MIRRI NEWS | Issue 4

Dear all,

six more months to go to finalize the MIRRI Preparatory Phase: needless to say that we now enter the most crucial phase of the project.

The past months brought some positive news for the MIRRI consortium: First of all, with Poland and Greece as third and fourth signatory of the Memorandum of Understanding the process of the MIRRI-ERIC application is about to start. Once all necessary underlying documents are finalised, this important step towards the Implementation Phase will be initiated. The second piece of good news is that the INFRADEV-4 application CORBEL (Coordinated Research Infrastructures Building Enduring Life-science services) has now been fully granted by the European Commission. The MIRRI Partners CAB International, CBS, DSMZ, and Jacobs University will closely collaborate with other ESFRI BMS infrastructures to guarantee the success of this project. It is envisaged to start CORBEL in September 2015.

As mentioned in previous issues of this newsletter, the implementation of the Nagoya Protocol and the EU Regulation No 511/2014 keeps us busy. Together with external experts, MIRRI will introduce recent developments of mBRC interest and react to expected needs of users of microbial material during two workshops. The first workshop will take place back-to-back with the annual ECCO meeting (27th of May in Paris), the second during the FEMS meeting (9th of June in Maastricht). Both workshops are free of charge. For more details please go to the Meet MIRRI section of this newsletter.

Kind regards,

Erko Stackebrandt
MIRRI Coordinator

The IRCCS AOU San Martino IST (USMI) is a Scientific Institute for Research, Hospitalization and Health Care of National interest. Its Technological Platform includes the core facility Biological Resource Centre, aimed at coordinating institutional biobank facilities. Among these, the Interlab Cell Line Collection (ICLC), was established in 1994. ICLC is a point of reference for biomedical researchers to whom it supplies: human and animal cell lines, STR profiling of human cell lines, safe and patent deposit of cell lines and hybridomas. The catalogue of services is on-line, and the cell lines are distributed all over the world. ICLC has contributed to the definition of the OECD Guidelines for the management of Biological Resource Centers, participates in the European Infrastructure of Biobanks and Biomolecular Resources (BBMRI-ERIC) and in MIRRI.
USMI is maintaining the CABRI web site. CABRI (Common Access to Biological Resources and Information) project was funded by the EU from 1996 to 1999. The project implemented a unified access to culture collection catalogues of partners, an online 'one-stop-shop' for biological resources where researchers can search, identify and pre-order strains. The CABRI web site currently includes 28 catalogues from height distinct European mBRCs. Overall, more than 130,000 resources are described. The majority of these are microbial strains, but there also are plasmids, phages, cell lines, plant cells and plant viruses. The CABRI web site is a pioneer model for an integrated, while distributed, database, which is searchable through a common gate.

The Service Public Fédéral de Programmation – Politique Scientifique or Belgian Science Policy Office (Belspo) has a longstanding engagement towards research on and preservation of biological diversity. This commitment is demonstrated through the support of the federal natural science museums, the establishment of an interface function between biodiversity researchers and policymakers, the realisation of dedicated research programmes as well as through the funding and coordination of the Belgian Coordinated Collections of Micro-organisms, BCCM.
Belspo has initiated the BCCM consortium in the early eighties. Since then the BCCM collections have developed from individual, research-based collections to a consortium of 7 public, service-oriented collections. Each collection forms a binomial with its host laboratory to exchange scientific expertise. The cooperation within the consortium ensures a harmonised approach to tackle issues of common interest. In this regard, a special role is set aside for the BCCM coordination cell that makes part of Belspo. This cell coordinates the ISO 9001 quality management system, information technology (e.g. LIMS), external and internal communication, international cooperation and legal aspects of the consortium.

For a small country like Belgium the integration of its researchers in international activities is a must. The BCCM collections work together with colleagues from other countries in the frame associations such as ECCO and WFCC. Belspo believes that close cooperation between European culture collections will benefit the many users and help stimulate the further development of biotechnology and life sciences. For this reason, they have participated in consecutive European projects like MINE, CABRI, EMBRC and EMbaRC. Within the MIRRI Preparatory Phase, Belspo is the only participating research funding organisation, clearly demonstrating its interest in the MIRRI infrastructure.

