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García-Tomsig NI, Lagares A, Becker A, Valverde C, Jiménez-Zurdo JI. An Integrated Affinity Chromatography-Based Approach to Unravel the sRNA Interactome in Nitrogen-Fixing Rhizobia. Methods Mol Biol 2024; 2741:363-380. [PMID: 38217663 DOI: 10.1007/978-1-0716-3565-0_19] [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] [Indexed: 01/15/2024]
Abstract
The activity mechanism and function of bacterial base-pairing small non-coding RNA regulators (sRNAs) are largely shaped by their main interacting cellular partners, i.e., proteins and mRNAs. We describe here an MS2 affinity chromatography-based procedure adapted to unravel the sRNA interactome in nitrogen-fixing legume endosymbiotic bacteria. The method consists of tagging of the bait sRNA at its 5'-end with the MS2 aptamer followed by pulse overexpression and immobilization of the chimeric transcript from cell lysates by an MS2-MBP fusion protein conjugated to an amylose resin. The sRNA-binding proteins and target mRNAs are further profiled by mass spectrometry and RNAseq, respectively.
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Affiliation(s)
- Natalia Isabel García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio Lagares
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Argentina
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas (LFGBBP), Centro de Bioquímica y Microbiología del Suelo (CBMS), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires, Argentina
| | - José Ignacio Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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2
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García-Tomsig NI, Guedes-García SK, Jiménez-Zurdo JI. A Workflow for the Functional Characterization of Noncoding RNAs in Legume Symbiotic Bacteria. Methods Mol Biol 2024; 2751:179-203. [PMID: 38265717 DOI: 10.1007/978-1-0716-3617-6_12] [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] [Indexed: 01/25/2024]
Abstract
Computational comparative genomics and, later, high-throughput transcriptome profiling (RNAseq) have uncovered a plethora of small noncoding RNA species (sRNAs) with potential regulatory roles in bacteria. A large fraction of sRNAs are differentially regulated in response to different biotic and abiotic stimuli and have the ability to fine-tune posttranscriptional reprogramming of gene expression through protein-assisted antisense interactions with trans-encoded target mRNAs. However, this level of gene regulation is still understudied in most non-model bacteria. Here, we compile experimental methods to detect expression, determine 5'/3'-ends, assess transcriptional regulation, generate mutants, and validate candidate target mRNAs of trans-acting sRNAs (trans-sRNAs) identified in the nitrogen-fixing α-rhizobium Sinorhizobium meliloti. The workflow, molecular tools, and methods are suited to investigate the function of newly identified base-pairing trans-sRNAs in phylogenetically related α-rhizobia.
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Affiliation(s)
- Natalia I García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Sabina K Guedes-García
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - José I Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain.
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3
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García-Tomsig NI, García-Rodriguez FM, Guedes-García SK, Millán V, Becker A, Robledo M, Jiménez-Zurdo JI. A double-negative feedback loop between NtrBC and a small RNA rewires nitrogen metabolism in legume symbionts. mBio 2023; 14:e0200323. [PMID: 37850753 PMCID: PMC10746234 DOI: 10.1128/mbio.02003-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
The nitrogen (N) status transduced via the NtrBC two-component system is a major signaling cue in the root nodule endosymbiosis of diazotrophic rhizobia with legumes. NtrBC is upregulated in the N-limiting rhizosphere environment at the onset of nodulation but silenced in nodules to favor the assimilation of the fixed N into plant biomass. We reported that the trans-acting sRNA NfeR1 (Nodule Formation Efficiency RNA) broadly influences the symbiotic performance of the α-rhizobium Sinorhizobium meliloti. Here, we show that NfeR1 is indeed an N-responsive sRNA that fine-tunes NtrBC output during the symbiotic transition. Biochemical and genetic approaches unveiled that NtrC and the