1
|
Ashaolu TJ, Malik T, Soni R, Prieto MA, Jafari SM. Extremophilic Microorganisms as a Source of Emerging Enzymes for the Food Industry: A Review. Food Sci Nutr 2025; 13:e4540. [PMID: 39803234 PMCID: PMC11716999 DOI: 10.1002/fsn3.4540] [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: 06/19/2024] [Revised: 09/27/2024] [Accepted: 10/02/2024] [Indexed: 01/16/2025] Open
Abstract
Modern-day consumers are interested in highly nutritious and safe foods with corresponding organoleptic qualities. Such foods are increasingly subjected to various processing techniques which include the use of enzymes. These enzymes like amylases, lipases, proteases, xylanases, laccases, pullulanase, chitinases, pectinases, esterases, isomerases, and dehydrogenases could be derived from extremophilic organisms such as thermophiles, psychrophiles, acidophiles, alkaliphiles, and halophiles. As these organisms can grow under severe environmental conditions, they can produce functional enzymes (extremozymes) used in producing safe foods (such as gluten-free, lactose-free, lower acrylamide, or lower trans-fat products). The extremozymes also enhance nutrient bioavailability and bioaccessibility (e.g., predigested nourishments like baby formulae), and improve nourishment functionalities such as surface, sensory, and bioactive properties. Therefore, exploring alternative sources of enzymes for better compatibility and long-term adaptability in the processing stages is a promising approach for obtaining novel food products. This review will establish novel discovery methods of extremozymes from psychrophiles, thermophiles, acidophiles, alkaliphiles, and halophiles, the enzymes' types, mechanisms of action, and their food applications. It will also contribute to their commercial relevance and the furtherance of their discovery.
Collapse
Affiliation(s)
- Tolulope Joshua Ashaolu
- Institute for Global Health InnovationsDuy Tan UniversityDa NangVietnam
- Faculty of MedicineDuy Tan UniversityDa NangVietnam
| | - Tanu Malik
- Centre of Food Science and TechnologyCCS Haryana Agricultural UniversityHisarHaryanaIndia
| | - Rakhi Soni
- Department of MicrobiologyCCS Haryana Agricultural UniversityHisarHaryanaIndia
| | - Miguel A. Prieto
- Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of ScienceUniversidade de VigoOurenseSpain
| | - Seid Mahdi Jafari
- Department of Food Materials and Process Design EngineeringGorgan University of Agricultural Sciences and Natural ResourcesGorganIran
- Halal Research Center of IRI, Iran Food and Drug Administration, Ministry of Health and Medical EducationTehranIran
| |
Collapse
|
2
|
Ma J, Wen L, Li X, Dai J, Song J, Wang Q, Xu K, Yuan H, Duan L. Different fates of particulate matters driven by marine hypoxia: A case study of oxygen minimum zone in the Western Pacific. MARINE ENVIRONMENTAL RESEARCH 2024; 200:106648. [PMID: 39043062 DOI: 10.1016/j.marenvres.2024.106648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/01/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024]
Abstract
The oxygen minimum zone (OMZ) is an important representative of marine hypoxia in the open ocean, and it is developing rapidly under the context of global warming. However, the research on OMZ in the Western Pacific is still deficient. This study focused on its basic characteristics and impact on the degradation of particulate matters in the M4 seamount of Western Pacific. The results showed that the OMZ is located at 290-1100 m, just below the high-salinity area and thermocline. The M4 seamount has a weak impact on the OMZ, and only the bottom waters contacting with the seamount have a weak decrease in dissolved oxygen (DO). With the increase of water depth, particulate nitrogen and phosphorus decrease first above and in the OMZ and then increase below the OMZ, while particulate organic carbon (POC) gradually decreases. The low-DO environment in the OMZ is not conducive to the degradation of particulate matters, which promotes the transport of particulate matters to the deep sea, and most particulate matters have the lowest degradation rate here. The waters above the OMZ have the fastest change rate of particulate matters, in which particulate organic phosphorus (POP) and particulate inorganic phosphorus (PIP) are preferentially degraded, and the degradation rate of them is significantly higher than particulate organic nitrogen (PON) and particulate inorganic nitrogen (PIN). The particulate nitrogen and phosphorus in the waters below the OMZ continue to increase, while PON/total particulate nitrogen (TPN) and POP/total particulate phosphorus (TPP) increase significantly, and the increase rate of PIN and PIP is far lower than PON and POP, indicating that the increase of organic matters in particulate matters is more significant. It is speculated that this phenomenon might be related to the input of Antarctic Bottom Water or the in-situ production by microorganisms. This study revealed the relationship between OMZ and different particulate matters, which may provide a valuable pathway for the biogeochemical effects of OMZ in the Western Pacific.
Collapse
Affiliation(s)
- Jun Ma
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Lilian Wen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuegang Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jiajia Dai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jinming Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Qidong Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Kuidong Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Huamao Yuan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Liqin Duan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| |
Collapse
|
3
|
Xiao Q, Xie Y, Hu F, Hu C. Current Status and Trends of Low-Temperature Steel Used in Polar Regions. MATERIALS (BASEL, SWITZERLAND) 2024; 17:3117. [PMID: 38998201 PMCID: PMC11242067 DOI: 10.3390/ma17133117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
The desire to explore the natural resources and geopolitical patterns of the North and South Poles has significantly increased the interest of experts and researchers in the development and utilization of the polar regions. In this article, we comprehensively analyzed the current state of the development of polar low-temperature steel around the world. We highlighted the challenges that must be addressed in the ongoing development efforts and summarized the expected future trends in this field. The main theme of this article involves the challenges encountered in polar environments primarily caused by the low-temperature toughness and seawater corrosion of marine steel.
Collapse
Affiliation(s)
| | - Yaozhou Xie
- Collaborative Innovation Center for Advanced Steels, Wuhan University of Science and Technology, Wuhan 430081, China; (Q.X.); (F.H.)
| | | | - Chengyang Hu
- Collaborative Innovation Center for Advanced Steels, Wuhan University of Science and Technology, Wuhan 430081, China; (Q.X.); (F.H.)
| |
Collapse
|
4
|
Kuddus M, Roohi, Bano N, Sheik GB, Joseph B, Hamid B, Sindhu R, Madhavan A. Cold-active microbial enzymes and their biotechnological applications. Microb Biotechnol 2024; 17:e14467. [PMID: 38656876 PMCID: PMC11042537 DOI: 10.1111/1751-7915.14467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024] Open
Abstract
Microorganisms known as psychrophiles/psychrotrophs, which survive in cold climates, constitute majority of the biosphere on Earth. Their capability to produce cold-active enzymes along with other distinguishing characteristics allows them to survive in the cold environments. Due to the relative ease of large-scale production compared to enzymes from plants and animals, commercial uses of microbial enzyme are alluring. The ocean depths, polar, and alpine regions, which make up over 85% of the planet, are inhabited to cold ecosystems. Microbes living in these regions are important for their metabolic contribution to the ecosphere as well as for their enzymes, which may have potential industrial applications. Cold-adapted microorganisms are a possible source of cold-active enzymes that have high catalytic efficacy at low and moderate temperatures at which homologous mesophilic enzymes are not active. Cold-active enzymes can be used in a variety of biotechnological processes, including food processing, additives in the detergent and food industries, textile industry, waste-water treatment, biopulping, environmental bioremediation in cold climates, biotransformation, and molecular biology applications with great potential for energy savings. Genetically manipulated strains that are suitable for producing a particular cold-active enzyme would be crucial in a variety of industrial and biotechnological applications. The potential advantage of cold-adapted enzymes will probably lead to a greater annual market than for thermo-stable enzymes in the near future. This review includes latest updates on various microbial source of cold-active enzymes and their biotechnological applications.
