Title Participants Abstract "Astrobiology in space : a comprehensive look at the solar system" "Maarten De Mol" "The field of astrobiology aims to understand the origin of life on Earth and searches for evidence of life beyond our planet. Although there is agreement on some of the requirements for life on Earth, the exact process by which life emerged from prebiotic conditions is still uncertain, leading to various theories. In order to expand our knowledge of life and our place in the universe, scientists look for signs of life through the use of biosignatures, observations that suggest the presence of past or present life. These biosignatures often require up-close investigation by orbiters and landers, which have been employed in various space missions. Mars, because of its proximity and Earth-like environment, has received the most attention and has been explored using (sub)surface sampling and analysis. Despite its inhospitable surface conditions, Venus has also been the subject of space missions due to the presence of potentially habitable conditions in its atmosphere. In addition, the discovery of habitable environments on icy moons has sparked interest in further study. This article provides an overview of the origin of life on Earth and the astrobiology studies carried out by orbiters and landers." "MariClus : your one-stop platform for information on marine natural products, their gene clusters and producing organisms" "Cedric Hermans, Maarten De Mol, Marieke Mispelaere, Anne-Sofie De Rop, Jeltien Rombaut, Tesneem Nusayr, Rebecca Creamer, Sofie De Maeseneire, Paco Hulpiau" "An exploratory in silico comparison of open-source codon harmonization tools" "Thomas Willems, Wim Hectors, Jeltien Rombaut, Anne-Sofie De Rop, Stijn Goegebeur, Tom Delmulle, Maarten De Mol, Sofie De Maeseneire, Wim Soetaert" "Background: Not changing the native constitution of genes prior to their expression by a heterologous host can affect the amount of proteins synthesized as well as their folding, hampering their activity and even cell viability. Over the past decades, several strategies have been developed to optimize the translation of heterologous genes by accommodating the difference in codon usage between species. While there have been a handful of studies assessing various codon optimization strategies, to the best of our knowledge, no research has been performed towards the evaluation and comparison of codon harmonization algorithms. To highlight their importance and encourage meaningful discussion, we compared different open-source codon harmonization tools pertaining to their in silico performance, and we investigated the influence of different gene-specific factors. Results: In total, 27 genes were harmonized with four tools toward two different heterologous hosts. The difference in %MinMax values between the harmonized and the original sequences was calculated (ΔMinMax), and statistical analysis of the obtained results was carried out. It became clear that not all tools perform similarly, and the choice of tool should depend on the intended application. Almost all biological factors under investigation (GC content, RNA secondary structures and choice of heterologous host) had a significant influence on the harmonization results and thus must be taken into account. These findings were substantiated using a validation dataset consisting of 8 strategically chosen genes. Conclusions: Due to the size of the dataset, no complex models could be developed. However, this initial study showcases significant differences between the results of various codon harmonization tools. Although more elaborate investigation is needed, it is clear that biological factors such as GC content, RNA secondary structures and heterologous hosts must be taken into account when selecting the codon harmonization tool." "Novel alkaloids from marine actinobacteria : discovery and characterization" "Anne-Sofie De Rop, Jeltien Rombaut, Thomas Willems, Marilyn De Graeve, Lynn Vanhaecke, Paco Hulpiau, Sofie De Maeseneire, Maarten De Mol, Wim Soetaert" "The marine environment is an excellent resource for natural products with therapeutic potential. Its microbial inhabitants, often associated with other marine organisms, are specialized in the synthesis of bioactive secondary metabolites. Similar to their terrestrial counterparts, marine Actinobacteria are a prevalent source of these natural products. Here, we discuss 77 newly discovered alkaloids produced by such marine Actinobacteria between 2017 and mid-2021, as well as the strategies employed in their elucidation. While 12 different classes of alkaloids were unraveled, indoles, diketopiperazines, glutarimides, indolizidines, and pyrroles were most dominant. Discoveries were mainly based on experimental approaches where microbial extracts were analyzed in relation to novel compounds. Although such experimental procedures have proven useful in the past, the methodologies need adaptations to limit the chance of compound rediscovery. On the other hand, genome mining provides a different angle for natural product discovery. While the technology is still relatively young compared to experimental screening, significant improvement has been made in recent years. Together with synthetic biology tools, both genome mining and extract screening provide excellent opportunities for continued drug discovery from marine Actinobacteria." "Alkaloids from marine fungi : promising antimicrobials" "Thomas Willems, Maarten De Mol, Aleksandar