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1.
Nat Commun ; 14(1): 1734, 2023 03 28.
Article in English | MEDLINE | ID: mdl-36977711

ABSTRACT

Severe acute respiratory syndrome 2 Omicron BA.4 and BA.5 are characterized by high transmissibility and ability to escape natural and vaccine induced immunity. Here we test the neutralizing activity of 482 human monoclonal antibodies isolated from people who received two or three mRNA vaccine doses or from people vaccinated after infection. The BA.4 and BA.5 variants are neutralized only by approximately 15% of antibodies. Remarkably, the antibodies isolated after three vaccine doses target mainly the receptor binding domain Class 1/2, while antibodies isolated after infection recognize mostly the receptor binding domain Class 3 epitope region and the N-terminal domain. Different B cell germlines are used by the analyzed cohorts. The observation that mRNA vaccination and hybrid immunity elicit a different immunity against the same antigen is intriguing and its understanding may help to design the next generation of therapeutics and vaccines against coronavirus disease 2019.


Subject(s)
COVID-19 , Humans , COVID-19/prevention & control , mRNA Vaccines , Antibodies, Monoclonal , Adaptive Immunity , Germ Cells , Antibodies, Neutralizing , Antibodies, Viral , Spike Glycoprotein, Coronavirus
2.
Nat Commun ; 14(1): 53, 2023 01 04.
Article in English | MEDLINE | ID: mdl-36599850

ABSTRACT

The continuous evolution of SARS-CoV-2 generated highly mutated variants able to escape natural and vaccine-induced primary immunity. The administration of a third mRNA vaccine dose induces a secondary response with increased protection. Here we investigate the longitudinal evolution of the neutralizing antibody response in four donors after three mRNA doses at single-cell level. We sorted 4100 spike protein specific memory B cells identifying 350 neutralizing antibodies. The third dose increases the antibody neutralization potency and breadth against all SARS-CoV-2 variants as observed with hybrid immunity. However, the B cell repertoire generating this response is different. The increases of neutralizing antibody responses is largely due to the expansion of B cell germlines poorly represented after two doses, and the reduction of germlines predominant after primary immunization. Our data show that different immunization regimens induce specific molecular signatures which should be considered while designing new vaccines and immunization strategies.


Subject(s)
Antibody Formation , B-Lymphocytes , COVID-19 Vaccines , COVID-19 , Humans , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/prevention & control , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Vaccination , COVID-19 Vaccines/immunology , B-Lymphocytes/immunology
3.
Nat Commun ; 13(1): 3375, 2022 06 13.
Article in English | MEDLINE | ID: mdl-35697673

ABSTRACT

SARS-CoV-2 vaccines, administered to billions of people worldwide, mitigate the effects of the COVID-19 pandemic, however little is known about the molecular basis of antibody cross-protection to emerging variants, such as Omicron BA.1, its sublineage BA.2, and other coronaviruses. To answer this question, 276 neutralizing monoclonal antibodies (nAbs), previously isolated from seronegative and seropositive donors vaccinated with BNT162b2 mRNA vaccine, were tested for neutralization against the Omicron BA.1 and BA.2 variants, and SARS-CoV-1 virus. Only 14.2, 19.9 and 4.0% of tested antibodies neutralize BA.1, BA.2, and SARS-CoV-1 respectively. These nAbs recognize mainly the SARS-CoV-2 receptor binding domain (RBD) and target Class 3 and Class 4 epitope regions on the SARS-CoV-2 spike protein. Interestingly, around 50% of BA.2 nAbs did not neutralize BA.1 and among these, several targeted the NTD. Cross-protective antibodies derive from a variety of germlines, the most frequents of which were the IGHV1-58;IGHJ3-1, IGHV2-5;IGHJ4-1 and IGHV1-69;IGHV4-1. Only 15.6, 20.3 and 7.8% of predominant gene-derived nAbs elicited against the original Wuhan virus cross-neutralize Omicron BA.1, BA.2 and SARS-CoV-1 respectively. Our data provide evidence, at molecular level, of the presence of cross-neutralizing antibodies induced by vaccination and map conserved epitopes on the S protein that can inform vaccine design.


