1
|
Ali R, Chaluvadi SR, Wang X, Hazzouri KM, Sudalaimuthuasari N, Rafi M, Al-Nuaimi M, Sasi S, Antepenko E, Bennetzen JL, Amiri KMA. Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree. Microbiol Spectr 2024; 12:e0361723. [PMID: 38624222 DOI: 10.1128/spectrum.03617-23] [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: 10/09/2023] [Accepted: 03/14/2024] [Indexed: 04/17/2024] Open
Abstract
We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.
Collapse
Affiliation(s)
- Rashid Ali
- Mitrix Bio., Inc., Farmington, Connecticut, USA
| | | | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | - Khaled M Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | | | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Mariam Al-Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
| | - Eric Antepenko
- Department of Genetics, University of Georgia, Athens, Georgia, USA
| | | | - Khaled M A Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, UAE
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, UAE
| |
Collapse
|
2
|
Pereira WJ, Boyd J, Conde D, Triozzi PM, Balmant KM, Dervinis C, Schmidt HW, Boaventura-Novaes C, Chakraborty S, Knaack SA, Gao Y, Feltus FA, Roy S, Ané JM, Frugoli J, Kirst M. The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula. Cell Rep 2024; 43:113747. [PMID: 38329875 DOI: 10.1016/j.celrep.2024.113747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/31/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Legumes establish a symbiotic relationship with nitrogen-fixing rhizobia by developing nodules. Nodules are modified lateral roots that undergo changes in their cellular development in response to bacteria, but the transcriptional reprogramming that occurs in these root cells remains largely uncharacterized. Here, we describe the cell-type-specific transcriptome response of Medicago truncatula roots to rhizobia during early nodule development in the wild-type genotype Jemalong A17, complemented with a hypernodulating mutant (sunn-4) to expand the cell population responding to infection and subsequent biological inferences. The analysis identifies epidermal root hair and stele sub-cell types associated with a symbiotic response to infection and regulation of nodule proliferation. Trajectory inference shows cortex-derived cell lineages differentiating to form the nodule primordia and, posteriorly, its meristem, while modulating the regulation of phytohormone-related genes. Gene regulatory analysis of the cell transcriptomes identifies new regulators of nodulation, including STYLISH 4, for which the function is validated.
Collapse
Affiliation(s)
- Wendell J Pereira
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Jade Boyd
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Daniel Conde
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28223 Madrid, Spain
| | - Paolo M Triozzi
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; PlantLab, Center of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy
| | - Kelly M Balmant
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA; Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Christopher Dervinis
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Henry W Schmidt
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | | | - Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Sara A Knaack
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA
| | - Yueyao Gao
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Frank Alexander Feltus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA; Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC, USA; Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53726, USA; Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Matias Kirst
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Yang J, Zhai N, Chen Y, Wang L, Chen R, Pan H. A signal peptide peptidase is required for ER-symbiosome proximal association and protein secretion. Nat Commun 2023; 14:4355. [PMID: 37468528 DOI: 10.1038/s41467-023-40008-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023] Open
Abstract
During legume-rhizobia symbiosis, differentiation of the symbiosome (engulfed intracellular rhizobia) is necessary for successful nitrogen fixation. To control symbiosome differentiation, host cell subcellular components, e.g., ER (endoplasmic reticulum), must adapt robustly to ensure large-scale host protein secretion to the new organelle. However, the key components controlling the adaption of ER in nodule cells remain elusive. We report that Medicago BID1, a nodule-specific signal peptide peptidase (SPP), is central to ER structural dynamics and host protein secretion. In bid1, symbiosome differentiation is blocked. BID1 localizes specifically to the ER membrane and expresses exclusively in nodule cells with symbiosomes. In the wild type ER forms proximal association structures with symbiosomes, but not in bid1. Consequently, in bid1 excessive ER stress responses are induced and ER-to-symbiosome protein secretion is impaired. In summary, a nodule-specific SPP is necessary for ER-symbiosome proximal association, host protein secretion, and symbiosome differentiation.
Collapse
Affiliation(s)
- Jian Yang
- College of Biology, Hunan University, Changsha, China
| | - Niu Zhai
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Yuhui Chen
- College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Luying Wang
- College of Biology, Hunan University, Changsha, China
| | - Rujin Chen
- College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Huairong Pan
- College of Biology, Hunan University, Changsha, China.
| |
Collapse
|
5
|
Riley AB, Grillo MA, Epstein B, Tiffin P, Heath KD. Discordant population structure among rhizobium divided genomes and their legume hosts. Mol Ecol 2023; 32:2646-2659. [PMID: 36161739 DOI: 10.1111/mec.16704] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022]
Abstract
Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.
Collapse
Affiliation(s)
- Alex B Riley
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| |
Collapse
|
6
|
Adaptive Evolution of Rhizobial Symbiosis beyond Horizontal Gene Transfer: From Genome Innovation to Regulation Reconstruction. Genes (Basel) 2023; 14:genes14020274. [PMID: 36833201 PMCID: PMC9957244 DOI: 10.3390/genes14020274] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence on integration mechanisms of symbiosis genes. Experimental evolution, in concert with reverse genetic studies based on pangenomics, suggests that gain of the same circuit of key symbiosis genes through horizontal gene transfer is necessary but sometimes insufficient for bacteria to establish an effective symbiosis with legumes. An intact genomic background of the recipient may not support the proper expression or functioning of newly acquired key symbiosis genes. Further adaptive evolution, through genome innovation and reconstruction of regulation networks, may confer the recipient of nascent nodulation and nitrogen fixation ability. Other accessory genes, either co-transferred with key symbiosis genes or stochastically transferred, may provide the recipient with additional adaptability in ever-fluctuating host and soil niches. Successful integrations of these accessory genes with the rewired core network, regarding both symbiotic and edaphic fitness, can optimize symbiotic efficiency in various natural and agricultural ecosystems. This progress also sheds light on the development of elite rhizobial inoculants using synthetic biology procedures.
Collapse
|
7
|
Taboada-Castro H, Gil J, Gómez-Caudillo L, Escorcia-Rodríguez JM, Freyre-González JA, Encarnación-Guevara S. Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network. Front Microbiol 2022; 13:947678. [PMID: 36312930 PMCID: PMC9611204 DOI: 10.3389/fmicb.2022.947678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30 and 20% of proteins with respect to genome content per pathway, respectively. These pathways were for energy and environmental compound metabolism, contributing to understand how Rhizobium is adapted to the different conditions. Metabolic maps based on orthology of the protein profiles, showed 101 and 74 functional homologous proteins in the MM and bacteroid profiles, respectively, which were grouped in 34 different isoenzymes showing a great impact in metabolism by covering 60 metabolic pathways in MM and symbiosis. Taking advantage of co-expression of transcriptional regulators (TF’s) in the profiles, by selection of genes whose matrices were clustered with matrices of TF’s, Transcriptional Regulatory networks (TRN´s) were deduced by the first time for these metabolic stages. In these clustered TF-MM and clustered TF-bacteroid networks, containing 654 and 246 proteins, including 93 and 46 TFs, respectively, showing valuable information of the TF’s and their regulated genes with high stringency. Isoenzymes were specific for adaptation to the different conditions and a different transcriptional regulation for MM and bacteroid was deduced. The parameters of the TRNs of these expected biological networks and biological networks of E. coli and B. subtilis segregate from the random theoretical networks. These are useful data to design experiments on TF gene–target relationships for bases to construct a TRN.
Collapse
Affiliation(s)
- Hermenegildo Taboada-Castro
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Jeovanis Gil
- Division of Oncology, Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden
| | - Leopoldo Gómez-Caudillo
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Juan Miguel Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Julio Augusto Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Sergio Encarnación-Guevara
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
- *Correspondence: Sergio Encarnacion Guevara,
| |
Collapse
|
8
|
Carvalho TLG, Rosman AC, Grativol C, de M. Nogueira E, Baldani JI, Hemerly AS. Sugarcane Genotypes with Contrasting Biological Nitrogen Fixation Efficiencies Differentially Modulate Nitrogen Metabolism, Auxin Signaling, and Microorganism Perception Pathways. PLANTS (BASEL, SWITZERLAND) 2022; 11:1971. [PMID: 35956449 PMCID: PMC9370643 DOI: 10.3390/plants11151971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Sugarcane is an economically important crop that is used for the production of fuel ethanol. Diazotrophic bacteria have been isolated from sugarcane tissues, without causing visible plant anatomical changes or disease symptoms. These bacteria can be beneficial to the plant by promoting root growth and an increase in plant yield. Different rates of Biological Nitrogen Fixation (BNF) were observed in different genotypes. The aim of this work was to conduct a comprehensive molecular and physiological analysis of two model genotypes for contrasting BNF efficiency in order to unravel plant genes that are differentially regulated during a natural association with diazotrophic bacteria. A next-generation sequencing of RNA samples from the genotypes SP70-1143 (high-BNF) and Chunee (low-BNF) was performed. A differential transcriptome analysis showed that several pathways were differentially regulated among the two BNF-contrasting genotypes, including nitrogen metabolism, hormone regulation and bacteria recognition. Physiological analyses, such as nitrogenase and GS activity quantification, bacterial colonization, auxin response and root architecture evaluation, supported the transcriptome expression analyses. The differences observed between the genotypes may explain, at least in part, the differences in BNF contributions. Some of the identified genes might be involved in key regulatory processes for a beneficial association and could be further used as tools for obtaining more efficient BNF genotypes.
