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Trotter VV, Shatsky M, Price MN, Juba TR, Zane GM, De León KB, Majumder ELW, Gui Q, Ali R, Wetmore KM, Kuehl JV, Arkin AP, Wall JD, Deutschbauer AM, Chandonia JM, Butland GP. Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough. Front Microbiol 2023; 14:1095191. [PMID: 37065130 PMCID: PMC10102598 DOI: 10.3389/fmicb.2023.1095191] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.
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Affiliation(s)
- Valentine V. Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maxim Shatsky
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Thomas R. Juba
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Kara B. De León
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Rida Ali
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jennifer V. Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Gareth P. Butland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Graham JE, Niks D, Zane GM, Gui Q, Hom K, Hille R, Wall JD, Raman CS. How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel E. Graham
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
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3
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Kosina SM, Rademacher P, Wetmore KM, de Raad M, Zemla M, Zane GM, Zulovich JJ, Chakraborty R, Bowen BP, Wall JD, Auer M, Arkin AP, Deutschbauer AM, Northen TR. Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms. Front Microbiol 2021; 12:757856. [PMID: 34956122 PMCID: PMC8696352 DOI: 10.3389/fmicb.2021.757856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.
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Affiliation(s)
- Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Rademacher
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcin Zemla
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | | | - Romy Chakraborty
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Manfred Auer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
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Wall JD, Zane GM, Juba TR, Kuehl JV, Ray J, Chhabra SR, Trotter VV, Shatsky M, De León KB, Keller KL, Bender KS, Butland G, Arkin AP, Deutschbauer AM. Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough. Microbiol Resour Announc 2021; 10:e00072-21. [PMID: 33737356 PMCID: PMC7975874 DOI: 10.1128/mra.00072-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/17/2021] [Indexed: 11/20/2022] Open
Abstract
The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community.
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Affiliation(s)
- Judy D Wall
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Grant M Zane
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Thomas R Juba
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Jennifer V Kuehl
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Swapnil R Chhabra
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Valentine V Trotter
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Maxim Shatsky
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kara B De León
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Kimberly L Keller
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Kelly S Bender
- Biochemistry Division, University of Missouri, Columbia, Missouri, USA
| | - Gareth Butland
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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5
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Zane GM, Wall JD, De León KB. Novel Mode of Molybdate Inhibition of Desulfovibrio vulgaris Hildenborough. Front Microbiol 2020; 11:610455. [PMID: 33391236 PMCID: PMC7774982 DOI: 10.3389/fmicb.2020.610455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/19/2020] [Indexed: 11/25/2022] Open
Abstract
Sulfate-reducing microorganisms (SRM) are found in multiple environments and play a major role in global carbon and sulfur cycling. Because of their growth capabilities and association with metal corrosion, controlling the growth of SRM has become of increased interest. One such mechanism of control has been the use of molybdate (MoO4 2-), which is thought to be a specific inhibitor of SRM. The way in which molybdate inhibits the growth of SRM has been enigmatic. It has been reported that molybdate is involved in a futile energy cycle with the sulfate-activating enzyme, sulfate adenylyl transferase (Sat), which results in loss of cellular ATP. However, we show here that a deletion of this enzyme in the model SRM, Desulfovibrio vulgaris Hildenborough, remained sensitive to molybdate. We performed several subcultures of the ∆sat strain in the presence of increasing concentrations of molybdate and obtained a culture with increased resistance to the inhibitor (up to 3 mM). The culture was re-sequenced and three single nucleotide polymorphisms (SNPs) were identified that were not present in the parental strain. Two of the SNPs seemed unlikely candidates for molybdate resistance due to a lack of conservation of the mutated residues in homologous genes of closely related strains. The remaining SNP was located in DVU2210, a protein containing two domains: a YcaO-like domain and a tetratricopeptide-repeat domain. The SNP resulted in a change of a serine residue to arginine in the ATP-hydrolyzing motif of the YcaO-like domain. Deletion mutants of each of the three genes apparently enriched with SNPs in the presence of inhibitory molybdate and combinations of these genes were generated in the Δsat and wild-type strains. Strains lacking both sat and DVU2210 became more resistant to molybdate. Deletions of the other two genes in which SNPs were observed did not result in increased resistance to molybdate. YcaO-like proteins are distributed across the bacterial and archaeal domains, though the function of these proteins is largely unknown. The role of this protein in D. vulgaris is unknown. Due to the distribution of YcaO-like proteins in prokaryotes, the veracity of molybdate as a specific SRM inhibitor should be reconsidered.
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Silveria MA, Large EE, Zane GM, White TA, Chapman MS. The Structure of an AAV5-AAVR Complex at 2.5 Å Resolution: Implications for Cellular Entry and Immune Neutralization of AAV Gene Therapy Vectors. Viruses 2020; 12:E1326. [PMID: 33218165 PMCID: PMC7698955 DOI: 10.3390/v12111326] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/28/2022] Open
Abstract
Adeno-Associated Virus is the leading vector for gene therapy. Although it is the vector for all in vivo gene therapies approved for clinical use by the US Food and Drug Administration, its biology is still not yet fully understood. It has been shown that different serotypes of AAV bind to their cellular receptor, AAVR, in different ways. Previously we have reported a 2.4Å structure of AAV2 bound to AAVR that shows ordered structure for only one of the two AAVR domains with which AAV2 interacts. In this study we present a 2.5Å resolution structure of AAV5 bound to AAVR. AAV5 binds to the first polycystic kidney disease (PKD) domain of AAVR that was not ordered in the AAV2 structure. Interactions of AAV5 with AAVR are analyzed in detail, and the implications for AAV2 binding are explored through molecular modeling. Moreover, we find that binding sites for the antibodies ADK5a, ADK5b, and 3C5 on AAV5 overlap with the binding site of AAVR. These insights provide a structural foundation for development of gene therapy agents to better evade immune neutralization without disrupting cellular entry.