Subject(s)
Antibodies, Neutralizing , COVID-19 , Antibodies, Viral , BNT162 Vaccine , COVID-19/prevention & control , COVID-19 Vaccines , Epitopes/genetics , Humans , Neutralization Tests , Pandemics/prevention & control , RNA, Messenger/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Vaccines, Synthetic , mRNA Vaccines
4.
Nature ; 600(7889): 530-535, 2021 12.
Article in English | MEDLINE | ID: mdl-34670266

ABSTRACT

The emergence of SARS-CoV-2 variants is jeopardizing the effectiveness of current vaccines and limiting the application of monoclonal antibody-based therapy for COVID-19 (refs. 1,2). Here we analysed the memory B cells of five naive and five convalescent people vaccinated with the BNT162b2 mRNA vaccine to investigate the nature of the B cell and antibody response at the single-cell level. Almost 6,000 cells were sorted, over 3,000 cells produced monoclonal antibodies against the spike protein and more than 400 cells neutralized the original SARS-CoV-2 virus first identified in Wuhan, China. The B.1.351 (Beta) and B.1.1.248 (Gamma) variants escaped almost 70% of these antibodies, while a much smaller portion was impacted by the B.1.1.7 (Alpha) and B.1.617.2 (Delta) variants. The overall loss of neutralization was always significantly higher in the antibodies from naive people. In part, this was due to the IGHV2-5;IGHJ4-1 germline, which was found only in people who were convalescent and generated potent and broadly neutralizing antibodies. Our data suggest that people who are seropositive following infection or primary vaccination will produce antibodies with increased potency and breadth and will be able to better control emerging SARS-CoV-2 variants.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Broadly Neutralizing Antibodies/immunology , Memory B Cells/immunology , SARS-CoV-2/immunology , Antibodies, Neutralizing/genetics , Antibodies, Neutralizing/isolation & purification , Antibodies, Viral/genetics , Antibodies, Viral/isolation & purification , BNT162 Vaccine/administration & dosage , BNT162 Vaccine/immunology , Broadly Neutralizing Antibodies/genetics , Broadly Neutralizing Antibodies/isolation & purification , Convalescence , Epitopes, B-Lymphocyte/chemistry , Epitopes, B-Lymphocyte/immunology , Female , Humans , Male , Neutralization Tests , Seroconversion , Single-Cell Analysis , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/immunology
5.
Cell ; 184(7): 1821-1835.e16, 2021 04 01.
Article in English | MEDLINE | ID: mdl-33667349

ABSTRACT

Human monoclonal antibodies are safe, preventive, and therapeutic tools that can be rapidly developed to help restore the massive health and economic disruption caused by the coronavirus disease 2019 (COVID-19) pandemic. By single-cell sorting 4,277 SARS-CoV-2 spike protein-specific memory B cells from 14 COVID-19 survivors, 453 neutralizing antibodies were identified. The most potent neutralizing antibodies recognized the spike protein receptor-binding domain, followed in potency by antibodies that recognize the S1 domain, the spike protein trimer, and the S2 subunit. Only 1.4% of them neutralized the authentic virus with a potency of 1-10 ng/mL. The most potent monoclonal antibody, engineered to reduce the risk of antibody-dependent enhancement and prolong half-life, neutralized the authentic wild-type virus and emerging variants containing D614G, E484K, and N501Y substitutions. Prophylactic and therapeutic efficacy in the hamster model was observed at 0.25 and 4 mg/kg respectively in absence of Fc functions.


Subject(s)
Antibodies, Monoclonal/administration & dosage , Antibodies, Neutralizing/administration & dosage , Antibodies, Viral/administration & dosage , B-Lymphocytes/immunology , COVID-19 , Convalescence , 3T3 Cells , Animals , Antibodies, Monoclonal/isolation & purification , Antibodies, Neutralizing/isolation & purification , Antibodies, Viral/isolation & purification , B-Lymphocytes/cytology , COVID-19/immunology , COVID-19/prevention & control , COVID-19/therapy , Chlorocebus aethiops , Disease Models, Animal , Female , HEK293 Cells , Humans , Immunoglobulin Fc Fragments/immunology , Male , Mice , Spike Glycoprotein, Coronavirus/immunology , Vero Cells
6.
Microbiome ; 7(1): 64, 2019 04 17.
Article in English | MEDLINE | ID: mdl-30995938

ABSTRACT

BACKGROUND: The population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply "skrei," lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world's largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or "fjord" cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromsø, Norway. RESULTS: Our analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are "Carbohydrates"; "Amino Acids and Derivatives"; "Protein Metabolism"; "Cofactors, Vitamins, Prosthetic, Groups, and Pigments"; and "DNA Metabolism," which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category "Protein Metabolism" is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol. CONCLUSION: We present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus (Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes.