LysR-type symbiotic regulator LsrB bind at distinct nearby sites in the NfeR1 promoter, acting antagonistically as repressor and activator of transcription, respectively. This complex transcriptional control specifies peak NfeR1 steady-state levels in N-starved and endosymbiotic bacteria. Furthermore, NfeR1 base pairs the translation initiation region of the histidine kinase coding mRNA ntrB, causing a decrease in both NtrB and NtrC abundance as assessed by double-plasmid genetic assays. In the context of endogenous regulation, NfeR1-mediated ntrBC silencing most likely amends the effective strength of the known operon autorepression exerted by NtrC. Accordingly, a lack of NfeR1 shifts the wild-type NtrBC output, restraining the fitness of free-living rhizobia under N stress and plant growth upon nodulation. The mixed NtrBC-NfeR1 double-negative feedback loop is thus an unprecedented adaptive network motif that helps α-rhizobia adjust N metabolism to the demands of an efficient symbiosis with legume plants. IMPORTANCE Root nodule endosymbioses between diazotrophic rhizobia and legumes provide the largest input of combined N to the biosphere, thus representing an alternative to harmful chemical fertilizers for sustainable crop production. Rhizobia have evolved intricate strategies to coordinate N assimilation for their own benefit with N2 fixation to sustain plant growth. The rhizobial N status is transduced by the NtrBC two-component system, the seemingly ubiquitous form of N signal transduction in Proteobacteria. Here, we show that the regulatory sRNA NfeR1 (nodule formation efficiency RNA) of the alfalfa symbiont Sinorhizobium meliloti is transcribed from a complex promoter repressed by NtrC in a N-dependent manner and feedback silences ntrBC by complementary base-pairing. These findings unveil a more prominent role of NtrC as a transcriptional repressor than hitherto anticipated and a novel RNA-based mechanism for NtrBC regulation. The NtrBC-NfeR1 double-negative feedback loop accurately rewires symbiotic S. meliloti N metabolism and is likely conserved in α-rhizobia.
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Affiliation(s)
- Natalia I. García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Fernando M. García-Rodriguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Sabina K. Guedes-García
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Vicenta Millán
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Marta Robledo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - José I. Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (RhizoRNA Lab), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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Ormazábal A, Pierdominici-Sottile G, Palma J. Recognition and Binding of RsmE to an AGGAC Motif of RsmZ: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:6614-6627. [PMID: 35470666 DOI: 10.1021/acs.jcim.2c00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
CsrA/RsmE is a post-transcriptional regulator protein widely distributed in bacteria. It impedes the expression of target mRNAs by attaching their 5' untranslated region. The translation is restored by small, noncoding RNAs that sequester CsrA/RsmE acting as sponges. In both cases, the protein recognizes and attaches to specific AGGAX and AXGGAX motifs, where X refers to any nucleotide. RsmZ of Pseudomonas protegens is one of these small RNAs. The structures of some of its complexes with RsmE were disclosed a few years ago. We have used umbrella sampling simulations to force the unbinding of RsmE from the AGGAC motif located in the single-stranded region sited between stem loops 2 and 3 of RsmZ. The calculations unveiled the identity of the main residues and nucleotides involved in the process. They also showed that the region adopts a hairpin-like conformation during the initial stages of the binding. The ability to acquire this conformation requires that the region has a length of at least nine nucleotides. Besides, we performed standard molecular dynamics simulations of the isolated fragments, analyzed their typical conformations, and characterized their movements. This analysis revealed that the free molecules oscillate along specific collective coordinates that facilitate the initial stages of the binding. The results strongly suggest that the flexibility of the single-stranded region of RsmZ crucially affects the ability of its binding motif to catch RsmE.