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Affiliation(s)
- Mark A. Silveria
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Edward E. Large
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
| | - Tommi A. White
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
- Electron Microscopy Core, University of Missouri, Columbia, MO 65211, USA
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; (M.A.S.); (E.E.L.); (G.M.Z.); (T.A.W.)
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Moon JW, Paradis CJ, Joyner DC, von Netzer F, Majumder EL, Dixon ER, Podar M, Ge X, Walian PJ, Smith HJ, Wu X, Zane GM, Walker KF, Thorgersen MP, Poole Ii FL, Lui LM, Adams BG, De León KB, Brewer SS, Williams DE, Lowe KA, Rodriguez M, Mehlhorn TL, Pfiffner SM, Chakraborty R, Arkin AP, Wall JD, Fields MW, Adams MWW, Stahl DA, Elias DA, Hazen TC. Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer. Chemosphere 2020; 255:126951. [PMID: 32417512 DOI: 10.1016/j.chemosphere.2020.126951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/17/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
The processing of sediment to accurately characterize the spatially-resolved depth profiles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, flow rate, and preferential flows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate- and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The fluctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.
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Affiliation(s)
- Ji-Won Moon
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA; current U.S. Geological Survey, National Minerals Information Center, Reston, VA, USA
| | - Charles J Paradis
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Dominique C Joyner
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Frederick von Netzer
- University of Washington, Department of Civil and Environmental Engineering, Seattle, WA, USA
| | - Erica L Majumder
- University of Missouri, Department of Biochemistry, Columbia, MO, USA
| | - Emma R Dixon
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Mircea Podar
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Xiaoxuan Ge
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
| | - Peter J Walian
- Lawrence Berkeley National Laboratory, Molecular Biophysics and Integrated Bioimaging, Berkeley, CA, USA
| | - Heidi J Smith
- Montana State University, Center for Biofilm Engineering, Department of Microbiology & Immunology, Bozeman, MT, USA
| | - Xiaoqin Wu
- Lawrence Berkeley National Laboratory, Department of Ecology, Earth and Environmental Sciences Area, Berkeley, CA, USA
| | - Grant M Zane
- University of Missouri, Department of Biochemistry, Columbia, MO, USA
| | - Kathleen F Walker
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Michael P Thorgersen
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
| | - Farris L Poole Ii
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
| | - Lauren M Lui
- Lawrence Berkeley National Laboratory Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Benjamin G Adams
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Kara B De León
- University of Missouri, Department of Biochemistry, Columbia, MO, USA
| | - Sheridan S Brewer
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Daniel E Williams
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Kenneth A Lowe
- Oak Ridge National Laboratory, Environmental Science Division, Oak Ridge, TN, USA
| | - Miguel Rodriguez
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Tonia L Mehlhorn
- Oak Ridge National Laboratory, Environmental Science Division, Oak Ridge, TN, USA
| | - Susan M Pfiffner
- University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA
| | - Romy Chakraborty
- Lawrence Berkeley National Laboratory, Department of Ecology, Earth and Environmental Sciences Area, Berkeley, CA, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Judy D Wall
- University of Missouri, Department of Biochemistry, Columbia, MO, USA
| | - Matthew W Fields
- Montana State University, Center for Biofilm Engineering, Department of Microbiology & Immunology, Bozeman, MT, USA
| | - Michael W W Adams
- University of Georgia, Department of Biochemistry and Molecular Biology, Athens, GA, USA
| | - David A Stahl
- University of Washington, Department of Civil and Environmental Engineering, Seattle, WA, USA
| | - Dwayne A Elias
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Terry C Hazen
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA; University of Tennessee, Departments of Earth & Planetary Sciences, Microbiology, Civil & Environmental Engineering, Methane Center, Knoxville, TN, USA.
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Meyer N, Davulcu O, Xie Q, Silveria M, Zane GM, Large E, Chapman MS. Expression and Purification of Adeno-associated Virus Virus-like Particles in a Baculovirus System and AAVR Ectodomain Constructs in E. coli. Bio Protoc 2020; 10:e3513. [PMID: 33654738 PMCID: PMC7842819 DOI: 10.21769/bioprotoc.3513] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/16/2019] [Accepted: 12/30/2019] [Indexed: 11/02/2022] Open
Abstract
Adeno-associated virus (AAV) is a promising gene therapy vector and the biophysical characterization of its interactions with host proteins is a critical foundation for engineering tissue targeting and immune escape. Presented here are protocols for the production of: (a) the outer protein shells (virus-like particles or VLPs) for serotype 2 (AAV-2) and (b) two fragments from the binding ectodomain of AAV's cellular receptor, AAVR. His6PKD1-2 comprises the first two polycystic kidney disease (PKD) domains, the minimal required for efficient binding of AAV, expressed with an N-terminal histidine tag. MBP-PKD1-5 is a fusion of the maltose binding protein with all five of the PKD domains of the AAVR receptor. Presented are the expression and purification of milligram quantities, ample for in vitro analyses. For AAV-2, the protocol offers an alternative to the use of (infectious) wild-type virus or transducing vectors. One of the methods for producing transducing vector is in Sf9 cells, and the production of VLPs is based on this. For AAVR, the protocols enable biochemical and biophysical characterization of virus-binding. The minimal two-domain construct allows more saturated binding to symmetry-equivalent sites on the virus, while the larger construct might be better expected to reflect the native receptor.
