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Bustamante JA, Ceron JS, Gao IT, Ramirez HA, Aviles MV, Bet Adam D, Brice JR, Cuellar RA, Dockery E, Jabagat MK, Karp DG, Lau JKO, Li S, Lopez-Magaña R, Moore RR, Morin BKR, Nzongo J, Rezaeihaghighi Y, Sapienza-Martinez J, Tran TTK, Huang Z, Duthoy AJ, Barnett MJ, Long SR, Chen JC. A protease and a lipoprotein jointly modulate the conserved ExoR-ExoS-ChvI signaling pathway critical in Sinorhizobium meliloti for symbiosis with legume hosts. PLoS Genet 2023; 19:e1010776. [PMID: 37871041 PMCID: PMC10659215 DOI: 10.1371/journal.pgen.1010776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/20/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Sinorhizobium meliloti is a model alpha-proteobacterium for investigating microbe-host interactions, in particular nitrogen-fixing rhizobium-legume symbioses. Successful infection requires complex coordination between compatible host and endosymbiont, including bacterial production of succinoglycan, also known as exopolysaccharide-I (EPS-I). In S. meliloti EPS-I production is controlled by the conserved ExoS-ChvI two-component system. Periplasmic ExoR associates with the ExoS histidine kinase and negatively regulates ChvI-dependent expression of exo genes, necessary for EPS-I synthesis. We show that two extracytoplasmic proteins, LppA (a lipoprotein) and JspA (a lipoprotein and a metalloprotease), jointly influence EPS-I synthesis by modulating the ExoR-ExoS-ChvI pathway and expression of genes in the ChvI regulon. Deletions of jspA and lppA led to lower EPS-I production and competitive disadvantage during host colonization, for both S. meliloti with Medicago sativa and S. medicae with M. truncatula. Overexpression of jspA reduced steady-state levels of ExoR, suggesting that the JspA protease participates in ExoR degradation. This reduction in ExoR levels is dependent on LppA and can be replicated with ExoR, JspA, and LppA expressed exogenously in Caulobacter crescentus and Escherichia coli. Akin to signaling pathways that sense extracytoplasmic stress in other bacteria, JspA and LppA may monitor periplasmic conditions during interaction with the plant host to adjust accordingly expression of genes that contribute to efficient symbiosis. The molecular mechanisms underlying host colonization in our model system may have parallels in related alpha-proteobacteria.
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Affiliation(s)
- Julian A. Bustamante
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Josue S. Ceron
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Ivan Thomas Gao
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Hector A. Ramirez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Milo V. Aviles
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Demsin Bet Adam
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Jason R. Brice
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rodrigo A. Cuellar
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Eva Dockery
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Miguel Karlo Jabagat
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Donna Grace Karp
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Kin-On Lau
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Suling Li
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Raymondo Lopez-Magaña
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rebecca R. Moore
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Bethany Kristi R. Morin
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Juliana Nzongo
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Yasha Rezaeihaghighi
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Sapienza-Martinez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Tuyet Thi Kim Tran
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Zhenzhong Huang
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Aaron J. Duthoy
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Melanie J. Barnett
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Sharon R. Long
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Joseph C. Chen
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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Slapakova M, Sgambati D, Pirone L, Russo V, D’Abrosca G, Valletta M, Russo R, Chambery A, Malgieri G, Pedone EM, Dame RT, Pedone PV, Baglivo I. MucR from Sinorhizobium meliloti: New Insights into Its DNA Targets and Its Ability to Oligomerize. Int J Mol Sci 2023; 24:14702. [PMID: 37834166 PMCID: PMC10572780 DOI: 10.3390/ijms241914702] [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: 08/24/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Proteins of the MucR/Ros family play a crucial role in bacterial infection or symbiosis with eukaryotic hosts. MucR from Sinorhizobium meliloti plays a regulatory role in establishing symbiosis with the host plant, both dependent and independent of Quorum Sensing. Here, we report the first characterization of MucR isolated from Sinorhizobium meliloti by mass spectrometry and demonstrate that this protein forms higher-order oligomers in its native condition of expression by SEC-MALS. We show that MucR purified from Sinorhizobium meliloti can bind DNA and recognize the region upstream of the ndvA gene in EMSA, revealing that this gene is a direct target of MucR. Although MucR DNA binding activity was already described, a detailed characterization of Sinorhizobium meliloti DNA targets has never been reported. We, thus, analyze sequences recognized by MucR in the rem gene promoter, showing that this protein recognizes AT-rich sequences and does not require a consensus sequence to bind DNA. Furthermore, we investigate the dependence of MucR DNA binding on the length of DNA targets. Taken together, our studies establish MucR from Sinorhizobium meliloti as a member of a new family of Histone-like Nucleoid Structuring (H-NS) proteins, thus explaining the multifaceted role of this protein in many species of alpha-proteobacteria.
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Affiliation(s)
- Martina Slapakova
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Domenico Sgambati
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino, 80134 Naples, Italy; (L.P.); (E.M.P.)
| | - Veronica Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Gianluca D’Abrosca
- Department of Clinical and Experimental Medicine, University of Foggia, Viale Pinto, 1, 71122 Foggia, Italy;
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino, 80134 Naples, Italy; (L.P.); (E.M.P.)
| | - Remus Thei Dame
- Leiden Institute of Chemistry, Leiden University, 2333 CC Leiden, The Netherlands;
- Centre for Microbial Cell Biology, Leiden University, 2333 CC Leiden, The Netherlands
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi, 43, 81100 Caserta, Italy; (M.S.); (D.S.); (V.R.); (M.V.); (R.R.); (A.C.); (G.M.); (P.V.P.)