Collapse
Affiliation(s)
- Mohammed Kuddus
- Department of Biochemistry, College of MedicineUniversity of HailHailSaudi Arabia
| | - Roohi
- Protein Research Laboratory, Department of BioengineeringIntegral UniversityLucknowIndia
| | - Naushin Bano
- Protein Research Laboratory, Department of BioengineeringIntegral UniversityLucknowIndia
| | | | - Babu Joseph
- Department of Clinical Laboratory Sciences, College of Applied Medical SciencesShaqra UniversityShaqraSaudi Arabia
| | - Burhan Hamid
- Center of Research for DevelopmentUniversity of KashmirSrinagarIndia
| | - Raveendran Sindhu
- Department of Food TechnologyTKM Institute of TechnologyKollamKeralaIndia
| | - Aravind Madhavan
- School of BiotechnologyAmrita Vishwa Vidyapeetham, AmritapuriKollamKeralaIndia
| |
Collapse
|
5
|
Maldonado-Ruiz K, Pedroza-Islas R, Pedraza-Segura L. Blue Biotechnology: Marine Bacteria Bioproducts. Microorganisms 2024; 12:697. [PMID: 38674641 PMCID: PMC11051736 DOI: 10.3390/microorganisms12040697] [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: 02/14/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The ocean is the habitat of a great number of organisms with different characteristics. Compared to terrestrial microorganisms, marine microorganisms also represent a vast and largely unexplored reservoir of bioactive compounds with diverse industrial applications like terrestrial microorganisms. This review examines the properties and potential applications of products derived from marine microorganisms, including bacteriocins, enzymes, exopolysaccharides, and pigments, juxtaposing them in some cases against their terrestrial counterparts. We discuss the distinct characteristics that set marine-derived products apart, including enhanced stability and unique structural features such as the amount of uronic acid and sulfate groups in exopolysaccharides. Further, we explore the uses of these marine-derived compounds across various industries, ranging from food and pharmaceuticals to cosmetics and biotechnology. This review also presents a broad description of biotechnologically important compounds produced by bacteria isolated from marine environments, some of them with different qualities compared to their terrestrial counterparts.
Collapse
Affiliation(s)
| | - Ruth Pedroza-Islas
- Department of Chemical, Industrial and Food Engineering, Universidad Iberoamericana, Prol. Paseo de la Reforma 880, Lomas de Santa Fe, Mexico City 01210, Mexico; (K.M.-R.); (L.P.-S.)
| | | |
Collapse
|
6
|
Camacho KF, de Melo Carlos L, Bernal SPF, de Oliveira VM, Ruiz JLM, Ottoni JR, Vieira R, Neto A, Rosa LH, Passarini MRZ. Antarctic marine sediment as a source of filamentous fungi-derived antimicrobial and antitumor compounds of pharmaceutical interest. Extremophiles 2024; 28:21. [PMID: 38532228 DOI: 10.1007/s00792-024-01339-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
Antarctica harbors a microbial diversity still poorly explored and of inestimable biotechnological value. Cold-adapted microorganisms can produce a diverse range of metabolites stable at low temperatures, making these compounds industrially interesting for biotechnological use. The present work investigated the biotechnological potential for antimicrobial and antitumor activity of filamentous fungi and bacteria isolated from marine sediment samples collected at Deception Island, Antarctica. A total of 89 microbial isolates were recovered from marine sediments and submitted to an initial screening for L-glutaminase with antitumoral activity and for antimicrobial metabolites. The isolates Pseudogymnoascus sp. FDG01, Pseudogymnoascus sp. FDG02, and Penicillium sp. FAD33 showed potential antiproliferative action against human pancreatic carcinoma cells while showing no toxic effect on non-tumor cells. The microbial extracts from unidentified three bacteria and four filamentous fungi showed antibacterial activity against at least one tested pathogenic bacterial strain. The isolate FDG01 inhibited four bacterial species, while the isolate FDG01 was active against Micrococcus luteus in the minimal inhibitory concentration of 0.015625 μg mL -1. The results pave the way for further optimization of enzyme production and characterization of enzymes and metabolites found and reaffirm Antarctic marine environments as a wealthy source of compounds potentially applicable in the healthcare and pharmaceutical industry.
Collapse
Affiliation(s)
- Karine Fernandes Camacho
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | - Layssa de Melo Carlos
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | - Suzan Prado Fernandes Bernal
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | | | - Jorge Luiz Maria Ruiz
- Laboratório de Biotecnologia da Saúde, Universidade Federal da Integração Latino-Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | - Júlia Ronzella Ottoni
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil
| | - Rosemary Vieira
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Arthur Neto
- Instituto de Geociências, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Michel Rodrigo Zambrano Passarini
- Laboratório de Biotecnologia Ambiental, Universidade Federal da Integração Latino-Americana - UNILA, Foz Do Iguaçu, PR, 85870-650, Brazil.
| |
Collapse
|
7
|
Daunoras J, Kačergius A, Gudiukaitė R. Role of Soil Microbiota Enzymes in Soil Health and Activity Changes Depending on Climate Change and the Type of Soil Ecosystem. BIOLOGY 2024; 13:85. [PMID: 38392304 PMCID: PMC10886310 DOI: 10.3390/biology13020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
The extracellular enzymes secreted by soil microorganisms play a pivotal role in the decomposition of organic matter and the global cycles of carbon (C), phosphorus (P), and nitrogen (N), also serving as indicators of soil health and fertility. Current research is extensively analyzing these microbial populations and enzyme activities in diverse soil ecosystems and climatic regions, such as forests, grasslands, tropics, arctic regions and deserts. Climate change, global warming, and intensive agriculture are altering soil enzyme activities. Yet, few reviews have thoroughly explored the key enzymes required for soil fertility and the effects of abiotic factors on their functionality. A comprehensive review is thus essential to better understand the role of soil microbial enzymes in C, P, and N cycles, and their response to climate changes, soil ecosystems, organic farming, and fertilization. Studies indicate that the soil temperature, moisture, water content, pH, substrate availability, and average annual temperature and precipitation significantly impact enzyme activities. Additionally, climate change has shown ambiguous effects on these activities, causing both reductions and enhancements in enzyme catalytic functions.
Collapse
Affiliation(s)
- Jokūbas Daunoras
- Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257 Vilnius, Lithuania
| | - Audrius Kačergius
- Lithuanian Research Centre for Agriculture and Forestry, Kedainiai Distr., LT-58344 Akademija, Lithuania
| | - Renata Gudiukaitė
- Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257 Vilnius, Lithuania
| |
Collapse
|
8
|
Hussain A, Ray MK. Functional activity of E. coli RNase R in the Antarctic Pseudomonas syringae Lz4W. J Genet Eng Biotechnol 2023; 21:101. [PMID: 37843651 PMCID: PMC10579198 DOI: 10.1186/s43141-023-00553-2] [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: 09/09/2022] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND In Antarctic P. syringae RNase R play an essential role in the processing of 16S and 5S rRNA, thereby playing an important role in cold-adapted growth of the bacterium. This study is focused on deciphering the in vivo functional activity of mesophilic exoribonuclease R and its catalytic domain (RNB) in an evolutionary distant psychrophilic bacterium Pseudomonas syringae Lz4W. RESULTS Our results confirm that E. coli RNase R complemented the physiological functions of the psychrophilic bacterium P. syringae RNase R and rescued the cold-sensitive phenotype of Pseudomonas syringae ∆rnr mutant. More importantly, the catalytic domain (RNB) of the E. coli RNase R is also capable of alleviating the cold-sensitive growth defects of ∆rnr mutant as seen with the catalytic domain (RNB) of the P. syringae enzyme. The Catalytic domain of E. coli RNase R was less efficient than the Catalytic domain of P. syringae RNase R in rescuing the cold-sensitive growth of ∆rnr mutant at 4°C, as the ∆rnr expressing the RNBEc (catalytic domain of E. coli RNase R) displayed longer lag phase than the RNBPs (Catalytic domain of P. syringae RNase R) complemented ∆rnr mutant at 4°C. Altogether it appears that the E. coli RNase R and P. syringae RNase R are functionally exchangeable for the growth requirements of P. syringae at low temperature (4°C). Our results also confirm that in P. syringae the requirement of RNase R for supporting the growth at 4°C is independent of the degradosomal complex. CONCLUSION E. coli RNase R (RNase REc) rescues the cold-sensitive phenotype of the P. syringae Δrnr mutant. Similarly, the catalytic domain of E. coli RNase R (RNBEc) is also capable of supporting the growth of Δrnr mutant at low temperatures. These findings have a vast scope in the design and development of low-temperature-based expression systems.