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Affiliation(s)
- Nancy Meyer
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
- Pacific Northwest Cryo-EM Center, OHSU Center for Spatial Systems Biomedicine, Portland, United States
| | - Omar Davulcu
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
- Pfizer, Chesterfield, United States
| | - Qing Xie
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States
| | - Mark Silveria
- Department of Biochemistry, University of Missouri, Columbia, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, United States
| | - Edward Large
- Department of Biochemistry, University of Missouri, Columbia, United States
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, United States
- Department of Biochemistry, University of Missouri, Columbia, United States
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9
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Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkov PS, Wall JD, Mukhopadhyay A. LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species. PLoS One 2019; 14:e0214960. [PMID: 30964892 PMCID: PMC6456213 DOI: 10.1371/journal.pone.0214960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 12/13/2018] [Accepted: 03/22/2019] [Indexed: 11/18/2022] Open
Abstract
The central carbon/lactate utilization pathway in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, is encoded by the highly conserved operon DVU3025-3033. Our earlier in vitro genome-wide study had suggested a network of four two-component system regulators that target this large operon; however, how these four regulators control this operon was not known. Here, we probe the regulation of the lactate utilization operon with mutant strains and DNA-protein binding assays. We show that the LurR response regulator is required for optimal growth and complete lactate utilization, and that it activates the DVU3025-3033 lactate oxidation operon as well as DVU2451, a lactate permease gene, in the presence of lactate. We show by electrophoretic mobility shift assays that LurR binds to three sites in the upstream region of DVU3025, the first gene of the operon. NrfR, a response regulator that is activated under nitrite stress, and LurR share similar binding site motifs and bind the same sites upstream of DVU3025. The DVU3025 promoter also has a binding site motif (Pho box) that is bound by PhoB, a two-component response regulator activated under phosphate limitation. The lactate utilization operon, the regulator LurR, and LurR binding sites are conserved across the order Desulfovibrionales whereas possible modulation of the lactate utilization genes by additional regulators such as NrfR and PhoB appears to be limited to D. vulgaris.
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Affiliation(s)
- Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Eric G. Luning
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Thomas R. Juba
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Alexey E. Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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10
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Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP. Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PLoS Genet 2019; 15:e1008106. [PMID: 30943208 PMCID: PMC6447180 DOI: 10.1371/journal.pgen.1008106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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11
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Rajeev L, Garber ME, Zane GM, Price MN, Dubchak I, Wall JD, Novichkov PS, Mukhopadhyay A, Kazakov AE. A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport. Environ Microbiol 2019; 21:784-799. [PMID: 30536693 DOI: 10.1111/1462-2920.14500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 11/30/2022]
Abstract
Bacterial genes for molybdenum-containing and tungsten-containing enzymes are often differentially regulated depending on the metal availability in the environment. Here, we describe a new family of transcription factors with an unusual DNA-binding domain related to excisionases of bacteriophages. These transcription factors are associated with genes for various molybdate and tungstate-specific transporting systems as well as molybdo/tungsto-enzymes in a wide range of bacterial genomes. We used a combination of computational and experimental techniques to study a member of the TF family, named TaoR (for tungsten-containing aldehyde oxidoreductase regulator). In Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, TaoR activates expression of aldehyde oxidoreductase aor and represses tungsten-specific ABC-type transporter tupABC genes under tungsten-replete conditions. TaoR binding sites at aor promoter were identified by electrophoretic mobility shift assay and DNase I footprinting. We also reconstructed TaoR regulons in 45 Deltaproteobacteria by comparative genomics approach and predicted target genes for TaoR family members in other Proteobacteria and Firmicutes.
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Affiliation(s)
- L Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - M E Garber
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Comparative Biochemistry, University of California, Berkeley, CA, 94720, USA
| | - G M Zane
- Biochemistry and Molecular Microbiology & Immunology Department, University of Missouri, Columbia, MO, 65211, USA
| | - M N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - I Dubchak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - J D Wall
- Biochemistry and Molecular Microbiology & Immunology Department, University of Missouri, Columbia, MO, 65211, USA
| | - P S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Energy, Knowledge Base, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - A Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Comparative Biochemistry, University of California, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - A E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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12
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Bertran E, Leavitt WD, Pellerin A, Zane GM, Wall JD, Halevy I, Wing BA, Johnston DT. Deconstructing the Dissimilatory Sulfate Reduction Pathway: Isotope Fractionation of a Mutant Unable of Growth on Sulfate. Front Microbiol 2018; 9:3110. [PMID: 30619187 PMCID: PMC6302107 DOI: 10.3389/fmicb.2018.03110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/30/2018] [Indexed: 11/13/2022] Open
Abstract
The sulfur isotope record provides key insight into the history of Earth's redox conditions. A detailed understanding of the metabolisms driving this cycle, and specifically microbial sulfate reduction (MSR), is crucial for accurate paleoenvironmental reconstructions. This includes a precise knowledge of the step-specific sulfur isotope effects during MSR. In this study, we aim at resolving the cellular-level fractionation factor during dissimilatory sulfite reduction to sulfide within MSR, and use this measured isotope effect as a calibration to enhance our understanding of the biochemistry of sulfite reduction. For this, we merge measured isotope effects associated with dissimilatory sulfite reduction with a quantitative model that explicitly links net fractionation, reaction reversibility, and intracellular metabolite levels. The highly targeted experimental aspect of this study was possible by virtue of the availability of a deletion mutant strain of the model sulfate reducer Desulfovibrio vulgaris (strain Hildenborough), in which the sulfite reduction step is isolated from the rest of the metabolic pathway owing to the absence of its QmoABC complex (ΔQmo). This deletion disrupts electron flux and prevents the reduction of adenosine phosphosulfate (APS) to sulfite. When grown in open-system steady-state conditions at 10% maximum growth rate in the presence of sulfite and lactate as electron donor, sulfur isotope fractionation factors averaged -15.9‰ (1 σ = 0.4), which appeared to be statistically indistinguishable from a pure enzyme study with dissimilatory sulfite reductase. We coupled these measurements with an understanding of step-specific equilibrium and kinetic isotope effects, and furthered our mechanistic understanding of the biochemistry of sulfite uptake and ensuing reduction. Our metabolically informed isotope model identifies flavodoxin as the most likely electron carrier performing the transfer of electrons to dissimilatory sulfite reductase. This is in line with previous work on metabolic strategies adopted by sulfate reducers under different energy regimes, and has implications for our understanding of the plasticity of this metabolic pathway at the center of our interpretation of modern and palaeo-environmental records.