Collapse
Affiliation(s)
- Thais Louise G. Carvalho
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - Aline C. Rosman
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - Clícia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
- Laboratório de Química e Funções de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes 28015-622, RJ, Brazil
| | - Eduardo de M. Nogueira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - José Ivo Baldani
- Laboratório de Genética e Bioquímica, Centro Nacional de Pesquisa de Agrobiologia, Embrapa Agrobiologia, Rio de Janeiro 23897-970, RJ, Brazil;
| | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| |
Collapse
|
9
|
Cheng X, Xie H, Zhang K, Wen J. Enabling Medicago truncatula forward genetics: identification of genetic crossing partner for R108 and development of mapping resources for Tnt1 mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:608-616. [PMID: 35510429 DOI: 10.1111/tpj.15797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/19/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
Though Medicago truncatula Tnt1 mutants are widely used by researchers in the legume community, they are mainly used for reverse genetics because of the availability of the BLAST-searchable large-scale flanking sequence tags database. However, these mutants should have also been used extensively for forward genetic screens, an effort that has been hindered due to the lack of a compatible genetic crossing partner for the M. truncatula genotype R108, from which Tnt1 mutants were generated. In this study, we selected three Medicago HapMap lines (HM017, HM018 and HM022) and performed reciprocal genetic crosses with R108. After phenotypic analyses in F1 and F2 progenies, HM017 was identified as a compatible crossing partner with R108. By comparing the assembled genomic sequences of HM017 and R108, we developed and confirmed 318 Indel markers evenly distributed across the eight chromosomes of the M. truncatula genome. To validate the effectiveness of these markers, by employing the map-based cloning approach, we cloned the causative gene in the dwarf mutant crs isolated from the Tnt1 mutant population, identifying it as gibberellin 3-β-dioxygenase 1, using some of the confirmed Indel markers. The primer sequences and the size difference of each marker were made available for users in the web-based database. The identification of the crossing partner for R108 and the generation of Indel markers will enhance the forward genetics and the overall usage of the Tnt1 mutants.
Collapse
Affiliation(s)
- Xiaofei Cheng
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Hongli Xie
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Kuihua Zhang
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Jiangqi Wen
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
- Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| |
Collapse
|
10
|
Abstract
The findings on the strategies employed by endophytic microbes have provided salient information to the researchers on the need to maximally explore them as bio-input in agricultural biotechnology. Biotic and abiotic factors are known to influence microbial recruitments from external plant environments into plant tissues. Endophytic microbes exhibit mutualism or antagonism association with host plants. The beneficial types contribute to plant growth and soil health, directly or indirectly. Strategies to enhance the use of endophytic microbes are desirable in modern agriculture, such that these microbes can be applied individually or combined as bioinoculants with bioprospecting in crop breeding systems. Scant information is available on the strategies for shaping the endophytic microbiome; hence, the need to unravel microbial strategies for yield enhancement and pathogen suppressiveness have become imperative. Therefore, this review focuses on the endophytic microbiome, mechanisms, factors influencing endophyte recruitment, and strategies for possible exploration as bioinoculants.
Collapse
|
11
|
Abstract
This article comments on: Tian L, Liu L, Xu S, Deng R, Wu P, Jiang H, Wu G, Chen Y. 2022. A d-pinitol transporter, LjPLT11, regulates plant growth and nodule development in Lotus japonicus. Journal of Experimental Botany 73, 351–365.
Collapse
Affiliation(s)
- Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Raphael Ledermann
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| |
Collapse
|
12
|
DNA Methylation in
Ensifer
Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with
Medicago
spp. mSystems 2022; 7:e0109221. [PMID: 35089065 PMCID: PMC8725594 DOI: 10.1128/msystems.01092-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Nitrogen fixation by rhizobia in symbiosis with legumes is economically and ecologically important. The symbiosis can involve a complex bacterial transformation—terminal differentiation—that includes major shifts in the transcriptome and cell cycle.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Webb IUC, Xu J, Sánchez-Cañizares C, Karunakaran R, Ramachandran VK, Rutten PJ, East AK, Huang WE, Watmough NJ, Poole PS. Regulation and Characterization of Mutants of fixABCX in Rhizobium leguminosarum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1167-1180. [PMID: 34110256 DOI: 10.1094/mpmi-02-21-0037-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Symbiosis between Rhizobium leguminosarum and Pisum sativum requires tight control of redox balance in order to maintain respiration under the microaerobic conditions required for nitrogenase while still producing the eight electrons and sixteen molecules of ATP needed for nitrogen fixation. FixABCX, a cluster of electron transfer flavoproteins essential for nitrogen fixation, is encoded on the Sym plasmid (pRL10), immediately upstream of nifA, which encodes the general transcriptional regulator of nitrogen fixation. There is a symbiotically regulated NifA-dependent promoter upstream of fixA (PnifA1), as well as an additional basal constitutive promoter driving background expression of nifA (PnifA2). These were confirmed by 5'-end mapping of transcription start sites using differential RNA-seq. Complementation of polar fixAB and fixX mutants (Fix- strains) confirmed expression of nifA from PnifA1 in symbiosis. Electron microscopy combined with single-cell Raman microspectroscopy characterization of fixAB mutants revealed previously unknown heterogeneity in bacteroid morphology within a single nodule. Two morphotypes of mutant fixAB bacteroids were observed. One was larger than wild-type bacteroids and contained high levels of polyhydroxy-3-butyrate, a complex energy/reductant storage product. A second bacteroid phenotype was morphologically and compositionally different and resembled wild-type infection thread cells. From these two characteristic fixAB mutant bacteroid morphotypes, inferences can be drawn on the metabolism of wild-type nitrogen-fixing bacteroids.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Isabel U C Webb
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Jiabao Xu
- Department of Engineering, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K
| | | | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Vinoy K Ramachandran
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Paul J Rutten
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Alison K East
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Wei E Huang
- Department of Engineering, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K
| | - Nicholas J Watmough
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, U.K
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| |
Collapse
|
15
|
Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
Collapse
Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
16
|
Dudeja SS, Suneja-Madan P, Paul M, Maheswari R, Kothe E. Bacterial endophytes: Molecular interactions with their hosts. J Basic Microbiol 2021; 61:475-505. [PMID: 33834549 DOI: 10.1002/jobm.202000657] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 01/19/2023]
Abstract
Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.
Collapse
Affiliation(s)
- Surjit S Dudeja
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Pooja Suneja-Madan
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Minakshi Paul
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Rajat Maheswari
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Erika Kothe
- Microbial Communication, Institute of Microbiology, Faculty for Biosciences, Friedrich Schiller University of Jena, Jena, Germany
| |
Collapse
|
17
|
Jarzyniak K, Banasiak J, Jamruszka T, Pawela A, Di Donato M, Novák O, Geisler M, Jasiński M. Early stages of legume-rhizobia symbiosis are controlled by ABCG-mediated transport of active cytokinins. NATURE PLANTS 2021; 7:428-436. [PMID: 33753904 DOI: 10.1038/s41477-021-00873-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
Growing evidence has highlighted the essential role of plant hormones, notably, cytokinins (CKs), in nitrogen-fixing symbiosis, both at early and late nodulation stages1,2. Despite numerous studies showing the central role of CK in nodulation, the importance of CK transport in the symbiosis is unknown. Here, we show the role of ABCG56, a full-size ATP-binding cassette (ABC) transporter in the early stages of the nodulation. MtABCG56 is expressed in roots and nodules and its messenger RNA levels increase upon treatment with symbiotic bacteria, isolated Nod factor and CKs, accumulating within the epidermis and root cortex. MtABCG56 exports bioactive CKs in an ATP-dependent manner over the plasma membrane and its disruption results in an impairment of nodulation. Our data indicate that ABCG-mediated cytokinin transport is important for proper establishment of N-fixing nodules.
