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Kurbessoian T, Stevenson D, Haro R, Ying S, Stajich JE. Draft genome sequence of a black yeast fungus Exophiala xenobiotica isolated from La Brea Tar Pits. Microbiol Resour Announc 2024; 13:e0091323. [PMID: 38179910 PMCID: PMC10868212 DOI: 10.1128/mra.00913-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/10/2023] [Indexed: 01/06/2024] Open
Abstract
A 30.28 Mb draft genome sequence was assembled and annotated for the melanized ascomycetous fungus Exophiala xenobiotica NRRL_64630 (Pezizomycotina; Chaetothyriales) isolated from La Brea Tar Pits, Los Angeles, California. Species identification was made by phylogenetic assessment of the Internal Transcribed Spacer. This is the first isolated fungal species from this historic space.
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Affiliation(s)
- Tania Kurbessoian
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Danielle Stevenson
- Department of Environmental Studies, University of California, Riverside, California, USA
| | - Renata Haro
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Samantha Ying
- Department of Environmental Studies, University of California, Riverside, California, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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Roy C, Islam RNU, Banerjee S, Bandyopadhyay AK. Underlying features for the enhanced electrostatic strength of the extremophilic malate dehydrogenase interface salt-bridge compared to the mesophilic one. J Biomol Struct Dyn 2023:1-16. [PMID: 38147414 DOI: 10.1080/07391102.2023.2295972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 12/28/2023]
Abstract
Malate dehydrogenase (MDH) exists in multimeric form in normal and extreme solvent conditions where residues of the interface are involved in specific interactions. The interface salt-bridge (ISB) and its microenvironment (ME) residues may have a crucial role in the stability and specificity of the interface. To gain insight into this, we have analyzed 218 ISBs from 42 interfaces of 15 crystal structures along with their sequences. Comparative analyses demonstrate that the ISB strength is ∼30 times greater in extremophilic cases than that of the normal one. To this end, the interface residue propensity, ISB design and pair selection, and ME-residue's types, i.e., type-I and type-II, are seen to be intrinsically involved. Although Type-I is a common type, Type-II appears to be extremophile-specific, where the net ME-residue count is much lower with an excessive net ME-energy contribution, which seems to be a novel interface compaction strategy. Furthermore, the interface strength can be enhanced by selecting the desired mutant from the net-energy profile of all possible mutations of an unfavorable ME-residue. The study that applies to other similar systems finds applications in protein-protein interaction and protein engineering.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chittran Roy
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
- Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Sahini Banerjee
- Department of Biological Sciences, Indian Statistical Institute, Kolkata, West Bengal, India
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Abstract
Hypersaline waters and glacial ice are inhospitable environments that have low water activity and high concentrations of osmolytes. They are inhabited by diverse microbial communities, of which extremotolerant and extremophilic fungi are essential components. Some fungi are specialized in only one of these two environments and can thrive in conditions that are lethal to most other life-forms. Others are generalists, highly adaptable species that occur in both environments and tolerate a wide range of extremes. Both groups efficiently balance cellular osmotic pressure and ion concentration, stabilize cell membranes, remodel cell walls, and neutralize intracellular oxidative stress. Some species use unusual reproductive strategies. Further investigation of these adaptations with new methods and carefully designed experiments under ecologically relevant conditions will help predict the role of fungi in hypersaline and glacial environments affected by climate change, decipher their stress resistance mechanisms and exploit their biotechnological potential.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
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Williams GB, Ma H, Khusnutdinova AN, Yakunin AF, Golyshin PN. Harnessing extremophilic carboxylesterases for applications in polyester depolymerisation and plastic waste recycling. Essays Biochem 2023; 67:715-729. [PMID: 37334661 PMCID: PMC10423841 DOI: 10.1042/ebc20220255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
The steady growth in industrial production of synthetic plastics and their limited recycling have resulted in severe environmental pollution and contribute to global warming and oil depletion. Currently, there is an urgent need to develop efficient plastic recycling technologies to prevent further environmental pollution and recover chemical feedstocks for polymer re-synthesis and upcycling in a circular economy. Enzymatic depolymerization of synthetic polyesters by microbial carboxylesterases provides an attractive addition to existing mechanical and chemical recycling technologies due to enzyme specificity, low energy consumption, and mild reaction conditions. Carboxylesterases constitute a diverse group of serine-dependent hydrolases catalysing the cleavage and formation of ester bonds. However, the stability and hydrolytic activity of identified natural esterases towards synthetic polyesters are usually insufficient for applications in industrial polyester recycling. This necessitates further efforts on the discovery of robust enzymes, as well as protein engineering of natural enzymes for enhanced activity and stability. In this essay, we discuss the current knowledge of microbial carboxylesterases that degrade polyesters (polyesterases) with focus on polyethylene terephthalate (PET), which is one of the five major synthetic polymers. Then, we briefly review the recent progress in the discovery and protein engineering of microbial polyesterases, as well as developing enzyme cocktails and secreted protein expression for applications in the depolymerisation of polyester blends and mixed plastics. Future research aimed at the discovery of novel polyesterases from extreme environments and protein engineering for improved performance will aid developing efficient polyester recycling technologies for the circular plastics economy.