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Affiliation(s)
- Emma Bertran
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MD, United States
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Cambridge, MD, United States.,Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Andre Pellerin
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, SC, United States
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, SC, United States
| | - Itay Halevy
- Department of Environmental Sciences and Energy Research, Weizmann Institute of Science, Rehovot, Israel
| | - Boswell A Wing
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, United States
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MD, United States
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13
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Ge X, Vaccaro BJ, Thorgersen MP, Poole FL, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW. Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle. Environ Microbiol 2018; 21:152-163. [PMID: 30289197 DOI: 10.1111/1462-2920.14435] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/24/2018] [Accepted: 09/27/2018] [Indexed: 11/25/2022]
Abstract
Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO4 2- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.
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Affiliation(s)
- Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Erica L Majumder
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Kara B De León
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Ji Won Moon
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Charles J Paradis
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98495, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98495, USA
| | - Paul D Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
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14
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Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 2018; 557:503-509. [PMID: 29769716 DOI: 10.1038/s41586-018-0124-0] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 04/09/2018] [Indexed: 01/25/2023]
Abstract
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because they are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.
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Affiliation(s)
- Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R Jordan Waters
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mark Callaghan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan A Melnyk
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jacob S Lamson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yumi Suh
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zuelma Esquivel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Harini Sadeeshkumar
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Benjamin E Rubin
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Axel Visel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California, Merced, CA, USA
| | - James Bristow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew J Blow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, CA, USA.
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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15
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Franco LC, Steinbeisser S, Zane GM, Wall JD, Fields MW. Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris. Appl Microbiol Biotechnol 2018; 102:2839-2850. [PMID: 29429007 PMCID: PMC5847207 DOI: 10.1007/s00253-017-8724-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 11/30/2022]
Abstract
Desulfovibrio spp. are capable of heavy metal reduction and are well-studied systems for understanding metal fate and transport in anaerobic environments. Desulfovibrio vulgaris Hildenborough was grown under environmentally relevant conditions (i.e., temperature, nutrient limitation) to elucidate the impacts on Cr(VI) reduction on cellular physiology. Growth at 20 °C was slower than 30 °C and the presence of 50 μM Cr(VI) caused extended lag times for all conditions, but once growth resumed the growth rate was similar to that without Cr(VI). Cr(VI) reduction rates were greatly diminished at 20 °C for both 50 and 100 μM Cr(VI), particularly for the electron acceptor limited (EAL) condition in which Cr(VI) reduction was much slower, the growth lag much longer (200 h), and viability decreased compared to balanced (BAL) and electron donor limited (EDL) conditions. When sulfate levels were increased in the presence of Cr(VI), cellular responses improved via a shorter lag time to growth. Similar results were observed between the different resource (donor/acceptor) ratio conditions when the sulfate levels were normalized (10 mM), and these results indicated that resource ratio (donor/acceptor) impacted D. vulgaris response to Cr(VI) and not merely sulfate limitation. The results suggest that temperature and resource ratios greatly impacted the extent of Cr(VI) toxicity, Cr(VI) reduction, and the subsequent cellular health via Cr(VI) influx and overall metabolic rate. The results also emphasized the need to perform experiments at lower temperatures with nutrient limitation to make accurate predictions of heavy metal reduction rates as well as physiological states in the environment.
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Affiliation(s)
- Lauren C Franco
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.,Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT, 59717, USA
| | - Sadie Steinbeisser
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA.,Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT, 59717, USA
| | - Grant M Zane
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Judy D Wall
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA.,ENIGMA, Berkeley, CA, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA. .,Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT, 59717, USA. .,ENIGMA, Berkeley, CA, USA, .
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16
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Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP. Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PLoS Genet 2018; 14:e1007147. [PMID: 29324779 PMCID: PMC5764234 DOI: 10.1371/journal.pgen.1007147] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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: 10/02/2017] [Accepted: 12/10/2017] [Indexed: 11/18/2022] Open
Abstract
For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes. For a few bacteria, it is well known how they can make all 20 of the standard amino acids (the building blocks of proteins). For many other bacteria, their genome sequence implies that there are gaps in these biosynthetic pathways, so that the bacteria cannot make all of the amino acids and would need to take up some of them from their environment instead. But many bacteria can grow in minimal media (without any amino acids) despite these apparent gaps. We studied 10 bacteria with predicted gaps in amino acid biosynthesis that nevertheless grow in minimal media. Most of these gaps were spurious, but 11 of the gaps were genuine and could not be explained by current knowledge. Using high-throughput genetics, we systematically identified genes that were required for growth in minimal media and identified the biosynthetic genes that fill 9 of the 11 gaps. We hope that this approach can be applied to many more bacteria and will eventually allow us to accurately predict the nutritional requirements of a bacterium from its genome sequence.
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Affiliation(s)
- Morgan N. Price
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail: (MNP); (AMD); (APA)
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Jennifer V. Kuehl
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Ryan A. Melnyk
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail: (MNP); (AMD); (APA)
| | - Adam P. Arkin
- Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail: (MNP); (AMD); (APA)
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17
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De León KB, Zane GM, Trotter VV, Krantz GP, Arkin AP, Butland GP, Walian PJ, Fields MW, Wall JD. Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough. mBio 2017; 8:e01696-17. [PMID: 29042504 PMCID: PMC5646257 DOI: 10.1128/mbio.01696-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 12/28/2022] Open
Abstract
Biofilms of sulfate-reducing bacteria (SRB) are of particular interest as members of this group are culprits in corrosion of industrial metal and concrete pipelines as well as being key players in subsurface metal cycling. Yet the mechanism of biofilm formation by these bacteria has not been determined. Here we show that two supposedly identical wild-type cultures of the SRB Desulfovibrio vulgaris Hildenborough maintained in different laboratories have diverged in biofilm formation. From genome resequencing and subsequent mutant analyses, we discovered that a single nucleotide change within DVU1017, the ABC transporter of a type I secretion system (T1SS), was sufficient to eliminate biofilm formation in D. vulgaris Hildenborough. Two T1SS cargo proteins were identified as likely biofilm structural proteins, and the presence of at least one (with either being sufficient) was shown to be required for biofilm formation. Antibodies specific to these biofilm structural proteins confirmed that DVU1017, and thus the T1SS, is essential for localization of these adhesion proteins on the cell surface. We propose that DVU1017 is a member of the lapB category of microbial surface proteins because of its phenotypic similarity to the adhesin export system described for biofilm formation in the environmental pseudomonads. These findings have led to the identification of two functions required for biofilm formation in D. vulgaris Hildenborough and focus attention on the importance of monitoring laboratory-driven evolution, as phenotypes as fundamental as biofilm formation can be altered.IMPORTANCE The growth of bacteria attached to a surface (i.e., biofilm), specifically biofilms of sulfate-reducing bacteria, has a profound impact on the economy of developed nations due to steel and concrete corrosion in industrial pipelines and processing facilities. Furthermore, the presence of sulfate-reducing bacteria in oil wells causes oil souring from sulfide production, resulting in product loss, a health hazard to workers, and ultimately abandonment of wells. Identification of the required genes is a critical step for determining the mechanism of biofilm formation by sulfate reducers. Here, the transporter by which putative biofilm structural proteins are exported from sulfate-reducing Desulfovibrio vulgaris Hildenborough cells was discovered, and a single nucleotide change within the gene coding for this transporter was found to be sufficient to completely stop formation of biofilm.
