The HotZyme Newsletter

Transcription

1 Issue The HotZyme Newsletter SYSTEMATIC SCREENING FOR NOVEL HYDROLASES FROM HOT ENVIRONMENTS From the Editor Dear readers, Welcome to the 12th edition of the HotZyme Newsletter. As we approach the end of a very productive year, allow us to take this opportunity to thank you for your continued interest and support. We have updates on a great project event in the coming year, as well as a quick look back on some of the achievements that came out of the project in the past few months. In this Issue Save the date! Updates on the upcoming project event HotZyme Symposium: Discovery of Extremophilic Novel Enzymes with Application for Industrial Biotechnology Showcasing academic papers and conference presentations resulted from the project and by its consortium members Project deliverable summaries and future schedules As always, the Editors welcome and encourage the submission of letters and research reports suitable for publication in the HotZyme Newsletter. The deadline for HotZyme s last newsletter is March 1, On behalf of the HotZyme consortium Haimo Gilbert (EuCRF) Editor, the HotZyme Newsletter Website: For more information about the project, its participating partners and events, please visit the project official website at: Contribution: What s your team up to? Please share the breakthroughs and other news with us by writing to haimo@eu- crf.net Forward this Do you know anyone who might be interested in receiving this quarterly newsletter? Please forward this PDF on and spread the word. Also, please send the e- mail address to haimo@eu- crf.net Contact: EuCRF - European Centre for Research & Financing. 2 Hamarva Street, Binyamina 30500; ISRAEL; Tel ; haimo@eu- crf.net

2 Issue SAVE the date: HotZyme Symposium Discovery of Extremophilic Novel Enzymes with Application for Industrial Biotechnology 9 & 10 February 2015 Nof Hotel, 101 Hanassi Avenue, Haifa The HotZyme project and its consortium are committed to the training of young scientists working in the discovery, characterisation and application of extremophilic enzymes. Therefore the project is sponsoring a symposium for young scientists where the issues dealt in the project and related topics are presented and discussed by the project experts, external leading specialists and the young scientists (mainly PhD students and post- doctoral fellows) themselves. This 2- day FREE event will be held on 9-10 February 2015 in Hotel Nof, in the highly attractive city of Haifa, Israel. The title of the symposium is: Discovery of Extremophilic Novel Enzymes with Application for Industrial Biotechnology. The opening lecture of the symposium will be given by Prof. Aharon Oren of the Hebrew University in Jerusalem, Israel, and his lecture is entitled "From Lot's wife to hypersaline biotechnology: Diversity, physiology and exploitation of life at high salt concentrations". The symposium will also feature presentations by the HotZyme experts of their work within the project and the industrial implications of the work done in the HotZyme project. In addition, a few guest experts will present their work in the area of extremophilic novel enzymes. The HotZyme academic and industrial experts include Prof. Mark Young of Montana State University (USA), Prof. Jennifer Littlechild of University of Exeter (UK), Prof. Elizaveta Bonch- Osmolovskaya of the Russian Academy of Sciences (Russia), Prof. Bettina Siebers of University Duisburg- Essen (Germany), Dr. Zalan Szabo of MicroDish (the Netherlands) and Dr. Roland Wohlgemuth of Sigma- Aldrich (Switzerland). Among the Israeli guest experts, there are Prof. Ayelet Fishman and Prof. Oded Beja of the Technion, Dr. Yoram Gerchman of University of Haifa, Dr. Mathew Weisman of Archaezyme Biotech Consulting and more.