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Affiliation(s)
- Gwion B Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Hairong Ma
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Anna N Khusnutdinova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Alexander F Yakunin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, U.K
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Ambrosino A, Chianese A, Zannella C, Piccolella S, Pacifico S, Giugliano R, Franci G, De Natale A, Pollio A, Pinto G, De Filippis A, Galdiero M. Galdieria sulphuraria: An Extremophilic Alga as a Source of Antiviral Bioactive Compounds. Mar Drugs 2023; 21:383. [PMID: 37504915 PMCID: PMC10381441 DOI: 10.3390/md21070383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
In the last decades, the interest in bioactive compounds derived from natural sources including bacteria, fungi, plants, and algae has significantly increased. It is well-known that aquatic or terrestrial organisms can produce, in special conditions, secondary metabolites with a wide range of biological properties, such as anticancer, antioxidant, anti-inflammatory, and antimicrobial activities. In this study, we focused on the extremophilic microalga Galdieria sulphuraria as a possible producer of bioactive compounds with antiviral activity. The algal culture was subjected to organic extraction with acetone. The cytotoxicity effect of the extract was evaluated by the 2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. The antiviral activity was assessed through a plaque assay against herpesviruses and coronaviruses as enveloped viruses and poliovirus as a naked one. The monolayer was treated with different concentrations of extract, ranging from 1 µg/mL to 200 µg/mL, and infected with viruses. The algal extract displayed strong antiviral activity at non-toxic concentrations against all tested enveloped viruses, in particular in the virus pre-treatment against HSV-2 and HCoV-229E, with IC50 values of 1.7 µg/mL and IC90 of 1.8 µg/mL, respectively. However, no activity against the non-enveloped poliovirus has been detected. The inhibitory effect of the algal extract was confirmed by the quantitative RT-PCR of viral genes. Preliminary chemical profiling of the extract was performed using ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS), revealing the enrichment in primary fatty acid amides (PFAA), such as oleamide, palmitamide, and pheophorbide A. These promising results pave the way for the further purification of the mixture to explore its potential role as an antiviral agent.
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Affiliation(s)
- Annalisa Ambrosino
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Annalisa Chianese
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Carla Zannella
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Simona Piccolella
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Severina Pacifico
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Rosa Giugliano
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi, Italy
| | - Antonino De Natale
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Antonino Pollio
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Gabriele Pinto
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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Pacheco S, Béhar G, Maillasson M, Mouratou B, Pecorari F. Affinity transfer to the archaeal extremophilic Sac7d protein by insertion of a CDR. Protein Eng Des Sel 2015; 27:431-8. [PMID: 25301962 DOI: 10.1093/protein/gzu042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Artificially transforming a scaffold protein into binders often consists of introducing diversity into its natural binding region by directed mutagenesis. We have previously developed the archaeal extremophilic Sac7d protein as a scaffold to derive affinity reagents (Affitins) by randomization of only a flat surface, or a flat surface and two short loops with natural lengths. Short loops are believed to contribute to stability of extremophilic proteins, and loop extension has been reported detrimental for the thermal and chemical stabilities of mesophilic proteins. In this work, we wanted to evaluate the possibility of designing target-binding proteins based on Sac7d by using a complementary determining region (CDR). To this aim, we inserted into three different loops a 10 residues CDR from the cAb-Lys3 anti-lysozyme camel antibody. The chimeras obtained were as stable as wild-type (WT) Sac7d at extreme pH and their structural integrity was supported. Chimeras were thermally stable, but with T(m)s from 60.9 to 66.3°C (cf. 91°C for Sac7d) which shows that loop extension is detrimental for thermal stability of Sac7d. The loop 3 enabled anti-lysozyme activity. These results pave the way for the use of CDR(s) from antibodies and/or extended randomized loop(s) to increase the potential of binding of Affitins.
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Affiliation(s)
- Sabino Pacheco
- CRCNA - UMR 892 INSERM, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France 6299 CNRS, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France University of Nantes, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France Institut Pasteur, CNRS UMR 3528, Unité de Microbiologie Structurale, 25 rue du Dr. Roux, 72724 Paris Cedex 15, France
| | - Ghislaine Béhar
- CRCNA - UMR 892 INSERM, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France 6299 CNRS, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France University of Nantes, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France
| | - Mike Maillasson
- CRCNA - UMR 892 INSERM, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France 6299 CNRS, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France University of Nantes, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France Plate-forme IMPACT Biogenouest, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France
| | - Barbara Mouratou
- CRCNA - UMR 892 INSERM, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France 6299 CNRS, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France University of Nantes, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France
| | - Frédéric Pecorari
- CRCNA - UMR 892 INSERM, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France 6299 CNRS, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France University of Nantes, 8 quai Moncousu, BP 70721, 44007 Nantes, Cedex 1, France
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Stierle AA, Stierle DB. Bioactive secondary metabolites from acid mine waste extremophiles. Nat Prod Commun 2014; 9:1037-1044. [PMID: 25230522 PMCID: PMC5156321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
The extremophilic microbes of the Berkeley Pit Lake are a valuable source of new and interesting secondary metabolites. It is of particular interest that these acidophilic microbes produce small molecule inhibitors of pathways associated with low pH and high Eh. These same small molecules also inhibit molecular pathways induced by reactive oxygen species (ROS) and inflammation in mammalian cells. Low pH is a hallmark of inflammation and high Eh is one of ROS, so the suitability of this collection as a source of bioactive metabolites is actually quite biorational. Compound isolation was guided by inhibition of caspase-1 and matrix metalloproteinase-3, and active compounds were sent to the National Cancer Institute-Developmental Therapeutics Program and Memorial Sloan Kettering Cancer center for evaluation as either antiproliferative or cytotoxic agents.
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