Collapse
Affiliation(s)
- Karolina Jarzyniak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
| | - Joanna Banasiak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Tomasz Jamruszka
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Aleksandra Pawela
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Martin Di Donato
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Olomouc, Czech Republic
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland.
| |
Collapse
|
18
|
Abstract
Rhizobia are a phylogenetically diverse group of soil bacteria that engage in mutualistic interactions with legume plants. Although specifics of the symbioses differ between strains and plants, all symbioses ultimately result in the formation of specialized root nodule organs which host the nitrogen-fixing microsymbionts called bacteroids. Inside nodules, bacteroids encounter unique conditions that necessitate global reprogramming of physiological processes and rerouting of their metabolism. Decades of research have addressed these questions using genetics, omics approaches, and more recently computational modelling. Here we discuss the common adaptations of rhizobia to the nodule environment that define the core principles of bacteroid functioning. All bacteroids are growth-arrested and perform energy-intensive nitrogen fixation fueled by plant-provided C4-dicarboxylates at nanomolar oxygen levels. At the same time, bacteroids are subject to host control and sanctioning that ultimately determine their fitness and have fundamental importance for the evolution of a stable mutualistic relationship.
Collapse
|
19
|
Dubey A, Malla MA, Kumar A, Dayanandan S, Khan ML. Plants endophytes: unveiling hidden agenda for bioprospecting toward sustainable agriculture. Crit Rev Biotechnol 2020; 40:1210-1231. [PMID: 32862700 DOI: 10.1080/07388551.2020.1808584] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Endophytic microbes are present in nearly all of the plant species known to date but how they enter and flourish inside a host plant and display multiple benefits like plant growth promotion (PGP), biodegradation, and stress alleviation are still unexplored. Until now, the majority of the research has been conducted assuming that the host-endophyte interaction is analogous to the PGP microbes, although, studies related to the mechanisms of their infection, colonization as well as conferring important traits to the plants are limited. It would be fascinating to explore the role of these endophytic microbes in host gene expression, metabolism, and the modulation of phenotypic traits, under abiotic and biotic stress conditions. In this review, we critically focused on the following areas: (i) endophytic lifestyle and the mechanism of their entry into plant tissues, (ii) how endophytes modulate the immune system of plants and affect the genotypic and phenotypic expression of host plants under abiotic and biotic stress condition, and (iii) the role of omics and other integrated genomic approaches in unraveling complex host-endophyte signaling crosstalk. Furthermore, we discussed their role in phytoremediation of heavy metal stress and whole genomic analysis based on an understanding of different metabolic pathways these endophytes utilize to combat stress.
Collapse
Affiliation(s)
- Anamika Dubey
- Department of Botany, Metagenomics and Secretomics Research Laboratory, Dr. Harisingh Gour University (A Central University), Sagar, India
| | - Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, India
| | - Ashwani Kumar
- Department of Botany, Metagenomics and Secretomics Research Laboratory, Dr. Harisingh Gour University (A Central University), Sagar, India
| | - Selvadurai Dayanandan
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, India.,Biology Department, Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Mohammad Latif Khan
- Department of Botany, Metagenomics and Secretomics Research Laboratory, Dr. Harisingh Gour University (A Central University), Sagar, India
| |
Collapse
|
20
|
Younginger BS, Friesen ML. Connecting signals and benefits through partner choice in plant-microbe interactions. FEMS Microbiol Lett 2020; 366:5626345. [PMID: 31730203 DOI: 10.1093/femsle/fnz217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
Abstract
Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.
Collapse
Affiliation(s)
- Brett S Younginger
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, PO Box 646420, 115 Johnson Hall, Pullman, WA 99164, USA
| |
Collapse
|
21
|
diCenzo GC, Tesi M, Pfau T, Mengoni A, Fondi M. Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium. Nat Commun 2020; 11:2574. [PMID: 32444627 PMCID: PMC7244743 DOI: 10.1038/s41467-020-16484-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/28/2020] [Indexed: 11/09/2022] Open
Abstract
The mutualistic association between leguminous plants and endosymbiotic rhizobial bacteria is a paradigmatic example of a symbiosis driven by metabolic exchanges. Here, we report the reconstruction and modelling of a genome-scale metabolic network of Medicago truncatula (plant) nodulated by Sinorhizobium meliloti (bacterium). The reconstructed nodule tissue contains five spatially distinct developmental zones and encompasses the metabolism of both the plant and the bacterium. Flux balance analysis (FBA) suggests that the metabolic costs associated with symbiotic nitrogen fixation are primarily related to supporting nitrogenase activity, and increasing N2-fixation efficiency is associated with diminishing returns in terms of plant growth. Our analyses support that differentiating bacteroids have access to sugars as major carbon sources, ammonium is the main nitrogen export product of N2-fixing bacteria, and N2 fixation depends on proton transfer from the plant cytoplasm to the bacteria through acidification of the peribacteroid space. We expect that our model, called 'Virtual Nodule Environment' (ViNE), will contribute to a better understanding of the functioning of legume nodules, and may guide experimental studies and engineering of symbiotic nitrogen fixation.
Collapse
Affiliation(s)
- George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Michelangelo Tesi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Thomas Pfau
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.
| |
Collapse
|
22
|
Abreu I, Mihelj P, Raimunda D. Transition metal transporters in rhizobia: tuning the inorganic micronutrient requirements to different living styles. Metallomics 2020; 11:735-755. [PMID: 30734808 DOI: 10.1039/c8mt00372f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A group of bacteria known as rhizobia are key players in symbiotic nitrogen fixation (SNF) in partnership with legumes. After a molecular exchange, the bacteria end surrounded by a plant membrane forming symbiosomes, organelle-like structures, where they differentiate to bacteroids and fix nitrogen. This symbiotic process is highly dependent on dynamic nutrient exchanges between the partners. Among these are transition metals (TM) participating as inorganic and organic cofactors of fundamental enzymes. While the understanding of how plant transporters facilitate TMs to the very near environment of the bacteroid is expanding, our knowledge on how bacteroid transporters integrate to TM homeostasis mechanisms in the plant host is still limited. This is significantly relevant considering the low solubility and scarcity of TMs in soils, and the in crescendo gradient of TM bioavailability rhizobia faces during the infection and bacteroid differentiation processes. In the present work, we review the main metal transporter families found in rhizobia, their role in free-living conditions and, when known, in symbiosis. We focus on discussing those transporters which could play a significant role in TM-dependent biochemical and physiological processes in the bacteroid, thus paving the way towards an optimized SNF.
Collapse
Affiliation(s)
- Isidro Abreu
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | | |
Collapse
|
23
|
Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria. Microorganisms 2020; 8:microorganisms8030384. [PMID: 32164262 PMCID: PMC7143759 DOI: 10.3390/microorganisms8030384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 01/21/2023] Open
Abstract
Small non-coding RNAs (sRNAs) are ubiquitous components of bacterial adaptive regulatory networks underlying stress responses and chronic intracellular infection of eukaryotic hosts. Thus, sRNA-mediated regulation of gene expression is expected to play a major role in the establishment of mutualistic root nodule endosymbiosis between nitrogen-fixing rhizobia and legume plants. However, knowledge about this level of genetic regulation in this group of plant-interacting bacteria is still rather scarce. Here, we review insights into the rhizobial non-coding transcriptome and sRNA-mediated post-transcriptional regulation of symbiotic relevant traits such as nutrient uptake, cell cycle, quorum sensing, or nodule development. We provide details about the transcriptional control and protein-assisted activity mechanisms of the functionally characterized sRNAs involved in these processes. Finally, we discuss the forthcoming research on riboregulation in legume symbionts.