Collapse
Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, India.
| | | |
Collapse
|
9
|
Rao H, Huan R, Chen Y, Xiao X, Li W, He H. Characteristics and Application of a Novel Cold-Adapted and Salt-Tolerant Protease EK4-1 Produced by an Arctic Bacterium Mesonia algae K4-1. Int J Mol Sci 2023; 24:ijms24097985. [PMID: 37175692 PMCID: PMC10178186 DOI: 10.3390/ijms24097985] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Mesonia algae K4-1 from the Arctic secretes a novel cold-adapted and salt-tolerant protease EK4-1. It has the highest sequence similarity with Stearolysin, an M4 family protease from Geobacillus stearothermophilus, with only 45% sequence identity, and is a novel M4 family protease. Ek4-1 has a low optimal catalytic temperature (40 °C) and is stable at low temperatures. Moreover, EK4-1 is still active in 4 mol/L NaCl solution and is tolerant to surfactants, oxidizing agents and organic solvents; furthermore, it prefers the hydrolysis of peptide bonds at the P1' position as the hydrophobic residues, such as Leu, Phe and Val, and amino acids with a long side chain, such as Phe and Tyr. Mn2+and Mg2+ significantly promoted enzyme activity, while Fe3+, Co+, Zn2+ and Cu2+ significantly inhibited enzyme activity. Amino acid composition analysis showed that EK4-1 had more small-side-chain amino acids and fewer large-side-chain amino acids. Compared with a thermophilic protease Stearolysin, the cold-adapted protease EK4-1 contains more random coils (48.07%) and a larger active pocket (727.42 Å3). In addition, the acidic amino acid content of protease EK4-1 was higher than that of the basic amino acid, which might be related to the salt tolerance of protease. Compared with the homologous proteases EB62 and E423, the cold-adapted protease EK4-1 was more efficient in the proteolysis of grass carp skin, salmon skin and casein at a low temperature, and produced a large number of antioxidant peptides, with DPPH, ·OH and ROO· scavenging activities. Therefore, cold-adapted and salt-tolerant protease EK4-1 offers wide application prospects in the cosmetic and detergent industries.
Collapse
Affiliation(s)
- Hailian Rao
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Ran Huan
- School of Life Sciences, Central South University, Changsha 410013, China
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100000, China
| | - Yidan Chen
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Xun Xiao
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Wenzhao Li
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Hailun He
- School of Life Sciences, Central South University, Changsha 410013, China
| |
Collapse
|
10
|
Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:6491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
Collapse
Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
| |
Collapse
|
11
|
Dopson M, González-Rosales C, Holmes DS, Mykytczuk N. Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies. Front Microbiol 2023; 14:1149903. [PMID: 37007468 PMCID: PMC10050440 DOI: 10.3389/fmicb.2023.1149903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.
Collapse
Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- *Correspondence: Mark Dopson
| | - Carolina González-Rosales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
| | - Nadia Mykytczuk
- Goodman School of Mines, Laurentian University, Sudbury, ON, Canada
| |
Collapse
|
12
|
Bisaccia M, Binda E, Rosini E, Caruso G, Dell'Acqua O, Azzaro M, Laganà P, Tedeschi G, Maffioli EM, Pollegioni L, Marinelli F. A novel promising laccase from the psychrotolerant and halotolerant Antarctic marine Halomonas sp. M68 strain. Front Microbiol 2023; 14:1078382. [PMID: 36846806 PMCID: PMC9950745 DOI: 10.3389/fmicb.2023.1078382] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/04/2023] [Indexed: 02/12/2023] Open
Abstract
Microbial communities inhabiting the Antarctic Ocean show psychrophilic and halophilic adaptations conferring interesting properties to the enzymes they produce, which could be exploited in biotechnology and bioremediation processes. Use of cold- and salt-tolerant enzymes allows to limit costs, reduce contaminations, and minimize pretreatment steps. Here, we report on the screening of 186 morphologically diverse microorganisms isolated from marine biofilms and water samples collected in Terra Nova Bay (Ross Sea, Antarctica) for the identification of new laccase activities. After primary screening, 13.4 and 10.8% of the isolates were identified for the ability to oxidize 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and the dye azure B, respectively. Amongst them, the marine Halomonas sp. strain M68 showed the highest activity. Production of its laccase-like activity increased six-fold when copper was added to culture medium. Enzymatic activity-guided separation coupled with mass spectrometry identified this intracellular laccase-like protein (named Ant laccase) as belonging to the copper resistance system multicopper oxidase family. Ant laccase oxidized ABTS and 2,6-dimethoxy phenol, working better at acidic pHs The enzyme showed a good thermostability, with optimal temperature in the 40-50°C range and maintaining more than 40% of its maximal activity even at 10°C. Furthermore, Ant laccase was salt- and organic solvent-tolerant, paving the way for its use in harsh conditions. To our knowledge, this is the first report concerning the characterization of a thermo- and halo-tolerant laccase isolated from a marine Antarctic bacterium.
Collapse
Affiliation(s)
- Melissa Bisaccia
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy,*Correspondence: Melissa Bisaccia,
| | - Elisa Binda
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
| | - Gabriella Caruso
- Institute of Polar Sciences (CNR-ISP), National Research Council, Messina, Italy
| | - Ombretta Dell'Acqua
- Institute of Polar Sciences (CNR-ISP), National Research Council, Venice, Italy
| | - Maurizio Azzaro
- Institute of Polar Sciences (CNR-ISP), National Research Council, Messina, Italy
| | - Pasqualina Laganà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine and Animal Science (DIVAS), University of Milan, Milan, Italy,Cimaina, University of Milan, Milan, Italy
| | - Elisa M. Maffioli
- Department of Veterinary Medicine and Animal Science (DIVAS), University of Milan, Milan, Italy,Cimaina, University of Milan, Milan, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, Varese, Italy
| |
Collapse
|
13
|
Li Z, Li C, Cheng P, Yu G. Rhodotorula mucilaginosa—alternative sources of natural carotenoids, lipids, and enzymes for industrial use. Heliyon 2022; 8:e11505. [DOI: 10.1016/j.heliyon.2022.e11505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/19/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
|
14
|
Embaby AM, Mahmoud HE. Recombinant acetylxylan esterase of Halalkalibacterium halodurans NAH-Egypt: molecular and biochemical study. AMB Express 2022; 12:135. [DOI: 10.1186/s13568-022-01476-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractAcetylxylan esterase plays a crucial role in xylan hydrolysis as the acetyl side-groups restrict endoxylanase action by stearic hindrance. In this study, an acetylxylan esterase (AXE-HAS10: 960 bp & 319 a.a) putative ORF from Halalkalibacterium halodurans NAH-Egypt was extensively studied through heterologous overexpression in Escherichia coli, biochemical characterization, and structural modeling. The AXE-HAS10 tertiary structure was predicted by the Local Meta Threading Server. AXE-HAS10 belongs to the carbohydrate esterase Family 7. Purified to homogeneity AXE-HAS10 showed specific activity (36.99 U/mg), fold purification (11.42), and molecular mass (41.39 kDa). AXE-HAS10 showed optimal pH (8.5) and temperature (40 oC). After 15 h of incubation at pH 7.0–9.0, AXE-HAS10 maintained 100% activity. After 120 min at 35 and 40 oC, the retained activity was 80 and 50%, respectively. At 10 mM Mn2+, Fe3+, K+, and Ca2+ after 30 min, retained activity was 329 ± 15, 212 ± 5.2, 123 ± 1.4, and 120 ± 3.0%, respectively. After 30 min of preincubation with triton x-100, SDS, and CTAB at 0.1% (v/v), the retained activity was 150 ± 19, 88 ± 4, and 82 ± 7%, respectively. At 6.0 M NaCl after 30 min, retained activity was 58%. A 1.44-fold enhancement of beechwood xylan hydrolysis was achieved by AXE-HAS10 and Penicillium chrysogenum DSM105774 β-xylanase concurrently. Present data underpins AXE-HAS10 as a promising AXE for industrial exploitation.
Collapse
|
15
|
Cold-Active Enzymes and Their Potential Industrial Applications-A Review. Molecules 2022; 27:molecules27185885. [PMID: 36144621 PMCID: PMC9501442 DOI: 10.3390/molecules27185885] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
More than 70% of our planet is covered by extremely cold environments, nourishing a broad diversity of microbial life. Temperature is the most significant parameter that plays a key role in the distribution of microorganisms on our planet. Psychrophilic microorganisms are the most prominent inhabitants of the cold ecosystems, and they possess potential cold-active enzymes with diverse uses in the research and commercial sectors. Psychrophiles are modified to nurture, replicate, and retain their active metabolic activities in low temperatures. Their enzymes possess characteristics of maximal activity at low to adequate temperatures; this feature makes them more appealing and attractive in biotechnology. The high enzymatic activity of psychrozymes at low temperatures implies an important feature for energy saving. These enzymes have proven more advantageous than their mesophilic and thermophilic counterparts. Therefore, it is very important to explore the efficiency and utility of different psychrozymes in food processing, pharmaceuticals, brewing, bioremediation, and molecular biology. In this review, we focused on the properties of cold-active enzymes and their diverse uses in different industries and research areas. This review will provide insight into the areas and characteristics to be improved in cold-active enzymes so that potential and desired enzymes can be made available for commercial purposes.
