1
|
Good N, Kang-Yun CS, Su MZ, Zytnick AM, Barber CC, Vu HN, Grace JM, Nguyen HH, Zhang W, Skovran E, Fan M, Park DM, Martinez-Gomez NC. Scalable and Consolidated Microbial Platform for Rare Earth Element Leaching and Recovery from Waste Sources. Environ Sci Technol 2024; 58:570-579. [PMID: 38150661 PMCID: PMC10785750 DOI: 10.1021/acs.est.3c06775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/29/2023]
Abstract
Chemical methods for the extraction and refinement of technologically critical rare earth elements (REEs) are energy-intensive, hazardous, and environmentally destructive. Current biobased extraction systems rely on extremophilic organisms and generate many of the same detrimental effects as chemical methodologies. The mesophilic methylotrophic bacterium Methylobacterium extorquens AM1 was previously shown to grow using electronic waste by naturally acquiring REEs to power methanol metabolism. Here we show that growth using electronic waste as a sole REE source is scalable up to 10 L with consistent metal yields without the use of harsh acids or high temperatures. The addition of organic acids increases REE leaching in a nonspecific manner. REE-specific bioleaching can be engineered through the overproduction of REE-binding ligands (called lanthanophores) and pyrroloquinoline quinone. REE bioaccumulation increases with the leachate concentration and is highly specific. REEs are stored intracellularly in polyphosphate granules, and genetic engineering to eliminate exopolyphosphatase activity increases metal accumulation, confirming the link between phosphate metabolism and biological REE use. Finally, we report the innate ability of M. extorquens to grow using other complex REE sources, including pulverized smartphones, demonstrating the flexibility and potential for use as a recovery platform for these critical metals.
Collapse
Affiliation(s)
- Nathan
M. Good
- Department
of Plant and Microbial Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Christina S. Kang-Yun
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Morgan Z. Su
- Department
of Plant and Microbial Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Alexa M. Zytnick
- Department
of Plant and Microbial Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Colin C. Barber
- Department
of Plant and Microbial Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Huong N. Vu
- Department
of Biological Sciences, San José
State University, San José, California 95192, United States
| | - Joseph M. Grace
- Department
of Biological Sciences, San José
State University, San José, California 95192, United States
| | - Hoang H. Nguyen
- Department
of Biological Sciences, San José
State University, San José, California 95192, United States
| | - Wenjun Zhang
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Elizabeth Skovran
- Department
of Biological Sciences, San José
State University, San José, California 95192, United States
| | - Maohong Fan
- Department
of Chemical and Biomedical Engineering, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Dan M. Park
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Norma Cecilia Martinez-Gomez
- Department
of Plant and Microbial Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
2
|
Abstract
Natural products are a diverse class of biologically produced compounds that participate in fundamental biological processes such as cell signaling, nutrient acquisition, and interference competition. Unique triple-bond functionalities like isonitriles and alkynes often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. Here, we focus our review on characterized biosynthetic pathways for isonitrile and alkyne functionalities, their bioorthogonal transformations, and prospects for engineering their biosynthetic machinery for biotechnological applications.
Collapse
Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Colin C. Barber
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | | | - Di Gu
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA,Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
3
|
Ehrenberg AJ, Moehle EA, Brook CE, Doudna Cate AH, Witkowsky LB, Sachdeva R, Hirsh A, Barry K, Hamilton JR, Lin-Shiao E, McDevitt S, Valentin-Alvarado L, Letourneau KN, Hunter L, Keller A, Pestal K, Frankino PA, Murley A, Nandakumar D, Stahl EC, Tsuchida CA, Gildea HK, Murdock AG, Hochstrasser ML, O’Brien E, Ciling A, Tsitsiklis A, Worden K, Dugast-Darzacq C, Hays SG, Barber CC, McGarrigle R, Lam EK, Ensminger DC, Bardet L, Sherry C, Harte A, Nicolette G, Giannikopoulos P, Hockemeyer D, Petersen M, Urnov FD, Ringeisen BR, Boots M, Doudna JA. Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus. PLoS One 2021; 16:e0251296. [PMID: 34038425 PMCID: PMC8153421 DOI: 10.1371/journal.pone.0251296] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/26/2021] [Indexed: 01/01/2023] Open
Abstract
Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to SARS-CoV-2 outbreak prevention on college and university campuses. Here we describe the voluntary saliva testing program instituted at the University of California, Berkeley during an early period of the SARS-CoV-2 pandemic in 2020. The program was administered as a research study ahead of clinical implementation, enabling us to launch surveillance testing while continuing to optimize the assay. Results of both the testing protocol itself and the study participants' experience show how the program succeeded in providing routine, robust testing capable of contributing to outbreak prevention within a campus community and offer strategies for encouraging participation and a sense of civic responsibility.