Collapse
|
24
|
Ng JLP, Welvaert A, Wen J, Chen R, Mathesius U. The Medicago truncatula PIN2 auxin transporter mediates basipetal auxin transport but is not necessary for nodulation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1562-1573. [PMID: 31738415 DOI: 10.1093/jxb/erz510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
The development of root nodules leads to an increased auxin response in early nodule primordia, which is mediated by changes in acropetal auxin transport in some legumes. Here, we investigated the role of root basipetal auxin transport during nodulation. Rhizobia inoculation significantly increased basipetal auxin transport in both Medicago truncatula and Lotus japonicus. In M. truncatula, this increase was dependent on functional Nod factor signalling through NFP, NIN, and NSP2, as well as ethylene signalling through SKL. To test whether increased basipetal auxin transport is required for nodulation, we examined a loss-of-function mutant of the M. truncatula PIN2 gene. The Mtpin2 mutant exhibited a reduction in basipetal auxin transport and an agravitropic phenotype. Inoculation of Mtpin2 roots with rhizobia still led to a moderate increase in basipetal auxin transport, but the mutant nodulated normally. No clear differences in auxin response were observed during nodule development. Interestingly, inoculation of wild-type roots increased lateral root numbers, whereas inoculation of Mtpin2 mutants resulted in reduced lateral root numbers compared with uninoculated roots. We conclude that the MtPIN2 auxin transporter is involved in basipetal auxin transport, that its function is not essential for nodulation, but that it plays an important role in the control of lateral root development.
Collapse
Affiliation(s)
- Jason L P Ng
- Division of Plant Science, Research School of Biology, Australian National University, Canberra, Australia
| | - Astrid Welvaert
- Division of Plant Science, Research School of Biology, Australian National University, Canberra, Australia
| | - Jiangqi Wen
- Noble Research Institute LLC, Ardmore, OK, USA
| | - Rujin Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ulrike Mathesius
- Division of Plant Science, Research School of Biology, Australian National University, Canberra, Australia
| |
Collapse
|
25
|
Vial L, Hommais F. Plasmid-chromosome cross-talks. Environ Microbiol 2019; 22:540-556. [PMID: 31782608 DOI: 10.1111/1462-2920.14880] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022]
Abstract
Plasmids can be acquired by recipient bacteria at a significant cost while conferring them advantageous traits. To counterbalance the costs of plasmid carriage, both plasmids and host bacteria have developed a tight regulatory network that may involve a cross-talk between the chromosome and the plasmids. Although plasmid regulation by chromosomal regulators is generally well known, chromosome regulation by plasmid has been far less investigated. Yet, a growing number of studies have highlighted an impact of plasmids on their host bacteria. Here, we describe the plasmid-chromosome cross-talk from the plasmid point of view. We summarize data about the chromosomal adaptive mutations generated by plasmid carriage; the impact of the loss of a domesticated plasmid or the gain of a new plasmid. Then, we present the control of plasmid-encoded regulators on chromosomal gene expression. The involvement of regulators homologous to chromosome-encoded proteins is illustrated by the H-NS-like proteins, and by the Rap-Phr system. Finally, plasmid-specific regulators of chromosomal gene expression are presented, which highlight the involvement of transcription factors and sRNAs. A comprehensive analysis of the mechanisms that allow a given plasmid to impact the chromosome of bacterium will help to understand the tight cross-talk between plasmids and the chromosome.
Collapse
Affiliation(s)
- Ludovic Vial
- Université de Lyon, 69622, Lyon, France.,Université Lyon 1, 69622, Villeurbanne, France.,CNRS, UMR 5557 Ecologie Microbienne, 69622, Villeurbanne, France.,INRA, UMR1418 Ecologie Microbienne, 69622, Villeurbanne, France
| | - Florence Hommais
- Université de Lyon, 69622, Lyon, France.,Université Lyon 1, 69622, Villeurbanne, France.,CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, 69622, Villeurbanne, France
| |
Collapse
|
26
|
Barton IS, Platt TG, Rusch DB, Fuqua C. Destabilization of the Tumor-Inducing Plasmid from an Octopine-Type Agrobacterium tumefaciens Lineage Drives a Large Deletion in the Co-resident At Megaplasmid. G3 (BETHESDA, MD.) 2019; 9:3489-3500. [PMID: 31451548 PMCID: PMC6778807 DOI: 10.1534/g3.119.400554] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/22/2019] [Indexed: 11/28/2022]
Abstract
Bacteria with multi-replicon genome organizations, including members of the family Rhizobiaceae, often carry a variety of niche-associated functions on large plasmids. While evidence exists for cross-replicon interactions and co-evolution between replicons in many of these systems, remarkable strain-to-strain variation is also observed for extrachromosomal elements, suggesting increased genetic plasticity. Here, we show that curing of the tumor-inducing virulence plasmid (pTi) of an octopine-type Agrobacterium tumefaciens lineage leads to a large deletion in the co-resident At megaplasmid (pAt). The deletion event is mediated by a repetitive IS-element, IS66, and results in a variety of environment-dependent fitness consequences, including loss of independent conjugal transfer of the plasmid. Interestingly, a related and otherwise wild-type A. tumefaciens strain is missing exactly the same large pAt segment as the pAt deletion derivatives, suggesting a similar event over its natural history. Overall, the findings presented here uncover a novel genetic interaction between the two large plasmids of A. tumefaciens and provide evidence for cross-replicon integration and co-evolution of these plasmids.
Collapse
Affiliation(s)
- Ian S Barton
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Thomas G Platt
- Division of Biology, Kansas State University, Manhattan, KS 66506, and
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana
| |
Collapse
|
27
|
A high-throughput system to identify inhibitors of Candidatus Liberibacter asiaticus transcription regulators. Proc Natl Acad Sci U S A 2019; 116:18009-18014. [PMID: 31427509 DOI: 10.1073/pnas.1905149116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Citrus greening disease, also known as huanglongbing (HLB), is the most devastating disease of Citrus worldwide. This incurable disease is caused primarily by the bacterium Candidatus Liberibacter asiaticus and spread by feeding of the Asian Citrus Psyllid, Diaphorina citri Ca L. asiaticus cannot be cultured; its growth is restricted to citrus phloem and the psyllid insect. Management of infected trees includes use of broad-spectrum antibiotics, which have disadvantages. Recent work has sought to identify small molecules that inhibit Ca L. asiaticus transcription regulators, based on a premise that at least some regulators control expression of genes necessary for virulence. We describe a synthetic, high-throughput screening system to identify compounds that inhibit activity of Ca L. asiaticus transcription activators LdtR, RpoH, and VisNR. Our system uses the closely related model bacterium, Sinorhizobium meliloti, as a heterologous host for expression of a Ca L. asiaticus transcription activator, the activity of which is detected through expression of an enhanced green fluorescent protein (EGFP) gene fused to a target promoter. We used this system to screen more than 120,000 compounds for compounds that inhibited regulator activity, but not growth. Our screen identified several dozen compounds that inhibit regulator activity in our assay. This work shows that, in addition to providing a means of characterizing Ca L. asiaticus regulators, an S. meliloti host can be used for preliminary identification of candidate inhibitory molecules.
Collapse
|
28
|
Wippel K, Long SR. Symbiotic Performance of Sinorhizobium meliloti Lacking ppGpp Depends on the Medicago Host Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:717-728. [PMID: 30576265 DOI: 10.1094/mpmi-11-18-0306-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Host specificity in the root-nodule symbiosis between legumes and rhizobia is crucial for the establishment of a successful interaction and ammonia provision to the plant. The specificity is mediated by plant-bacterial signal exchange during early stages of interaction. We observed that a Sinorhizobium meliloti mutant ∆relA, which is deficient in initiating the bacterial stringent response, fails to nodulate Medicago sativa (alfalfa) but successfully infects Medicago truncatula. We used biochemical, histological, transcriptomic, and imaging approaches to compare the behavior of the S. meliloti ∆relA mutant and wild type (WT) on the two plant hosts. ∆relA performed almost WT-like on M. truncatula, except for reduced nitrogen-fixation capacity and a disorganized positioning of bacteroids within nodule cells. In contrast, ∆relA showed impaired root colonization on alfalfa and failed to infect nodule primordia. Global transcriptome analyses of ∆relA cells treated with the alfalfa flavonoid luteolin and of mature nodules induced by the mutant on M. truncatula revealed normal nod gene expression but overexpression of exopolysaccharide biosynthesis genes and a slight suppression of plant defense-like reactions. Many RelA-dependent transcripts overlap with the hypo-osmolarity-related FeuP regulon or are characteristic of stress responses. Based on our findings, we suggest that RelA is not essential until the late stages of symbiosis with M. truncatula, in which it may be involved in processes that optimize nitrogen fixation.