Collapse
|
16
|
Wu Y, Zhou H, Sun W, Zhao Q, Liang M, Chen W, Guo Z, Jiang Y, Jiang Y, Liu G, Xue S. Temperature sensitivity of soil enzyme kinetics under N and P fertilization in an alpine grassland, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156042. [PMID: 35597335 DOI: 10.1016/j.scitotenv.2022.156042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/14/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Soil nutrient cycling can be best studied by supplementing the soil with N and P fertilizers. Soil enzyme kinetic parameters (Vmax and Km) can be used to reflect the maximum reaction rates and affinities of soil enzymes. However, how N and P fertilizers affect the temperature sensitivity of soil enzyme kinetics is poorly understood. Therefore, our study investigated the response of soil enzyme kinetic temperature sensitivity relevant to C, N, and P cycles based on a 9-year fertilization (N and P) experiment performed in an alpine grassland on the Qinghai-Tibetan Plateau in China. Our results showed the following: N and P addition positively affected the Km of β-glucosidase (BG); P and NP interaction significantly increased the Km of phosphatase (AP), indicating that N and P addition significantly negatively affected the substrate affinity of soil enzymes. The temperature sensitivity of Michaelis-Menten kinetics was different for different enzymes. N and P fertilization decreased the temperature sensitivity of Km of BG but increased the temperature sensitivity of the Km of N-acetyl-glucosaminidase (NAG) and AP. In our study, P and NP fertilization increased the temperature sensitivity and activation energy of the Vmax of BG, indicating that P elements promoted the secretion of more extracellular enzymes by soil microbes to cope with temperature changes. The enzymes involved in the soil N and P cycle responded to the exogenous N and P through increases and decreases in the temperature sensitivity of the Km and Vmax, respectively. This study is crucial for investigating the impact of nutrient input on soil ecosystem functions under future climate warming conditions.
Collapse
Affiliation(s)
- Yang Wu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - HuaKun Zhou
- Qinghai Provincial Key Laboratory of Restoration Ecology in Cold Regions, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810000, PR China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810000, PR China
| | - Wei Sun
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - QiFan Zhao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - Meng Liang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - WenJing Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - ZiQi Guo
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China
| | - YaoKun Jiang
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry Water Resources, Yangling 712100, PR China
| | - Yue Jiang
- College of Economics & Management, Northwest A&F University, Yangling 712100, PR China
| | - GuoBin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry Water Resources, Yangling 712100, PR China
| | - Sha Xue
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, PR China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry Water Resources, Yangling 712100, PR China.
| |
Collapse
|
17
|
Matrawy AA, Khalil AI, Embaby AM. Molecular study on recombinant cold-adapted, detergent- and alkali stable esterase (EstRag) from Lysinibacillus sp.: a member of family VI. World J Microbiol Biotechnol 2022; 38:217. [PMID: 36070019 PMCID: PMC9452428 DOI: 10.1007/s11274-022-03402-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022]
Abstract
Cold-adapted esterases have potential industrial applications. To fulfil the global continuous demand for these enzymes, a cold-adapted esterase member of family VI from Lysinibacillus sp. YS11 was cloned on pET-28b (+) vector and expressed in E. coli BL21(DE3) Rosetta cells for the first time. The open reading frame (654 bp: GenBank MT120818.1) encodes a polypeptide (designated EstRag: 217 amino acid residues). EstRag amino acid sequence has conserved esterase signature motifs: pentapeptide (GFSQG) and catalytic triad Ser110-Asp163-His194. EstRag 3D predicted model, built with LOMETS3 program, showed closest structural similarity to PDB 1AUO_A (esterase: Pseudomonas fluorescens); TM-align score program inferences. Purified EstRag to 9.28-fold, using Ni2+affinity agarose matrix, showed a single protein band (25 kDa) on SDS-PAGE, Km (0.031 mM) and Kcat/Km (657.7 s−1 mM−1) on p-NP-C2. Temperature and pH optima of EstRag were 35 °C and 8.0, respectively. EstRag was fully stable at 5–30 °C for 120 min and at pH(s) 8.0–10.0 after 24 h. EstRag activity (391.46 ± 0.009%) was impressively enhanced after 30 min preincubation with 5 mM Cu2+. EstRag retained full stability after 30 min pre-incubation with 0.1%(v/v) SDS, Triton X-100, and Tween-80. EstRag promising characteristics motivate performing guided evolution and industrial applications prospective studies.
Collapse
Affiliation(s)
- Amira A Matrawy
- Environmental Studies Department, Institute of Graduate Studies and Research, Alexandria University, 163 Horreya Avenue, P.O. Box 832, Chatby, 21526, Alexandria, Egypt
| | - Ahmed I Khalil
- Environmental Studies Department, Institute of Graduate Studies and Research, Alexandria University, 163 Horreya Avenue, P.O. Box 832, Chatby, 21526, Alexandria, Egypt
| | - Amira M Embaby
- Biotechnology Department, Institute of Graduate Studies and Research, Alexandria University, 163 Horreya Avenue, P.O. Box 832, Chatby, 21526, Alexandria, Egypt.
| |
Collapse
|
18
|
Masnoddin M, Ling CMWV, Yusof NA. Functional Analysis of Conserved Hypothetical Proteins from the Antarctic Bacterium, Pedobacter cryoconitis Strain BG5 Reveals Protein Cold Adaptation and Thermal Tolerance Strategies. Microorganisms 2022; 10:microorganisms10081654. [PMID: 36014072 PMCID: PMC9415557 DOI: 10.3390/microorganisms10081654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/04/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Pedobacter cryoconitis BG5 is an obligate psychrophilic bacterium that was first isolated on King George Island, Antarctica. Over the last 50 years, the West Antarctic, including King George Island, has been one of the most rapidly warming places on Earth, hence making it an excellent area to measure the resilience of living species in warmed areas exposed to the constantly changing environment due to climate change. This bacterium encodes a genome of approximately 5694 protein-coding genes. However, 35% of the gene models for this species are found to be hypothetical proteins (HP). In this study, three conserved HP genes of P. cryoconitis, designated pcbg5hp1, pcbg5hp2 and pcbg5hp12, were cloned and the proteins were expressed, purified and their functions and structures were evaluated. Real-time quantitative PCR analysis revealed that these genes were expressed constitutively, suggesting a potentially important role where the expression of these genes under an almost constant demand might have some regulatory functions in thermal stress tolerance. Functional analysis showed that these proteins maintained their activities at low and moderate temperatures. Meanwhile, a low citrate synthase aggregation at 43 °C in the presence of PCBG5HP1 suggested the characteristics of chaperone activity. Furthermore, our comparative structural analysis demonstrated that the HPs exhibited cold-adapted traits, most notably increased flexibility in their 3D structures compared to their counterparts. Concurrently, the presence of a disulphide bridge and aromatic clusters was attributed to PCBG5HP1’s unusual protein stability and chaperone activity. Thus, this suggested that the HPs examined in this study acquired strategies to maintain a balance between molecular stability and structural flexibility. Conclusively, this study has established the structure–function relationships of the HPs produced by P. cryoconitis and provided crucial experimental evidence indicating their importance in thermal stress response.
Collapse
Affiliation(s)
- Makdi Masnoddin
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
- Preparatory Centre for Science and Technology, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
| | | | - Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
- Correspondence:
| |
Collapse
|
19
|
KINASZ CAMILAT, KREUSCH MARIANNEG, BENDIA AMANDAG, PELLIZARI VIVIANH, DUARTE RUBENST. Taxonomic and functional diversity from Antarctic ice-tephra microbial community: ecological insights and potential for bioprospection. AN ACAD BRAS CIENC 2022; 94:e20210621. [DOI: 10.1590/0001-3765202220210621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
|
20
|
Shen L, Zhang S, Chen G. Regulated strategies of cold-adapted microorganisms in response to cold: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68006-68024. [PMID: 34648167 DOI: 10.1007/s11356-021-16843-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There are a large number of active cold-adapted microorganisms in the perennial cold environment. Due to their high-efficiency and energy-saving catalytic properties, cold-adapted microorganisms have become valuable natural resources with potential in various biological fields. In this study, a series of cold response strategies for microorganisms were summarized. This mainly involves the regulation of cell membrane fluidity, synthesis of cold adaptation proteins, regulators and metabolic changes, energy supply, and reactive oxygen species. Also, the potential of biocatalysts produced by cold-adapted microorganisms including cold-active enzymes, ice-binding proteins, polyhydroxyalkanoates, and surfactants was introduced, which provided a guidance for expanding its application values. Overall, new insights were obtained on response strategies of microorganisms to cold environments in this review. This will deepen the understanding of the cold tolerance mechanism of cold-adapted microorganisms, thus promoting the establishment and application of low-temperature biotechnology.