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Chávez-Jacobo VM, Becerra-Rivera VA, Guerrero G, Dunn MF. The Sinorhizobium meliloti NspS-MbaA system affects biofilm formation, exopolysaccharide production and motility in response to specific polyamines. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001293. [PMID: 36748569 PMCID: PMC9993111 DOI: 10.1099/mic.0.001293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We previously showed that specific polyamines (PAs) present in the extracellular environment markedly affect extracellular polysaccharide (EPS) production, biofilm formation and motility in Sinorhizobium meliloti Rm8530. We hypothesized that extracellular PA signals were sensed and transduced by the NspS and MbaA proteins, respectively, which are homologs of the PA-sensing, c-di-GMP modulating NspS-MbaA proteins described in Vibrio cholerae. Here we show that the decrease in biofilm formation and EPS production in the quorum-sensing (QS)-deficient S. meliloti wild-type strain 1021 in cultures containing putrescine or spermine did not occur in a 1021 nspS mutant (1021 nspS). The transcriptional expression of nspS in strain 1021 was significantly increased in cultures containing either of these polyamines, but not by exogenous cadaverine, 1,3-diaminopropane (DAP), spermidine (Spd) or norspermidine (NSpd). Cell aggregation in liquid cultures did not differ markedly between strain 1021 and 1021 nspS in the presence or absence of PAs. The S. meliloti QS-proficient Rm8530 wild-type and nspS mutant (Rm8530 nspS) produced similar levels of biofilm under control conditions and 3.2- and 2.2-fold more biofilm, respectively, in cultures with NSpd, but these changes did not correlate with EPS production. Cells of Rm8530 nspS aggregated from two- to several-fold more than the wild-type in cultures without PAs or in those containing Spm. NSpd, Spd and DAP differently affected swimming and swarming motility in strains 1021 and Rm8530 and their respective nspS mutants. nspS transcription in strain Rm8530 was greatly reduced by exogenous Spm. Bioinformatic analysis revealed similar secondary structures and functional domains in the MbaA proteins of S. meliloti and V. cholerae, while their NspS proteins differed in some residues implicated in polyamine recognition in the latter species. NspS-MbaA homologs occur in a small subset of soil and aquatic bacterial species that commonly interact with eukaryotes. We speculate that the S. meliloti NspS-MbaA system modulates biofilm formation, EPS production and motility in response to environmental or host plant-produced PAs.
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Affiliation(s)
- Víctor M Chávez-Jacobo
- Programa en Genómica Funcional de Procariotes, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Víctor A Becerra-Rivera
- Programa en Genómica Funcional de Procariotes, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Gabriela Guerrero
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Michael F Dunn
- Programa en Genómica Funcional de Procariotes, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
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4
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Calvopina-Chavez DG, Howarth RE, Memmott AK, Pech Gonzalez OH, Hafen CB, Jensen KT, Benedict AB, Altman JD, Burnside BS, Childs JS, Dallon SW, DeMarco AC, Flindt KC, Grover SA, Heninger E, Iverson CS, Johnson AK, Lopez JB, Meinzer MA, Moulder BA, Moulton RI, Russell HS, Scott TM, Shiobara Y, Taylor MD, Tippets KE, Vainerere KM, Von Wallwitz IC, Wagley M, Wiley MS, Young NJ, Griffitts JS. A large-scale genetic screen identifies genes essential for motility in Agrobacterium fabrum. PLoS One 2023; 18:e0279936. [PMID: 36598925 PMCID: PMC9812332 DOI: 10.1371/journal.pone.0279936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/17/2022] [Indexed: 01/05/2023] Open
Abstract
The genetic and molecular basis of flagellar motility has been investigated for several decades, with innovative research strategies propelling advances at a steady pace. Furthermore, as the phenomenon is examined in diverse bacteria, new taxon-specific regulatory and structural features are being elucidated. Motility is also a straightforward bacterial phenotype that can allow undergraduate researchers to explore the palette of molecular genetic tools available to microbiologists. This study, driven primarily by undergraduate researchers, evaluated hundreds of flagellar motility mutants in the Gram-negative plant-associated bacterium Agrobacterium fabrum. The nearly saturating screen implicates a total of 37 genes in flagellar biosynthesis, including genes of previously unknown function.
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Affiliation(s)
- Diana G. Calvopina-Chavez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Robyn E. Howarth
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Audrey K. Memmott
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Oscar H. Pech Gonzalez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Caleb B. Hafen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Kyson T. Jensen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Alex B. Benedict
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Jessica D. Altman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Brittany S. Burnside
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Justin S. Childs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Samuel W. Dallon
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Alexa C. DeMarco
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Kirsten C. Flindt
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Sarah A. Grover
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Elizabeth Heninger
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Christina S. Iverson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Abigail K. Johnson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Jack B. Lopez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - McKay A. Meinzer
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Brook A. Moulder
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Rebecca I. Moulton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Hyrum S. Russell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Tiana M. Scott
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Yuka Shiobara
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Mason D. Taylor
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Kathryn E. Tippets
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Kayla M. Vainerere
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Isabella C. Von Wallwitz
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Madison Wagley
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Megumi S. Wiley
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Naomi J. Young
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States of America
- * E-mail:
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5
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The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions. Int J Mol Sci 2022; 23:ijms232415536. [PMID: 36555178 PMCID: PMC9779718 DOI: 10.3390/ijms232415536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Ros/MucR is a widespread family of bacterial zinc-finger-containing proteins that integrate multiple functions, such as symbiosis, virulence, transcription regulation, motility, production of surface components, and various other physiological processes in cells. This regulatory protein family is conserved in bacteria and is characterized by its zinc-finger motif, which has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure has evolved. The first prokaryotic zinc-finger domain found in the transcription regulator Ros was identified in Agrobacterium tumefaciens. In the past decades, a large body of evidence revealed Ros/MucR as pleiotropic transcriptional regulators that mainly act as repressors through oligomerization and binding to AT-rich target promoters. The N-terminal domain and the zinc-finger-bearing C-terminal region of these regulatory proteins are engaged in oligomerization and DNA binding, respectively. These properties of the Ros/MucR proteins are similar to those of xenogeneic silencers, such as H-NS, MvaT, and Lsr2, which are mainly found in other lineages. In fact, a novel functional model recently proposed for this protein family suggests that they act as H-NS-'like' gene silencers. The prokaryotic zinc-finger domain exhibits interesting structural and functional features that are different from that of its eukaryotic counterpart (a βββα topology), as it folds in a significantly larger zinc-binding globular domain (a βββαα topology). Phylogenetic analysis of Ros/MucR homologs suggests an ancestral origin of this type of protein in α-Proteobacteria. Furthermore, multiple duplications and lateral gene transfer events contributing to the diversity and phyletic distribution of these regulatory proteins were found in bacterial genomes.