Collapse
Affiliation(s)
- Kathrin Wippel
- Department of Biology, Stanford University, Stanford, CA 94305, U.S.A
| | - Sharon R Long
- Department of Biology, Stanford University, Stanford, CA 94305, U.S.A
| |
Collapse
|
29
|
Critical symbiont signals drive both local and systemic changes in diel and developmental host gene expression. Proc Natl Acad Sci U S A 2019; 116:7990-7999. [PMID: 30833394 DOI: 10.1073/pnas.1819897116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The colonization of an animal's tissues by its microbial partners creates networks of communication across the host's body. We used the natural binary light-organ symbiosis between the squid Euprymna scolopes and its luminous bacterial partner, Vibrio fischeri, to define the impact of colonization on transcriptomic networks in the host. A night-active predator, E. scolopes coordinates the bioluminescence of its symbiont with visual cues from the environment to camouflage against moon and starlight. Like mammals, this symbiosis has a complex developmental program and a strong day/night rhythm. We determined how symbiont colonization impacted gene expression in the light organ itself, as well as in two anatomically remote organs: the eye and gill. While the overall transcriptional signature of light organ and gill were more alike, the impact of symbiosis was most pronounced and similar in light organ and eye, both in juvenile and adult animals. Furthermore, the presence of a symbiosis drove daily rhythms of transcription within all three organs. Finally, a single mutation in V. fischeri-specifically, deletion of the lux operon, which abrogates symbiont luminescence-reduced the symbiosis-dependent transcriptome of the light organ by two-thirds. In addition, while the gills responded similarly to light-organ colonization by either the wild-type or mutant, luminescence was required for all of the colonization-associated transcriptional responses in the juvenile eye. This study defines not only the impact of symbiont colonization on the coordination of animal transcriptomes, but also provides insight into how such changes might impact the behavior and ecology of the host.
Collapse
|
30
|
Cherni AE, Perret X. Deletion of rRNA Operons of Sinorhizobium fredii Strain NGR234 and Impact on Symbiosis With Legumes. Front Microbiol 2019; 10:154. [PMID: 30814981 PMCID: PMC6381291 DOI: 10.3389/fmicb.2019.00154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/22/2019] [Indexed: 01/08/2023] Open
Abstract
During their lifecycle, from free-living soil bacteria to endosymbiotic nitrogen-fixing bacteroids of legumes, rhizobia must colonize, and cope with environments where nutrient concentrations and compositions vary greatly. Bacterial colonization of legume rhizospheres and of root surfaces is subject to a fierce competition for plant exudates. By contrast root nodules offer to rhizobia sheltered nutrient-rich environments within which the cells that successfully propagated via infection threads can rapidly multiply. To explore the effects on symbiosis of a slower rhizobia growth and metabolism, we deleted one or two copies of the three functional rRNA operons of the promiscuous Sinorhizobium fredii strain NGR234 and examined the impact of these mutations on free-living and symbiotic lifestyles. Strains with two functional rRNA operons (NGRΔrRNA1 and NGRΔrRNA3) grew almost as rapidly as NGR234, and NGRΔrRNA1 was as proficient as the parent strain on all of the five legume species tested. By contrast, the NGRΔrRNA1,3 double mutant, which carried a single rRNA operon and grew significantly slower than NGR234, had a reduced symbiotic proficiency on Cajanus cajan, Macroptilium atropurpureum, Tephrosia vogelii, and Vigna unguiculata. In addition, while NGRΔrRNA1 and NGR234 equally competed for nodulation of V. unguiculata, strain NGRΔrRNA1,3 was clearly outcompeted by wild-type. Surprisingly, on Leucaena leucocephala, NGRΔrRNA1,3 was the most proficient strain and competed equally NGR234 for nodule occupation. Together, these results indicate that for strains with otherwise identical repertoires of symbiotic genes, a faster growth on roots and/or inside plant tissues may contribute to secure access to nodules of some hosts. By contrast, other legumes such as L. leucocephala appear as less selective and capable of providing symbiotic environments susceptible to accommodate strains with a broader spectrum of competences.
Collapse
Affiliation(s)
- Ala Eddine Cherni
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Xavier Perret
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| |
Collapse
|
31
|
Green RT, East AK, Karunakaran R, Downie JA, Poole PS. Transcriptomic analysis of Rhizobium leguminosarum bacteroids in determinate and indeterminate nodules. Microb Genom 2019; 5:e000254. [PMID: 30777812 PMCID: PMC6421345 DOI: 10.1099/mgen.0.000254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 01/25/2023] Open
Abstract
Two common classes of nitrogen-fixing legume root nodules are those that have determinate or indeterminate meristems, as in Phaseolus bean and pea, respectively. In indeterminate nodules, rhizobia terminally differentiate into bacteroids with endoreduplicated genomes, whereas bacteroids from determinate nodules are less differentiated and can regrow. We used RNA sequencing to compare bacteroid gene expression in determinate and indeterminate nodules using two Rhizobium leguminosarum strains whose genomes differ due to replacement of the symbiosis (Sym) plasmid pRP2 (strain Rlp4292) with pRL1 (strain RlvA34), thereby switching symbiosis hosts from Phaseolus bean (determinate nodules) to pea (indeterminate nodules). Both bacteroid types have gene expression patterns typical of a stringent response, a stressful environment and catabolism of dicarboxylates, formate, amino acids and quaternary amines. Gene expression patterns were indicative that bean bacteroids were more limited for phosphate, sulphate and iron than pea bacteroids. Bean bacteroids had higher levels of expression of genes whose products are predicted to be associated with metabolite detoxification or export. Pea bacteroids had increased expression of genes associated with DNA replication, membrane synthesis and the TCA (tricarboxylic acid) cycle. Analysis of bacteroid-specific transporter genes was indicative of distinct differences in sugars and other compounds in the two nodule environments. Cell division genes were down-regulated in pea but not bean bacteroids, while DNA synthesis was increased in pea bacteroids. This is consistent with endoreduplication of pea bacteroids and their failure to regrow once nodules senesce.
Collapse
Affiliation(s)
- R. T. Green
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - A. K. East
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - R. Karunakaran
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - J. A. Downie
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - P. S. Poole
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| |
Collapse
|
32
|
diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
Collapse
Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| |
Collapse
|
33
|
Libault M. Transcriptional Reprogramming of Legume Genomes: Perspective and Challenges Associated With Single-Cell and Single Cell-Type Approaches During Nodule Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1600. [PMID: 30467509 PMCID: PMC6237103 DOI: 10.3389/fpls.2018.01600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/17/2018] [Indexed: 05/11/2023]
Abstract
Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate picture of the transcriptome, epigenome, proteome, and metabolome of the cells infected by rhizobia and cells composing the nodule, there is a need to implement plant single-cell and single cell-types strategies and methods. Accessing such information would allow a better understanding of the infection of plant cells by rhizobia and will help understanding the complex interactions existing between rhizobia and the plant cells. In this mini-review, we are reporting the current knowledge on legume nodulation gained by plant scientists at the level of single cell-types, and provide perspectives on single cell/single cell-type approaches when applied to legume nodulation.
Collapse
Affiliation(s)
- Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Centre for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
- Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| |
Collapse
|
34
|
Ratib NR, Sabio EY, Mendoza C, Barnett MJ, Clover SB, Ortega JA, Dela Cruz FM, Balderas D, White H, Long SR, Chen EJ. Genome-wide identification of genes directly regulated by ChvI and a consensus sequence for ChvI binding in Sinorhizobium meliloti. Mol Microbiol 2018; 110:596-615. [PMID: 30192418 DOI: 10.1111/mmi.14119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/16/2018] [Accepted: 09/04/2018] [Indexed: 12/11/2022]
Abstract
ExoS/ChvI two-component signaling in the nitrogen-fixing α-proteobacterium Sinorhizobium meliloti is required for symbiosis and regulates exopolysaccharide production, motility, cell envelope integrity and nutrient utilization in free-living bacteria. However, identification of many ExoS/ChvI direct transcriptional target genes has remained elusive. Here, we performed chromatin immunoprecipitation followed by microarray analysis (chIP-chip) to globally identify DNA regions bound by ChvI protein in S. meliloti. We then performed qRT-PCR with chvI mutant strains to test ChvI-dependent expression of genes downstream of the ChvI-bound DNA regions. We identified 64 direct target genes of ChvI, including exoY, rem and chvI itself. We also identified ChvI direct target candidates, like exoR, that are likely controlled by additional regulators. Analysis of upstream sequences from the 64 ChvI direct target genes identified a 15 bp-long consensus sequence. Using electrophoretic mobility shift assays and transcriptional fusions with exoY, SMb21440, SMc00084, SMc01580, chvI, and ropB1, we demonstrated this consensus sequence is important for ChvI binding to DNA and transcription of ChvI direct target genes. Thus, we have comprehensively identified ChvI regulon genes and a 'ChvI box' bound by ChvI. Many ChvI direct target genes may influence the cell envelope, consistent with the critical role of ExoS/ChvI in growth and microbe-host interactions.
