- Patricia Bubner
- Glycobiology, Enzymology, Filamentous Fungi, Carbohydrate Active Enzymes, Plants
- Postdoc | C. Somerville Lab
- Energy Biosciences Building, 2151 Berkeley Way
- Berkeley, California 94704
- Phone 510.642.1241
- Lab Phone 510.642.1241
I am a passionate scientist with a strong background in Biotechnology and Chemistry. I am especially intrigued by the various important roles sugars play in the chemistry of life. I envision a future where we will be able to do rational “glycoengineering” for the production of tailored glycoproteins of industrial and/or therapeutic relevance.
I have pursued my interests in glycobiology and enzymology from a variety of angles for eight years. I have expertise in the biology and biochemistry of a variety of fungi, bacteria, archaea and plants, as well as detailed knowledge about their glycobiology, carbohydrate active enzymes and other associated enzymes that are key in their carbohydrate metabolism. My undergraduate training in Chemistry enables me to comfortably work at the intersection of Chemistry and Biology. My Ph.D. research focused on the deconstruction of cellulose, a polysaccharide, by microbial enzymes and on developing high-throughput screening assays for glycosyltransferases. During my postdoctoral research, I have been expanding my training in carbohydrate active enzymes by incorporating a system level glycobiology approach. I have pioneered new methodologies and achieved the first complete characterization of an archaeal cellulase expressed in and purified from plants. Moreover, I have collaborated successfully with international colleagues and departmental colleagues. I have also demonstrated my ability to seek funding for my research and have been awarded grants and fellowships.
I am a Co-PI on an agriculture and food systems project (themilletproject.org), where our focus lies in diversifying agriculture and our diet by cultivation & consumption of lesser-known grains such as millets. I am motivated by concerns about climate change and think that lack of diversity in agriculture is ultimately reflected in our diet and leads to multifaceted health and ecological issues. I think that rediscovering the variety of grains humans have cultivated in the past will be a critically important “wedge” in a pie of solutions.
My current research on plant & fungal glycobiology and glycoengineering under the mentorship of Prof. Chris Somerville at UC Berkeley has two aspects. First, I am studying glycosylation in the filamentous model fungus Neurospora crassa and in plants. Second, I am studying the properties of cellulases heterologously produced in plants, among them a hyperthermostable cellulase from archaea.
I approach this research from various angles: complementation & knockout studies, enzyme characterization, advanced microscopy, and quantitative proteomic and glycomic techniques employing mass spectrometry. The most significant hurdle in my research has been the lack of knowledge about glycosylation in filamentous fungi, and that it is significantly different from what is known in yeast. To overcome this, I have identified several putative glycosyltransferases and other enzymes involved in glycosylation in the filamentous fungus N. crassa, and developed a workflow for analysis of these genes and their influence on cellulase glycosylation & secretion. The main aim of my research has been to gain a better understanding of the poorly understood O-glycosylation in filamentous fungi and the consequences of differences in O-glycosylation on cellulase secretion, activity and binding. To this end, we first characterized the O-glycans of N. crassa CBHI, the major secreted enzyme of this fungus (published in Glycobiology 2016). This gave us the basic information necessary to target specific enzymes involved in glycosylation. I envision that we eventually will be able to do rational glycoengineering in plants & fungi for the production of tailored glycosylated proteins of industrial and/or therapeutic relevance.
During my time as a Ph.D. student at TU Graz, Austria, I became fascinated by the mechanisms of crystalline cellulose deconstruction. I pioneered visualization of enzymatic cellulose degradation using atomic force microscopy (AFM). I designed a model substrate and built a collaboration with a group specialized in AFM that is still ongoing; I also built the core team and acquired funding through a co-authored grant application. We studied a variety of fungal cellulases, lytic polysaccharide monooxygenases and bacterial cellulosomes (see publications). During my time at TU Graz, I also served as a teaching assistant, teaching an introductory biotechnology and bioengineering lab course and a module in an advanced lab course.
After finishing my M.S. at TU Graz, Austria, I evaluated over 50 different fungal and bacterial strains for biomass degrading capabilities in an industrial collaboration with Südchemie (now Clariant Ltd.). In my masters thesis, I showed that a single amino acid substitution leads to inversion of the co-substrate preference of Pseudomonas fluorescens mannitol 2-dehydrogenase (Bubner P et al, 2007).
Tang S, Bubner P, Bauer S, Somerville CR (2016). O-Glycan analysis of cellobiohydrolase I from Neurospora crassa. Glycobiology. Accepted, Advance Access: doi: 10.1093/glycob/cww004
Eibinger M*, Ganner T*, Bubner P*, Rošker S, Kracher D, Haltrich D, Ludwig R, Plank H, Nidetzky B. (2014) Cellulose surface degradation by a lytic polysaccharide monooxygenase and its effect on cellulase hydrolytic activity. *Co-first authors. J. Biol. Chem. 289(52):35929-38.
Ganner T, Aschl T, Eibinger M, Bubner P, Meingast A, Chernev B, Mayrhofer C, Nidetzky B, Plank H. (2014) Tunable mixed amorphous-crystalline cellulose substrates (MACS) for dynamic degradation studies by atomic force microscopy in liquid environments. Cellulose. 21(6):3927-39.
Eibinger M, Bubner P, Ganner T, Plank H, Nidetzky B. (2014) Surface structural dynamics of enzymatic cellulose degradation, revealed by combined kinetic and atomic force microscopy studies. FEBS J. 281(1):275-90.
Bubner P#, Plank H, Nidetzky B#. (2013) Visualizing cellulase activity. #co-corresponding authors. Biotechnol. Bioeng. 110(6):1529-49.
Ganner T*, Bubner P*, Eibinger M*, Mayrhofer C, Plank H, Nidetzky B. (2012) Dissecting and reconstructing synergism: in situ visualization of cooperativity among cellulases. *Co-first authors. J. Biol. Chem. (2012) 287(52):43215-22.
Bubner P, Dohr J, Plank H, Mayrhofer C, Nidetzky B. (2012) Cellulases dig deep: In situ observation of the mesoscopic structural dynamics of enzymatic cellulose degradation. J. Biol. Chem. 287(4):2759-65.
Krahulec S, Armao GC, Bubner P, Klimacek M, Nidetzky B. (2009) Polyol-specific long-chain dehydrogenases/reductases of mannitol metabolism in Aspergillus fumigatus: biochemical characterization and pH studies of mannitol 2-dehydrogenase and mannitol-1-phosphate 5-dehydrogenase. Chem. Biol. Interact. 178(1-3):274-82.
Bubner P, Klimacek M, Nidetzky B. (2008) Structure-guided engineering of the coenzyme specificity of Pseudomonas fluorescens mannitol 2-dehydrogenase to enable efficient utilization of NAD(H) and NADP(H). FEBS Lett. 582(2):233-237.