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Affiliation(s)
- Agustín Ormazábal
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Sáenz Peña 352, Bernal B1876BXD, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, CABA C1425FQB, Argentina
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Sequential uptake of aldoses over fructose and enhanced phosphate solubilization in Rhizobium sp. RM. Appl Microbiol Biotechnol 2022; 106:4251-4268. [DOI: 10.1007/s00253-022-11997-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022]
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Evguenieva-Hackenberg E. Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1696. [PMID: 34651439 DOI: 10.1002/wrna.1696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022]
Abstract
Gene expression strategies ensuring bacterial survival and competitiveness rely on cis- and trans-acting RNA-regulators (riboregulators). Among the cis-acting riboregulators are transcriptional and translational attenuators, and antisense RNAs (asRNAs). The trans-acting riboregulators are small RNAs (sRNAs) that bind proteins or base pairs with other RNAs. This classification is artificial since some regulatory RNAs act both in cis and in trans, or function in addition as small mRNAs. A prominent example is the archetypical, ribosome-dependent attenuator of tryptophan (Trp) biosynthesis genes. It responds by transcription attenuation to two signals, Trp availability and inhibition of translation, and gives rise to two trans-acting products, the attenuator sRNA rnTrpL and the leader peptide peTrpL. In Escherichia coli, rnTrpL links Trp availability to initiation of chromosome replication and in Sinorhizobium meliloti, it coordinates regulation of split tryptophan biosynthesis operons. Furthermore, in S. meliloti, peTrpL is involved in mRNA destabilization in response to antibiotic exposure. It forms two types of asRNA-containing, antibiotic-dependent ribonucleoprotein complexes (ARNPs), one of them changing the target specificity of rnTrpL. The posttranscriptional role of peTrpL indicates two emerging paradigms: (1) sRNA reprograming by small molecules and (2) direct involvement of antibiotics in regulatory RNPs. They broaden our view on RNA-based mechanisms and may inspire new approaches for studying, detecting, and using antibacterial compounds. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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7
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Robledo M, García-Tomsig NI, Matia-González AM, García-Rodríguez FM, Jiménez-Zurdo JI. Synthetase of the methyl donor S-adenosylmethionine from nitrogen-fixing α-rhizobia can bind functionally diverse RNA species. RNA Biol 2021; 18:1111-1123. [PMID: 33043803 PMCID: PMC8244774 DOI: 10.1080/15476286.2020.1829365] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Function of bacterial small non-coding RNAs (sRNAs) and overall RNA metabolism is largely shaped by a vast diversity of RNA-protein interactions. However, in non-model bacteria with defined non-coding transcriptomes the sRNA interactome remains almost unexplored. We used affinity chromatography to capture proteins associated in vivo with MS2-tagged trans-sRNAs that regulate nutrient uptake (AbcR2 and NfeR1) and cell cycle (EcpR1) mRNAs by antisense-based translational inhibition in the nitrogen-fixing α-rhizobia Sinorhizobium meliloti. The three proteomes were rather distinct, with that of EcpR1 particularly enriched in cell cycle-related enzymes, whilst sharing several transcription/translation-related proteins recurrently identified associated with sRNAs. Strikingly, MetK, the synthetase of the major methyl donor S-adenosylmethionine, was reliably recovered as a binding partner of the three sRNAs, which reciprocally co-immunoprecipitated with a FLAG-tagged MetK variant. Induced (over)expression of the trans-sRNAs and MetK depletion did not influence canonical riboregulatory traits, `for example, protein titration or sRNA stability, respectively. An in vitro filter assay confirmed binding of AbcR2, NfeR1 and EcpR1 to MetK and further revealed interaction of the protein with other non-coding and coding transcripts but not with the 5S rRNA. These findings uncover a broad specificity for RNA binding as an unprecedented feature of this housekeeping prokaryotic enzyme.
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MESH Headings
- Gene Expression Regulation, Bacterial
- Methionine Adenosyltransferase/genetics
- Methionine Adenosyltransferase/metabolism
- Nitrogen Fixation/physiology
- Plant Root Nodulation/physiology
- Plants/microbiology
- Protein Binding
- Protein Interaction Mapping
- RNA, Bacterial/classification
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- S-Adenosylmethionine/metabolism
- Sinorhizobium meliloti/enzymology
- Sinorhizobium meliloti/genetics
- Symbiosis/physiology
- Transcriptome
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Affiliation(s)
- Marta Robledo
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Natalia I. García-Tomsig
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Ana M. Matia-González
- Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Fernando M. García-Rodríguez
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - José I. Jiménez-Zurdo
- Structure, Dynamics and Function of Rhizobacterial Genomes (Grupo de Ecología Genética de la Rizosfera), Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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Eisfeld J, Kraus A, Ronge C, Jagst M, Brandenburg VB, Narberhaus F. A LysR-type transcriptional regulator controls the expression of numerous small RNAs in Agrobacterium tumefaciens. Mol Microbiol 2021; 116:126-139. [PMID: 33560537 DOI: 10.1111/mmi.14695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 01/08/2023]
Abstract
Small RNAs (sRNAs) are universal posttranscriptional regulators of gene expression and hundreds of sRNAs are frequently found in each and every bacterium. In order to coordinate cellular processes in response to ambient conditions, many sRNAs are differentially expressed. Here, we asked how these small regulators are regulated using Agrobacterium tumefaciens as a model system. Among the best-studied sRNAs in this plant pathogen are AbcR1 regulating numerous ABC transporters and PmaR, a regulator of peptidoglycan biosynthesis, motility, and ampicillin resistance. We report that the LysR-type regulator VtlR (also known as LsrB) controls expression of AbcR1 and PmaR. A vtlR/lsrB deletion strain showed growth defects, was sensitive to antibiotics and severely compromised in plant tumor formation. Transcriptome profiling by RNA-sequencing revealed more than 1,200 genes with altered expression in the mutant. Consistent with the function of VtlR/LsrB as regulator of AbcR1, many ABC transporter genes were affected. Interestingly, the transcription factor did not only control the expression of AbcR1 and PmaR. In the mutant, 102 sRNA genes were significantly up- or downregulated. Thus, our study uncovered VtlR/LsrB as the master regulator of numerous sRNAs. Thereby, the transcriptional regulator harnesses the regulatory power of sRNAs to orchestrate the expression of distinct sub-regulons.