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Shi WT, Zhang B, Li ML, Liu KH, Jiao J, Tian CF. The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes. Nucleic Acids Res 2022; 50:8580-8598. [PMID: 36007892 PMCID: PMC9410896 DOI: 10.1093/nar/gkac664] [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: 12/03/2021] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial adaptation is largely shaped by horizontal gene transfer, xenogeneic silencing mediated by lineage-specific DNA bridgers (H-NS, Lsr2, MvaT and Rok), and various anti-silencing mechanisms. No xenogeneic silencing DNA bridger is known for α-proteobacteria, from which mitochondria evolved. By investigating α-proteobacterium Sinorhizobium fredii, a facultative legume microsymbiont, here we report the conserved zinc-finger bearing MucR as a novel xenogeneic silencing DNA bridger. Self-association mediated by its N-terminal domain (NTD) is required for DNA–MucR–DNA bridging complex formation, maximizing MucR stability, transcriptional silencing, and efficient symbiosis in legume nodules. Essential roles of NTD, CTD (C-terminal DNA-binding domain), or full-length MucR in symbiosis can be replaced by non-homologous NTD, CTD, or full-length protein of H-NS from γ-proteobacterium Escherichia coli, while NTD rather than CTD of Lsr2 from Gram-positive Mycobacterium tuberculosis can replace the corresponding domain of MucR in symbiosis. Chromatin immunoprecipitation sequencing reveals similar recruitment profiles of H-NS, MucR and various functional chimeric xenogeneic silencers across the multipartite genome of S. fredii, i.e. preferring AT-rich genomic islands and symbiosis plasmid with key symbiosis genes as shared targets. Collectively, the convergently evolved DNA bridger MucR predisposed α-proteobacteria to integrate AT-rich foreign DNA including symbiosis genes, horizontal transfer of which is strongly selected in nature.
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Affiliation(s)
- Wen-Tao Shi
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Biliang Zhang
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Meng-Lin Li
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Ke-Han Liu
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University , Beijing , China
- MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University , Beijing , China
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7
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The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity. THE ISME JOURNAL 2022; 16:738-749. [PMID: 34584215 PMCID: PMC8857273 DOI: 10.1038/s41396-021-01118-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 02/08/2023]
Abstract
Foreign AT-rich genes drive bacterial adaptation to new niches while challenging the existing regulation network. Here we report that MucR, a conserved regulator in α-proteobacteria, balances adaptation and regulatory integrity in Sinorhizobium fredii, a facultative microsymbiont of legumes. Chromatin immunoprecipitation sequencing coupled with transcriptomic data reveal that average transcription levels of both target and non-target genes, under free-living and symbiotic conditions, increase with their conservation levels. Targets involved in environmental adaptation and symbiosis belong to genus or species core and can be repressed or activated by MucR in a condition-dependent manner, implying regulatory integrations. However, most targets are enriched in strain-specific genes of lower expression levels and higher AT%. Within each conservation levels, targets have higher AT% and average transcription levels than non-target genes and can be further up-regulated in the mucR mutant. This is consistent with higher AT% of spacers between -35 and -10 elements of promoters for target genes, which enhances transcription. The MucR recruitment level linearly increases with AT% and the number of a flexible pattern (with periodic repeats of Ts) of target sequences. Collectively, MucR directly represses AT-rich foreign genes with predisposed high transcription potential while progressive erosions of its target sites facilitate regulatory integrations of foreign genes.
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8
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Pirhanov GG. Sinorhizobium meliloti AS A PERSPECTIVE OBJECT FOR MODERN BIOTECHNOLOGY. BIOTECHNOLOGIA ACTA 2021. [DOI: 10.15407/biotech14.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sinorhizobium meliloti is a Gram-negative soil nitrogen-fixing bacterium that increases the yield of legumes. There is information in the literature about the complete genome sequence of this bacterium, in addition, the polysaccharide composition of the biofilm, which is actively involved in nitrogen fixation, has been studied. The well-known nucleotide sequence, as well as the genetic and biochemical features of S. meliloti make this organism an ideal model for biotechnological research. The purpose of this work was to analyze the current data provided in the literature on the symbiotic interaction of Sinorhizobium meliloti with the host plant, and to characterize the main directions of the use of this bacterium in agriculture, bioremediation and medicine.
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9
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Identification of a Novel Pyruvyltransferase Using 13C Solid-State Nuclear Magnetic Resonance To Analyze Rhizobial Exopolysaccharides. J Bacteriol 2021; 203:e0040321. [PMID: 34606371 DOI: 10.1128/jb.00403-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The alphaproteobacterium Sinorhizobium meliloti secretes two acidic exopolysaccharides (EPSs), succinoglycan (EPSI) and galactoglucan (EPSII), which differentially enable it to adapt to a changing environment. Succinoglycan is essential for invasion of plant hosts and, thus, for the formation of nitrogen-fixing root nodules. Galactoglucan is critical for population-based behaviors such as swarming and biofilm formation and can facilitate invasion in the absence of succinoglycan on some host plants. The biosynthesis of galactoglucan is not as completely understood as that of succinoglycan. We devised a pipeline to identify putative pyruvyltransferase and acetyltransferase genes, construct genomic deletions in strains engineered to produce either succinoglycan or galactoglucan, and analyze EPS from mutant bacterial strains. EPS samples were examined by 13C cross-polarization magic-angle spinning (CPMAS) solid-state nuclear magnetic resonance (NMR). CPMAS NMR is uniquely suited to defining chemical composition in complex samples and enables the detection and quantification of distinct EPS functional groups. Galactoglucan was isolated from mutant strains with deletions in five candidate acyl/acetyltransferase genes (exoZ, exoH, SMb20810, SMb21188, and SMa1016) and a putative pyruvyltransferase (wgaE or SMb21322). Most samples were similar in composition to wild-type EPSII by CPMAS NMR analysis. However, galactoglucan produced from a strain lacking wgaE exhibited a significant reduction in pyruvylation. Pyruvylation was restored through the ectopic expression of plasmid-borne wgaE. Our work has thus identified WgaE as a galactoglucan pyruvyltransferase. This exemplifies how the systematic combination of genetic analyses and solid-state NMR detection is a rapid means to identify genes responsible for modification of rhizobial exopolysaccharides. IMPORTANCE Nitrogen-fixing bacteria are crucial for geochemical cycles and global nitrogen nutrition. Symbioses between legumes and rhizobial bacteria establish root nodules, where bacteria convert dinitrogen to ammonia for plant utilization. Secreted exopolysaccharides (EPSs) produced by Sinorhizobium meliloti (succinoglycan and galactoglucan) play important roles in soil and plant environments. The biosynthesis of galactoglucan is not as well characterized as that of succinoglycan. We employed solid-state nuclear magnetic resonance (NMR) to examine intact EPS from wild-type and mutant S. meliloti strains. NMR analysis of EPS isolated from a wgaE gene mutant revealed a novel pyruvyltransferase that modifies galactoglucan. Few EPS pyruvyltransferases have been characterized. Our work provides insight into the biosynthesis of an important S. meliloti EPS and expands the knowledge of enzymes that modify polysaccharides.
