Universiteit Leiden

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Arthur Ram

Director of education / associate professor

Name
Dr. A.F.J. Ram
Telephone
+31 71 527 4914
E-mail
a.f.j.ram@biology.leidenuniv.nl

I am associate professor Molecular Microbiology and Biotechnology at the Institute of Biology (IBL). I am interested in the several aspects related to the growth and development of the filamentous fungi. These include elucidation of molecular mechanisms related to the transcriptional regulation of enzymes involved in plant polysaccharide degradation, polarized secretion and cell growth, and mechanisms related to fungal cell wall biosynthesis and remodeling.

More information about Arthur Ram

Brief Biography

I obtained my PhD in 1996 at the University of Amsterdam with molecular genetic study on Isolation and characterization of cell wall mutants in Saccharomyces cerevisiae. The biosynthesis and remodeling of the fungal cell wall is still in important part of my research area, focusing on signal transduction pathway responsible for cell wall remodeling and identification of enzymes important for biosynthesis and crosslinking of cell wall polymers such as alpha glucan, chitin and galactomannan. In 1999 moved to Leiden after a two-years post doc at TNO Nutrition in Zeist, to start, together with Prof Kees van den Hondel and developed two other research lines in relation to transcriptional regulation of plant polysaccharides degrading enzyme networks and in relation to polarized growth and protein secretion in the filamentous fungus Aspergillus niger.

At Leiden University I’m currently head of the departments Molecular Microbiology and Biotechnology serve as Director of Education for the bachelor program Biology.

Research

My research is focused at the understanding of the molecular mechanisms that underlay cellular processes which are specific for filamentous fungi. Aspergillus niger is chosen as our main model system due its fascinating biology in terms of growth and development and its many applications in biotechnology related to protein and metabolite production. The cellular processes that are studied include processes related to enzyme production, polarized growth, cell wall biosynthesis, and carbon utilization.  In the last years we have also included as a model species Aspergillus fumigatus as this fungus is the most commonly found fungus in human patients and therir medically relevant. We are also studying Trichoderma reesei as another important industrial fungus.

To study these fundamental processes, we have developed many important molecular and cell-biological tools including i) state of the art molecular tools to analyze gene function (creating knockout strain, tools for targeting integration, controlled expression and fluorescent protein labeling, CRSIPR/CAS technology), ii) use of available microscope infrastructure within the IBL to perform protein localization studies in time and space, iii) develop classical genetic tools such as bulk segregant analysis, to perform mutant identification via whole genome sequencing approaches, iv) we have build-up and financed a state-of-the art bioreactor cultivation platform for filamentous fungi, Such a platform is an absolute requirement for microbiological research in the field of filamentous fungi as such as system is the only way by which the growth of the fungus can be adequately controlled.

Research Interests

1. Transcription regulation of carbohydrate modifying enzymes

Filamentous fungi, including Aspergillus niger are well known for its ability to secrete a wide variety of plant-polysaccharide modifying enzymes. The secreted enzymes are able to degrade the plant cell wall polysaccharides pectin, hemicellulose and cellulose, as well as plant storage polysaccharides like starch and inulin. We are interested in the mechanism(s) by which the fungus can sense and transport the presence of different (often complex) carbon sources in its vicinity and how the presence of a certain carbohydrate activates the expression of a network of genes encoding enzymes to degrade the carbon source. Special focus is on the identification of so-called inducer molecules and transcription factors that are required for expression of enzyme networks involved in the breakdown and uptake of starch, inulin and pectin. In 2016, we identified a novel transcription factor and repressor module that controls the expression of pectin degrading enzymes in A. niger.

Related projects:

  • New regulators involved in plant cell wall degradation (Jing Niu, PhD, Ebru Alazi, PhD)
  • Responses to carbon starvation (Annemarie Burggraaf, PhD)
  • Improving the filamentous fungus Aspergillus niger as cell factory for starch degrading jean paul enzymes (Mark Arentshorst)

2. Morphology  and enzyme production

Cell morphology and secretion capacity are two important parameters in relation to optimizing enzyme production in filamentous fungi . Fundamental research on fungal morphology and secretion in the industrial host Aspergillus niger is aimed at a much deeper understanding of the mechanisms that temporally and spatially regulate different steps of the hyphal morphogenesis and secretion. Knowledge of the complex networks and molecular interactions will generate new possibilities to control and manipulate the morphology of A. niger for industrial applications. The cell wall of filamentous fungi is an essential part of the cell protecting its integrity, forming a barrier with the surrounding environment and permitting interactions with possible substrates and hosts to be infected.  Recent research in the group has revealed that galactofuranose is essential for the integrity of the cell wall and is required for proper morphology. In its absence the mycelium grows much slower and forms abnormal hyphae with increased branching.

Related projects:

  • Cell architecture and pathways for parallel secretion in the  filamentous fungus Aspergillus niger (Min Jin Kwon PhD, Vera Meyer)
  • Galactofuranose biosynthesis in the filamentous fungus Aspergillus niger (Joohae Park PhD)
  • Cell Wall Dynamics in Aspergillus niger (Benjamin Nitsche PhD)
  • Efficient targeting of the Trichoderma genome for industrial protein engineering (Jean Paul Ouedraogo, post-doc)

3 Robustness of the Fungal Cell Factory

The cell wall of yeasts and fungi is of vital importance to the cell. It is required to resist the turgor pressure of the protoplasts to prevent cell lysis. It further protects against potentially damaging enzymes from the environment and acts as a scaffold for exposing cell wall proteins that play a role during cell-cell interactions. The cell wall strength and permeability  is mainly accomplished by crosslinking of individual cell wall components to each other. We are interested in the crosslinking of these components with the aim to improve enzyme production and increase extractability of cell wall components such as chitin. The cell wall of spores of A. niger is much more resistant to environmental stress (heat stress and oxidative stress) compared to vegetative cells. We are interested in the cell wall related adaptation that create the stress tolerance of spores as well as understanding mechanisms that are important to create the heterogeneity of stress resistance among fungal spores.

Related projects:

  • Cell wall strength in Aspergillus niger (Tim van  Leeuwe, PhD)
  • Heterogeneity of resistance in spores of food spoilage fungi (Sjoerd  Seekles, PhD)

Director of education / associate professor

  • Wiskunde en Natuurwetenschappen
  • Instituut Biologie Leiden
  • IBL Biotechnology & Health

Work address

Sylvius
Sylviusweg 72
2333 BE Leiden
Room number 4.4.14

Contact

  • Stichting Eurofung Bestuurslid en penningmeester

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