3 Issue The symposium will also allow young scientists PhD students and post- doctoral fellows to present their own work in short talks and posters and allow them to get a closer look and to get to know other leading experts in their fields of interest. Event Schedule: Day 1 Monday, 9 February : Registration 09: Opening Lecture - Prof. Aharon Oren, HUJI 09: Coffee break 10:00-12:00 Presentations by young scientists (PhD students; Post Docs) 12:00-13:00 Meetings of students with consortium members & guest scientists 13: Lunch 14: Prof. Mark Young, Montana State University Prof. Jenny Littlechild, University of Exeter or Israeli scientist (tbc) Prof. Bettina Siebers, University of Duisburg- Essen or Israeli scientist (tbc) 15: Coffee break 15:45-17:15 Presentations by young scientists (PhD students; Post Docs) 17:15-18:30 Meetings of students with consortium members & guest scientists 19: late Dinner All guests from abroad are invited to a walk on Panorama Street in Haifa after dinner Day 2 Tuesday, 10 February : Dr. Roland Wohlgemuth, Sigma Aldrich (tbc) Lecture by Israeli scientist - Dr. Yoram Gerchman, University of Haifa 09: Coffee break 10:15-12:00 Presentations of consortium members (Prof. Elizaveta Bonch- Osmolovskaya; Dr. Zalan Szabo; Prof. Fragiskos Kolisis) 12: Conclusion Call for Participants - EXTENDED: Submissions of applications are invited from young scientists (age 35 years or less) on discovery, characterisation and application of extremophilic enzymes. Applications must include short curriculum vitae that include present position, highest degree held and papers published in the last 5 years, presentation title and abstracts not exceeding 300 words. Applications for financial support for travelling will be considered. Please submit the application materials to Haimo Gilbert via haimo@eu- crf.net by 22 December 2014 with subject HotZyme Symposium application + your last name. Successful applications will be notified by 10 January Additional information including details about symposium arrangements and programme will also be provided at that time to participants.

4 Issue Project Progress Current and Upcoming Reports One regular feature of the HotZyme Newsletter is to update readers of our project s deliverable summaries. The following summaries are of deliverable reports that were submitted since our last issue in September D6.4 - Evaluation of stability of selected hydrolase enzymes under the conditions required for specific industrial processes: (Completed by partners UNEXE, ICRM, UDE and NHRF) Several new thermostable esterase enzymes with varying specificity have been identified and characterized and are suitable for use in industrial biocatalysis. One is already being used in a thermophilic cell factory synthetic biology approach. New thermostable lactonase activities have been discovered belonging to three different enzyme folds: the phosphotriesterase quorum sensing lactonase, the enol lactonase and the gluconolactonase. These enzymes offer a new type of hydrolase enzyme that is of industrial interest to the pharmaceutical industries. These activities are not commercially available to date. Three new thermostable epoxide hydrolases have been identified and characterized. Two of these belong to the limonene type and offer more stable alternatives than the currently used Rhodococcus enzyme for industrial biocatalysis and offer different substrate preference and enantioselectivity. One belongs to a different α/β hydrolase fold family and also has applications for biocatalysis. Two novel thermophilic cellulases have been identified and characterized which have interest to our industrial partner Novozymes. Below is a summary of one of HotZyme project s regular 6- month progress report this one is for the period of April- October 2014: D HotZyme 6- Month Progress Report #7: Main achievements during the last 6- month period include - Big effort has been dedicated to close the genomes of Thermococcus and Planctomycetes isolated earlier during HotZyme project. DNA has been prepared from the organisms that are difficult to cultivate, and sent for closing the gaps.