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10
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Li ML, Jiao J, Zhang B, Shi WT, Yu WH, Tian CF. Global Transcriptional Repression of Diguanylate Cyclases by MucR1 Is Essential for Sinorhizobium-Soybean Symbiosis. mBio 2021; 12:e0119221. [PMID: 34700374 PMCID: PMC8546604 DOI: 10.1128/mbio.01192-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/22/2021] [Indexed: 11/20/2022] Open
Abstract
The ubiquitous bacterial second messenger c-di-GMP is intensively studied in pathogens but less so in mutualistic bacteria. Here, we report a genome-wide investigation of functional diguanylate cyclases (DGCs) synthesizing c-di-GMP from two molecules of GTP in Sinorhizobium fredii CCBAU45436, a facultative microsymbiont fixing nitrogen in nodules of diverse legumes, including soybean. Among 25 proteins harboring a putative GGDEF domain catalyzing the biosynthesis of c-di-GMP, eight functional DGCs were identified by heterogenous expression in Escherichia coli in a Congo red binding assay. This screening result was further verified by in vitro enzymatic assay with purified full proteins or the GGDEF domains from representative functional and nonfunctional DGCs. In the same in vitro assay, a functional EAL domain catalyzing the degradation of c-di-GMP into pGpG was identified in a protein that has an inactive GGDEF domain but with an active phosphodiesterase (PDE) function. The identified functional DGCs generally exhibited low transcription levels in soybean nodules compared to free-living cultures, as revealed in transcriptomes. An engineered upregulation of a functional DGC in nodules led to a significant increase of c-di-GMP level and symbiotic defects, which were not observed when a functional EAL domain was upregulated at the same level. Further transcriptional analysis and gel shift assay demonstrated that these functional DGCs were all transcriptionally repressed in nodules by a global pleiotropic regulator, MucR1, that is essential in Sinorhizobium-soybean symbiosis. These findings shed novel insights onto the systematic regulation of c-di-GMP biosynthesis in mutualistic symbiosis. IMPORTANCE The ubiquitous second messenger c-di-GMP is well-known for its role in biofilm formation and host adaptation of pathogens, whereas it is less investigated in mutualistic symbioses. Here, we reveal a cocktail of eight functional diguanylate cyclases (DGCs) catalyzing the biosynthesis of c-di-GMP in a broad-host-range Sinorhizobium that can establish nitrogen-fixing nodules on soybean and many other legumes. These functional DGCs are generally transcribed at low levels in soybean nodules compared to free-living conditions. The engineered nodule-specific upregulation of DGC can elevate the c-di-GMP level and cause symbiotic defects, while the upregulation of a phosphodiesterase that quenches c-di-GMP has no detectable symbiotic defects. Moreover, eight functional DGCs located on two different replicons are all directly repressed in nodules by a global silencer, MucR1, that is essential for Sinorhizobium-soybean symbiosis. These findings represent a novel mechanism of a strategic regulation of the c-di-GMP biosynthesis arsenal in prokaryote-eukaryote interactions.
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Affiliation(s)
- Meng-Lin Li
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Biliang Zhang
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Tao Shi
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Hao Yu
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
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11
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Pan L, Gardner CL, Beliakoff R, da Silva D, Zuo R, Pagliai FA, Padgett-Pagliai KA, Merli ML, Bahadiroglu E, Gonzalez CF, Lorca GL. PrbP modulates biofilm formation in Liberibacter crescens. Environ Microbiol 2021; 23:7121-7138. [PMID: 34431209 DOI: 10.1111/1462-2920.15740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 12/31/2022]
Abstract
In Liberibacter asiaticus, PrbP is a transcriptional regulatory protein involved in survival and persistence during host infection. Tolfenamic acid was previously found to inhibit interactions between PrbP and the promotor region of rplK, resulting in reduced survival of L. asiaticus in the citrus host. In this study, we performed transcriptome analyses to elucidate the PrbP regulon in L. crescens, as it is phylogenetically the closest related species to L. asiaticus that can be grown in laboratory conditions. Chemical inhibition of PrbP with tolfenamic acid revealed that PrbP is involved in the regulation of diverse cellular processes, including stress response, cell motility, cell cycle and biofilm formation. In vitro DNA binding and bacterial two-hybrid assays also suggested that PrbP is a global regulator of multiple transcription factors (RpoH, VisN, PleD, MucR, MocR and CtrA) at both transcriptional and/or post-transcriptional levels. Sub-lethal concentrations of tolfenamic acid significantly reduced the attachment of L. crescens during biofilm formation and decreased long-term persistence in biofilm structures. Overall, our findings show the importance of PrbP in regulating diverse biological processes through direct and indirect interactions with other transcriptional regulators in L. crescens.
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Affiliation(s)
- Lei Pan
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Christopher L Gardner
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Reagan Beliakoff
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Danilo da Silva
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Ran Zuo
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Fernando A Pagliai
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Kaylie A Padgett-Pagliai
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Marcelo L Merli
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Erol Bahadiroglu
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Claudio F Gonzalez
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
| | - Graciela L Lorca
- Microbiology and Cell Science Department, Genetics Institute, Institute of Food and Agricultural Science, University of Florida, Gainesville, FL, USA
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12
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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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Krol E, Schäper S, Becker A. Cyclic di-GMP signaling controlling the free-living lifestyle of alpha-proteobacterial rhizobia. Biol Chem 2021; 401:1335-1348. [PMID: 32990642 DOI: 10.1515/hsz-2020-0232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger which has been associated with a motile to sessile lifestyle switch in many bacteria. Here, we review recent insights into c-di-GMP regulated processes related to environmental adaptations in alphaproteobacterial rhizobia, which are diazotrophic bacteria capable of fixing nitrogen in symbiosis with their leguminous host plants. The review centers on Sinorhizobium meliloti, which in the recent years was intensively studied for its c-di-GMP regulatory network.