Subject(s)
Animal Migration , Gadus morhua/microbiology , Gastrointestinal Microbiome , Metagenomics , Photobacterium/classification , Animals , DNA, Bacterial/genetics , Female , Genetic Variation , Genome, Bacterial , Male , Norway , Proteomics , Sequence Analysis, DNA
7.
Sci Rep ; 7(1): 17278, 2017 12 08.
Article in English | MEDLINE | ID: mdl-29222424

ABSTRACT

The family 15 carbohydrate esterase (CE15) MZ0003, which derives from a marine Arctic metagenome, has a broader substrate scope than other members of this family. Here we report the crystal structure of MZ0003, which reveals that residues comprising the catalytic triad differ from previously-characterized fungal homologs, and resolves three large loop regions that are unique to this bacterial sub-clade. The catalytic triad of the bacterial CE15, which includes Asp 332 as its third member, closely resembles that of family 1 carbohydrate esterases (CE1), despite the overall lower structural similarity with members of this family. Two of the three loop regions form a subdomain that deepens the active site pocket and includes several basic residues that contribute to the high positive charge surrounding the active site. Docking simulations predict specific interactions with the sugar moiety of glucuronic-acid substrates, and with aromatically-substituted derivatives that serve as model compounds for the lignin-carbohydrate complex of plant cell walls. Molecular dynamics simulations indicate considerable flexibility of the sub-domain in the substrate-bound form, suggesting plasticity to accommodate different substrates is possible. The findings from this first reported structure of a bacterial member of the CE15 family provide insight into the basis of its broader substrate specificity.


Subject(s)
Bacteria/genetics , Esterases/chemistry , Esterases/genetics , Metagenome , Amino Acid Sequence , Bacteria/enzymology , Catalytic Domain , Crystallography, X-Ray , Esterases/metabolism , Hydrolysis , Molecular Docking Simulation , Substrate Specificity
8.
Stand Genomic Sci ; 11(1): 62, 2016.
Article in English | MEDLINE | ID: mdl-27610212

ABSTRACT

The marine Arctic isolate Halomonas sp. R5-57 was sequenced as part of a bioprospecting project which aims to discover novel enzymes and organisms from low-temperature environments, with potential uses in biotechnological applications. Phenotypically, Halomonas sp. R5-57 exhibits high salt tolerance over a wide range of temperatures and has extra-cellular hydrolytic activities with several substrates, indicating it secretes enzymes which may function in high salinity conditions. Genome sequencing identified the genes involved in the biosynthesis of the osmoprotectant ectoine, which has applications in food processing and pharmacy, as well as those involved in production of polyhydroxyalkanoates, which can serve as precursors to bioplastics. The percentage identity of these biosynthetic genes from Halomonas sp. R5-57 and current production strains varies between 99 % for some to 69 % for others, thus it is plausible that R5-57 may have a different production capacity to currently used strains, or that in the case of PHAs, the properties of the final product may vary. Here we present the finished genome sequence (LN813019) of Halomonas sp. R5-57 which will facilitate exploitation of this bacterium; either as a whole-cell production host, or by recombinant expression of its individual enzymes.

