Biocatalysis and Biotransformation of Extremozymes

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Biocatalysis".

Deadline for manuscript submissions: closed (20 June 2022) | Viewed by 13620

Special Issue Editors


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Guest Editor
Department of Biology, University of Naples “Federico II", Via Cinthia 26, Ed. 7, 80126 Naples, Italy
Interests: expression; purification and characterization of DNA- and carbohydrate-active enzymes from (hyper)thermophilic organisms; protein engineering for enzyme optimization employed as biotechnological tools

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Guest Editor
School of Molecular and Cellular Biology, University of Illinois, Champaign, IL, USA
Interests: molecular biology and biochemistry of archaeal DNA replication; enzymes of plant cell wall hydrolysis

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Co-Guest Editor
Institute of Biosciences and BioResources, National Research Council of Italy, Rome, Italy
Interests: DNA metabolism and biochemical analysis of proteins and enzymes in particular related to DNA structure regulation and to the safeguard of genomic stability in (hyper)thermophiles

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Co-Guest Editor
Institute of Biosciences and BioResources, National Research Council of Italy, Rome, Italy
Interests: structure and function of cold-adapted proteins in marine organisms; evolutionary and physiological adaptations; oxidative/nitrosative stress; NO biology

Special Issue Information

Dear Colleagues,

Normal is passé, extreme is chic”, as NASA’s Lynn J. Rothschild and Rocco L. Mancinelli said some years ago. The discovery of extreme environments and organisms which thrive in them had an impact on science similar to that on the refutation of the Ptolemaic vision. The awareness that the definition of life was very far from its "anthropocentric" connotation has in fact given a huge boost in various fields of knowledge, from basic research on the origin of life to astrobiology (life outside the Earth).

Undoubtedly, extremophilic microorganisms represent an impressive "treasure chest" of new enzymes, and their associated studies have led to the realization that biocatalysis goes beyond mild conditions, pushing the boundaries of pH, temperature, pressure, ionic environments and solvents, thought before to be destructive to biomolecules. Although yet to be fully realized, our understanding of the tenets underlying enzymatic function under extreme reaction conditions has led to the identification of some of the molecular mechanisms that play key roles in the success of extremozymes. Our expanded knowledge of the evolutionary trajectories of diverse enzymes across different environmental gradients therefore offers the opportunity to improve enzymes in terms of stability and activity, and/or the development of efficient, sustainable, and environmentally friendly industrial technologies.

This Special Issue is devoted to basic research on enzymes that function under harsh reaction conditions, for example in DNA transactions at high temperatures and/or radiations, or cellular metabolism under freezing water. We further welcome applied research that employs these biocatalysts in different “biotech” fields, including in the decomposition of hardly soluble and insoluble polymers for sustainable energy production and in food and detergent industries.

Reviews and original research papers from fundamental research to industrial application are welcome.

The main topics include but are not limited to:

- Enzyme evolution and adaptation;

- Catalysis at temperature extremes;

- Stabilization of mesophilic enzymes by protein engineering;

- DNA-associated extremozymes;

- Enzymes in polar environments;

- Extremophiles catalysts for sustainable bio-refineries;

- Novel and sustainable enzymes from marine extremophilic sources;

- Biotechnology of extremozymes.

Submit your paper and select the Journal “Catalysts” and the Special Issue “Biocatalysis and Biotransformation of Extremozymes” via: MDPI submission system. Please contact the Guest Editor or the journal editor ([email protected]) for any queries. Our papers will be published on a rolling basis and we will be pleased to receive your submission once you have finished it.


Dr. Giuseppe Perugino
Prof. Dr. Isaac Cann
Dr. Anna Valenti
Dr. Cinzia Verde
Guest Editors

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Keywords

  • extremozyme
  • biotechnological tools
  • biotransformation in harsh conditions
  • rational and irrational enzyme engineering
  • enzyme evolution
  • origin of life
  • biocatalysis

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Published Papers (4 papers)