Collapse
Affiliation(s)
- Nicole R Ratib
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Erich Y Sabio
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Carolina Mendoza
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | | | - Sarah B Clover
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Jesus A Ortega
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Francesca M Dela Cruz
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - David Balderas
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Holly White
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| | - Sharon R Long
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Esther J Chen
- Department of Biological Science, Center for Applied Biotechnology Studies, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, USA
| |
Collapse
|
35
|
Checcucci A, diCenzo GC, Ghini V, Bazzicalupo M, Becker A, Decorosi F, Döhlemann J, Fagorzi C, Finan TM, Fondi M, Luchinat C, Turano P, Vignolini T, Viti C, Mengoni A. Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti. ACS Synth Biol 2018; 7:2365-2378. [PMID: 30223644 DOI: 10.1021/acssynbio.8b00158] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.
Collapse
Affiliation(s)
- Alice Checcucci
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - George C. diCenzo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Veronica Ghini
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Marco Bazzicalupo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Anke Becker
- LOEWE − Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Francesca Decorosi
- Department of Agri-food Production and Environmental Science, University of Florence, 50019 Florence, Italy
| | | | - Camilla Fagorzi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Marco Fondi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
- CERM and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Paola Turano
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
- CERM and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Tiziano Vignolini
- European Laboratory for Non-Linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
| | - Carlo Viti
- Department of Agri-food Production and Environmental Science, University of Florence, 50019 Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
36
|
Abstract
Fixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [σs]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress. Bacteria must sense alterations in their environment and respond with changes in function and/or structure in order to cope. Extracytoplasmic function sigma factors (ECF σs) modulate transcription in response to cellular and environmental signals. The symbiotic nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti carries genes for 11 ECF-like σs (RpoE1 to -E10 and FecI). We hypothesized that some of these play a role in mediating the interaction between the bacterium and its plant symbiotic partner. The bacterium senses changes in its immediate environment as it establishes contact with the plant root, initiates invasion of the plant as the root nodule is formed, traverses several root cell layers, and enters plant cortical cells via endocytosis. We used genetics, transcriptomics, and functionality to characterize the entire S. meliloti cohort of ECF σs. We discovered new targets for individual σs, confirmed others by overexpressing individual ECF σs, and identified or confirmed putative promoter motifs for nine of them. We constructed precise deletions of each ECF σ gene and its demonstrated or putative anti-σ gene and also a strain in which all 11 ECF σ and anti-σ genes were deleted. This all-ECF σ deletion strain showed no major defects in free-living growth, in Biolog Phenotype MicroArray assays, or in response to multiple stresses. None of the ECF σs were required for symbiosis on the host plants Medicago sativa and Medicago truncatula: the strain deleted for all ECF σ and anti-σ genes was symbiotically normal. IMPORTANCE Fixed (reduced) soil nitrogen plays a critical role in soil fertility and successful food growth. Much soil fertility relies on symbiotic nitrogen fixation: the bacterial partner infects the host plant roots and reduces atmospheric dinitrogen in exchange for host metabolic fuel, a process that involves complex interactions between the partners mediated by changes in gene expression in each partner. Here we test the roles of a family of 11 extracytoplasmic function (ECF) gene regulatory proteins (sigma factors [σs]) that interact with RNA polymerase to determine if they play a significant role in establishing a nitrogen-fixing symbiosis or in responding to various stresses, including cell envelope stress. We discovered that symbiotic nitrogen fixation occurs even when all 11 of these regulatory genes are deleted, that most ECF sigma factors control accessory functions, and that none of the ECF sigma factors are required to survive envelope stress.
Collapse
|
37
|
Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia. High Throughput 2018; 7:ht7020015. [PMID: 29783718 PMCID: PMC6023288 DOI: 10.3390/ht7020015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 01/24/2023] Open
Abstract
Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).
Collapse
|
38
|
Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome. G3-GENES GENOMES GENETICS 2018; 8:1711-1720. [PMID: 29563186 PMCID: PMC5940162 DOI: 10.1534/g3.117.300405] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Integration of newly acquired genes into existing regulatory networks is necessary for successful horizontal gene transfer (HGT). Ten percent of bacterial species contain at least two DNA replicons over 300 kilobases in size, with the secondary replicons derived predominately through HGT. The Sinorhizobium meliloti genome is split between a 3.7 Mb chromosome, a 1.7 Mb chromid consisting largely of genes acquired through ancient HGT, and a 1.4 Mb megaplasmid consisting primarily of recently acquired genes. Here, RNA-sequencing is used to examine the transcriptional consequences of massive, synthetic genome reduction produced through the removal of the megaplasmid and/or the chromid. Removal of the pSymA megaplasmid influenced the transcription of only six genes. In contrast, removal of the chromid influenced expression of ∼8% of chromosomal genes and ∼4% of megaplasmid genes. This was mediated in part by the loss of the ETR DNA region whose presence on pSymB is due to a translocation from the chromosome. No obvious functional bias among the up-regulated genes was detected, although genes with putative homologs on the chromid were enriched. Down-regulated genes were enriched in motility and sensory transduction pathways. Four transcripts were examined further, and in each case the transcriptional change could be traced to loss of specific pSymB regions. In particularly, a chromosomal transporter was induced due to deletion of bdhA likely mediated through 3-hydroxybutyrate accumulation. These data provide new insights into the evolution of the multipartite bacterial genome, and more generally into the integration of horizontally acquired genes into the transcriptome.
Collapse
|
39
|
Gao M, Benge A, Mesa JM, Javier R, Liu FX. Use of RNA Immunoprecipitation Method for Determining Sinorhizobium meliloti RNA -Hfq Protein Associations In Vivo. Biol Proced Online 2018; 20:8. [PMID: 29743820 PMCID: PMC5928592 DOI: 10.1186/s12575-018-0075-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/05/2018] [Indexed: 01/05/2023] Open
Abstract
Background Soil bacterium Sinorhizobium meliloti (S. meliloti) forms an endosymbiotic partnership with Medicago truncatula (M. truncatula) roots which results in root nodules. The bacteria live within root nodules where they function to fix atmospheric N2 and supply the host plant with reduced nitrogen. The bacterial RNA-binding protein Hfq (Hfq) is an important regulator for the effectiveness of the nitrogen fixation. RNA immunoprecipitation (RIP) method is a powerful method for detecting the association of Hfq protein with specific RNA in cultured bacteria, yet a RIP method for bacteria living in root nodules remains to be described. Results A modified S. meliloti gene encoding a His-tagged Hfq protein (HfqHis) was placed under the regulation of the native Hfq gene promoter (Phfqsm). The trans produced HfqHis protein was accumulated at its nature levels during all stages of the symbiosis, allowing RNAs that associated with the given protein to be immunoprecipitated with the anti-His antibody against the protein from root nodule lysates. RNAs that associated with the protein were selectively enriched in the immunoprecipitated sample. The RNAs were recovered by a simple method using heat and subsequently analyzed by RT-PCR. The nature of PCR products was determined by DNA sequencing. Hfq association with specific RNAs can be analyzed at different conditions (e. g. young or older root nodules) and/or in wild-type versus mutant strains. Conclusions This article describes the RIP method for determining Sinorhizobium meliloti RNA-Hfq associations in vivo. It is also applicable to other rhizobia living in planta, although some tissue-specific modification related to sample disruption and homogenization may be needed.