9.
PLoS One ; 11(7): e0159345, 2016.
Article in English | MEDLINE | ID: mdl-27433797

ABSTRACT

BACKGROUND: The glucuronoyl esterase enzymes of wood-degrading fungi (Carbohydrate Esterase family 15; CE15) form part of the hemicellulolytic and cellulolytic enzyme systems that break down plant biomass, and have possible applications in biotechnology. Homologous enzymes are predicted in the genomes of several bacteria, however these have been much less studied than their fungal counterparts. Here we describe the recombinant production and biochemical characterization of a bacterial CE15 enzyme denoted MZ0003, which was identified by in silico screening of a prokaryotic metagenome library derived from marine Arctic sediment. MZ0003 has high similarity to several uncharacterized gene products of polysaccharide-degrading bacterial species, and phylogenetic analysis indicates a deep evolutionary split between these CE15s and fungal homologs. RESULTS: MZ0003 appears to differ from previously-studied CE15s in some aspects. Some glucuronoyl esterase activity could be measured by qualitative thin-layer chromatography which confirms its assignment as a CE15, however MZ0003 can also hydrolyze a range of other esters, including p-nitrophenyl acetate, which is not acted upon by some fungal homologs. The structure of MZ0003 also appears to differ as it is predicted to have several large loop regions that are absent in previously studied CE15s, and a combination of homology-based modelling and site-directed mutagenesis indicate its catalytic residues deviate from the conserved Ser-His-Glu triad of many fungal CE15s. Taken together, these results indicate that potentially unexplored diversity exists among bacterial CE15s, and this may be accessed by investigation of the microbial metagenome. The combination of low activity on typical glucuronoyl esterase substrates, and the lack of glucuronic acid esters in the marine environment suggest that the physiological substrate of MZ0003 and its homologs is likely to be different from that of related fungal enzymes.


Subject(s)
Esterases/genetics , Geologic Sediments/microbiology , Metagenome/genetics , Phylogeny , Amino Acid Sequence/genetics , Arctic Regions , Biotechnology , Carbohydrates/chemistry , Chromatography, Thin Layer , Esterases/chemistry , Hydrolysis , Lignin/chemistry , Mutagenesis, Site-Directed , Schizophyllum/enzymology , Schizophyllum/genetics , Substrate Specificity
10.
Extremophiles ; 20(3): 323-36, 2016 May.
Article in English | MEDLINE | ID: mdl-27016194

ABSTRACT

A gene encoding an esterase, ThaEst2349, was identified in the marine psychrophilic bacterium Thalassospira sp. GB04J01. The gene was cloned and overexpressed in E. coli as a His-tagged fusion protein. The recombinant enzyme showed optimal activity at 45 °C and the thermal stability displayed a retention of 75 % relative activity at 40 °C after 2 h. The optimal pH was 8.5 but the enzyme kept more than 75 % of its maximal activity between pH 8.0 and 9.5. ThaEst2349 also showed remarkable tolerance towards high concentrations of salt and it was active against short-chain p-nitrophenyl esters, displaying optimal activity with the acetate. The enzyme was tested for tolerance of organic solvents and the results are suggesting that it could function as an interesting candidate for biotechnological applications. The crystal structure of ThaEst2349 was determined to 1.69 Å revealing an asymmetric unit containing two chains, which also is the biological unit. The structure has a characteristic cap domain and a catalytic triad comprising Ser158, His285 and Asp255. To explain the cold-active nature of the enzyme, we compared it against thermophilic counterparts. Our hypothesis is that a high methionine content, less hydrogen bonds and less ion pairs render the enzyme more flexible at low temperatures.


Subject(s)
Bacterial Proteins/metabolism , Cold Temperature , Esterases/metabolism , Rhodospirillaceae/enzymology , Salt Tolerance , Bacterial Proteins/chemistry , Catalytic Domain , Esterases/chemistry
11.
BMC Biochem ; 17: 1, 2016 Jan 19.
Article in English | MEDLINE | ID: mdl-26782782

ABSTRACT

BACKGROUND: The use of metagenomics in enzyme discovery constitutes a powerful approach to access to genomes of unculturable community of microorganisms and isolate novel valuable biocatalysts for use in a wide range of biotechnological and pharmaceutical fields. RESULTS: Here we present a novel esterase gene (lip3) identified by functional screening of three fosmid metagenomic libraries, constructed from three marine sediment samples. The sequenced positive fosmid revealed an enzyme of 281 amino acids with similarity to class 3 lipases. The 3D modeling of Lip3 was generated by homology modeling on the basis of four lipases templates [PDB ID: 3O0D, 3NGM, 3G7N, 2QUB] to unravel structural features of this novel enzyme. The catalytic triad of Lip3 was predicted to be Asp207, His267 and the catalytic nucleophile Ser150 in a conserved pentapeptide (GXSXG). The 3D model highlighted the presence of a one-helix lid able to regulate the access of the substrate to the active site when the enzyme binds a hydrophobic interface. Moreover an analysis of the external surface of Lip3 model showed that the majority of the surface regions were hydrophobic (59.6 %) compared with homologous lipases (around 35 %) used as templates. The recombinant Lip3 esterase, expressed and purified from Escherichia coli, preferentially hydrolyzed short and medium length p-nitrophenyl esters with the best substrate being p-nitrophenyl acetate. Further characterization revealed a temperature optimum of 35 °C and a pH optimum of 8.0. Lip3 exhibits a broad temperature stability range and tolerates the presence of DTT, EDTA, PMSF, ß-mercaptoethanol and high concentrations of salt. The enzyme was also highly activated by NaCl. CONCLUSIONS: The biochemical characterization and homology model reveals a novel esterase originating from the marine Arctic metagenomics libraries with features of a cold-active, relatively thermostable and highly halotolerant enzyme. Taken together, these results suggest that this esterase could be a highly valuable candidate for biotechnological applications such as organic synthesis reactions and cheese ripening processes.