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Affiliation(s)
- Kara B De León
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Valentine V Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Gregory P Krantz
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Gareth P Butland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Peter J Walian
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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18
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Thorgersen MP, Lancaster WA, Ge X, Zane GM, Wetmore KM, Vaccaro BJ, Poole FL, Younkin AD, Deutschbauer AM, Arkin AP, Wall JD, Adams MWW. Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions. Front Microbiol 2017; 8:1529. [PMID: 28848534 PMCID: PMC5554334 DOI: 10.3389/fmicb.2017.01529] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/28/2017] [Indexed: 01/03/2023] Open
Abstract
Chromium and uranium are highly toxic metals that contaminate many natural environments. We investigated their mechanisms of toxicity under anaerobic conditions using nitrate-reducing Pseudomonas stutzeri RCH2, which was originally isolated from a chromium-contaminated aquifer. A random barcode transposon site sequencing library of RCH2 was grown in the presence of the chromate oxyanion (Cr[VI]O42−) or uranyl oxycation (U[VI]O22+). Strains lacking genes required for a functional nitrate reductase had decreased fitness as both metals interacted with heme-containing enzymes required for the later steps in the denitrification pathway after nitrate is reduced to nitrite. Cr[VI]-resistance also required genes in the homologous recombination and nucleotide excision DNA repair pathways, showing that DNA is a target of Cr[VI] even under anaerobic conditions. The reduced thiol pool was also identified as a target of Cr[VI] toxicity and psest_2088, a gene of previously unknown function, was shown to have a role in the reduction of sulfite to sulfide. U[VI] resistance mechanisms involved exopolysaccharide synthesis and the universal stress protein UspA. As the first genome-wide fitness analysis of Cr[VI] and U[VI] toxicity under anaerobic conditions, this study provides new insight into the impact of Cr[VI] and U[VI] on an environmental isolate from a chromium contaminated site, as well as into the role of a ubiquitous protein, Psest_2088.
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Affiliation(s)
- Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - Grant M Zane
- Department of Biochemistry, University of MissouriColumbia, MO, United States
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
| | - Adam D Younkin
- Department of Biochemistry, University of MissouriColumbia, MO, United States
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Judy D Wall
- Department of Biochemistry, University of MissouriColumbia, MO, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthens, GA, United States
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19
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Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, Baliga NS. Mechanism for microbial population collapse in a fluctuating resource environment. Mol Syst Biol 2017; 13:919. [PMID: 28320772 PMCID: PMC5371734 DOI: 10.15252/msb.20167058] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Managing trade-offs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. To investigate this hypothesis, we imposed a fluctuating environment that required the sulfate-reducer Desulfovibrio vulgaris to undergo repeated ecologically relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen-consuming Methanococcus maripaludis Strikingly, the microbial community became progressively less proficient at restoring the environmentally relevant physiological state after each perturbation and most cultures collapsed within 3-7 shifts. Counterintuitively, the collapse phenomenon was prevented by a single regulatory mutation. We have characterized the mechanism for collapse by conducting RNA-seq analysis, proteomics, microcalorimetry, and single-cell transcriptome analysis. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Drew Gorman-Lewis
- Earth and Space Sciences, University of Washington, Seattle, WA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | | | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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20
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Vaccaro BJ, Lancaster WA, Thorgersen MP, Zane GM, Younkin AD, Kazakov AE, Wetmore KM, Deutschbauer A, Arkin AP, Novichkov PS, Wall JD, Adams MWW. Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri. Appl Environ Microbiol 2016; 82:6046-56. [PMID: 27474723 PMCID: PMC5038046 DOI: 10.1128/aem.01845-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/27/2016] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED Metal ion transport systems have been studied extensively, but the specificity of a given transporter is often unclear from amino acid sequence data alone. In this study, predicted Cu(2+) and Zn(2+) resistance systems in Pseudomonas stutzeri strain RCH2 are compared with those experimentally implicated in Cu(2+) and Zn(2+) resistance, as determined by using a DNA-barcoded transposon mutant library. Mutant fitness data obtained under denitrifying conditions are combined with regulon predictions to yield a much more comprehensive picture of Cu(2+) and Zn(2+) resistance in strain RCH2. The results not only considerably expand what is known about well-established metal ion exporters (CzcCBA, CzcD, and CusCBA) and their accessory proteins (CzcI and CusF), they also reveal that isolates with mutations in some predicted Cu(2+) resistance systems do not show decreased fitness relative to the wild type when exposed to Cu(2+) In addition, new genes are identified that have no known connection to Zn(2+) (corB, corC, Psest_3226, Psest_3322, and Psest_0618) or Cu(2+) resistance (Mrp antiporter subunit gene, Psest_2850, and Psest_0584) but are crucial for resistance to these metal cations. Growth of individual deletion mutants lacking corB, corC, Psest_3226, or Psest_3322 confirmed the observed Zn-dependent phenotypes. Notably, to our knowledge, this is the first time a bacterial homolog of TMEM165, a human gene responsible for a congenital glycosylation disorder, has been deleted and the resulting strain characterized. Finally, the fitness values indicate Cu(2+)- and Zn(2+)-based inhibition of nitrite reductase and interference with molybdenum cofactor biosynthesis for nitrate reductase. These results extend the current understanding of Cu(2+) and Zn(2+) efflux and resistance and their effects on denitrifying metabolism. IMPORTANCE In this study, genome-wide mutant fitness data in P. stutzeri RCH2 combined with regulon predictions identify several proteins of unknown function that are involved in resisting zinc and copper toxicity. For zinc, these include a member of the UPF0016 protein family that was previously implicated in Ca(2+)/H(+) antiport and a human congenital glycosylation disorder, CorB and CorC, which were previously linked to Mg(2+) transport, and Psest_3322 and Psest_0618, two proteins with no characterized homologs. Experiments using mutants lacking Psest_3226, Psest_3322, corB, corC, or czcI verified their proposed functions, which will enable future studies of these little-characterized zinc resistance determinants. Likewise, Psest_2850, annotated as an ion antiporter subunit, and the conserved hypothetical protein Psest_0584 are implicated in copper resistance. Physiological connections between previous studies and phenotypes presented here are discussed. Functional and mechanistic understanding of transport proteins improves the understanding of systems in which members of the same protein family, including those in humans, can have different functions.