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Affiliation(s)
- Elizaveta Krol
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Simon Schäper
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
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14
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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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15
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Rosier A, Beauregard PB, Bais HP. Quorum Quenching Activity of the PGPR Bacillus subtilis UD1022 Alters Nodulation Efficiency of Sinorhizobium meliloti on Medicago truncatula. Front Microbiol 2021; 11:596299. [PMID: 33519732 PMCID: PMC7843924 DOI: 10.3389/fmicb.2020.596299] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) have enormous potential for solving some of the myriad challenges facing our global agricultural system. Intense research efforts are rapidly moving the field forward and illuminating the wide diversity of bacteria and their plant beneficial activities. In the development of better crop solutions using these PGPR, producers are including multiple different species of PGPR in their formulations in a "consortia" approach. While the intention is to emulate more natural rhizomicrobiome systems, the aspect of bacterial interactions has not been properly regarded. By using a tri-trophic model of Medicago truncatula A17 Jemalong, its nitrogen (N)-fixing symbiont Sinorhizobium meliloti Rm8530, and the PGPR Bacillus subtilis UD1022, we demonstrate indirect influences between the bacteria affecting their plant growth-promoting activities. Co-cultures of UD1022 with Rm8530 significantly reduced Rm8530 biofilm formation and downregulated quorum sensing (QS) genes responsible for symbiotically active biofilm production. This work also identifies the presence and activity of a quorum quenching lactonase in UD1022 and proposes this as the mechanism for non-synergistic activity of this model "consortium." These interspecies interactions may be common in the rhizosphere and are critical to understand as we seek to develop new sustainable solutions in agriculture.
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Affiliation(s)
- Amanda Rosier
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, United States
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
| | | | - Harsh P. Bais
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, United States
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
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16
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Jiao J, Tian CF. Ancestral zinc-finger bearing protein MucR in alpha-proteobacteria: A novel xenogeneic silencer? Comput Struct Biotechnol J 2020; 18:3623-3631. [PMID: 33304460 PMCID: PMC7710501 DOI: 10.1016/j.csbj.2020.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulator that integrating multiple functions such as virulence, symbiosis, cell cycle and various physiological processes. Scattered reports indicate that MucR mainly acts as a repressor, through oligomerization and binding to multiple sites of AT-rich target promoters. The N-terminal region and zinc-finger bearing C-terminal region of MucR mediate oligomerization and DNA-binding, respectively. These features are convergent to those of xenogeneic silencers such as H-NS, MvaT, Lsr2 and Rok, which are mainly found in other lineages. Phylogenetic analysis of MucR homologs suggests an ancestral origin of MucR in alpha- and delta-proteobacteria. Multiple independent duplication and lateral gene transfer events contribute to the diversity and phyletic distribution of MucR. Finally, we posed questions which remain unexplored regarding the putative roles of MucR as a xenogeneic silencer and a general manager in balancing adaptation and regulatory integration in the pangenome context.
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Affiliation(s)
- Jian Jiao
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.,MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.,MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, China Agricultural University, Beijing, China
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Structural Insight of the Full-Length Ros Protein: A Prototype of the Prokaryotic Zinc-Finger Family. Sci Rep 2020; 10:9283. [PMID: 32518326 PMCID: PMC7283297 DOI: 10.1038/s41598-020-66204-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022] Open
Abstract
Ros/MucR is a widespread family of bacterial zinc-finger (ZF) containing proteins that integrate multiple functions such as virulence, symbiosis and/or cell cycle transcription. NMR solution structure of Ros DNA-binding domain (region 56–142, i.e. Ros87) has been solved by our group and shows that the prokaryotic ZF domain shows interesting structural and functional features that differentiate it from its eukaryotic counterpart as it folds in a significantly larger zinc-binding globular domain. We have recently proposed a novel functional model for this family of proteins suggesting that they may act as H-NS-‘like’ gene silencers. Indeed, the N-terminal region of this family of proteins appears to be responsible for the formation of functional oligomers. No structural characterization of the Ros N-terminal domain (region 1–55) is available to date, mainly because of serious solubility problems of the full-length protein. Here we report the first structural characterization of the N-terminal domain of the prokaryotic ZF family examining by means of MD and NMR the structural preferences of the full-length Ros protein from Agrobacterium tumefaciens.
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Bioinspired reorientation strategies for application in micro/nanorobotic control. JOURNAL OF MICRO-BIO ROBOTICS 2020. [DOI: 10.1007/s12213-020-00130-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractEngineers have recently been inspired by swimming methodologies of microorganisms in creating micro-/nanorobots for biomedical applications. Future medicine may be revolutionized by the application of these small machines in diagnosing, monitoring, and treating diseases. Studies over the past decade have often concentrated on propulsion generation. However, there are many other challenges to address before the practical use of robots at the micro-/nanoscale. The control and reorientation ability of such robots remain as some of these challenges. This paper reviews the strategies of swimming microorganisms for reorientation, including tumbling, reverse and flick, direction control of helical-path swimmers, by speed modulation, using complex flagella, and the help of mastigonemes. Then, inspired by direction change in microorganisms, methods for orientation control for microrobots and possible directions for future studies are discussed. Further, the effects of solid boundaries on the swimming trajectories of microorganisms and microrobots are examined. In addition to propulsion systems for artificial microswimmers, swimming microorganisms are promising sources of control methodologies at the micro-/nanoscale.
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Marczak M, Żebracki K, Koper P, Turska-Szewczuk A, Mazur A, Wydrych J, Wójcik M, Skorupska A. Mgl2 Is a Hypothetical Methyltransferase Involved in Exopolysaccharide Production, Biofilm Formation, and Motility in Rhizobium leguminosarum bv. trifolii. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:899-911. [PMID: 30681888 DOI: 10.1094/mpmi-01-19-0026-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, functional characterization of the mgl2 gene located near the Pss-I exopolysaccharide biosynthesis region in Rhizobium leguminosarum bv. trifolii TA1 is described. The hypothetical protein encoded by the mgl2 gene was found to be similar to methyltransferases (MTases). Protein homology and template-based modeling facilitated prediction of the Mgl2 structure, which greatly resembled class I MTases with a S-adenosyl-L-methionine-binding cleft. The Mgl2 protein was engaged in exopolysaccharide, but not lipopolysaccharide, synthesis. The mgl2 deletion mutant produced exopolysaccharide comprised of only low molecular weight fractions, while overexpression of mgl2 caused overproduction of exopolysaccharide with a normal low to high molecular weight ratio. The deletion of the mgl2 gene resulted in disturbances in biofilm formation and a slight increase in motility in minimal medium. Red clover (Trifolium pratense) inoculated with the mgl2 mutant formed effective nodules, and the appearance of the plants indicated active nitrogen fixation. The mgl2 gene was preceded by an active and strong promoter. Mgl2 was defined as an integral membrane protein and formed homodimers in vivo; however, it did not interact with Pss proteins encoded within the Pss-I region. The results are discussed in the context of the possible involvement of the newly described potential MTase in various metabolic traits, such as the exopolysaccharide synthesis and motility that are important for rhizobial saprophytic and symbiotic relationships.