Collapse
Affiliation(s)
- Mengsheng Gao
- Soil and Water Science Department, Cancer and Genetics Research Complex, Room 330E, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, 32610 USA
| | - Anne Benge
- Soil and Water Science Department, Cancer and Genetics Research Complex, Room 330E, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, 32610 USA
| | - Julia M Mesa
- Soil and Water Science Department, Cancer and Genetics Research Complex, Room 330E, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, 32610 USA
| | - Regina Javier
- Soil and Water Science Department, Cancer and Genetics Research Complex, Room 330E, University of Florida-Institute of Food and Agricultural Sciences, Gainesville, 32610 USA
| | - Feng-Xia Liu
- 2Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 People's Republic of China
| |
Collapse
|
40
|
OxyR-Dependent Transcription Response of Sinorhizobium meliloti to Oxidative Stress. J Bacteriol 2018; 200:JB.00622-17. [PMID: 29358497 DOI: 10.1128/jb.00622-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/11/2018] [Indexed: 11/20/2022] Open
Abstract
Reactive oxygen species such as peroxides play an important role in plant development, cell wall maturation, and defense responses. During nodulation with the host plant Medicago sativa, Sinorhizobium meliloti cells are exposed to H2O2 in infection threads and developing nodules (R. Santos, D. Hérouart, S. Sigaud, D. Touati, and A. Puppo, Mol Plant Microbe Interact 14:86-89, 2001, https://doi.org/10.1094/MPMI.2001.14.1.86). S. meliloti cells likely also experience oxidative stress, from both internal and external sources, during life in the soil. Here, we present microarray transcription data for S. meliloti wild-type cells compared to a mutant deficient in the key oxidative regulatory protein OxyR, each in response to H2O2 treatment. Several alternative sigma factor genes are upregulated in the response to H2O2; the stress sigma gene rpoE2 shows OxyR-dependent induction by H2O2, while rpoH1 expression is induced by H2O2 irrespective of the oxyR genotype. The activity of the RpoE2 sigma factor in turn causes increased expression of two more sigma factor genes, rpoE5 and rpoH2 Strains with deletions of rpoH1 showed improved survival in H2O2 as well as increased levels of oxyR and total catalase expression. These results imply that ΔrpoH1 strains are primed to deal with oxidative stress. This work presents a global view of S. meliloti gene expression changes, and of regulation of those changes, in response to H2O2IMPORTANCE Like all aerobic organisms, the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti experiences oxidative stress throughout its complex life cycle. This report describes the global transcriptional changes that S. meliloti makes in response to H2O2 and the roles of the OxyR transcriptional regulator and the RpoH1 sigma factor in regulating those changes. By understanding the complex regulatory response of S. meliloti to oxidative stress, we may further understand the role that reactive oxygen species play as both stressors and potential signals during symbiosis.
Collapse
|
41
|
Ng JLP, Mathesius U. Acropetal Auxin Transport Inhibition Is Involved in Indeterminate But Not Determinate Nodule Formation. FRONTIERS IN PLANT SCIENCE 2018; 9:169. [PMID: 29497432 PMCID: PMC5818462 DOI: 10.3389/fpls.2018.00169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/30/2018] [Indexed: 05/23/2023]
Abstract
Legumes enter into a symbiotic relationship with nitrogen-fixing rhizobia, leading to nodule development. Two main types of nodules have been widely studied, indeterminate and determinate, which differ in the location of the first cell division in the root cortex, and persistency of the nodule meristem. Here, we compared the control of auxin transport, content, and response during the early stages of indeterminate and determinate nodule development in the model legumes Medicago truncatula and Lotus japonicus, respectively, to investigate whether differences in auxin transport control could explain the differences in the location of cortical cell divisions. While auxin responses were activated in dividing cortical cells during nodulation of both nodule types, auxin (indole-3-acetic acid) content at the nodule initiation site was transiently increased in M. truncatula, but transiently reduced in L. japonicus. Root acropetal auxin transport was reduced in M. truncatula at the very start of nodule initiation, in contrast to a prolonged increase in acropetal auxin transport in L. japonicus. The auxin transport inhibitors 2,3,5-triiodobenzoic acid and 1-N-naphthylphthalamic acid (NPA) only induced pseudonodules in legume species forming indeterminate nodules, but failed to elicit such structures in a range of species forming determinate nodules. The development of these pseudonodules in M. truncatula exhibited increased auxin responses in a small primordium formed from the pericycle, endodermis, and inner cortex, similar to rhizobia-induced nodule primordia. In contrast, a diffuse cortical auxin response and no associated cortical cell divisions were found in L. japonicus. Collectively, we hypothesize that a step of acropetal auxin transport inhibition is unique to the process of indeterminate nodule development, leading to auxin responses in pericycle, endodermis, and inner cortex cells, while increased auxin responses in outer cortex cells likely require a different mechanism during the formation of determinate nodules.
Collapse
Affiliation(s)
- Jason L. P. Ng
- Division of Plant Sciences, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | |
Collapse
|
42
|
Lang C, Smith LS, Haney CH, Long SR. Characterization of Novel Plant Symbiosis Mutants Using a New Multiple Gene-Expression Reporter Sinorhizobium meliloti Strain. FRONTIERS IN PLANT SCIENCE 2018; 9:76. [PMID: 29467773 PMCID: PMC5808326 DOI: 10.3389/fpls.2018.00076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
The formation of nitrogen fixing root nodules by Medicago truncatula and Sinorhizobium meliloti requires communication between both organisms and coordinated differentiation of plant and bacterial cells. After an initial signal exchange, the bacteria invade the tissue of the growing nodule via plant-derived tubular structures, called infection threads. The bacteria are released from the infection threads into invasion-competent plant cells, where they differentiate into nitrogen-fixing bacteroids. Both organisms undergo dramatic transcriptional, metabolic and morphological changes during nodule development. To identify plant processes that are essential for the formation of nitrogen fixing nodules after nodule development has been initiated, large scale mutageneses have been conducted to discover underlying plant symbiosis genes. Such screens yield numerous uncharacterized plant lines with nitrogen fixation deficient nodules. In this study, we report construction of a S. meliloti strain carrying four distinct reporter constructs to reveal stages of root nodule development. The strain contains a constitutively expressed lacZ reporter construct; a PexoY-mTFP fusion that is expressed in infection threads but not in differentiated bacteroids; a PbacA-mcherry construct that is expressed in infection threads and during bacteroid differentiation; and a PnifH-uidA construct that is expressed during nitrogen fixation. We used this strain together with fluorescence microscopy to study nodule development over time in wild type nodules and to characterize eight plant mutants from a fast neutron bombardment screen. Based on the signal intensity and the localization patterns of the reporter genes, we grouped mutants with similar phenotypes and placed them in a developmental context.
Collapse
Affiliation(s)
| | | | | | - Sharon R. Long
- Gilbert Lab, Department of Biology, Stanford University, Stanford, CA, United States
| |
Collapse
|
43
|
Klonowska A, Melkonian R, Miché L, Tisseyre P, Moulin L. Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history. BMC Genomics 2018; 19:105. [PMID: 29378510 PMCID: PMC5789663 DOI: 10.1186/s12864-018-4487-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called "alpha" and "beta"-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adaptation toward symbiotic nitrogen fixation in beta-rhizobia compared to alpha-rhizobia. In a previous study (Melkonian et al., Environ Microbiol 16:2099-111, 2014) we described the symbiotic competitiveness of M. pudica symbionts belonging to Burkholderia, Cupriavidus and Rhizobium species. RESULTS In this article we present a comparative analysis of the transcriptomes (by RNAseq) of B. phymatum STM815 (BP), C. taiwanensis LMG19424 (CT) and R. mesoamericanum STM3625 (RM) in conditions mimicking the early steps of symbiosis (i.e. perception of root exudates). BP exhibited the strongest transcriptome shift both quantitatively and qualitatively, which mirrors its high competitiveness in the early steps of symbiosis and its ancient evolutionary history as a symbiont, while CT had a minimal response which correlates with its status as a younger symbiont (probably via acquisition of symbiotic genes from a Burkholderia ancestor) and RM had a typical response of Alphaproteobacterial rhizospheric bacteria. Interestingly, the upregulation of nodulation genes was the only common response among the three strains; the exception was an up-regulated gene encoding a putative fatty acid hydroxylase, which appears to be a novel symbiotic gene specific to Mimosa symbionts. CONCLUSION The transcriptional response to root exudates was correlated to each strain nodulation competitiveness, with Burkholderia phymatum appearing as the best specialised symbiont of Mimosa pudica.
Collapse
Affiliation(s)
| | - Rémy Melkonian
- IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France
| | - Lucie Miché
- IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France.,Present address: Aix Marseille University, University of Avignon, CNRS, IRD, IMBE, Marseille, France
| | | | - Lionel Moulin
- IRD, Cirad, University of Montpellier, IPME, Montpellier, France.
| |
Collapse
|
44
|
Abstract
Rhizobia are some of the best-studied plant microbiota. These oligotrophic Alphaproteobacteria or Betaproteobacteria form symbioses with their legume hosts. Rhizobia must exist in soil and compete with other members of the microbiota before infecting legumes and forming N2-fixing bacteroids. These dramatic lifestyle and developmental changes are underpinned by large genomes and even more complex pan-genomes, which encompass the whole population and are subject to rapid genetic exchange. The ability to respond to plant signals and chemoattractants and to colonize nutrient-rich roots are crucial for the competitive success of these bacteria. The availability of a large body of genomic, physiological, biochemical and ecological studies makes rhizobia unique models for investigating community interactions and plant colonization.