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Affiliation(s)
- Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Adam D Younkin
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
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21
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Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME J 2015; 9:2360-72. [PMID: 25848870 DOI: 10.1038/ismej.2015.45] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/07/2015] [Accepted: 02/26/2015] [Indexed: 01/19/2023]
Abstract
To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.
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Affiliation(s)
- Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Wendy Schackwitz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Grant M Zane
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Qiao Ma
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Yuanyuan Qu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Judy D Wall
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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22
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Brileya KA, Camilleri LB, Zane GM, Wall JD, Fields MW. Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy. Front Microbiol 2014; 5:693. [PMID: 25566209 PMCID: PMC4266047 DOI: 10.3389/fmicb.2014.00693] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/22/2014] [Indexed: 12/03/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) can interact syntrophically with other community members in the absence of sulfate, and interactions with hydrogen-consuming methanogens are beneficial when these archaea consume potentially inhibitory H2 produced by the SRB. A dual continuous culture approach was used to characterize population structure within a syntrophic biofilm formed by the SRB Desulfovibrio vulgaris Hildenborough and the methanogenic archaeum Methanococcus maripaludis. Under the tested conditions, monocultures of D. vulgaris formed thin, stable biofilms, but monoculture M. maripaludis did not. Microscopy of intact syntrophic biofilm confirmed that D. vulgaris formed a scaffold for the biofilm, while intermediate and steady-state images revealed that M. maripaludis joined the biofilm later, likely in response to H2 produced by the SRB. Close interactions in structured biofilm allowed efficient transfer of H2 to M. maripaludis, and H2 was only detected in cocultures with a mutant SRB that was deficient in biofilm formation (ΔpilA). M. maripaludis produced more carbohydrate (uronic acid, hexose, and pentose) as a monoculture compared to total coculture biofilm, and this suggested an altered carbon flux during syntrophy. The syntrophic biofilm was structured into ridges (∼300 × 50 μm) and models predicted lactate limitation at ∼50 μm biofilm depth. The biofilm had structure that likely facilitated mass transfer of H2 and lactate, yet maximized biomass with a more even population composition (number of each organism) when compared to the bulk-phase community. Total biomass protein was equivalent in lactate-limited and lactate-excess conditions when a biofilm was present, but in the absence of biofilm, total biomass protein was significantly reduced. The results suggest that multispecies biofilms create an environment conducive to resource sharing, resulting in increased biomass retention, or carrying capacity, for cooperative populations.
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Affiliation(s)
- Kristen A Brileya
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA ; Center for Biofilm Engineering, Montana State University Bozeman, MT, USA
| | - Laura B Camilleri
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA ; Center for Biofilm Engineering, Montana State University Bozeman, MT, USA
| | - Grant M Zane
- Division of Biochemistry, University of Missouri Columbia, MO, USA
| | - Judy D Wall
- Division of Biochemistry, University of Missouri Columbia, MO, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA ; Center for Biofilm Engineering, Montana State University Bozeman, MT, USA ; Thermal Biology Institute, Montana State University Bozeman, MT, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; National Center for Genome Resources Santa Fe, NM, USA
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23
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Hillesland KL, Lim S, Flowers JJ, Turkarslan S, Pinel N, Zane GM, Elliott N, Qin Y, Wu L, Baliga NS, Zhou J, Wall JD, Stahl DA. Erosion of functional independence early in the evolution of a microbial mutualism. Proc Natl Acad Sci U S A 2014; 111:14822-7. [PMID: 25267659 PMCID: PMC4205623 DOI: 10.1073/pnas.1407986111] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Many species have evolved to function as specialized mutualists, often to the detriment of their ability to survive independently. However, there are few, if any, well-controlled observations of the evolutionary processes underlying the genesis of new mutualisms. Here, we show that within the first 1,000 generations of initiating independent syntrophic interactions between a sulfate reducer (Desulfovibrio vulgaris) and a hydrogenotrophic methanogen (Methanococcus maripaludis), D. vulgaris frequently lost the capacity to grow by sulfate respiration, thus losing the primary physiological attribute of the genus. The loss of sulfate respiration was a consequence of mutations in one or more of three key genes in the pathway for sulfate respiration, required for sulfate activation (sat) and sulfate reduction to sulfite (apsA or apsB). Because loss-of-function mutations arose rapidly and independently in replicated experiments, and because these mutations were correlated with enhanced growth rate and productivity, gene loss could be attributed to natural selection, even though these mutations should significantly restrict the independence of the evolved D. vulgaris. Together, these data present an empirical demonstration that specialization for a mutualistic interaction can evolve by natural selection shortly after its origin. They also demonstrate that a sulfate-reducing bacterium can readily evolve to become a specialized syntroph, a situation that may have often occurred in nature.
