SFB 1664:  Plant Proteoform Diversity - SNP2Prot

• Subject Area: Biology
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 514901783

The global challenge of sustaining food security and nutritional quality requires efficient plant production amidst climate change, resource constraints, and population growth. Leveraging genome information of plant species is crucial for resource-efficient agriculture. Advances in DNA sequencing and bioinformatics have enriched our understanding of genome organisation and gene discovery. Single nucleotide polymorphisms (SNPs) contribute significantly to genomic diversity, especially in protein-coding sequences. These SNPs result in proteoform variations that likely aid plants in adapting to diverse conditions. However, while a wealth of genetic variation, often in the form of SNPs, has been correlated to phenotypic variation in genome-wide association studies, consequences of SNPs on protein function are poorly understood. The CRC initiative therefore aims to decipher how coding sequence variation translates into functionally diverse proteoforms - SNP2Prot, bridging plant and protein research. The focus of SNP2Prot will be laid on deciphering of functional differences between proteoforms primarily in the model plant Arabidopsis thaliana, often based on the elucidation of 3-D protein structures or their prediction by structural modelling. The interdisciplinary collaboration targets areas like 'proteoforms interacting with nucleic acids', 'proteoforms mediating signalling processes', and 'proteoforms with enzymatic functions', but also genome- and proteome-wide approaches generating resources and supporting the transition into future funding periods. The long-term goal is to inform plant breeding or molecular pharming through rational proteoform design. With expertise from MLU Halle, Leibniz Institutes (IPB and IPK), and Leipzig University (UL), the initiative stands poised for impactful research.

• DFG Programme: Collaborative Research Centres

Current projects

• A01 - Structure-function analyses of NAC transcription factor proteoforms (Project Heads Balbach, Jochen ;  Delker, Carolin )
• A02 - Functional proteoform variation in thermomorphogenesis master regulators (Project Heads Quint, Marcel ;  Sinz, Andrea )
• A03 - Mutation-Sensitive Prediction of Transcription Factor-DNA Interactions in Plants (Project Heads Große, Ivo ;  Meiler, Jens )
• A04 - Quantitative cytogenetic characterization and structural analysis of REC8 proteoforms in plant meiosis (Project Heads Dreissig, Steven ;  Kastritis, Panagiotis L. )
• A05 - Targeting of function and structure of Arabidopsis dicing complex proteoforms on microRNA biogenesis (Project Heads Laubinger, Sascha ;  Schoeder, Clara )
• B01 - Natural allelic variation of PI4P 5-kinases modulating plasma membrane-associated processes in plants (Project Heads Heilmann, Ingo ;  Sinz, Andrea )
• B02 - Allelic variation in the control of calcium-dependent protein kinase activity and function in plant-environment interactions (Project Heads Romeis, Tina ;  Sinz, Andrea )
• B03 - Allelic variation of a vacuolar cation channel modulating ion homeostasis and calcium signalling in plants (Project Heads Peiter, Edgar ;  Romeis, Tina )
• B04 - Impact of JAZ9 allelic variation on proteoform structure, JA-Ile co-receptor assembly and plant performance (Project Heads Balbach, Jochen ;  Gasperini, Debora )
• B05 - Role of plant SRO proteoforms in tolerance to oxidative and salinity stress (Project Heads Stubbs, Milton T. ;  Wirthmüller, Lennart )
• C01 - Climate-associated functional polymorphisms of terpene synthases (Project Heads Degenhardt, Jörg ;  Weissenborn, Martin )
• C02 - Relevance of natural allelic variation in YUCCA genes for proteoform modulation, local auxin biosynthesis and phenotypic variation in natural Arabidopsis accessions (Project Heads Stubbs, Milton T. ;  von Wirén, Nicolaus )
• C03 - Impact of natural LPR1 proteoforms on Fe-dependent phosphate sensing (Project Heads Abel, Steffen ;  Naumann, Christin ;  Stubbs, Milton T. )
• C04 - Function of mevalonate kinase proteoforms in the adaptation to specific climates (Project Heads Kastritis, Panagiotis L. ;  Tissier, Alain )
• C05 - Impact of natural allelic variation on structure and function of the immune proteases SAP1 and SAP2 (Project Heads Ihling, Christian ;  Schuster, Mariana )
• D01 - Modelling, understanding, and predicting >2 million Arabidopsis proteoforms in the post-genomic era (Project Heads Kastritis, Panagiotis L. ;  Künze, Georg )
• D02 - Development of SNPstar 2.0 and computational prediction of putative proteoform candidates with high functional proteoform variation (Project Heads Große, Ivo ;  Quint, Marcel )
• MGK - Integrated Research Training Group PROTEOFORuM - Bridging plant and protein sciences (Project Head Delker, Carolin )
• Z01 - Central Tasks of the Collaborative Research Centre (Project Head Quint, Marcel )
• Z02 - Protein Expression, Purification and Analysis [Z02a] Proteomics/Protein Mass Spectrometry [Z02b] (Project Heads Fuszard, Matt ;  Pietzsch, Markus )

• Applicant Institution: Martin-Luther-Universität Halle-Wittenberg
• Participating University: Universität Leipzig
• Participating Institution: Leibniz-Institut für Pflanzenbiochemie (IPB); Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
• Spokesperson: Professor Dr. Marcel Quint