Subject(s)
Cold Temperature , Esterases/metabolism , Metagenomics , Amino Acid Sequence , Arctic Regions , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cloning, Molecular , DNA, Bacterial/genetics , DNA, Bacterial/isolation & purification , DNA, Bacterial/metabolism , Escherichia coli/metabolism , Esterases/chemistry , Esterases/genetics , Gene Library , Geologic Sediments/microbiology , Hydrogen-Ion Concentration , Molecular Sequence Data , Protein Stability , Protein Structure, Tertiary , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Sequence Alignment , Sodium Chloride/chemistry , Substrate Specificity
12.
J Basic Microbiol ; 56(3): 238-53, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26662844

ABSTRACT

We have investigated the biotechnological potential of Arctic marine bacteria for their ability to produce a broad spectrum of cold-active enzymes. Marine bacteria exhibiting these features are of great interest for both fundamental research and industrial applications. Macrobiota, water and sediment samples have been collected during 2010 and 2011 expeditions around the Lofoten and Svalbard islands. Bacteria were isolated from this material and identified through 16S rRNA gene sequence analysis for the purpose of establishing a culture collection of marine Arctic bacteria. Herein, we present the functional screening for different extracellular enzymatic activities from 100 diversely chosen microbial isolates incubated at 4 and 20 °C. The production of esterase/lipase, DNase, and protease activities were revealed in 67, 53, and 56% of the strains, respectively, while 41, 23, 9, and 7% of the strains possessed amylase, chitinase, cellulase, and xylanase activities, respectively. Our findings show that phylogenetically diverse bacteria, including many new species, could be cultured from the marine arctic environment. The Arctic polar environment is still an untapped reservoir of biodiversity for bioprospecting.


Subject(s)
Bacteria/enzymology , Bacteria/isolation & purification , Bacterial Proteins/metabolism , Bioprospecting , Enzymes/metabolism , Arctic Regions , Bacteria/classification , Bacteria/genetics , Bacterial Proteins/biosynthesis , Bacterial Proteins/genetics , Base Sequence , Biodiversity , Cold Temperature , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Enzyme Activation , Enzyme Assays , Enzymes/biosynthesis , Enzymes/genetics , Geologic Sediments/microbiology , Islands , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Seawater/microbiology , Sequence Analysis, DNA
13.
Biotechnol Prog ; 31(4): 890-9, 2015.
Article in English | MEDLINE | ID: mdl-25920073

ABSTRACT

A salt-tolerant esterase, designated H9Est, was identified from a metagenomic library of the Karuola glacier. H9Est gene comprised 1071 bp and encoded a polypeptide of 357 amino acids with a molecular mass of 40 kDa. Sequence analysis revealed that H9Est belonged to the family IV of bacterial lypolitic enzyme. H9Est was overexpressed in Escherichia coli and the purified enzyme showed hydrolytic activity towards p-nitrophenyl esters with carbon chain from 2 to 8. The optimal esterase activity was at 40°C and pH 8.0 and the enzyme retained its activity towards some miscible organic solvents such as polyethylene glycol. A three-dimensional model of H9Est revealed that S200, D294, and H324 formed the H9Est catalytic triad. Circular Dichroism spectra and molecular dynamic simulation indicated that the esterase had a wide denaturation temperature range and flexible loops that would be beneficial for H9Est performance at low temperatures while retaining heat-resistant features.