5 Issue Comprehensive analysis of the metagenomic sequences including both the cellular part and the viral part. Two manuscripts are being prepared. Identified potentially interesting enzymes from the viral sequences present in the metagenomes. Several genes have been cloned into pet30a expression vector and attempts were made to purify the proteins. With the purpose of obtaining toxins that can cause cell lysis to facilitate enzyme purification, we identified the first CRISPR toxin from hyperthermophilic archaeon Sulfolobus. What to Expect Next Deliverables due before the project ends (March 2015): D6.5 - Crystallographic analysis of selected proteins: Crystallographic analysis will be performed for selected proteins and the structures will be reported. D6.6 - Production of protein variants by rational design based on modeling and structural analysis: Protein variants will be produced by rational design based on modeling and structural analysis. D9.1 - Interest groups and interests: Identifying and mapping interest groups and their respective interests. These will include such commercial / industrial parties and groupings, political local, national and regional parties and groupings, including regulatory and policy- making parties, etc. For each identifiable party its potential and actual interests will be mapped and indicated. D9.2 - Policy- related consideration: The report will analyse the various consideration that pertain to socio- political decision processes that would potentially influence such decisions affecting the potential uses of the project results, like heritage consideration that might affect possible restrictions on use or environmental vs. employment consideration pertaining to industries to which the project result are related. D9.3 - Potential markets and use: In conjunction with the commercialisation consideration, potential markets, clientele, users, etc. will be mapped so as to determine the potential market developmental trends and directions, with reference to the various socio- economic considerations that might affect such market developmental patterns and direction. HIGHLIGHTING Paper Publications and Conference Presentation by HotZyme Member Teams: Poster Presentations Discovery of Cellulase CellDZ1 and Esterase EstDZ1 Members of HotZyme teams recently attended and presented at the 10th International Congress on Extremophiles (Saint Petersburg, Russia, 7-11 September, 2014) and 4 th International conference on Novel Enzymes. (Ghent, Belgium, October, 2014). At both conferences, Dimitra Zarafeta of the NTUA team made a poster presentation titled Discovery of novel thermostable enzymes of industrial interest by metagenomic screening, highlight of which is the discovery of the two novel enzymes - the cellulase celldz1 and the esterase estdz1. Other authors of the work mentioned in the presentation were Efthymios Ladoukakis, Dimitrios Kissas, Soley R. Gudbergsdottir, Sergey Gavrilov, Aristotelis Chatziioannou, Elizaveta A. Bonch- Osmolovskaya, Xu Peng, Georgios Skretas*, Fragiskos N. Kolisis* (2014).

6 Issue International Journal of Systematic and Evolutionary Microbiology, July 2014 HotZyme consortium member Prof. Elizaveta Bonch- Osmolovskaya collaborated on the paper Thermosipho activus sp. nov., a novel thermophilic anaerobic hydrolytic bacterium isolated from a deep- sea sample Guaymas Basin, Gulf of California. The complete reference for the paper is as follows: Podosokorskaya OA, Bonch- Osmolovskaya EA, Godfroy A, Gavrilov SN, Beskorovaynaya DA, Sokolova TG, Kolganova TV, Toshchakov SV, Kublanov IV. Thermosipho activus sp. nov., a thermophilic, anaerobic, hydrolytic bacterium isolated from a deep- sea sample. Int J Syst Evol Microbiol., 2014, 64: Paper Abstract: A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain Rift- s3t, was isolated from a deep- sea sample containing Riftia pachyptila sheath from Guaymas Basin, Gulf of California. Cells of new isolate were rods μm in width and μm in length surrounded by a sheath- like structure (toga). Strain Rift- s3t grew at temperature range from 44 to 75 C, ph from 5.5 to 8.0, and NaCl concentration from 3 to 60 g l- 1. At optimum conditions (65 C, ph 6.0, NaCl 25 g l- 1) the doubling time was 30 min. The isolate was able to ferment mono-, oligo- and polysaccharides including cellulose, chitin, xylan, pectin and proteins including β- keratins, casein, gelatin. Acetate, hydrogen and carbon dioxide were the main products of glucose fermentation. G+C content of DNA was 30 mol %. Phylogenetic analysis of 16S rrna gene sequences of strain Rift- s3t and relatives showed its affiliation with the genus Thermosipho. Thermosipho atlanticus was its closest relative (96.5 % identity of 16S rrna gene sequences). Based on the phylogenetic analysis and physiological properties of the novel isolate we propose a novel species Thermosipho activus Rift- s3t (= DSM 26467T = VKM В- 2803T). International Journal of Systematic and Evolutionary Microbiology (Online), November 2014 Prof. Elizaveta Bonch- Osmolovskaya is involved in several more collaborated papers, one such published paper is titled Tepidisphaera mucosa gen. nov., sp. nov., a new moderately thermophilic member of Phycisphaerae class in the Planctomycetes, and proposal of a new family Tepidisphaeraceae and a new order Tepidisphaerales. Collaborators of this paper are Olga L. Kovaleval, Alexander Merkell, Andrei Novikov, Roman Baslerov, Stepan Toshchakov, and Elizaveta A. Bonch- Osmolovskaya. Paper Abstract: Three strains of facultatively aerobic moderately thermophilic bacteria were isolated from terrestrial hot springs in Baikal Lake region and Kamchatka (Russia). Cells of new isolates were cocci reproducing by binary fission. The temperature range for growth was between 20 and 56 C and of ph from 4.5 to 8.5 with the optimum at C and ph The organisms were chemoheterotrophs preferring sugars and polysaccharides as growth substrates. 16S rrna genes of the strains 2842, 2813 and 2918Kr were nearly identical ( % similarity) and indicated the belonging of strains to Planctomycetes phylum. The closest cultivated relatives were Algisphaera agarilytica 06SJR6-2T and Phycisphaera mikurensis FYK2301M01T with 16S rrna gene similarity value of 82.4 and 80.3%, respectively. New strains differed from them by higher growth temperature, sensitivity to NaCl concentration above 3.0% and by cellular fatty acids profile. On the base of phylogenetic and physiology data it is proposed that strains 2842T, 2813 and 2918Kr represent a novel genus and species for which we propose the name Tepidisphaera mucosa. The type strain is 2842T (= VKM B- 2832T = JCM 19875T). We also propose that Tepidisphaera is the type genus of a novel family Tepidisphaeraceae and a novel order Tepidisphaerales.