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Research

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13 pages, 3334 KiB  
Article
Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis
by Wakao Fukuda, Mamoru Osaki, Yusuke Yasuda, Ryota Hidese, Tsunehiko Higuchi, Naoki Umezawa, Shinsuke Fujiwara and Eiichi Mizohata
Catalysts 2022, 12(5), 567; https://doi.org/10.3390/catal12050567 - 20 May 2022
Cited by 1 | Viewed by 2767
Abstract
The facultative anaerobic hyperthermophilic crenarchaeon Pyrobaculum calidifontis possesses norspermine (333), norspermidine (33), and spermidine (34) as intracellular polyamines (where the number in parentheses represents the number of methylene CH2 chain units between NH2, or [...] Read more.
The facultative anaerobic hyperthermophilic crenarchaeon Pyrobaculum calidifontis possesses norspermine (333), norspermidine (33), and spermidine (34) as intracellular polyamines (where the number in parentheses represents the number of methylene CH2 chain units between NH2, or NH). In this study, the polyamine biosynthesis pathway of P. calidifontis was predicted on the basis of the enzymatic properties and crystal structures of an aminopropyltransferase from P. calidifontis (Pc-SpeE). Pc-SpeE shared 75% amino acid identity with the thermospermine synthase from Pyrobaculum aerophilum, and recombinant Pc-SpeE could synthesize both thermospermine (334) and spermine (343) from spermidine and decarboxylated S-adenosyl methionine (dcSAM). Recombinant Pc-SpeE showed high enzymatic activity when aminopropylagmatine and norspermidine were used as substrates. By comparison, Pc-SpeE showed low affinity toward putrescine, and putrescine was not stably bound in its active site. Norspermidine was produced from thermospermine by oxidative degradation using a cell-free extract of P. calidifontis, whereas 1,3-diaminopropane (3) formation was not detected. These results suggest that thermospermine was mainly produced from arginine via agmatine, aminopropylagmatine, and spermidine. Norspermidine was produced from thermospermine by an unknown polyamine oxidase/dehydrogenase followed by norspermine formation by Pc-SpeE. Full article
(This article belongs to the Special Issue Biocatalysis and Biotransformation of Extremozymes)
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21 pages, 3692 KiB  
Article
Xylan Deconstruction by Thermophilic Thermoanaerobacterium bryantii Hemicellulases Is Stimulated by Two Oxidoreductases
by Zhuolin Yi, Xiaoyun Su, Abigail E. Asangba, Ahmed M. Abdel-Hamid, Siddhartha Chakraborty, Dylan Dodd, Peter G. Stroot, Roderick I. Mackie and Isaac Cann
Catalysts 2022, 12(2), 182; https://doi.org/10.3390/catal12020182 - 31 Jan 2022
Cited by 6 | Viewed by 3460
Abstract
Thermoanaerobacterium bryantii strain mel9T is a thermophilic bacterium isolated from a waste pile of a corn-canning factory. The genome of T. bryantii mel9T was sequenced and a hemicellulase gene cluster was identified. The cluster encodes seven putative enzymes, which are likely an [...] Read more.
Thermoanaerobacterium bryantii strain mel9T is a thermophilic bacterium isolated from a waste pile of a corn-canning factory. The genome of T. bryantii mel9T was sequenced and a hemicellulase gene cluster was identified. The cluster encodes seven putative enzymes, which are likely an endoxylanase, an α-glucuronidase, two oxidoreductases, two β-xylosidases, and one acetyl xylan esterase. These genes were designated tbxyn10A, tbagu67A, tbheoA, tbheoB, tbxyl52A, tbxyl39A, and tbaxe1A, respectively. Only TbXyn10A released reducing sugars from birchwood xylan, as shown by thin-layer chromatography analysis. The five components of the hemicellulase cluster (TbXyn10A, TbXyl39A, TbXyl52A, TbAgu67A, and TbAxe1A) functioned in synergy to hydrolyze birchwood xylan. Surprisingly, the two putative oxidoreductases increased the enzymatic activities of the gene products from the xylanolytic gene cluster in the presence of NADH and manganese ions. The two oxidoreductases were therefore named Hemicellulase-Enhancing Oxidoreductases (HEOs). All seven enzymes were thermophilic and acted in synergy to degrade xylans at 60 °C. Except for TbXyn10A, the other enzymes encoded by the gene cluster were conserved with high amino acid identities (85–100%) in three other Thermoanaerobacterium species. The conservation of the gene cluster is, therefore, suggestive of an important role of these enzymes in xylan degradation by these bacteria. The mechanism for enhancement of hemicellulose degradation by the HEOs is under investigation. It is anticipated, however, that the discovery of these new actors in hemicellulose deconstruction will have a significant impact on plant cell wall deconstruction in the biofuel industry. Full article