Subject(s)
Esterases/chemistry , Esterases/genetics , Ice Cover/microbiology , Metagenome/genetics , Salt Tolerance/genetics , Amino Acid Sequence , Biotechnology , Cold Temperature , Enzyme Stability , Escherichia coli/genetics , Escherichia coli/metabolism , Esterases/classification , Esterases/metabolism , Gene Library , Molecular Dynamics Simulation , Molecular Sequence Data , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment
14.
Stand Genomic Sci ; 9(3): 676-86, 2014 Jun 15.
Article in English | MEDLINE | ID: mdl-25197453

ABSTRACT

Here we report the 8 Mb high quality draft genome of Streptomyces sp. strain AW19M42, together with specific properties of the organism and the generation, annotation and analysis of its genome sequence. The genome encodes 7,727 putative open reading frames, of which 6,400 could be assigned with COG categories. Also, 62 tRNA genes and 8 rRNA operons were identified. The genome harbors several gene clusters involved in the production of secondary metabolites. Functional screening of the isolate was positive for several enzymatic activities, and some candidate genes coding for those activities are listed in this report. We find that this isolate shows biotechnological potential and is an interesting target for bioprospecting.

15.
Appl Biochem Biotechnol ; 172(6): 3054-68, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24488777

ABSTRACT

The special features of cold-adapted lipolytic biocatalysts have made their use possible in several industrial applications. In fact, cold-active enzymes are known to be able to catalyze reactions at low temperatures, avoiding side reactions taking place at higher temperatures and preserving the integrity of products. A lipolytic gene was isolated from the Arctic marine bacterium Rhodococcus sp. AW25M09 and expressed in Escherichia coli as inclusion bodies. The recombinant enzyme (hereafter called RhLip) showed interesting cold-active esterase activity. The refolded purified enzyme displayed optimal activity at 30 °C and was cold-active with retention of 50% activity at 10 °C. It is worth noting that the optimal pH was 11, and the low relative activity below pH 10 revealed that RhLip was an alkaliphilic esterase. The enzyme was active toward short-chain p-nitrophenyl esters (C2-C6), displaying optimal activity with the butyrate (C4) ester. In addition, the enzyme revealed a good organic solvent and salt tolerance. These features make this an interesting enzyme for exploitation in some industrial applications.


Subject(s)
Bacterial Proteins/chemistry , Lipase/chemistry , Rhodococcus/chemistry , Amino Acid Sequence , Aquatic Organisms , Arctic Regions , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Cloning, Molecular , Cold Temperature , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Hydrogen-Ion Concentration , Inclusion Bodies/chemistry , Kinetics , Lipase/genetics , Lipase/metabolism , Models, Molecular , Molecular Sequence Data , Protein Refolding , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Rhodococcus/enzymology , Salt Tolerance , Sequence Homology, Amino Acid , Substrate Specificity
16.
Biochimie ; 95(9): 1795-806, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23796575

ABSTRACT

The ciliated protozoon Euplotes focardii, originally isolated from the coastal seawaters of Terra Nova Bay in Antarctica, shows a strictly psychrophilic phenotype, including optimal survival and multiplication rates at 4-5 °C. This characteristic makes E. focardii an ideal model species for identifying the molecular bases of cold adaptation in psychrophilic organisms, as well as a suitable source of novel cold-active enzymes for industrial applications. In the current study, we characterized the patatin-like phospholipase from E. focardii (EfPLP), and its enzymatic activity was compared to that of the homologous protein from the mesophilic congeneric species Euplotes crassus (EcPLP). Both EfPLP and EcPLP have consensus motifs conserved in other patatin-like phospholipases. By analyzing both esterase and phospholipase A2 activity, we determined the thermostability and the optimal pH, temperature dependence and substrates of these enzymes. We demonstrated that EfPLP shows the characteristics of a psychrophilic phospholipase. Furthermore, we analyzed the enzymatic activity of three engineered versions of the EfPLP, in which unique residues of EfPLP, Gly80, Ala201 and Val204, were substituted through site-directed mutagenesis with residues found in the E. crassus homolog (Glu, Pro and Ile, respectively). Additionally, three corresponding mutants of EcPLP were also generated and characterized. These analyses showed that the substitution of amino acids with rigid and bulky charged/hydrophobic side chain in the psychrophilic EfPLP confers enzymatic properties similar to those of the mesophilic patatin-like phospholipase, and vice versa. This is the first report on the isolation and characterization of a cold-adapted patatin-like phospholipase from eukaryotes. The results reported in this paper support the idea that enzyme thermal-adaptation is based mainly on some amino acid residues that influence the structural flexibility of polypeptides and that EfPLP is an attractive biocatalyst for industrial processes at low temperatures.