7 Issue Paper under review Currently there are a number of academic paper written by HotZyme Consortium scientists and based on work conducted within this project that are under publication review. One such paper is a true collaboration of HotZyme members, it is titled Comparative metagenomics of eight geographically remote terrestrial hot springs. Contributing authors are: Peter Menzel, Sóley Ruth Guðbergsdóttir, Anne Gunn Rike, Lianbing Lin, Qi Zhang, Patrizia Contursi, Marco Moracci, Jakob K. Kristjansson, Benjamin Bolduc, Sergey Gavrilov, Nikolai Ravin, Andrey Mardanov, Elizaveta Bonch- Osmolovskaya, Mark Young, Anders Krogh, and Xu Peng. Paper Abstract: Hot springs are natural habitats for thermophilic Archaea and Bacteria. In this paper, we present the metagenomic analysis of eight globally distributed terrestrial hot springs from China, Iceland, Italy, Russia, and the USA with a temperature range between 61ºC and 92ºC and ph between 1.8 and 7. A comparison of the biodiversity and community composition generally showed a decrease in biodiversity with increasing temperature and decreasing ph. Species belonging to the crenarchaeal order Thermoprotei were detected in all eight hot springs, whereas no single bacterial species was found in all samples; suggesting a better adaptation of certain archaeal species to different thermophilic environments. Two hot springs show high abundance of Acidithiobacillus, supporting the idea of a true thermophilic Acidithiobacillus species that can thrive in hyperthermophilic environments. Depending on the sample, up to 58% of sequencing reads could not be assigned to a known phylum, reinforcing the fact that a large number of microorganisms in nature including hot environments remain to be isolated and characterized. Last But Not Least Season s Greetings to All! As the holiday season approaches, on behalf of the entire HotZyme Consortium, we'd like to take this opportunity to thank you for your continued interest and support. May your holiday season and the New Year be filled with much joy, happiness and success. We look forward to connect and work with you in the coming year. Happy Holidays Everyone!

8 Issue HotZyme Partners: Copenhagen University Microdish BV Norwegian Geotechnical Institute Winogradsky Institute of Microbiology (RAS) National Research Council of Italy National Technical University of Athens EuCRF European Centre for Research & Financing European Commission Scientific Officer Dr. Herman VAN MELLAERT This is a newsletter distributed by the HotZyme project consortium to those interested in our EU FP7 coordination action project on Systematic Screening for Novel Hydrolases from Hot Environments. HotZyme (GA: ) is a project supported by the 7th Framework Programme for Research and Technological Development (FP7) of the European Union. The research project is a large scale integrating project collaborative project - on the systematic screening for novel hydrolases from hot environments.