Abstract
Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature is typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for lignin catabolism remain unclear. Improved understanding of this biological process would aid in our collective knowledge of both carbon cycling and microbial strategies to valorize lignin to value-added compounds. Here, we examine lignin modifications and the exoproteome of three aromatic–catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. P. putida cultivation in lignin-rich media is characterized by an abundant exoproteome that is dynamically and selectively packaged into outer membrane vesicles (OMVs). Interestingly, many enzymes known to exhibit activity toward lignin-derived aromatic compounds are enriched in OMVs from early to late stationary phase, corresponding to the shift from bioavailable carbon to oligomeric lignin as a carbon source. In vivo and in vitro experiments demonstrate that enzymes contained in the OMVs are active and catabolize aromatic compounds. Taken together, this work supports OMV-mediated catabolism of lignin-derived aromatic compounds as an extracellular strategy for nutrient acquisition by soil bacteria and suggests that OMVs could potentially be useful tools for synthetic biology and biotechnological applications.
| Original language | English |
|---|---|
| Pages (from-to) | 9302-9310 |
| Number of pages | 9 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Volume | 117 |
| Issue number | 17 |
| DOIs | |
| State | Published - Apr 28 2020 |
Funding
ACKNOWLEDGMENTS. This work was authored in part by Alliance for Sustainable Energy, LLC, the manager and operator of the National Renewable Energy Laboratory for the US Department of Energy (DOE) under Contract DE-AC36-08GO28308. Funding for the time-resolved exoproteomics efforts was provided by the US DOE, Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office. The isolation and proteomics study of the OMVs and OMV assays were funded by The Center for Bioenergy Innovation, a US DOE Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. The exoproteomics of the three bacteria was done at the Environmental Molecular Sciences Laboratory (EMSL) (grid.436923.9), a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research. Portions of the microscopy and light scattering work were supported in part by Laboratory Directed Research and Development funding from Argonne National Laboratory provided by the Director, Office of Science, of the US DOE under Contract DE-AC02-06CH11357. Use of the Center for Nanoscale Materials, an Office of Science user facility, was supported by the US DOE, Office of Science, Basic Energy Sciences, under the same contract. We thank Christopher W. Johnson and Payal Khanna for sharing the P. putida deletion strains. We thank Darren Peterson and David Brandner for providing the alkaline pretreated lignin liquor. We thank Samantha Peters and Payal Chirania for their assistance in proteomic sample preparation at Oak Ridge National Laboratory (ORNL). We thank Adam Guss for providing materials and laboratory space to conduct part of this work at ORNL. We thank Gregory A. Tira for support of initial P. putida OMV characterization experiments at Argonne National Laboratory. We thank Therese Clauss and Rosey Chu at EMSL for help with the proteomics measurements.
| Funders | Funder number |
|---|---|
| DOE Office of Science | |
| Office of Biological and Environmental Research | |
| Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office | |
| DOE Office of Science | DE-AC02-06CH11357 |
| US Department of Energy | |
| U.S. Department of Energy | DE-AC36-08GO28308 |
| Office of Science | |
| Office of Energy Efficiency and Renewable Energy | |
| Basic Energy Sciences | |
| Biological and Environmental Research | |
| Argonne National Laboratory | |
| Oak Ridge National Laboratory | |
| National Renewable Energy Laboratory | |
| Laboratory Directed Research and Development | |
| Center for Bioenergy Innovation |
Keywords
- Biological funneling
- Extracellular vesicle
- Lignin valorization
- Outer membrane vesicle
- Pseudomonas putida