Collapse
Affiliation(s)
- Lijun Shen
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
| |
Collapse
|
21
|
Noby N, Auhim HS, Winter S, Worthy HL, Embaby AM, Saeed H, Hussein A, Pudney CR, Rizkallah PJ, Wells SA, Jones DD. Structure and in silico simulations of a cold-active esterase reveals its prime cold-adaptation mechanism. Open Biol 2021; 11:210182. [PMID: 34847772 PMCID: PMC8633780 DOI: 10.1098/rsob.210182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/02/2021] [Indexed: 01/09/2023] Open
Abstract
Here we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1. EstN7 is a dimer with a classical α/β hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entropy at lower temperatures. The conformation of the functionally important cap region is significantly different to EstN7's closest relatives, forming a bridge-like structure with reduced helical content providing greater access to the active site through more than one substrate access tunnel. However, dynamics do not appear to play a major role in cold adaption. Molecular dynamics at different temperatures, rigidity analysis, normal mode analysis and geometric simulations of motion confirm the flexibility of the cap region but suggest that the rest of the protein is largely rigid. Rigidity analysis indicates the distribution of hydrophobic tethers is appropriate to colder conditions, where the hydrophobic effect is weaker than in mesophilic conditions due to reduced water entropy. Thus, it is likely that increased substrate accessibility and tolerance to changes in water entropy are important for of EstN7's cold adaptation rather than changes in dynamics.
Collapse
Affiliation(s)
- Nehad Noby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
- School of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff CF10 3AX, UK
| | - Husam Sabah Auhim
- School of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff CF10 3AX, UK
- Department of Biology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Samuel Winter
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Harley L. Worthy
- School of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff CF10 3AX, UK
| | - Amira M. Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Hesham Saeed
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Ahmed Hussein
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | | | | | | | - D. Dafydd Jones
- School of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff CF10 3AX, UK
| |
Collapse
|
22
|
Kumari M, Padhi S, Sharma S, Phukon LC, Singh SP, Rai AK. Biotechnological potential of psychrophilic microorganisms as the source of cold-active enzymes in food processing applications. 3 Biotech 2021; 11:479. [PMID: 34790503 DOI: 10.1007/s13205-021-03008-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
Microorganisms striving in extreme environments and exhibiting optimal growth and reproduction at low temperatures, otherwise known as psychrophilic microorganisms, are potential sources of cold-active enzymes. Owing to higher stability and cold activity, these enzymes are gaining enormous attention in numerous industrial bioprocesses. Applications of several cold-active enzymes have been established in the food industry, e.g., β-galactosidase, pectinase, proteases, amylases, xylanases, pullulanases, lipases, and β-mannanases. The enzyme engineering approaches and the accumulating knowledge of protein structure and function have made it possible to improve the catalytic properties of interest and express the candidate enzyme in a heterologous host for a higher level of enzyme production. This review compiles the relevant and recent information on the potential uses of different cold-active enzymes in the food industry.
Collapse
Affiliation(s)
- Megha Kumari
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Swati Sharma
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| |
Collapse
|
23
|
Green Oxidation of Amines by a Novel Cold-Adapted Monoamine Oxidase MAO P3 from Psychrophilic Fungi Pseudogymnoascus sp. P3. Molecules 2021; 26:molecules26206237. [PMID: 34684818 PMCID: PMC8538783 DOI: 10.3390/molecules26206237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022] Open
Abstract
The use of monoamine oxidases (MAOs) in amine oxidation is a great example of how biocatalysis can be applied in the agricultural or pharmaceutical industry and manufacturing of fine chemicals to make a shift from traditional chemical synthesis towards more sustainable green chemistry. This article reports the screening of fourteen Antarctic fungi strains for MAO activity and the discovery of a novel psychrozyme MAOP3 isolated from the Pseudogymnoascus sp. P3. The activity of the native enzyme was 1350 ± 10.5 U/L towards a primary (n-butylamine) amine, and 1470 ± 10.6 U/L towards a secondary (6,6-dimethyl-3-azabicyclohexane) amine. MAO P3 has the potential for applications in biotransformations due to its wide substrate specificity (aliphatic and cyclic amines, pyrrolidine derivatives). The psychrozyme operates at an optimal temperature of 30 °C, retains 75% of activity at 20 °C, and is rather thermolabile, which is beneficial for a reduction in the overall costs of a bioprocess and offers a convenient way of heat inactivation. The reported biocatalyst is the first psychrophilic MAO; its unique biochemical properties, substrate specificity, and effectiveness predispose MAO P3 for use in environmentally friendly, low-emission biotransformations.
Collapse
|
24
|
Varga A, Csuka P, Sonesouphap O, Bánóczi G, Toşa MI, Katona G, Molnár Z, Bencze LC, Poppe L, Paizs C. A novel phenylalanine ammonia-lyase from Pseudozyma antarctica for stereoselective biotransformations of unnatural amino acids. Catal Today 2021. [DOI: 10.1016/j.cattod.2020.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
25
|
Medium Optimization and Proteome Analysis of Protease Production by Janthinobacterium sp. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0110-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
26
|
Rizzo C, Lo Giudice A. The Variety and Inscrutability of Polar Environments as a Resource of Biotechnologically Relevant Molecules. Microorganisms 2020; 8:microorganisms8091422. [PMID: 32947905 PMCID: PMC7564310 DOI: 10.3390/microorganisms8091422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
The application of an ever-increasing number of methodological approaches and tools is positively contributing to the development and yield of bioprospecting procedures. In this context, cold-adapted bacteria from polar environments are becoming more and more intriguing as valuable sources of novel biomolecules, with peculiar properties to be exploited in a number of biotechnological fields. This review aims at highlighting the biotechnological potentialities of bacteria from Arctic and Antarctic habitats, both biotic and abiotic. In addition to cold-enzymes, which have been intensively analysed, relevance is given to recent advances in the search for less investigated biomolecules, such as biosurfactants, exopolysaccharides and antibiotics.
Collapse
Affiliation(s)
- Carmen Rizzo
- Stazione Zoologica Anton Dohrn, Department Marine Biotechnology, National Institute of Biology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy
- Correspondence:
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata San Raineri 86, 98122 Messina, Italy;
| |
Collapse
|
27
|
Zucconi L, Canini F, Temporiti ME, Tosi S. Extracellular Enzymes and Bioactive Compounds from Antarctic Terrestrial Fungi for Bioprospecting. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17186459. [PMID: 32899827 PMCID: PMC7558612 DOI: 10.3390/ijerph17186459] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022]
Abstract
Antarctica, one of the harshest environments in the world, has been successfully colonized by extremophilic, psychrophilic, and psychrotolerant microorganisms, facing a range of extreme conditions. Fungi are the most diverse taxon in the Antarctic ecosystems, including soils. Genetic adaptation to this environment results in the synthesis of a range of metabolites, with different functional roles in relation to the biotic and abiotic environmental factors, some of which with new biological properties of potential biotechnological interest. An overview on the production of cold-adapted enzymes and other bioactive secondary metabolites from filamentous fungi and yeasts isolated from Antarctic soils is here provided and considerations on their ecological significance are reported. A great number of researches have been carried out to date, based on cultural approaches. More recently, metagenomics approaches are expected to increase our knowledge on metabolic potential of these organisms, leading to the characterization of unculturable taxa. The search on fungi in Antarctica deserves to be improved, since it may represent a useful strategy for finding new metabolic pathways and, consequently, new bioactive compounds.
Collapse
Affiliation(s)
- Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence: (L.Z.); (F.C.); Tel.: +39-328-2741247 (L.Z.); +39-347-9288247 (F.C.)
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence: (L.Z.); (F.C.); Tel.: +39-328-2741247 (L.Z.); +39-347-9288247 (F.C.)
| | - Marta Elisabetta Temporiti
- Department of Earth and Environmental Sciences, University of Pavia, via S. Epifanio 14, 27100 Pavia, Italy; (M.E.T.); (S.T.)
| | - Solveig Tosi
- Department of Earth and Environmental Sciences, University of Pavia, via S. Epifanio 14, 27100 Pavia, Italy; (M.E.T.); (S.T.)
| |
Collapse
|
28
|
Abe T, Akazawa Y, Toyoda A, Niki H, Baba T. Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes. Front Microbiol 2020; 11:1486. [PMID: 32719664 PMCID: PMC7350273 DOI: 10.3389/fmicb.2020.01486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/08/2020] [Indexed: 02/05/2023] Open
Abstract
Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.