The LMG Bacteria Collection was one of the founding partners of the Belgian Coordinated Collections of Microorganisms (BCCM) in 1983 and has since then developed into a well-known Microbial Biological Resource Centre (mBRC) specialized in bacteria, holding and offering over 25,000 well-characterized bacterial strains. It receives an excellent international recognition as repository of important groups of bacteria and for its strong expertise in bacterial characterization. The strain holdings are very diverse and serve the needs of both academia and various R&D sectors, including green, red, blue and white biotechnology. The strategic acquisition policy of BCCM/LMG is supported by an ISO 9001 certification for accession, control, preservation, storage and supply of biological material and related information in the frame of public deposits, safe deposits and patent deposits.
A glimpse on the BCCM/LMG EU project track record (MINE, CABRI, EBRCN, EmBaRC) clearly illustrates that BCCM/LMG supports the establishment of a pan-European Research Infrastructure for supporting both academia and bio-industry. In MIRRI, BCCM/LMG focusses on strategies for the reduction of gaps in holdings, development of services and outputs, and it also actively contributes to the data resources management work package.

ELIXIR is the ESFRI Research Infrastructure for life science data. It aims to coordinate, sustain and integrate Europe’s bioinformatics resources by linking major bioinformatics institutes such as EMBL-EBI with the national bioinformatics infrastructures developed within each country. The volume and diversity of data being generated now in life sciences is too big for any one country to handle alone and researchers increasingly require access to data from several resources to be able to conduct their research.
There are over 1,800 life science databases and analysis tools in Europe, which range from major data archives such as the European Nucleotide Archive (ENA), to widely used knowledge bases such as Ensembl through to niche databases and analysis tools used by smaller communities of researchers. ELIXIR works to coordinate these resources by operating a series of service platforms for ‘data’, ‘tools’, ‘standards’, ‘compute’ and ‘training’. ELIXIR’s Innovation and SME programme provides direct support to research-intensive companies in accessing and using ELIXIR’s resources.

ELIXIR shares many synergies with MIRRI and there are several existing and future avenues for collaboration. ELIXIR will work closely with MIRRI on the EUR 14.5 million CORBEL grant, awarded by the European Commission, which will officially kick off later in 2015. This grant will ensure that common data bridges, shared access, ELSI services and innovation activities are developed between partnering organisations. This will allow for direct ELIXIR – MIRRI collaboration. On issues such as predictive systems for pharmacology for safer drugs and chemical products, ELIXIR will build curated reference datasets and annotations, tools for big data and literature mining and data storage, whilst MIRRI will provide world-class access to cell cultures, microbes and genomes. ELIXIR has also funded a Pilot Action on ‘Marine metagenomics: towards user centric services’. MIRRI is seen as a key infrastructure in this field, and as the Pilot Action expands, partners will seek to engage MIRRI’s experts closely in the development of new databases. Equally, MIRRI’s expertise in aspects such as the Nagoya Protocol is invaluable to ELIXIR’s partners.
Some of ELIXIR’s services may also be of interest to MIRRI’s users. The ELIXIR Tools and Data Services registry allows researchers to search for the right database and tool including those for microbial data. The emerging ELIXIR TeSS portal will allow users to identify and access relevant training courses and e-learning content run by ELIXIR partners, and again many of these will be of relevance to experts in microbial resources.

Mucor circinelloides MUT44, an effective biocatalyst for C=C double bonds and carboxylic acids/esters reduction

In the framework of the modern bioeconomy, the reduction of waste and by-product formation as process costs and energy requirements is a central goal and an actual challenge. The deficiencies shown by chemical synthesis are indeed overcoming by the focused development of biocatalytic processes based on fungi. Mucor circinelloides (picture shows sporangium of M. circinelloides MUT44) belongs to Zygomycota, and recently raised biotechnological attention due to its capability to accumulate poly-unsaturated fatty acids (Carvalho et al. 2015) and carotenoids (Torres-Martínez et al. 2012). Several strains of M. circinelloides efficiently reduce C=C double bonds, carboxylic acids and esters, carrying out crucial reactions of organic chemistry industry on both conventional and unconventional (i.e. not transformed by bacterial and yeast enzymes) substrates (Romagnolo et al. 2015). Many compounds with different electron-withdrawing groups and substituents nearby the C=C or COOR bounds can be efficiently transformed. The enoate reductase (EC1.3.1.31) and carboxylate reductase (EC1.2.99.6) activity, putatively expressed by those strains, have been rarely reported in filamentous fungi and, to our knowledge, this is the first report on M. circinelloides. Given its high reduction yields towards not conventional substrates, the expressed enoate reductase activity pattern by M. circinelloides MUT44 was investigated by RT-PCR. Ten putative genes were found; the expression of three of them was strongly and rapidly activated in presence of cyclohexanone, concurrently to its actual biotransformation, highlighting the active role of these enzymes. These reactions enrich the enzymatic toolbox available to organic synthetic chemistry for the development of green processes aimed to produce natural flavours and fragrances, satisfying the EU requisite for the natural labelling of the corresponding products.