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Affiliation(s)
- Małgorzata Marczak
- 1 Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St, 20-033 Lublin, Poland
| | - Kamil Żebracki
- 1 Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St, 20-033 Lublin, Poland
| | - Piotr Koper
- 1 Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St, 20-033 Lublin, Poland
| | - Anna Turska-Szewczuk
- 1 Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St, 20-033 Lublin, Poland
| | - Andrzej Mazur
- 1 Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St, 20-033 Lublin, Poland
| | - Jerzy Wydrych
- 2 Department of Comparative Anatomy and Anthropology, Institute of Biology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University
| | - Magdalena Wójcik
- 1 Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St, 20-033 Lublin, Poland
| | - Anna Skorupska
- 1 Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St, 20-033 Lublin, Poland
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20
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McIntosh M, Serrania J, Lacanna E. A novel LuxR-type solo of Sinorhizobium meliloti, NurR, is regulated by the chromosome replication coordinator, DnaA and activates quorum sensing. Mol Microbiol 2019; 112:678-698. [PMID: 31124196 DOI: 10.1111/mmi.14312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2019] [Indexed: 12/16/2022]
Abstract
The genome of Sinorhizobium meliloti, a model for studying plant-bacteria symbiosis, contains eight genes coding for LuxR-like proteins. Two of these, SinR and ExpR, are essential for quorum sensing (QS). Roles and regulation surrounding the others are mostly unknown. Here, we reveal the DNA recognition sequence and regulon of the LuxR-like protein SMc00877. Unlike ExpR, which uses the long-chain acyl homoserine lactones (AHLs) as inducers, SMc00877 functioned independently of AHLs and was even functional in Escherichia coli. A target of SMc00877 is SinR, the major regulator of AHL production in S. meliloti. Disruption of SMc00877 decreased AHL production. A weaker production of AHLs resulted in smaller microcolonies, starting from single cells, and delayed AHL-dependent regulation. SMc00877 was expressed only in growing cells in the presence of replete nutrients. Therefore, we renamed it NurR (nutrient sensitive LuxR-like regulator). We traced this nutrient-sensitive expression to transcription control by the DNA replication initiation factor, DnaA, which is essential for growth. These results indicate that NurR has a role in modulating the threshold of QS activation according to growth. We propose growth behavior as an additional prerequisite to population density for the activation of QS in S. meliloti.
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Affiliation(s)
- Matthew McIntosh
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, 35043, Germany.,Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany.,Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Javier Serrania
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, 35043, Germany.,Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Egidio Lacanna
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, 35043, Germany.,Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
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An Osmoregulatory Mechanism Operating through OmpR and LrhA Controls the Motile-Sessile Switch in the Plant Growth-Promoting Bacterium Pantoea alhagi. Appl Environ Microbiol 2019; 85:AEM.00077-19. [PMID: 30902852 DOI: 10.1128/aem.00077-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/14/2019] [Indexed: 11/20/2022] Open
Abstract
Adaptation to osmotic stress is crucial for bacterial growth and survival in changing environments. Although a large number of osmotic stress response genes have been identified in various bacterial species, how osmotic changes affect bacterial motility, biofilm formation, and colonization of host niches remains largely unknown. In this study, we report that the LrhA regulator is an osmoregulated transcription factor that directly binds to the promoters of the flhDC, eps, and opgGH operons and differentially regulates their expression, thus inhibiting motility and promoting exopolysaccharide (EPS) production, synthesis of osmoregulated periplasmic glucans (OPGs), biofilm formation, and root colonization of the plant growth-promoting bacterium Pantoea alhagi LTYR-11Z. Further, we observed that the LrhA-regulated OPGs control RcsCD-RcsB activation in a concentration-dependent manner, and a high concentration of OPGs induced by increased medium osmolarity is maintained to achieve the high level of activation of the Rcs phosphorelay, which results in enhanced EPS synthesis and decreased motility in P. alhagi Moreover, we showed that the osmosensing regulator OmpR directly binds to the promoter of lrhA and promotes its expression, while lrhA expression is feedback inhibited by the activated Rcs phosphorelay system. Overall, our data support a model whereby P. alhagi senses environmental osmolarity changes through the EnvZ-OmpR two-component system and LrhA to regulate the synthesis of OPGs, EPS production, and flagellum-dependent motility, thereby employing a hierarchical signaling cascade to control the transition between a motile lifestyle and a biofilm lifestyle.IMPORTANCE Many motile bacterial populations form surface-attached biofilms in response to specific environmental cues, including osmotic stress in a range of natural and host-related systems. However, cross talk between bacterial osmosensing, swimming, and biofilm formation regulatory networks is not fully understood. Here, we report that the pleiotropic regulator LrhA in Pantoea alhagi is involved in the regulation of flagellar motility, biofilm formation, and host colonization and responds to osmotic upshift. We further show that this sensing relies on the EnvZ-OmpR two-component system that was known to detect changes in external osmotic stress. The EnvZ-OmpR-LrhA osmosensing signal transduction cascade is proposed to increase bacterial fitness under hyperosmotic conditions inside the host. Our work proposes a novel regulatory mechanism that links osmosensing and motile-sessile lifestyle transitions, which may provide new approaches to prevent or promote the formation of biofilms and host colonization in P. alhagi and other bacteria possessing a similar osmoregulatory mechanism.
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Bettenworth V, Steinfeld B, Duin H, Petersen K, Streit WR, Bischofs I, Becker A. Phenotypic Heterogeneity in Bacterial Quorum Sensing Systems. J Mol Biol 2019; 431:4530-4546. [PMID: 31051177 DOI: 10.1016/j.jmb.2019.04.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/11/2022]
Abstract
Quorum sensing is usually thought of as a collective behavior in which all members of a population partake. However, over the last decade, several reports of phenotypic heterogeneity in quorum sensing-related gene expression have been put forward, thus challenging this view. In the respective systems, cells of isogenic populations did not contribute equally to autoinducer production or target gene activation, and in some cases, the fraction of contributing cells was modulated by environmental factors. Here, we look into potential origins of these incidences and into how initial cell-to-cell variations might be amplified to establish distinct phenotypic heterogeneity. We furthermore discuss potential functions heterogeneity in bacterial quorum sensing systems could serve: as a preparation for environmental fluctuations (bet hedging), as a more cost-effective way of producing public goods (division of labor), as a loophole for genotypic cooperators when faced with non-contributing mutants (cheat protection), or simply as a means to fine-tune the output of the population as a whole (output modulation). We illustrate certain aspects of these recent developments with the model organisms Sinorhizobium meliloti, Sinorhizobium fredii and Bacillus subtilis, which possess quorum sensing systems of different complexity, but all show phenotypic heterogeneity therein.