Collapse
Affiliation(s)
- Takashi Abe
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Yu Akazawa
- Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan.,Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, National Institute of Genetics, Mishima, Japan
| | - Tomoya Baba
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan.,Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Tokyo, Japan
| |
Collapse
|
29
|
Pellerin A, Antler G, Marietou A, Turchyn AV, Jørgensen BB. The effect of temperature on sulfur and oxygen isotope fractionation by sulfate reducing bacteria (Desulfococcus multivorans). FEMS Microbiol Lett 2020; 367:5817845. [PMID: 32267916 DOI: 10.1093/femsle/fnaa061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 04/04/2020] [Indexed: 11/14/2022] Open
Abstract
Temperature influences microbiological growth and catabolic rates. Between 15 and 35 °C the growth rate and cell specific sulfate reduction rate of the sulfate reducing bacterium Desulfococcus multivorans increased with temperature. Sulfur isotope fractionation during sulfate reduction decreased with increasing temperature from 27.2 ‰ at 15 °C to 18.8 ‰ at 35 °C which is consistent with a decreasing reversibility of the metabolic pathway as the catabolic rate increases. Oxygen isotope fractionation, in contrast, decreased between 15 and 25 °C and then increased again between 25 and 35 °C, suggesting increasing reversibility in the first steps of the sulfate reducing pathway at higher temperatures. This points to a decoupling in the reversibility of sulfate reduction between the steps from the uptake of sulfate into the cell to the formation of sulfite, relative to the whole pathway from sulfate to sulfide. This observation is consistent with observations of increasing sulfur isotope fractionation when sulfate reducing bacteria are living near their upper temperature limit. The oxygen isotope decoupling may be a first signal of changing physiology as the bacteria cope with higher temperatures.
Collapse
Affiliation(s)
- André Pellerin
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark.,Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P. O. Box 653, Beer-Sheva 84105, Israel
| | - Gilad Antler
- Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P. O. Box 653, Beer-Sheva 84105, Israel.,The Interuniversity Institute for Marine Sciences of Eilat, PO Box 469, Eilat 88103, Israel
| | - Angeliki Marietou
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark
| | - Alexandra V Turchyn
- Cambridge University, Downing Street, Cambridge, CB2 3EQ, Departement of Earth Sciences, Cambridge, UK
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark
| |
Collapse
|
30
|
Giordano D, Boubeta FM, di Prisco G, Estrin DA, Smulevich G, Viappiani C, Verde C. Conformational Flexibility Drives Cold Adaptation in Pseudoalteromonas haloplanktis TAC125 Globins. Antioxid Redox Signal 2020; 32:396-411. [PMID: 31578873 DOI: 10.1089/ars.2019.7887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Significance: Temperature is one of the most important drivers in shaping protein adaptations. Many biochemical and physiological processes are influenced by temperature. Proteins and enzymes from organisms living at low temperature are less stable in comparison to high-temperature adapted proteins. The lower stability is generally due to greater conformational flexibility. Recent Advances: Adaptive changes in the structure of cold-adapted proteins may occur at subunit interfaces, distant from the active site, thus producing energy changes associated with conformational transitions transmitted to the active site by allosteric modulation, valid also for monomeric proteins in which tertiary structural changes may play an essential role. Critical Issues: Despite efforts, the current experimental and computational methods still fail to produce general principles on protein evolution, since many changes are protein and species dependent. Environmental constraints or other biological cellular signals may override the ancestral information included in the structure of the protein, thus introducing inaccuracy in estimates and predictions on the evolutionary adaptations of proteins in response to cold adaptation. Future Directions: In this review, we describe the studies and approaches used to investigate stability and flexibility in the cold-adapted globins of the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125. In fact, future research directions will be prescient on more detailed investigation of cold-adapted proteins and the role of fluctuations between different conformational states.
Collapse
Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Fernando Martín Boubeta
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parma, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| |
Collapse
|
31
|
Noby N, Hussein A, Saeed H, Embaby AM. "Recombinant cold -adapted halotolerant, organic solvent-stable esterase (estHIJ) from Bacillus halodurans. Anal Biochem 2020; 591:113554. [PMID: 31863727 DOI: 10.1016/j.ab.2019.113554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/08/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022]
Abstract
Esterases and lipases enduring harsh conditions, including low temperature and extreme tolerance to organic solvents, have attracted great attention in recent times. In the current study, a full open reading frame of 747 bp that encodes a novel, cold-adapted esterase (estHIJ) of 248 amino acids from Bacillus halodurans strain NAH-Egypt was heterologously cloned and expressed in E. coli BL21 (DE3) Rosetta. Amino acid sequence analysis revealed that estHIJ belongs to family XIII of lipolytic enzymes, with a characteristic pentapeptide motif (G-L-S-L-G). The recombinant estHIJ was purified using Ni-affinity chromatography to homogeneity with purification fold, yield, specific activity, and molecular weight (MW) of 3.5, 47.5%, 19.8 U/mg and 29 kDa, respectively. The enzyme showed preferential substrate specificity towards pNP-acetate (C2), with catalytic efficiency of 46,825 min-1 mM-1 estHIJ displayed optimal activity at 30 °C and pH (7.0-8.0). estHIJ demonstrated robust stability in the presence of 50% (v/v) non-polar solvents and 4 M NaCl after 15 h and 6 h of incubation, respectively. The promising features of the recombinant estHIJ underpin its potential in several fields, e.g., the synthesis of pharmaceutical compounds and the food industry.
Collapse
Affiliation(s)
- Nehad Noby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Ahmed Hussein
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Hesham Saeed
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Amira M Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt.
| |
Collapse
|
32
|
Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019; 17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.
Collapse
|
33
|
Han Z, Shang-Guan F, Yang J. Molecular and Biochemical Characterization of a Bimodular Xylanase From Marinifilaceae Bacterium Strain SPP2. Front Microbiol 2019; 10:1507. [PMID: 31312196 PMCID: PMC6614494 DOI: 10.3389/fmicb.2019.01507] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 06/17/2019] [Indexed: 01/31/2023] Open
Abstract
In this study, the first xylantic enzyme from the family Marinifilaceae, XynSPP2, was identified from Marinifilaceae bacterium strain SPP2. Amino acid sequence analysis revealed that XynSPP2 is a rare Fn3-fused xylanase, consisting of a signal peptide, a fibronectin type-III domain (Fn3), and a C-terminal catalytic domain belonging to glycoside hydrolase family 10 (GH10). The catalytic domain shared 17–46% identities to those of biochemically characterized GH10 xylanases. Structural analysis revealed that the conserved asparagine and glutamine at the glycone −2/−3 subsite of GH10 xylanases are substituted by a tryptophan and a serine, respectively, in XynSPP2. Full-length XynSPP2 and its Fn3-deleted variant (XynSPP2ΔFn3) were overexpressed in Escherichia coli and purified by Ni-affinity chromatography. The optimum temperature and pH for both recombinant enzymes were 50°C and 6, respectively. The enzymes were stable under alkaline condition and at temperature lower than 50°C. With beechwood xylan as the substrate, XynSPP2 showed 2.8 times the catalytic efficiency of XynSPP2ΔFn3, indicating that the Fn3 module promotes xylanase activity. XynSPP2 was active toward xylooligosaccharides (XOSs) longer than xylotriose. Such a substrate preference can be explained by the unique −2/−3 subsite composition in the enzyme which provides new insight into subsite interaction within the GH10 family. XynSPP2 hydrolyzed beechwood xylan into small XOSs (xylotriose and xylotetraose as major products). No monosaccharide was detected by thin-layer chromatography which may be ascribed to putative transxylosylation activity of XynSPP2. Preferring long XOS substrate and lack of monosaccharide production suggest its potential in probiotic XOS manufacture.
Collapse
Affiliation(s)
- Zhenggang Han
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Fang Shang-Guan
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jiangke Yang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| |
Collapse
|
34
|
Rapid detection and control of psychrotrophic microorganisms in cold storage foods: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
35
|
Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
Collapse
|
36
|
Pischedda A, Ramasamy KP, Mangiagalli M, Chiappori F, Milanesi L, Miceli C, Pucciarelli S, Lotti M. Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes. Sci Rep 2018; 8:14721. [PMID: 30283056 PMCID: PMC6170424 DOI: 10.1038/s41598-018-33127-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/20/2018] [Indexed: 11/09/2022] Open
Abstract
Oxidative stress is a particularly severe threat to Antarctic marine polar organisms because they are exposed to high dissolved oxygen and to intense UV radiation. This paper reports the features of three superoxide dismutases from the Antarctic psychrophilic ciliate Euplotes focardii that faces two environmental challenges, oxidative stress and low temperature. Two out of these are Cu,Zn superoxide dismutases (named Ef-SOD1a and Ef-SOD1b) and one belongs to the Mn-containing group (Ef-SOD2). Ef-SOD1s and Ef-SOD2 differ in their evolutionary history, expression and overall structural features. Ef-SOD1 genes are expressed at different levels, with Ef-SOD1b mRNA 20-fold higher at the ciliate optimal temperature of growth (4 °C). All Ef-SOD enzymes are active at 4 °C, consistent with the definition of cold-adapted enzymes. At the same time, they display temperatures of melting in the range 50-70 °C and retain residual activity after incubation at 65-75 °C. Supported by data of molecular dynamics simulation, we conclude that the E. focardii SODs combine cold activity, local molecular flexibility and thermo tolerance.