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Affiliation(s)
| | - Sujung Lim
- Biological Sciences, University of Washington Bothell, Bothell, WA 98011
| | | | | | - Nicolas Pinel
- Civil and Environmental Engineering, and Institute for Systems Biology, Seattle, WA 98109-5234
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO 65211
| | | | - Yujia Qin
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA 98109-5234; Departments of Biology and Microbiology, Molecular and Cellular Biology Program, University of Washington Seattle, Seattle, WA 98195; Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019; Earth Science Division, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO 65211
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24
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Rajeev L, Luning EG, Altenburg S, Zane GM, Baidoo EEK, Catena M, Keasling JD, Wall JD, Fields MW, Mukhopadhyay A. Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. Front Microbiol 2014; 5:382. [PMID: 25120537 PMCID: PMC4114195 DOI: 10.3389/fmicb.2014.00382] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/09/2014] [Indexed: 01/02/2023] Open
Abstract
We surveyed the eight putative cyclic-di-GMP-modulating response regulators (RRs) in Desulfovibrio vulgaris Hildenborough that are predicted to function via two-component signaling. Using purified proteins, we examined cyclic-di-GMP (c-di-GMP) production or turnover in vitro of all eight proteins. The two RRs containing only GGDEF domains (DVU2067, DVU0636) demonstrated c-di-GMP production activity in vitro. Of the remaining proteins, three RRs with HD-GYP domains (DVU0722, DVUA0086, and DVU2933) were confirmed to be Mn2+-dependent phosphodiesterases (PDEs) in vitro and converted c-di-GMP to its linear form, pGpG. DVU0408, containing both c-di-GMP production (GGDEF) and degradation domains (EAL), showed c-di-GMP turnover activity in vitro also with production of pGpG. No c-di-GMP related activity could be assigned to the RR DVU0330, containing a metal-dependent phosphohydrolase HD-OD domain, or to the HD-GYP domain RR, DVU1181. Studies included examining the impact of overexpressed cyclic-di-GMP-modulating RRs in the heterologous host E. coli and led to the identification of one RR, DVU0636, with increased cellulose production. Evaluation of a transposon mutant in DVU0636 indicated that the strain was impaired in biofilm formation and demonstrated an altered carbohydrate:protein ratio relative to the D. vulgaris wild type biofilms. However, grown in liquid lactate/sulfate medium, the DVU0636 transposon mutant showed no growth impairment relative to the wild-type strain. Among the eight candidates, only the transposon disruption mutant in the DVU2067 RR presented a growth defect in liquid culture. Our results indicate that, of the two diguanylate cyclases (DGCs) that function as part of two-component signaling, DVU0636 plays an important role in biofilm formation while the function of DVU2067 has pertinence in planktonic growth.
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Affiliation(s)
- Lara Rajeev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eric G Luning
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Sara Altenburg
- Center for Biofilm Engineering, Montana State University Bozeman, MT, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri Columbia, MO, USA
| | - Edward E K Baidoo
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Michela Catena
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jay D Keasling
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California Berkeley, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri Columbia, MO, USA
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University Bozeman, MT, USA ; Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA
| | - Aindrila Mukhopadhyay
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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25
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Korte HL, Fels SR, Christensen GA, Price MN, Kuehl JV, Zane GM, Deutschbauer AM, Arkin AP, Wall JD. Genetic basis for nitrate resistance in Desulfovibrio strains. Front Microbiol 2014; 5:153. [PMID: 24795702 PMCID: PMC4001038 DOI: 10.3389/fmicb.2014.00153] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/21/2014] [Indexed: 12/31/2022] Open
Abstract
Nitrate is an inhibitor of sulfate-reducing bacteria (SRB). In petroleum production sites, amendments of nitrate and nitrite are used to prevent SRB production of sulfide that causes souring of oil wells. A better understanding of nitrate stress responses in the model SRB, Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20, will strengthen predictions of environmental outcomes of nitrate application. Nitrate inhibition of SRB has historically been considered to result from the generation of small amounts of nitrite, to which SRB are quite sensitive. Here we explored the possibility that nitrate might inhibit SRB by a mechanism other than through nitrite inhibition. We found that nitrate-stressed D. vulgaris cultures grown in lactate-sulfate conditions eventually grew in the presence of high concentrations of nitrate, and their resistance continued through several subcultures. Nitrate consumption was not detected over the course of the experiment, suggesting adaptation to nitrate. With high-throughput genetic approaches employing TnLE-seq for D. vulgaris and a pooled mutant library of D. alaskensis, we determined the fitness of many transposon mutants of both organisms in nitrate stress conditions. We found that several mutants, including homologs present in both strains, had a greatly increased ability to grow in the presence of nitrate but not nitrite. The mutated genes conferring nitrate resistance included the gene encoding the putative Rex transcriptional regulator (DVU0916/Dde_2702), as well as a cluster of genes (DVU0251-DVU0245/Dde_0597-Dde_0605) that is poorly annotated. Follow-up studies with individual D. vulgaris transposon and deletion mutants confirmed high-throughput results. We conclude that, in D. vulgaris and D. alaskensis, nitrate resistance in wild-type cultures is likely conferred by spontaneous mutations. Furthermore, the mechanisms that confer nitrate resistance may be different from those that confer nitrite resistance.