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Affiliation(s)
- Jessica Eisfeld
- Microbial Biology, Ruhr University Bochum, Bochum, Germany.,Medical Microbiology, Ruhr University Bochum, Bochum, Germany
| | | | | | - Michelle Jagst
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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Pervasive RNA Regulation of Metabolism Enhances the Root Colonization Ability of Nitrogen-Fixing Symbiotic α-Rhizobia. mBio 2021; 13:e0357621. [PMID: 35164560 PMCID: PMC8844928 DOI: 10.1128/mbio.03576-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The rhizosphere and rhizoplane are nutrient-rich but selective environments for the root microbiome. Here, we deciphered a posttranscriptional network regulated by the homologous trans-small RNAs (sRNAs) AbcR1 and AbcR2, which rewire the metabolism of the nitrogen-fixing α-rhizobium Sinorhizobium meliloti during preinfection stages of symbiosis with its legume host alfalfa. The LysR-type regulator LsrB, which transduces the cell redox state, is indispensable for AbcR1 expression in actively dividing bacteria, whereas the stress-induced transcription of AbcR2 depends on the alternative σ factor RpoH1. MS2 affinity purification coupled with RNA sequencing unveiled exceptionally large and overlapping AbcR1/2 mRNA interactomes, jointly representing ⁓6% of the S. meliloti protein-coding genes. Most mRNAs encode transport/metabolic proteins whose translation is silenced by base pairing to two distinct anti-Shine Dalgarno motifs that function independently in both sRNAs. A metabolic model-aided analysis of the targetomes predicted changes in AbcR1/2 expression driven by shifts in carbon/nitrogen sources, which were confirmed experimentally. Low AbcR1/2 levels in some defined media anticipated overexpression growth phenotypes linked to the silencing of specific mRNAs. As a proof of principle, we confirmed AbcR1/2-mediated downregulation of the l-amino acid AapQ permease. AbcR1/2 interactomes are well represented in rhizosphere-related S. meliloti transcriptomic signatures. Remarkably, a lack of AbcR1 specifically compromised the ability of S. meliloti to colonize the root rhizoplane. The AbcR1 regulon likely ranks the utilization of available substrates to optimize metabolism, thus conferring on S. meliloti an advantage for efficient rhizosphere/rhizoplane colonization. AbcR1 regulation is predicted to be conserved in related α-rhizobia, which opens unprecedented possibilities for engineering highly competitive biofertilizers. IMPORTANCE Nitrogen-fixing root nodule symbioses between rhizobia and legume plants provide more than half of the combined nitrogen incorporated annually into terrestrial ecosystems, rendering plant growth independent of environmentally unfriendly chemical fertilizers. The success of symbiosis depends primarily on the capacity of rhizobia to establish competitive populations in soil and rhizosphere environments. Here, we provide insights into the regulation and architecture of an extensive RNA posttranscriptional network that fine-tunes the metabolism of the alfalfa symbiont S. meliloti, thereby enhancing the ability of this beneficial bacterium to colonize nutrient-rich but extremely selective niches, such as the rhizosphere of its host plant. This pervasive RNA regulation of metabolism is a major adaptive mechanism, predicted to operate in diverse rhizobial species. Because RNA regulation relies on modifiable base-pairing interactions, our findings open unexplored avenues for engineering the legumes rhizobiome within sustainable agricultural practices.