De Bruycker, Sofie De Maeseneire, Wim Soetaert" "Resistance of pathogenic microorganisms against antimicrobials is a major threat to contemporary human society. It necessitates a perpetual influx of novel antimicrobial compounds. More specifically, Gram(-)pathogens emerged as the most exigent danger. In our continuing quest to search for novel antimicrobial molecules, alkaloids from marine fungi show great promise. However, current reports of such newly discovered alkaloids are often limited to cytotoxicity studies and, moreover, neglect to discuss the enigma of their biosynthesis. Yet, the latter is often a prerequisite to make them available through sufficiently efficient processes. This review aims to summarize novel alkaloids with promising antimicrobial properties discovered in the past five years and produced by marine fungi. Several discovery strategies are summarized, and knowledge gaps in biochemical production routes are identified. Finally, links between the structure of the newly discovered molecules and their activity are proposed. Since 2015, a total of 35 new antimicrobial alkaloids from marine fungi were identified, of which 22 showed an antibacterial activity against Gram(-)microorganisms. Eight of them can be classified as narrow-spectrum Gram(-)antibiotics. Despite this promising ratio of novel alkaloids active against Gram(-)microorganisms, the number of newly discovered antimicrobial alkaloids is low, due to the narrow spectrum of discovery protocols that are used and the fact that antimicrobial properties of newly discovered alkaloids are barely characterized. Alternatives are proposed in this review. In conclusion, this review summarizes novel findings on antimicrobial alkaloids from marine fungi, shows their potential as promising therapeutic candidates, and hints on how to further improve this potential." "Engineering yeast factories towards improved robustness" "Maarten De Mol" "An orthogonal transcription system for Saccharomyces cerevisiae" "Maarten De Mol, Veerle De Clercq, Sofie De Maeseneire, Joeri Beauprez" "Metabolic engineering of microbial production hosts with long, heterologous pathways strongly increases the burden on a production strain. Thus, genomic stability and robust expression tools (decoupled from the host metabolism and regulation) are key for the creation of robust production strains. Here we describe the development of an orthogonal transcription system using short promoters for Saccharomyces cerevisiae. This system is based on an endogenous transcription system found in baker's yeast and is similar to the bacteriophage T7 expression system for E. coli. An additional copy of the polymerase coding sequence and the one of its transcription factor were introduced into the genome of S. cerevisiae, together with the mOrange coding sequence. The latter was placed under the control of such a short promoter. The absence of mOrange fluorescence in cells expressing the mOrange gene under control of this short promoter, with and without expression of the polymerase proved the orthogonality of the transcription system. Further characterization of the promoter structure, fine tuning of the transcription factor expression and the construction of promoter libraries will enable the full exploitation of this tool in yeast synthetic biology approaches. Finally, it will increase the genomic stability and performance robustness of industrial production strains." "Where to introduce genetic pathways into the genome of Saccharomyces cerevisiae?" "Maarten De Mol, Victoria Marcoen, Isabelle Maryns, Sofie De Maeseneire, Joeri Beauprez" "Directional multipart in vivo assembly and genome integration using Saccharomyces cerevisiae" "Maarten De Mol, Sofie De Maeseneire, Joeri Beauprez" "Although various state-of-the-art metabolic engineering tools are by now well established for Saccharomyces cerevisiae, the introduction of multiple genes in its genome is still a laborious task. Yet, this is crucial for the stable expression of balanced biosynthesis pathways, i.e. for the efficient production of target molecules. To tackle this problem, we are developing a new technique called genomic Serine Integrase Recombinational Assembly (gSIRA). By exploiting the Streptomyces phiC31 integrase and its att sites as landing paths in the yeastU+2019s genome, a whole pathway of genes can be directionally assembled and integrated at a desired locus. This is tested first with fluorescent proteins and will later on be evaluated for a small pathway of up to five genes. Benefits of this new assembly technique are 1) its time-saving nature (no vector intermediate needed), 2) its ability to manage multi-part assemblies and 3) the fact that it can be extended to introduce multiple copies of a pathway at various locations in the same single step. The only prerequisite is that one needs a library of bakerU+2019s yeast strains with the inducible integrase and specific att sites at specific genome locations. Thus, future research will also include the construction of a library of different att sites, to increase stability of the yeast strains using multiple landing paths. This technique can hence be used to quickly develop an industrially stable production strain of Saccharomyces cerevisiae." "Serine integrase recombinational engineering (SIRE) : a versatile toolbox for genome editing" "Nico Snoeck, Maarten De Mol, Dries Van Herpe, Anke Goormans, Isabelle Maryns, Pieter Coussement, Gert Peters, Joeri Beauprez, Sofie De Maeseneire"