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Affiliation(s)
- Vera Bettenworth
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35043 Marburg, Germany; Faculty of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany.
| | - Benedikt Steinfeld
- BioQuant Center of the University of Heidelberg, 69120 Heidelberg, Germany; Center for Molecular Biology (ZMBH), University of Heidelberg, 69120 Heidelberg, Germany; Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
| | - Hilke Duin
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Katrin Petersen
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany.
| | - Ilka Bischofs
- BioQuant Center of the University of Heidelberg, 69120 Heidelberg, Germany; Center for Molecular Biology (ZMBH), University of Heidelberg, 69120 Heidelberg, Germany; Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany.
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, 35043 Marburg, Germany; Faculty of Biology, Philipps-Universität Marburg, 35043 Marburg, Germany.
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23
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A Bifunctional UDP-Sugar 4-Epimerase Supports Biosynthesis of Multiple Cell Surface Polysaccharides in Sinorhizobium meliloti. J Bacteriol 2019; 201:JB.00801-18. [PMID: 30833352 DOI: 10.1128/jb.00801-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/25/2019] [Indexed: 01/19/2023] Open
Abstract
Sinorhizobium meliloti produces multiple extracellular glycans, including among others, lipopolysaccharides (LPS), and the exopolysaccharides (EPS) succinoglycan (SG) and galactoglucan (GG). These polysaccharides serve cell protective roles. Furthermore, SG and GG promote the interaction of S. meliloti with its host Medicago sativa in root nodule symbiosis. ExoB has been suggested to be the sole enzyme catalyzing synthesis of UDP-galactose in S. meliloti (A. M. Buendia, B. Enenkel, R. Köplin, K. Niehaus, et al. Mol Microbiol 5:1519-1530, 1991, https://doi.org/10.1111/j.1365-2958.1991.tb00799.x). Accordingly, exoB mutants were previously found to be affected in the synthesis of the galactose-containing glycans LPS, SG, and GG and consequently, in symbiosis. Here, we report that the S. meliloti Rm2011 uxs1-uxe-apsS-apsH1-apsE-apsH2 (SMb20458-63) gene cluster directs biosynthesis of an arabinose-containing polysaccharide (APS), which contributes to biofilm formation, and is solely or mainly composed of arabinose. Uxe has previously been identified as UDP-xylose 4-epimerase. Collectively, our data from mutational and overexpression analyses of the APS biosynthesis genes and in vitro enzymatic assays indicate that Uxe functions as UDP-xylose 4- and UDP-glucose 4-epimerase catalyzing UDP-xylose/UDP-arabinose and UDP-glucose/UDP-galactose interconversions, respectively. Overexpression of uxe suppressed the phenotypes of an exoB mutant, evidencing that Uxe can functionally replace ExoB. We suggest that under conditions stimulating expression of the APS biosynthesis operon, Uxe contributes to the synthesis of multiple glycans and thereby to cell protection, biofilm formation, and symbiosis. Furthermore, we show that the C2H2 zinc finger transcriptional regulator MucR counteracts the previously reported CuxR-c-di-GMP-mediated activation of the APS biosynthesis operon. This integrates the c-di-GMP-dependent control of APS production into the opposing regulation of EPS biosynthesis and swimming motility in S. meliloti IMPORTANCE Bacterial extracellular polysaccharides serve important cell protective, structural, and signaling roles. They have particularly attracted attention as adhesives and matrix components promoting biofilm formation, which significantly contributes to resistance against antibiotics. In the root nodule symbiosis between rhizobia and leguminous plants, extracellular polysaccharides have a signaling function. UDP-sugar 4-epimerases are important enzymes in the synthesis of the activated sugar substrates, which are frequently shared between multiple polysaccharide biosynthesis pathways. Thus, these enzymes are potential targets to interfere with these pathways. Our finding of a bifunctional UDP-sugar 4-epimerase in Sinorhizobium meliloti generally advances the knowledge of substrate promiscuity of such enzymes and specifically of the biosynthesis of extracellular polysaccharides involved in biofilm formation and symbiosis in this alphaproteobacterium.
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Identifying the region responsible for Brucella abortus MucR higher-order oligomer formation and examining its role in gene regulation. Sci Rep 2018; 8:17238. [PMID: 30467359 PMCID: PMC6250670 DOI: 10.1038/s41598-018-35432-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/05/2018] [Indexed: 11/09/2022] Open
Abstract
MucR is a member of the Ros/MucR family of prokaryotic zinc-finger proteins found in the α-proteobacteria which regulate the expression of genes required for the successful pathogenic and symbiotic interactions of these bacteria with the eukaryotic hosts. The structure and function of their distinctive zinc-finger domain has been well-studied, but only recently the quaternary structure of the full length proteins was investigated demonstrating their ability to form higher-order oligomers. The aim of this study was to identify the region of MucR involved in higher-order oligomer formation by analysing deletion and point mutants of this protein by Light Scattering, and to determine the role that MucR oligomerization plays in the regulatory function of this protein. Here we demonstrate that a conserved hydrophobic region at the N-terminus of MucR is responsible for higher-order oligomer formation and that MucR oligomerization is essential for its regulatory function in Brucella. All these features of MucR are shared by the histone-like nucleoid structuring protein, (H-NS), leading us to propose that the prokaryotic zinc-finger proteins in the MucR/Ros family control gene expression employing a mechanism similar to that used by the H-NS proteins, rather than working as classical transcriptional regulators.
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25
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Bettenworth V, McIntosh M, Becker A, Eckhardt B. Front-propagation in bacterial inter-colony communication. CHAOS (WOODBURY, N.Y.) 2018; 28:106316. [PMID: 30384658 DOI: 10.1063/1.5040068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/09/2018] [Indexed: 06/08/2023]
Abstract
Many bacterial species exchange signaling molecules to coordinate population-wide responses. For this process, known as quorum sensing, the concentration of the respective molecules is crucial. Here, we consider the interaction between spatially distributed bacterial colonies so that the spreading of the signaling molecules in space becomes important. The exponential growth of the signal-producing populations and the corresponding increase in signaling molecule production result in an exponential concentration profile that spreads with uniform speed. The theoretical predictions are supported by experiments with different strains of the soil bacterium Sinorhizobium meliloti that display fluorescence when either producing or responding to the signaling molecules.