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10
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Vandana UK, Rajkumari J, Singha LP, Satish L, Alavilli H, Sudheer PD, Chauhan S, Ratnala R, Satturu V, Mazumder PB, Pandey P. The Endophytic Microbiome as a Hotspot of Synergistic Interactions, with Prospects of Plant Growth Promotion. BIOLOGY 2021; 10:101. [PMID: 33535706 PMCID: PMC7912845 DOI: 10.3390/biology10020101] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
The plant root is the primary site of interaction between plants and associated microorganisms and constitutes the main components of plant microbiomes that impact crop production. The endophytic bacteria in the root zone have an important role in plant growth promotion. Diverse microbial communities inhabit plant root tissues, and they directly or indirectly promote plant growth by inhibiting the growth of plant pathogens, producing various secondary metabolites. Mechanisms of plant growth promotion and response of root endophytic microorganisms for their survival and colonization in the host plants are the result of complex plant-microbe interactions. Endophytic microorganisms also assist the host to sustain different biotic and abiotic stresses. Better insights are emerging for the endophyte, such as host plant interactions due to advancements in 'omic' technologies, which facilitate the exploration of genes that are responsible for plant tissue colonization. Consequently, this is informative to envisage putative functions and metabolic processes crucial for endophytic adaptations. Detection of cell signaling molecules between host plants and identification of compounds synthesized by root endophytes are effective means for their utilization in the agriculture sector as biofertilizers. In addition, it is interesting that the endophytic microorganism colonization impacts the relative abundance of indigenous microbial communities and suppresses the deleterious microorganisms in plant tissues. Natural products released by endophytes act as biocontrol agents and inhibit pathogen growth. The symbiosis of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) affects plant symbiotic signaling pathways and root colonization patterns and phytohormone synthesis. In this review, the potential of the root endophytic community, colonization, and role in the improvement of plant growth has been explained in the light of intricate plant-microbe interactions.
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Affiliation(s)
- Udaya Kumar Vandana
- Department of Biotechnology, Assam University Silchar, Assam 788011, India; (U.K.V.); (P.B.M.)
| | - Jina Rajkumari
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
| | - L. Paikhomba Singha
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
| | - Lakkakula Satish
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Hemasundar Alavilli
- Department of Biochemistry and Molecular Biology, College of Medicine, Korea Molecular Medicine and Nutrition Research Institute, Korea University, Seoul 02841, Korea;
| | - Pamidimarri D.V.N. Sudheer
- Amity Institute of Biotechnology, Amity University Chhattisgarh, Raipur 493225, India; (P.D.V.N.S.); (S.C.)
| | - Sushma Chauhan
- Amity Institute of Biotechnology, Amity University Chhattisgarh, Raipur 493225, India; (P.D.V.N.S.); (S.C.)
| | - Rambabu Ratnala
- TATA Institute for Genetics and Society, Bangalore 560065, India;
| | - Vanisri Satturu
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India;
| | - Pranab Behari Mazumder
- Department of Biotechnology, Assam University Silchar, Assam 788011, India; (U.K.V.); (P.B.M.)
| | - Piyush Pandey
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
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11
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McQuail J, Switzer A, Burchell L, Wigneshweraraj S. The RNA-binding protein Hfq assembles into foci-like structures in nitrogen starved Escherichia coli. J Biol Chem 2020; 295:12355-12367. [PMID: 32532816 PMCID: PMC7458820 DOI: 10.1074/jbc.ra120.014107] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/09/2020] [Indexed: 11/13/2022] Open
Abstract
The initial adaptive responses to nutrient depletion in bacteria often occur at the level of gene expression. Hfq is an RNA-binding protein present in diverse bacterial lineages that contributes to many different aspects of RNA metabolism during gene expression. Using photoactivated localization microscopy and single-molecule tracking, we demonstrate that Hfq forms a distinct and reversible focus-like structure in Escherichia coli specifically experiencing long-term nitrogen starvation. Using the ability of T7 phage to replicate in nitrogen-starved bacteria as a biological probe of E. coli cell function during nitrogen starvation, we demonstrate that Hfq foci have a role in the adaptive response of E. coli to long-term nitrogen starvation. We further show that Hfq foci formation does not depend on gene expression once nitrogen starvation has set in and occurs indepen-dently of the transcription factor N-regulatory protein C, which activates the initial adaptive response to N starvation in E. coli These results serve as a paradigm to demonstrate that bacterial adaptation to long-term nutrient starvation can be spatiotemporally coordinated and can occur independently of de novo gene expression during starvation.
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Affiliation(s)
- Josh McQuail
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Amy Switzer
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Lynn Burchell
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Sivaramesh Wigneshweraraj
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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