World J Microbiol Biotechnol 2018; 34:124. [PMID: 30083971 DOI: 10.1007/s11274-018-2513-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/01/2018] [Indexed: 10/28/2022]
Abstract
One novel protease sin3406-1 was identified from Streptomyces niveus SCSIO 3406, which was isolated from the deep sea of the South China Sea, and heterologously expressed in E. coli BL21(DE3). Protease sin3406-1 was further used as a green biocatalyst in the kinetic resolution of racemic ethyl-3-hydroxybutyrate. After careful process optimization, chiral product ethyl (S)-3-hydroxybutyrate was generated with an enantiomeric excess of over 99% and a conversion rate of up to 50% through direct hydrolysis of inexpensive racemic ethyl-3-hydroxybutyrate catalyzed by sin3406-1. Interestingly, protease sin3406-1 exhibited the same enantio-preference as that of esterase PHE21 during the asymmetric hydrolysis of the ester bonds of racemic ethyl-3-hydroxybutyrate. Through mutation studies and molecular docking, we also demonstrated that the four residues close to the catalytic center, S85, A86, Q87 and Y254, played key roles in both the hydrolytic activity and the enantioselectivity of protease sin3406-1, possibly through forming hydrogen bonds between the enzyme and the substrates. Deep-sea microbial proteases represented by sin3406-1 are new contributions to the biocatalyst library for the preparation of valuable chiral drug intermediates and chemicals through enzymatic kinetic resolution.
Collapse
Affiliation(s)
- Jinlong Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,College of Life Science, Guangxi Normal University, Guilin, 541004, People's Republic of China
| | - Yongkai Xu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, People's Republic of China
| | - Yun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Aijun Sun
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.,Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
| | - Yunfeng Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China. .,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Guangzhou, People's Republic of China.
| |
Collapse
|
5
|
Tavano OL, Berenguer-Murcia A, Secundo F, Fernandez-Lafuente R. Biotechnological Applications of Proteases in Food Technology. Compr Rev Food Sci Food Saf 2018; 17:412-436. [DOI: 10.1111/1541-4337.12326] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Olga Luisa Tavano
- Faculty of Nutrition; Alfenas Federal Univ.; 700 Gabriel Monteiro da Silva St Alfenas MG 37130-000 Brazil
| | - Angel Berenguer-Murcia
- Inorganic Chemistry Dept. and Materials Science Inst.; Alicante Univ.; Ap. 99 E-03080 Alicante Spain
| | - Francesco Secundo
- Istit. di Chimica del Riconoscimento Molecolare; CNR; v. Mario Bianco 9 20131 Milan Italy
| | | |
Collapse
|
6
|
Devi SG, Fathima AA, Sanitha M, Iyappan S, Curtis WR, Ramya M. Expression and characterization of alkaline protease from the metagenomic library of tannery activated sludge. J Biosci Bioeng 2016; 122:694-700. [PMID: 27323930 DOI: 10.1016/j.jbiosc.2016.05.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 11/17/2022]
Abstract
Metagenomics has the potential to facilitate the discovery of novel enzymes; however, to date, only a few alkaline proteases have been characterized from environmentally-sourced DNA. We report the identification and characterization of an alkaline serine protease designated as Prt1A from the metagenomic library of tannery activated sludge. Sequence analysis revealed that Prt1A is closely related to S8A family subtilisins with a catalytic triad of Asp143, His173, and Ser326. The putative protease gene (prt-1A) was subcloned in pET 28a (+) vector and overexpressed in Escherichia coli BL21(DE3)pLysS cells. This 38.8 KDa recombinant protease was purified to homogeneity by nickel affinity chromatography and exhibited optimal enzyme activity at elevated pH (11.0) and temperature (55°C). The enzyme activity was enhanced by the addition of 5 mM Ca2+ ions, and was stable in the presence of anionic detergent, oxidizing agent and various organic solvents. The enzyme displayed high affinity and catalytic efficiency for casein under standard assay conditions (Vmax = 279 U/mg/min, Km = 1.70 mg/mL) and was also compatible with commercial detergents. These results suggest that Prt1A protease could act as an efficient enzyme in various industrial applications.
Collapse
Affiliation(s)
| | | | - Mary Sanitha
- Department of Genetic Engineering, SRM University, Tamilnadu 603203, India
| | - Sellamuthu Iyappan
- Department of Genetic Engineering, SRM University, Tamilnadu 603203, India
| | - Wayne R Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mohandass Ramya
- Department of Genetic Engineering, SRM University, Tamilnadu 603203, India.
| |
Collapse
|