Subject(s)
Adaptation, Physiological , Cold Temperature , Euplotes/physiology , Phospholipases/metabolism , Sequence Homology, Amino Acid , Amino Acid Sequence , Cloning, Molecular , Enzyme Stability , Euplotes/enzymology , Euplotes/genetics , Hydrogen-Ion Concentration , Kinetics , Models, Molecular , Molecular Sequence Data , Mutation , Phospholipases/chemistry , Phospholipases/genetics , Phospholipases/isolation & purification , Protein Conformation , Sequence Analysis
17.
Mar Genomics ; 8: 15-22, 2012 Dec.
Article in English | MEDLINE | ID: mdl-23199876

ABSTRACT

The term bioprospecting has been adopted for systematic searches in nature for new bioactive compounds, genes, proteins, microorganisms and other products with potential for commercial use. Much effort has been focused on microorganisms able to thrive under harsh conditions, including the Polar environments. Both the lipid and protein cellular building blocks of Polar microorganisms are shaped by their adaptation to the permanently low temperatures. In addition, strongly differing environments, such as permafrost, glaciers and sea ice, have contributed to additional functional diversity. Emerging massive-parallel sequencing technologies have revealed the existence of a huge, hitherto unseen diversity of low-abundance phylotypes--the rare biosphere--even in the Polar environments. This realization has further strengthened the need to employ cultivation-independent approaches, including metagenomics and single-cell genomic sequencing, to get comprehensive access to the genetic diversity of microbial communities for bioprospecting purposes. In this review, we present an updated snapshot of recent findings on the molecular basis for adaptation to the cold and the phylogenetic diversities of different Polar environments. Novel approaches in bioprospecting are presented and we conclude by showing recent bioprospecting outcomes in terms of new molecules patented or applied by some biotech companies.


Subject(s)
Bacteria/classification , Bacteria/genetics , Biodiversity , Adaptation, Physiological , Antarctic Regions , Arctic Regions , Biological Products/chemistry , Biological Products/metabolism , Genetic Variation , Metagenomics , Phylogeny
18.
Fish Shellfish Immunol ; 33(5): 1183-91, 2012 Nov.
Article in English | MEDLINE | ID: mdl-22982327

ABSTRACT

Antimicrobial peptides (AMPs) are considered one of the most ancient components of the innate immune system. They are able to exert their protection activity against a variety of microorganisms, and are widely distributed in both vertebrates and invertebrates. In this paper we focused on an AMP identified in the Antarctic teleost Chionodraco hamatus, an icefish species. The cDNA sequence of the AMP, named chionodracine, is comprised of 515 bp and translates for a putative protein precursor of 80 amino acids, with a signal peptide of 22 amino acids. The structural features evidenced in the primary sequence of chionodracine lead to the inclusion of the peptide in the antimicrobial family of piscidins. The analysis by real-time PCR of the basal gene transcripts of chionodracine in different icefish tissues showed that the highest expression was found in gills, followed by head kidney. The chionodracine expression levels in head kidney leukocytes were up-regulated in vitro both by LPS and poly I:C, and in vivo by LPS. A putative chionodracine mature peptide was synthesized and employed to obtain a polyclonal antiserum, which was used in immunohistochemistry of gills sections and revealed a significant positivity associated with mast cells. The bactericidal activity of the peptide was investigated and found significant against Antarctic psychrophilic bacteria strains (Psychrobacter sp. TAD1 and TA144), the Gram-positive Bacillus cereus, and at a lesser extent against the Gram-negative Escherichia coli. Interestingly, the haemolytic activity of chionodracine was tested in vitro on human erythrocytes and no significant lysis occurred until peptide concentration of 50 µM.