Collapse
Affiliation(s)
- Alexander J. Ehrenberg
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Erica A. Moehle
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Cara E. Brook
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Lea B. Witkowsky
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Rohan Sachdeva
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Ariana Hirsh
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Kerrie Barry
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jennifer R. Hamilton
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Enrique Lin-Shiao
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Shana McDevitt
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Luis Valentin-Alvarado
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Lauren Hunter
- University of California, Berkeley, California, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Kathleen Pestal
- University of California, Berkeley, California, United States of America
| | | | - Andrew Murley
- University of California, Berkeley, California, United States of America
| | - Divya Nandakumar
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Elizabeth C. Stahl
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Connor A. Tsuchida
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Holly K. Gildea
- University of California, Berkeley, California, United States of America
| | - Andrew G. Murdock
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Megan L. Hochstrasser
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Elizabeth O’Brien
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Alison Ciling
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Kurtresha Worden
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | | | - Stephanie G. Hays
- University of California, Berkeley, California, United States of America
| | - Colin C. Barber
- University of California, Berkeley, California, United States of America
| | - Riley McGarrigle
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Emily K. Lam
- University of California, Berkeley, California, United States of America
| | - David C. Ensminger
- University of California, Berkeley, California, United States of America
| | - Lucie Bardet
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Carolyn Sherry
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Anna Harte
- University of California, Berkeley, California, United States of America
- University Health Services, University of California, Berkeley, California, United States of America
| | - Guy Nicolette
- University of California, Berkeley, California, United States of America
- University Health Services, University of California, Berkeley, California, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Dirk Hockemeyer
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Maya Petersen
- University of California, Berkeley, California, United States of America
| | - Fyodor D. Urnov
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Bradley R. Ringeisen
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Mike Boots
- University of California, Berkeley, California, United States of America
| | - Jennifer A. Doudna
- University of California, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | | |
Collapse
|
4
|
Mondo SJ, Lastovetsky OA, Gaspar ML, Schwardt NH, Barber CC, Riley R, Sun H, Grigoriev IV, Pawlowska TE. Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. Nat Commun 2017; 8:1843. [PMID: 29184190 PMCID: PMC5705715 DOI: 10.1038/s41467-017-02052-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 11/03/2017] [Indexed: 11/09/2022] Open
Abstract
Many heritable mutualisms, in which beneficial symbionts are transmitted vertically between host generations, originate as antagonisms with parasite dispersal constrained by the host. Only after the parasite gains control over its transmission is the symbiosis expected to transition from antagonism to mutualism. Here, we explore this prediction in the mutualism between the fungus Rhizopus microsporus (Rm, Mucoromycotina) and a beta-proteobacterium Burkholderia, which controls host asexual reproduction. We show that reproductive addiction of Rm to endobacteria extends to mating, and is mediated by the symbiont gaining transcriptional control of the fungal ras2 gene, which encodes a GTPase central to fungal reproductive development. We also discover candidate G-protein-coupled receptors for the perception of trisporic acids, mating pheromones unique to Mucoromycotina. Our results demonstrate that regulating host asexual proliferation and modifying its sexual reproduction are sufficient for the symbiont's control of its own transmission, needed for antagonism-to-mutualism transition in heritable symbioses. These properties establish the Rm-Burkholderia symbiosis as a powerful system for identifying reproductive genes in Mucoromycotina.
Collapse
Affiliation(s)
- Stephen J Mondo
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, NY, 14853, USA
- US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Olga A Lastovetsky
- Graduate Field of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Maria L Gaspar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Nicole H Schwardt
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Colin C Barber
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Robert Riley
- US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Hui Sun
- US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Teresa E Pawlowska
- School of Integrative Plant Science, Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|