Collapse
Affiliation(s)
- Alessandro Pischedda
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Kesava Priyan Ramasamy
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | | | | | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 1, 62032, Camerino (MC), Italy.
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| |
Collapse
|
37
|
Bacteria Associated with Marine Benthic Invertebrates from Polar Environments: Unexplored Frontiers for Biodiscovery? DIVERSITY-BASEL 2018. [DOI: 10.3390/d10030080] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ecological function of bacteria-invertebrate interactions in Polar areas remains poorly understood, despite increasing evidence that microbial metabolites may play pivotal roles in host-associated chemical defense and in shaping the symbiotic community structure. The metabolic and physiological changes that these organisms undergo in response to adapting to extreme conditions result in the production of structurally and functionally novel biologically active molecules. Deepening our knowledge on the interactions between bacteria and their invertebrate host would be highly helpful in providing the rationale for why (e.g., competition or cooperative purpose) and which (whether secondary metabolites, enzymes, or proteins) bioactive compounds are produced. To date, cold-adapted bacteria associated with marine invertebrates from the Arctic and Antarctica have not been given the attention they deserve and the versatility of their natural products remains virtually unexplored, even if they could represent a new attractive frontier in the search for novel natural compounds. This review is aimed at showcasing the diversity of cold-adapted bacteria associated with benthic invertebrates from Polar marine areas, highlighting the yet unexplored treasure they represent for biodiscovery.
Collapse
|
38
|
Molecular Cloning and Characterization of a Novel α-Amylase from Antarctic Sea Ice Bacterium Pseudoalteromonas sp. M175 and Its Primary Application in Detergent. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3258383. [PMID: 30050926 PMCID: PMC6040283 DOI: 10.1155/2018/3258383] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/06/2018] [Accepted: 05/02/2018] [Indexed: 11/17/2022]
Abstract
A novel cold-adapted and salt-tolerant α-amylase gene (amy175) from Antarctic sea ice bacterium Pseudoalteromonas sp. M175 was successfully cloned and expressed. The open reading frame (ORF) of amy175 had 1722 bp encoding a protein of 573 amino acids residues. Multiple alignments indicated Amy175 had seven highly conserved sequences and the putative catalytic triad (Asp244, Glu286, and Asp372). It was the first identified member of GH13_36 subfamily which contained QPDLN in the CSR V. The recombinant enzyme (Amy175) was purified to homogeneity with a molecular mass of about 62 kDa on SDS-PAGE. It had a mixed enzyme specificity of α-amylase and α-glucosidase. Amy175 displayed highest activity at pH 8.0 and 25°C and exhibited extreme salt-resistance with the maximum activity at 1 M NaCl. Amy175 was strongly stimulated by Mg2+, Ni2+, K+, 1 mM Ca2+, 1 mM Ba2+, 1 mM Pb2+, 1 mM sodium dodecyl sulphate (SDS), and 10% dimethyl sulfoxide (DMSO) but was significantly inhibited by Cu2+, Mn2+, Hg2+, 10 mM β-mercaptoethanol (β-ME), and 10% Tween 80. Amy175 demonstrated excellent resistance towards all the tested commercial detergents, and wash performance analysis displayed that the addition of Amy175 improved the stain removal efficiency. This study demonstrated that Amy175 would be proposed as a novel α-amylase source for industrial application in the future.
Collapse
|
39
|
Hashim NHF, Mahadi NM, Illias RM, Feroz SR, Abu Bakar FD, Murad AMA. Biochemical and structural characterization of a novel cold-active esterase-like protein from the psychrophilic yeast Glaciozyma antarctica. Extremophiles 2018; 22:607-616. [DOI: 10.1007/s00792-018-1021-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/11/2018] [Indexed: 02/04/2023]
|
40
|
Psychrotrophic Microbiomes: Molecular Diversity and Beneficial Role in Plant Growth Promotion and Soil Health. MICROORGANISMS FOR SUSTAINABILITY 2018. [DOI: 10.1007/978-981-10-7146-1_11] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
41
|
Araújo FVDE, Netto MCM, Azevedo GP, Jayme MMA, Nunes-Carvalho MC, Silva MM, Carmo FLDO. Ecology and biotechnological potential of bacterial community from three marine sponges of the coast of Rio de Janeiro, Brazil. AN ACAD BRAS CIENC 2017; 89:2785-2792. [PMID: 29236862 DOI: 10.1590/0001-3765201720170462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/11/2017] [Indexed: 11/22/2022] Open
Abstract
Marine sponges has been a large reservoir of microbial diversity, with the presence of many species specific populations as well as producing biologically active compounds, which has attracted great biotechnological interest. In order to verify the influence of the environment in the composition of the bacterial community present in marine sponges and biotechnological potential of bacteria isolated from these organisms, three species of sponges and the waters surrounding them were collected in different beaches of Rio de Janeiro, Brazil. The profile of the bacterial community present in sponges and water was obtained by PCR-DGGE technique and the biotechnological potential of the strains isolated by producing amylase, cellulase, protease and biosurfactants. The results showed that despite the influence of the environment in the composition of the microbial community, studied marine sponges shown to have specific bacterial populations, with some, showing potential in the production of substances of biotechnological applications.
Collapse
Affiliation(s)
- Fábio V DE Araújo
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Marcelle C M Netto
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Gustavo P Azevedo
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Marcelly M A Jayme
- Departamento de Microbiologia, Imunologia e Parasitologia, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rua São Francisco Xavier, 524, 3° andar , Maracanã, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Monica C Nunes-Carvalho
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Av. Athos da Silveira Ramos, 149, 21044-020 Rio de Janeiro, RJ, Brazil
| | - Mariana M Silva
- Departamento de Ciências, Faculdade de Formação de Professores, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, Patronato, 24435-005 São Gonçalo, RJ, Brazil
| | - Flávia L DO Carmo
- Departamento de Microbiologia Geral, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, RJ, Brazil
| |
Collapse
|
42
|
Duarte AWF, Dos Santos JA, Vianna MV, Vieira JMF, Mallagutti VH, Inforsato FJ, Wentzel LCP, Lario LD, Rodrigues A, Pagnocca FC, Pessoa Junior A, Durães Sette L. Cold-adapted enzymes produced by fungi from terrestrial and marine Antarctic environments. Crit Rev Biotechnol 2017; 38:600-619. [PMID: 29228814 DOI: 10.1080/07388551.2017.1379468] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antarctica is the coldest, windiest, and driest continent on Earth. In this sense, microorganisms that inhabit Antarctica environments have to be adapted to harsh conditions. Fungal strains affiliated with Ascomycota and Basidiomycota phyla have been recovered from terrestrial and marine Antarctic samples. They have been used for the bioprospecting of molecules, such as enzymes. Many reports have shown that these microorganisms produce cold-adapted enzymes at low or mild temperatures, including hydrolases (e.g. α-amylase, cellulase, chitinase, glucosidase, invertase, lipase, pectinase, phytase, protease, subtilase, tannase, and xylanase) and oxidoreductases (laccase and superoxide dismutase). Most of these enzymes are extracellular and their production in the laboratory has been carried out mainly under submerged culture conditions. Several studies showed that the cold-adapted enzymes exhibit a wide range in optimal pH (1.0-9.0) and temperature (10.0-70.0 °C). A myriad of methods have been applied for cold-adapted enzyme purification, resulting in purification factors and yields ranging from 1.70 to 1568.00-fold and 0.60 to 86.20%, respectively. Additionally, some fungal cold-adapted enzymes have been cloned and expressed in host organisms. Considering the enzyme-producing ability of microorganisms and the properties of cold-adapted enzymes, fungi recovered from Antarctic environments could be a prolific genetic resource for biotechnological processes (industrial and environmental) carried out at low or mild temperatures.