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Affiliation(s)
- Hannah L Korte
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Samuel R Fels
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA
| | - Geoff A Christensen
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Morgan N Price
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jennifer V Kuehl
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA
| | - Adam M Deutschbauer
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Adam P Arkin
- Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri Columbia, MO, USA ; Ecosystems and Networks Integrated with Genes and Molecular Assemblies Berkeley, CA, USA ; Department of Molecular Microbiology and Immunology, University of Missouri Columbia, MO, USA
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26
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Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson JJ, Auer M, Wall JD, Mukhopadhyay A. Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility. Front Microbiol 2014; 5:77. [PMID: 24639670 PMCID: PMC3944678 DOI: 10.3389/fmicb.2014.00077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 02/12/2014] [Indexed: 01/07/2023] Open
Abstract
Sulfate-reducing bacteria such as Desulfovibrio vulgaris Hildenborough are often found in environments with limiting growth nutrients. Using lactate as the electron donor and carbon source, and sulfate as the electron acceptor, wild type D. vulgaris shows motility on soft agar plates. We evaluated this phenotype with mutants resulting from insertional inactivation of genes potentially related to motility. Our study revealed that the cheA3 (DVU2072) kinase mutant was impaired in the ability to form motility halos. Insertions in two other cheA loci did not exhibit a loss in this phenotype. The cheA3 mutant was also non-motile in capillary assays. Complementation with a plasmid-borne copy of cheA3 restores wild type phenotypes. The cheA3 mutant displayed a flagellum as observed by electron microscopy, grew normally in liquid medium, and was motile in wet mounts. In the growth conditions used, the D. vulgaris ΔfliA mutant (DVU3229) for FliA, predicted to regulate flagella-related genes including cheA3, was defective both in flagellum formation and in forming the motility halos. In contrast, a deletion of the flp gene (DVU2116) encoding a pilin-related protein was similar to wild type. We conclude that wild type D. vulgaris forms motility halos on solid media that are mediated by flagella-related mechanisms via the CheA3 kinase. The conditions under which the CheA1 (DVU1594) and CheA2 (DVU1960) kinase function remain to be explored.
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Affiliation(s)
- Jayashree Ray
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | | | - Michela Catena
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Thomas R Juba
- Biochemistry Division, University of Missouri Columbia, MO, USA
| | - Marcin Zemla
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Lara Rajeev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Bernhard Knierim
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Grant M Zane
- Biochemistry Division, University of Missouri Columbia, MO, USA
| | | | - Manfred Auer
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Judy D Wall
- Biochemistry Division, University of Missouri Columbia, MO, USA
| | - Aindrila Mukhopadhyay
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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27
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Sim MS, Wang DT, Zane GM, Wall JD, Bosak T, Ono S. Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking hydrogenases or type I tetraheme cytochrome c 3. Front Microbiol 2013; 4:171. [PMID: 23805134 PMCID: PMC3691511 DOI: 10.3389/fmicb.2013.00171] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/04/2013] [Indexed: 11/13/2022] Open
Abstract
The sulfur isotope effect produced by sulfate reducing microbes is commonly used to trace biogeochemical cycles of sulfur and carbon in aquatic and sedimentary environments. To test the contribution of intracellular coupling between carbon and sulfur metabolisms to the overall magnitude of the sulfur isotope effect, this study compared sulfur isotope fractionations by mutants of Desulfovibrio vulgaris Hildenborough. We tested mutant strains lacking one or two periplasmic (Hyd, Hyn-1, Hyn-2, and Hys) or cytoplasmic hydrogenases (Ech and CooL), and a mutant lacking type I tetraheme cytochrome (TpI-c 3). In batch culture, wild-type D. vulgaris and its hydrogenase mutants had comparable growth kinetics and produced the same sulfur isotope effects. This is consistent with the reported redundancy of hydrogenases in D. vulgaris. However, the TpI-c 3 mutant (ΔcycA) exhibited slower growth and sulfate reduction rates in batch culture, and produced more H2 and an approximately 50% larger sulfur isotope effect, compared to the wild type. The magnitude of sulfur isotope fractionation in the CycA deletion strain, thus, increased due to the disrupted coupling of the carbon oxidation and sulfate reduction pathways. In continuous culture, wild-type D. vulgaris and the CycA mutant produced similar sulfur isotope effects, underscoring the influence of environmental conditions on the relative contribution of hydrogen cycling to the electron transport. The large sulfur isotope effects associated with the non-ideal stoichiometry of sulfate reduction in this study imply that simultaneous fermentation and sulfate reduction may be responsible for some of the large naturally-occurring sulfur isotope effects. Overall, mutant strains provide a powerful tool to test the effect of specific redox proteins and pathways on sulfur isotope fractionation.
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Affiliation(s)
- Min Sub Sim
- Department of Earth and Planetary Sciences, Northwestern University Evanston, IL, USA ; Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology Cambridge, MA, USA
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Zane GM, Yen HCB, Wall JD. Effect of the deletion of qmoABC and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 2010; 76:5500-9. [PMID: 20581180 PMCID: PMC2918943 DOI: 10.1128/aem.00691-10] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 06/18/2010] [Indexed: 12/24/2022] Open
Abstract
The pathway of electrons required for the reduction of sulfate in sulfate-reducing bacteria (SRB) is not yet fully characterized. In order to determine the role of a transmembrane protein complex suggested to be involved in this process, a deletion in Desulfovibrio vulgaris Hildenborough was created by marker exchange mutagenesis that eliminated four genes putatively encoding the QmoABC complex and a hypothetical protein (DVU0851). The Qmo (quinone-interacting membrane-bound oxidoreductase) complex is proposed to be responsible for transporting electrons to the dissimilatory adenosine-5'-phosphosulfate reductase in SRB. In support of the predicted role of this complex, the deletion mutant was unable to grow using sulfate as its sole electron acceptor with a range of electron donors. To explore a possible role for the hypothetical protein in sulfate reduction, a second mutant was constructed that had lost only the gene that codes for the DVU0851 protein. The second constructed mutant grew with sulfate as the sole electron acceptor; however, there was a lag that was not present with the wild-type or complemented strain. Neither deletion strain was significantly impaired for growth with sulfite or thiosulfate as the terminal electron acceptor. Complementation of the Delta(qmoABC-DVU0851) mutant with all four genes or only the qmoABC genes restored its ability to grow by sulfate respiration. These results confirmed the prediction that the Qmo complex is in the electron pathway for sulfate reduction and revealed that no other transmembrane complex could compensate when Qmo was lacking.
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Affiliation(s)
- Grant M. Zane
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
| | - Huei-che Bill Yen
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
| | - Judy D. Wall
- University of Missouri, Columbia, Missouri, the Virtual Institute for Microbial Stress and Survival‡
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