Subject(s)
Antimicrobial Cationic Peptides/genetics , Antimicrobial Cationic Peptides/metabolism , Gene Expression Regulation/immunology , Perciformes/immunology , Amino Acid Sequence , Animals , Antarctic Regions , Base Sequence , DNA Primers/genetics , Enzyme-Linked Immunosorbent Assay/veterinary , Erythrocytes/drug effects , Gene Expression Profiling , Gene Expression Regulation/drug effects , Gills/metabolism , Head Kidney/metabolism , Hemolysis/immunology , Humans , Immunohistochemistry/veterinary , Lipopolysaccharides/toxicity , Molecular Sequence Data , Perciformes/genetics , Poly I-C/toxicity , Real-Time Polymerase Chain Reaction , Sequence Analysis, DNA
19.
Biotechnol Prog ; 28(4): 946-52, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22718288

ABSTRACT

Cold-adapted enzymes possess high specific activity at low and moderate temperatures with respect to their mesophilic and thermophilic homologs; it is accepted that they have a less rigid and more flexible structure in the region surrounding the active site. However, the low stability of such molecules could represent the main barrier for their application in some industrial bioprocesses. The aim of this article was to investigate the ability of the naturally occurring osmolytes to increase the thermal stability and the specific activity of the cold-active lipase from Psychrobacter sp. TA144 (PsyHSL), which belongs to the hormone-sensitive lipase group. The effect of trimethylamine N-oxide (TMAO), betaine, and L-proline addition on the activity and thermal stability of PsyHSL was investigated by means of biochemical and biophysical techniques. It turned out that in the presence of 3 M TMAO, the enzyme specific activity enhanced up to 250% at 50°C, while the addition of 1 M TMAO increased the thermostability fivefold at 45°C. Our experiments demonstrated that, even in the case of a psychrophilic enzyme, osmoprotectants, particularly TMAO, addition may be considered an efficient strategy to improve the protein thermal stability and specific activity at higher temperatures.


Subject(s)
Bacterial Proteins/chemistry , Psychrobacter/enzymology , Sterol Esterase/chemistry , Bacterial Proteins/isolation & purification , Enzyme Stability , Hot Temperature , Kinetics , Molecular Sequence Data , Psychrobacter/chemistry , Sterol Esterase/isolation & purification
20.
Biochem Biophys Res Commun ; 420(3): 542-6, 2012 Apr 13.
Article in English | MEDLINE | ID: mdl-22440394

ABSTRACT

Psychrobacter, a micro-organism originally isolated from Antarctic sea water, expresses an extremely active hormone-sensitive lipase (HSL) which catalyzes the hydrolysis of fatty acid esters at very low temperature and is therefore of great potential industrial and pharmaceutical interest. An insoluble form of the entire enzyme has previously been cloned and expressed in Escherichia coli, subsequently refolded and shown to be active, whilst a shorter but completely inactive version, lacking the N-terminal 98 amino acids has been expressed in soluble form. In this study the entire enzyme has been expressed as a fully soluble protein in E. coli in the presence of either the osmolyte trehalose, plus high salt concentration, or the membrane fluidizer benzyl alcohol. Trehalose promotes protein mono-dispersion by increasing the viscosity of the growth medium for bacterial cells, thereby helping circumvent protein aggregation, whilst the heat-shock inducer benzyl alcohol stimulates the production of a network of endogenous chaperones which actively prevent protein misfolding, whilst also converting recombinant aggregates to native, correctly folded proteins. The resultant recombinant protein proved to be more stable than its previously expressed counterpart, as shown by CD and enzymatic activity data which proved the enzyme to be more active at a higher temperature than its refolded counterpart. By light scattering analysis it was shown that the newly expressed protein was monomeric. The stability of the full length native protein will help in understanding the structure of PsyHSL and the role of its regulatory N-terminal for eventual application in a myriad of biotechnological processes.


Subject(s)
Psychrobacter/enzymology , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Sterol Esterase/biosynthesis , Sterol Esterase/chemistry , Circular Dichroism , Enzyme Stability , Escherichia coli/drug effects , Escherichia coli/growth & development , Escherichia coli/metabolism , Light , Protein Structure, Secondary , Recombinant Proteins/isolation & purification , Scattering, Radiation , Solubility , Sterol Esterase/isolation & purification , Trehalose/pharmacology
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