Collapse
Affiliation(s)
- Alysson Wagner Fernandes Duarte
- a Universidade Federal de Alagoas, Campus Arapiraca , Arapiraca , Brazil.,b Divisão de Recursos Microbianos , Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas , Paulínia , Brazil
| | - Juliana Aparecida Dos Santos
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Marina Vitti Vianna
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Juliana Maíra Freitas Vieira
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Vitor Hugo Mallagutti
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Fabio José Inforsato
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Lia Costa Pinto Wentzel
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Luciana Daniela Lario
- d Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario , Rosario , Argentina.,e Departamento de Tecnologia Bioquímico-Farmacêutica , Faculdade de Ciências Farmacêuticas, Universidade de São Paulo , São Paulo , Brazil
| | - Andre Rodrigues
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Fernando Carlos Pagnocca
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| | - Adalberto Pessoa Junior
- e Departamento de Tecnologia Bioquímico-Farmacêutica , Faculdade de Ciências Farmacêuticas, Universidade de São Paulo , São Paulo , Brazil
| | - Lara Durães Sette
- c Departamento de Bioquímica e Microbiologia , Universidade Estadual Paulistra (UNESP), Câmpus de Rio Claro , Rio Claro , Brazil
| |
Collapse
|
43
|
Predicting the biotechnological potential of bacteria isolated from Antarctic soils, including the rhizosphere of vascular plants. Polar Biol 2017. [DOI: 10.1007/s00300-016-2065-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
44
|
Baraúna RA, Freitas DY, Pinheiro JC, Folador ARC, Silva A. A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7. Proteomes 2017; 5:proteomes5010009. [PMID: 28248259 PMCID: PMC5372230 DOI: 10.3390/proteomes5010009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/24/2016] [Accepted: 12/05/2016] [Indexed: 11/30/2022] Open
Abstract
Since the publication of one of the first studies using 2D gel electrophoresis by Patrick H. O’Farrell in 1975, several other studies have used that method to evaluate cellular responses to different physicochemical variations. In environmental microbiology, bacterial adaptation to cold environments is a “hot topic” because of its application in biotechnological processes. As in other fields, gel-based and gel-free proteomic methods have been used to determine the molecular mechanisms of adaptation to cold of several psychrotrophic and psychrophilic bacterial species. In this review, we aim to describe and discuss these main molecular mechanisms of cold adaptation, referencing proteomic studies that have made significant contributions to our current knowledge in the area. Furthermore, we use Exiguobacterium antarcticum B7 as a model organism to present the importance of integrating genomic, transcriptomic, and proteomic data. This species has been isolated in Antarctica and previously studied at all three omic levels. The integration of these data permitted more robust conclusions about the mechanisms of bacterial adaptation to cold.
Collapse
Affiliation(s)
- Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Dhara Y Freitas
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Juliana C Pinheiro
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| |
Collapse
|
45
|
Swain MR, Natarajan V, Krishnan C. Marine Enzymes and Microorganisms for Bioethanol Production. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 80:181-197. [PMID: 28215326 DOI: 10.1016/bs.afnr.2016.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bioethanol is a potential alternative fuel to fossil fuels. Bioethanol as a fuel has several economic and environmental benefits. Though bioethanol is produced using starch and sugarcane juice, these materials are in conflict with food availability. To avoid food-fuel conflict, the second-generation bioethanol production by utilizing nonfood lignocellulosic materials has been extensively investigated. However, due to the complexity of lignocellulose architecture, the process is complicated and not economically competitive. The cultivation of lignocellulosic energy crops indirectly affects the food supplies by extensive land use. Marine algae have attracted attention to replace the lignocellulosic feedstock for bioethanol production, since the algae grow fast, do not use land, avoid food-fuel conflict and have several varieties to suit the cultivation environment. The composition of algae is not as complex as lignocellulose due to the absence of lignin, which renders easy hydrolysis of polysaccharides to fermentable sugars. Marine organisms also produce cold-active enzymes for hydrolysis of starch, cellulose, and algal polysaccharides, which can be employed in bioethanol process. Marine microoorganisms are also capable of fermenting sugars under high salt environment. Therefore, marine biocatalysts are promising for development of efficient processes for bioethanol production.
Collapse
Affiliation(s)
- M R Swain
- Indian Institute of Technology Madras, Chennai, India
| | - V Natarajan
- Indian Institute of Technology Madras, Chennai, India
| | - C Krishnan
- Indian Institute of Technology Madras, Chennai, India.
| |
Collapse
|
46
|
Bai X, Yuan X, Wen A, Li J, Bai Y, Shao T. Efficient expression and characterization of a cold-active endo-1, 4-β-glucanase from Citrobacter farmeri by co-expression of Myxococcus xanthus protein S. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
47
|
Santiago M, Ramírez-Sarmiento CA, Zamora RA, Parra LP. Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. Front Microbiol 2016; 7:1408. [PMID: 27667987 PMCID: PMC5016527 DOI: 10.3389/fmicb.2016.01408] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 08/25/2016] [Indexed: 11/17/2022] Open
Abstract
Cold-active enzymes constitute an attractive resource for biotechnological applications. Their high catalytic activity at temperatures below 25°C makes them excellent biocatalysts that eliminate the need of heating processes hampering the quality, sustainability, and cost-effectiveness of industrial production. Here we provide a review of the isolation and characterization of novel cold-active enzymes from microorganisms inhabiting different environments, including a revision of the latest techniques that have been used for accomplishing these paramount tasks. We address the progress made in the overexpression and purification of cold-adapted enzymes, the evolutionary and molecular basis of their high activity at low temperatures and the experimental and computational techniques used for their identification, along with protein engineering endeavors based on these observations to improve some of the properties of cold-adapted enzymes to better suit specific applications. We finally focus on examples of the evaluation of their potential use as biocatalysts under conditions that reproduce the challenges imposed by the use of solvents and additives in industrial processes and of the successful use of cold-adapted enzymes in biotechnological and industrial applications.
Collapse
Affiliation(s)
- Margarita Santiago
- Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Universidad de ChileSantiago, Chile
| | - César A. Ramírez-Sarmiento
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Ricardo A. Zamora
- Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
| |
Collapse
|
48
|
Baweja M, Nain L, Kawarabayasi Y, Shukla P. Current Technological Improvements in Enzymes toward Their Biotechnological Applications. Front Microbiol 2016; 7:965. [PMID: 27379087 PMCID: PMC4909775 DOI: 10.3389/fmicb.2016.00965] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
Enzymes from extremophiles are creating interest among researchers due to their unique properties and the enormous power of catalysis at extreme conditions. Since community demands are getting more intensified, therefore, researchers are applying various approaches viz. metagenomics to increase the database of extremophilic species. Furthermore, the innovations are being made in the naturally occurring enzymes utilizing various tools of recombinant DNA technology and protein engineering, which allows redesigning of the enzymes for its better fitment into the process. In this review, we discuss the biochemical constraints of psychrophiles during survival at the lower temperature. We summarize the current knowledge about the sources of such enzymes and their in vitro modification through mutagenesis to explore their biotechnological potential. Finally, we recap the microbial cell surface display to enhance the efficiency of the process in cost effective way.
Collapse
Affiliation(s)
- Mehak Baweja
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi India
| | - Yutaka Kawarabayasi
- National Institute of Advanced Industrial Science and Technology, Tsukuba Japan
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
| |
Collapse
|
49
|
Robador A, Müller AL, Sawicka JE, Berry D, Hubert CRJ, Loy A, Jørgensen BB, Brüchert V. Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments. THE ISME JOURNAL 2016; 10:796-809. [PMID: 26359912 PMCID: PMC4796921 DOI: 10.1038/ismej.2015.157] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/18/2015] [Accepted: 07/25/2015] [Indexed: 11/09/2022]
Abstract
Temperature has a fundamental impact on the metabolic rates of microorganisms and strongly influences microbial ecology and biogeochemical cycling in the environment. In this study, we examined the catabolic temperature response of natural communities of sulfate-reducing microorganisms (SRM) in polar, temperate and tropical marine sediments. In short-term sediment incubation experiments with (35)S-sulfate, we demonstrated how the cardinal temperatures for sulfate reduction correlate with mean annual sediment temperatures, indicating specific thermal adaptations of the dominant SRM in each of the investigated ecosystems. The community structure of putative SRM in the sediments, as revealed by pyrosequencing of bacterial 16S rRNA gene amplicons and phylogenetic assignment to known SRM taxa, consistently correlated with in situ temperatures, but not with sediment organic carbon concentrations or C:N ratios of organic matter. Additionally, several species-level SRM phylotypes of the class Deltaproteobacteria tended to co-occur at sites with similar mean annual temperatures, regardless of geographic distance. The observed temperature adaptations of SRM imply that environmental temperature is a major controlling variable for physiological selection and ecological and evolutionary differentiation of microbial communities.
Collapse
Affiliation(s)
- Alberto Robador
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Albert L Müller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Wien, Austria
| | - Joanna E Sawicka
- Department of Geological Sciences, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Wien, Austria
| | - Casey R J Hubert
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Wien, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus C, Denmark
| | - Volker Brüchert
- Department of Geological Sciences, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| |
Collapse
|
50
|
Cold-Active β-Galactosidases: Sources, Biochemical Properties and Their Biotechnological Potential. BIOTECHNOLOGY OF EXTREMOPHILES: 2016. [DOI: 10.1007/978-3-319-13521-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|