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Bhat A, Sharma R, Desigan K, Lucas MM, Mishra A, Bowers RM, Woyke T, Epstein B, Tiffin P, Pueyo JJ, Paape T. Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria. BMC Microbiol 2024; 24:247. [PMID: 38971740 PMCID: PMC11227200 DOI: 10.1186/s12866-024-03391-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 07/08/2024] Open
Abstract
BACKGROUND Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg. RESULTS Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg. CONCLUSIONS Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.
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Affiliation(s)
- Aditi Bhat
- Brookhaven National Laboratory, Upton, USA
| | | | | | | | - Ankita Mishra
- Institute for Advancing Health Through Agriculture, Texas A&M, College Station, TX, USA
| | - Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brendan Epstein
- Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - José J Pueyo
- Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Tim Paape
- Institute for Advancing Health Through Agriculture, Texas A&M, College Station, TX, USA.
- USDA-ARS Children's Nutrition Research Center, Houston, TX, USA.
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Bustamante JA, Ceron JS, Gao IT, Ramirez HA, Aviles MV, Bet Adam D, Brice JR, Cuellar RA, Dockery E, Jabagat MK, Karp DG, Lau JKO, Li S, Lopez-Magaña R, Moore RR, Morin BKR, Nzongo J, Rezaeihaghighi Y, Sapienza-Martinez J, Tran TTK, Huang Z, Duthoy AJ, Barnett MJ, Long SR, Chen JC. A protease and a lipoprotein jointly modulate the conserved ExoR-ExoS-ChvI signaling pathway critical in Sinorhizobium meliloti for symbiosis with legume hosts. PLoS Genet 2023; 19:e1010776. [PMID: 37871041 PMCID: PMC10659215 DOI: 10.1371/journal.pgen.1010776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/20/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Sinorhizobium meliloti is a model alpha-proteobacterium for investigating microbe-host interactions, in particular nitrogen-fixing rhizobium-legume symbioses. Successful infection requires complex coordination between compatible host and endosymbiont, including bacterial production of succinoglycan, also known as exopolysaccharide-I (EPS-I). In S. meliloti EPS-I production is controlled by the conserved ExoS-ChvI two-component system. Periplasmic ExoR associates with the ExoS histidine kinase and negatively regulates ChvI-dependent expression of exo genes, necessary for EPS-I synthesis. We show that two extracytoplasmic proteins, LppA (a lipoprotein) and JspA (a lipoprotein and a metalloprotease), jointly influence EPS-I synthesis by modulating the ExoR-ExoS-ChvI pathway and expression of genes in the ChvI regulon. Deletions of jspA and lppA led to lower EPS-I production and competitive disadvantage during host colonization, for both S. meliloti with Medicago sativa and S. medicae with M. truncatula. Overexpression of jspA reduced steady-state levels of ExoR, suggesting that the JspA protease participates in ExoR degradation. This reduction in ExoR levels is dependent on LppA and can be replicated with ExoR, JspA, and LppA expressed exogenously in Caulobacter crescentus and Escherichia coli. Akin to signaling pathways that sense extracytoplasmic stress in other bacteria, JspA and LppA may monitor periplasmic conditions during interaction with the plant host to adjust accordingly expression of genes that contribute to efficient symbiosis. The molecular mechanisms underlying host colonization in our model system may have parallels in related alpha-proteobacteria.
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Affiliation(s)
- Julian A. Bustamante
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Josue S. Ceron
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Ivan Thomas Gao
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Hector A. Ramirez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Milo V. Aviles
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Demsin Bet Adam
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Jason R. Brice
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rodrigo A. Cuellar
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Eva Dockery
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Miguel Karlo Jabagat
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Donna Grace Karp
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Kin-On Lau
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Suling Li
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Raymondo Lopez-Magaña
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rebecca R. Moore
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Bethany Kristi R. Morin
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Juliana Nzongo
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Yasha Rezaeihaghighi
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Sapienza-Martinez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Tuyet Thi Kim Tran
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Zhenzhong Huang
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Aaron J. Duthoy
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Melanie J. Barnett
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Sharon R. Long
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Joseph C. Chen
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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3
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Yang J, Zhang Q, Zhang G, Shang G. Recombineering-Mediated Sinorhizobium meliloti Rm1021 Gene Deletion. Curr Microbiol 2023; 80:76. [PMID: 36650293 DOI: 10.1007/s00284-023-03188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
Sinorhizobium meliloti Rm1021 (S. meliloti Rm1021) is a Gram-negative, soil-dwelling α-proteobacterium which serves as a model microorganism for the studies of symbiotic nitrogen fixation. The S. meliloti Rm1021 genome consists of one chromosome and two megaplasmids, pSymA and pSymB. Gene deletion is an essential tool for the elucidation of gene function and generation of mutants with improved properties. However, only two gene deletion methods, counterselectable marker sacB-based and FLP/FRT, Cre/loxP site-specific recombination, have been reported for S. meliloti Rm1021 gene deletion. Both methods require time-consuming and tedious gene cloning and conjugation steps. Herein, a λ Red recombineering-mediated gene deletion strategy is reported. The mutant was obtained via electroporating overlap-extension PCR-generated linear targeting DNA into Red-proficient cells. One gene each from the S. meliloti Rm1021 chromosome, megaplasmid SymA and pSymB was deleted, with deletion efficiency up to 100%. The straightforward and highly efficient recombineering procedure holds the promise to be a general gene manipulation method for S. meliloti Rm1021.
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Affiliation(s)
- Jun Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Rd., Xixia District, Nanjing, 210023, Jiangsu, People's Republic of China
| | - Qiong Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Rd., Xixia District, Nanjing, 210023, Jiangsu, People's Republic of China
| | - Guoyi Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Rd., Xixia District, Nanjing, 210023, Jiangsu, People's Republic of China
| | - Guangdong Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, No. 1 Wenyuan Rd., Xixia District, Nanjing, 210023, Jiangsu, People's Republic of China.
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Yurgel SN, Qu Y, Rice JT, Ajeethan N, Zink EM, Brown JM, Purvine S, Lipton MS, Kahn ML. Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1409-1422. [PMID: 34402628 DOI: 10.1094/mpmi-07-21-0180-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent anabolic metabolism. Tricarboxylic acid cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in S. meliloti Rm1021 were detected, and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Svetlana N Yurgel
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, P.O. Box 550, Truro, Nova Scotia, B2N 5E3, Canada
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
| | - Yi Qu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Jennifer T Rice
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
| | - Nivethika Ajeethan
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, P.O. Box 550, Truro, Nova Scotia, B2N 5E3, Canada
- Faculty of Technology, University of Jaffna, Sri Lanka
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Joseph M Brown
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Sam Purvine
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Mary S Lipton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, U.S.A
| | - Michael L Kahn
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, U.S.A
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, U.S.A
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