Collapse
|
45
|
Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides in Sinorhizobium meliloti. J Bacteriol 2018; 200:JB.00501-17. [PMID: 29158240 DOI: 10.1128/jb.00501-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022] Open
Abstract
Sinorhizobium meliloti is a soil-dwelling alphaproteobacterium that engages in a nitrogen-fixing root nodule symbiosis with leguminous plants. Cell surface polysaccharides are important both for adapting to stresses in the soil and for the development of an effective symbiotic interaction. Among the polysaccharides characterized to date, the acidic exopolysaccharides I (EPS-I; succinoglycan) and II (EPS-II; galactoglucan) are particularly important for protection from abiotic stresses, biofilm formation, root colonization, and infection of plant roots. Previous genetic screens discovered mutants with impaired EPS production, allowing the delineation of EPS biosynthetic pathways. Here we report on a genetic screen to isolate mutants with mucoid colonial morphologies that suggest EPS overproduction. Screening with Tn5-110, which allows the recovery of both null and upregulation mutants, yielded 47 mucoid mutants, most of which overproduce EPS-I; among the 30 unique genes and intergenic regions identified, 14 have not been associated with EPS production previously. We identified a new protein-coding gene, emmD, which may be involved in the regulation of EPS-I production as part of the EmmABC three-component regulatory circuit. We also identified a mutant defective in EPS-I production, motility, and symbiosis, where Tn5-110 was not responsible for the mutant phenotypes; these phenotypes result from a missense mutation in rpoA corresponding to the domain of the RNA polymerase alpha subunit known to interact with transcription regulators.IMPORTANCE The alphaproteobacterium Sinorhizobium meliloti converts dinitrogen to ammonium while inhabiting specialized plant organs termed root nodules. The transformation of S. meliloti from a free-living soil bacterium to a nitrogen-fixing plant symbiont is a complex developmental process requiring close interaction between the two partners. As the interface between the bacterium and its environment, the S. meliloti cell surface plays a critical role in adaptation to varied soil environments and in interaction with plant hosts. We isolated and characterized S. meliloti mutants with increased production of exopolysaccharides, key cell surface components. Our diverse set of mutants suggests roles for exopolysaccharide production in growth, metabolism, cell division, envelope homeostasis, biofilm formation, stress response, motility, and symbiosis.
Collapse
|
46
|
Burks D, Azad R, Wen J, Dickstein R. The Medicago truncatula Genome: Genomic Data Availability. Methods Mol Biol 2018; 1822:39-59. [PMID: 30043295 DOI: 10.1007/978-1-4939-8633-0_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Medicago truncatula emerged in 1990 as a model for legumes, comprising the third largest land plant family. Most legumes form symbiotic nitrogen-fixing root nodules with compatible soil bacteria and thus are important contributors to the global nitrogen cycle and sustainable agriculture. Legumes and legume products are important sources for human and animal protein as well as for edible and industrial oils. In the years since M. truncatula was chosen as a legume model, many genetic, genomic, and molecular resources have become available, including reference quality genome sequences for two widely used genotypes. Accessibility of genomic data is important for many different types of studies with M. truncatula as well as for research involving crop and forage legumes. In this chapter, we discuss strategies to obtain archived M. truncatula genomic data originally deposited into custom databases that are no longer maintained but are now accessible in general databases. We also review key current genomic databases that are specific to M. truncatula as well as those that contain M. truncatula data in addition to data from other plants.
Collapse
Affiliation(s)
- David Burks
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Rajeev Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.,Department of Mathematics, University of North Texas, Denton, TX, USA
| | | | - Rebecca Dickstein
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
| |
Collapse
|
47
|
Transcriptomic Studies of the Effect of nod Gene-Inducing Molecules in Rhizobia: Different Weapons, One Purpose. Genes (Basel) 2017; 9:genes9010001. [PMID: 29267254 PMCID: PMC5793154 DOI: 10.3390/genes9010001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/07/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
Simultaneous quantification of transcripts of the whole bacterial genome allows the analysis of the global transcriptional response under changing conditions. RNA-seq and microarrays are the most used techniques to measure these transcriptomic changes, and both complement each other in transcriptome profiling. In this review, we exhaustively compiled the symbiosis-related transcriptomic reports (microarrays and RNA sequencing) carried out hitherto in rhizobia. This review is specially focused on transcriptomic changes that takes place when five rhizobial species, Bradyrhizobium japonicum (=diazoefficiens) USDA 110, Rhizobium leguminosarum biovar viciae 3841, Rhizobium tropici CIAT 899, Sinorhizobium (=Ensifer) meliloti 1021 and S. fredii HH103, recognize inducing flavonoids, plant-exuded phenolic compounds that activate the biosynthesis and export of Nod factors (NF) in all analysed rhizobia. Interestingly, our global transcriptomic comparison also indicates that each rhizobial species possesses its own arsenal of molecular weapons accompanying the set of NF in order to establish a successful interaction with host legumes.
Collapse
|
48
|
Vargas-Lagunas C, Mora Y, Díaz R, Martínez-Batallar G, Girard L, Encarnación S, Peralta H, Mora J. Overproduction of Sinorhizobium meliloti ArgC (N-acetyl-gamma-glutamyl phosphate reductase) promotes growth delay and inefficient nodules. FEMS Microbiol Lett 2017; 364:4600503. [PMID: 29121239 DOI: 10.1093/femsle/fnx233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/06/2017] [Indexed: 11/13/2022] Open
Abstract
argC encodes N-acetyl-gamma-glutamyl phosphate reductase, the enzyme that catalyzes the high-energy-consuming third step in the arginine synthesis pathway. A comparative analysis revealed two translation start sites in argC from Sinorhizobium meliloti. To determine whether both protein versions are synthesized in the organism and their functional role, we obtained genetic constructs with one (1S) or two (2S) start sites, with promoters of low (pspeB) or high (plac) transcriptional rate. The constructs were transferred to the S. meliloti 1021 derivative argC mutant strain. Both protein versions were found in the free-living proteomes, but only ArgC 1S showed post-translational modification. Expression levels from argC 1S were five times higher than those of 2S, when transcribed by plac, and in concordance, its protein activity was 3-fold greater. The overexpression of both versions under plac delayed cellular growth. Inoculation of Medicago sativa plants with the S. meliloti strain harboring the argC 1S under plac induced nodulation but not nitrogen fixation. However, the strain with the argC 2S under the same promoter had a positive phenotype. Overproduction of ArgC protein for the synthesis of arginine induced physiological and symbiotic effects.
Collapse
|
49
|
diCenzo GC, Finan TM. The Divided Bacterial Genome: Structure, Function, and Evolution. Microbiol Mol Biol Rev 2017; 81:e00019-17. [PMID: 28794225 PMCID: PMC5584315 DOI: 10.1128/mmbr.00019-17] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.
Collapse
Affiliation(s)
- George C diCenzo
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
50
|
Thomloudi EE, Skagia A, Venieraki A, Katinakis P, Dimou M. Functional analysis of the two cyclophilin isoforms of Sinorhizobium meliloti. World J Microbiol Biotechnol 2017; 33:28. [PMID: 28058638 DOI: 10.1007/s11274-016-2201-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/23/2016] [Indexed: 11/24/2022]
Abstract
The nitrogen fixing Sinorhizobium meliloti possesses two genes, ppiA and ppiB, encoding two cyclophilin isoforms which belong to the superfamily of peptidyl prolyl cis/trans isomerases (PPIase, EC: 5.2.1.8). Here, we functionally characterize the two proteins and we demonstrate that both recombinant cyclophilins are able to isomerise the Suc-AAPF-pNA synthetic peptide but neither of them displays chaperone function in the citrate synthase thermal aggregation assay. Furthermore, we observe that the expression of both enzymes increases the viability of E. coli BL21 in the presence of abiotic stress conditions such as increased heat and salt concentration. Our results support and strengthen previous high-throughput studies implicating S. meliloti cyclophilins in various stress conditions.
Collapse
Affiliation(s)
- Eirini-Evangelia Thomloudi
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Aggeliki Skagia
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Anastasia Venieraki
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Panagiotis Katinakis
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Maria Dimou
- Laboratory of General and Agricultural Microbiology, Faculty of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece.
| |
Collapse
|