(This article belongs to the Special Issue Biocatalysis and Biotransformation of Extremozymes)
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20 pages, 3118 KiB  
Article
Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius
by Shoji Suzuki, Norio Kurosawa, Takeshi Yamagami, Shunsuke Matsumoto, Tomoyuki Numata, Sonoko Ishino and Yoshizumi Ishino
Catalysts 2022, 12(1), 34; https://doi.org/10.3390/catal12010034 - 29 Dec 2021
Cited by 1 | Viewed by 2010
Abstract
Homologous recombination (HR) refers to the process of information exchange between homologous DNA duplexes and is composed of four main steps: end resection, strand invasion and formation of a Holliday junction (HJ), branch migration, and resolution of the HJ. Within each step of [...] Read more.
Homologous recombination (HR) refers to the process of information exchange between homologous DNA duplexes and is composed of four main steps: end resection, strand invasion and formation of a Holliday junction (HJ), branch migration, and resolution of the HJ. Within each step of HR in Archaea, the helicase-promoting branch migration is not fully understood. Previous biochemical studies identified three candidates for archaeal helicase promoting branch migration in vitro: Hjm/Hel308, PINA, and archaeal long helicase related (aLhr) 2. However, there is no direct evidence of their involvement in HR in vivo. Here, we identified a novel helicase encoded by Saci_0814, isolated from the thermophilic crenarchaeon Sulfolobus acidocaldarius; the helicase dissociated a synthetic HJ. Notably, HR frequency in the Saci_0814-deleted strain was lower than that of the parent strain (5-fold decrease), indicating that Saci_0814 may be involved in HR in vivo. Saci_0814 is classified as an aLhr1 under superfamily 2 helicases; its homologs are conserved among Archaea. Purified protein produced in Escherichia coli showed branch migration activity in vitro. Based on both genetic and biochemical evidence, we suggest that aLhr1 is involved in HR and may function as a branch migration helicase in S. acidocaldarius. Full article
(This article belongs to the Special Issue Biocatalysis and Biotransformation of Extremozymes)
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17 pages, 1600 KiB  
Review
Promotion of Carbon Dioxide Biofixation through Metabolic and Enzyme Engineering
by Xin Pu and Yejun Han
Catalysts 2022, 12(4), 399; https://doi.org/10.3390/catal12040399 - 3 Apr 2022
Cited by 13 | Viewed by 4452
Abstract
Carbon dioxide is a major greenhouse gas, and its fixation and transformation are receiving increasing attention. Biofixation of CO2 is an eco–friendly and efficient way to reduce CO2, and six natural CO2 fixation pathways have been identified in microorganisms [...] Read more.
Carbon dioxide is a major greenhouse gas, and its fixation and transformation are receiving increasing attention. Biofixation of CO2 is an eco–friendly and efficient way to reduce CO2, and six natural CO2 fixation pathways have been identified in microorganisms and plants. In this review, the six pathways along with the most recent identified variant pathway were firstly comparatively characterized. The key metabolic process and enzymes of the CO2 fixation pathways were also summarized. Next, the enzymes of Rubiscos, biotin-dependent carboxylases, CO dehydrogenase/acetyl-CoA synthase, and 2-oxoacid:ferredoxin oxidoreductases, for transforming inorganic carbon (CO2, CO, and bicarbonate) to organic chemicals, were specially analyzed. Then, the factors including enzyme properties, CO2 concentrating, energy, and reducing power requirements that affect the efficiency of CO2 fixation were discussed. Recent progress in improving CO2 fixation through enzyme and metabolic engineering was then summarized. The artificial CO2 fixation pathways with thermodynamical and/or energetical advantages or benefits and their applications in biosynthesis were included as well. The challenges and prospects of CO2 biofixation and conversion are discussed. Full article
(This article belongs to the Special Issue Biocatalysis and Biotransformation of Extremozymes)
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