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Affiliation(s)
- Vera Bettenworth
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg
| | - Matthew McIntosh
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg
| | - Anke Becker
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg
| | - Bruno Eckhardt
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg
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26
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Calatrava-Morales N, McIntosh M, Soto MJ. Regulation Mediated by N-Acyl Homoserine Lactone Quorum Sensing Signals in the Rhizobium-Legume Symbiosis. Genes (Basel) 2018; 9:genes9050263. [PMID: 29783703 PMCID: PMC5977203 DOI: 10.3390/genes9050263] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 02/06/2023] Open
Abstract
Soil-dwelling bacteria collectively referred to as rhizobia synthesize and perceive N-acyl-homoserine lactone (AHL) signals to regulate gene expression in a population density-dependent manner. AHL-mediated signaling in these bacteria regulates several functions which are important for the establishment of nitrogen-fixing symbiosis with legume plants. Moreover, rhizobial AHL act as interkingdom signals triggering plant responses that impact the plant-bacteria interaction. Both the regulatory mechanisms that control AHL synthesis in rhizobia and the set of bacterial genes and associated traits under quorum sensing (QS) control vary greatly among the rhizobial species. In this article, we focus on the well-known QS system of the alfalfa symbiont Sinorhizobium(Ensifer)meliloti. Bacterial genes, environmental factors and transcriptional and posttranscriptional regulatory mechanisms that control AHL production in this Rhizobium, as well as the effects of the signaling molecule on bacterial phenotypes and plant responses will be reviewed. Current knowledge of S. meliloti QS will be compared with that of other rhizobia. Finally, participation of the legume host in QS by interfering with rhizobial AHL perception through the production of molecular mimics will also be addressed.
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Affiliation(s)
- Nieves Calatrava-Morales
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC; Granada 18008, Spain.
| | - Matthew McIntosh
- Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, 35392 Giessen, Germany.
| | - María J Soto
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC; Granada 18008, Spain.
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27
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Robledo M, Schlüter JP, Loehr LO, Linne U, Albaum SP, Jiménez-Zurdo JI, Becker A. An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA. Front Microbiol 2018; 9:763. [PMID: 29740411 PMCID: PMC5928217 DOI: 10.3389/fmicb.2018.00763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 04/04/2018] [Indexed: 11/13/2022] Open
Abstract
Adjustment of cell cycle progression is crucial for bacterial survival and adaptation under adverse conditions. However, the understanding of modulation of cell cycle control in response to environmental changes is rather incomplete. In α-proteobacteria, the broadly conserved cell cycle master regulator CtrA underlies multiple levels of control, including coupling of cell cycle and cell differentiation. CtrA levels are known to be tightly controlled through diverse transcriptional and post-translational mechanisms. Here, small RNA (sRNA)-mediated post-transcriptional regulation is uncovered as an additional level of CtrA fine-tuning. Computational predictions as well as transcriptome and proteome studies consistently suggested targeting of ctrA and the putative cold shock chaperone cspA5 mRNAs by the trans-encoded sRNA (trans-sRNA) GspR (formerly SmelC775) in several Sinorhizobium species. GspR strongly accumulated in the stationary growth phase, especially in minimal medium (MM) cultures. Lack of the gspR locus confers a fitness disadvantage in competition with the wild type, while its overproduction hampers cell growth, suggesting that this riboregulator interferes with cell cycle progression. An eGFP-based reporter in vivo assay, involving wild-type and mutant sRNA and mRNA pairs, experimentally confirmed GspR-dependent post-transcriptional down-regulation of ctrA and cspA5 expression, which most likely occurs through base-pairing to the respective mRNA. The energetically favored secondary structure of GspR is predicted to comprise three stem-loop domains, with stem-loop 1 and stem-loop 3 targeting ctrA and cspA5 mRNA, respectively. Moreover, this work reports evidence for post-transcriptional control of ctrA by CspA5. Thus, this regulation and GspR-mediated post-transcriptional repression of ctrA and cspA5 expression constitute a coherent feed-forward loop, which may enhance the negative effect of GspR on CtrA levels. This novel regulatory circuit involving the riboregulator GspR, CtrA, and a cold shock chaperone may contribute to fine-tuning of ctrA expression.
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Affiliation(s)
- Marta Robledo
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany.,Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Jan-Philip Schlüter
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Lars O Loehr
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Uwe Linne
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Stefan P Albaum
- Bioinformatics Resource Facility, Center for Biotechnology, Universität Bielefeld, Bielefeld, Germany
| | - José I Jiménez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
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28
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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.
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29
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Saramago M, Peregrina A, Robledo M, Matos RG, Hilker R, Serrania J, Becker A, Arraiano CM, Jiménez-Zurdo JI. Sinorhizobium meliloti YbeY is an endoribonuclease with unprecedented catalytic features, acting as silencing enzyme in riboregulation. Nucleic Acids Res 2017; 45:1371-1391. [PMID: 28180335 PMCID: PMC5388416 DOI: 10.1093/nar/gkw1234] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 01/23/2023] Open
Abstract
Structural and biochemical features suggest that the almost ubiquitous bacterial YbeY protein may serve catalytic and/or Hfq-like protective functions central to small RNA (sRNA)-mediated regulation and RNA metabolism. We have biochemically and genetically characterized the YbeY ortholog of the legume symbiont Sinorhizobium meliloti (SmYbeY). Co-immunoprecipitation (CoIP) with a FLAG-tagged SmYbeY yielded a poor enrichment in RNA species, compared to Hfq CoIP-RNA uncovered previously by a similar experimental setup. Purified SmYbeY behaved as a monomer that indistinctly cleaved single- and double-stranded RNA substrates, a unique ability among bacterial endoribonucleases. SmYbeY-mediated catalysis was supported by the divalent metal ions Mg2+, Mn2+ and Ca2+, which influenced in a different manner cleavage efficiency and reactivity patterns, with Ca2+ specifically blocking activity on double-stranded and some structured RNA molecules. SmYbeY loss-of-function compromised expression of core energy and RNA metabolism genes, whilst promoting accumulation of motility, late symbiotic and transport mRNAs. Some of the latter transcripts are known Hfq-binding sRNA targets and might be SmYbeY substrates. Genetic reporter and in vitro assays confirmed that SmYbeY is required for sRNA-mediated down-regulation of the amino acid ABC transporter prbA mRNA. We have thus discovered a bacterial endoribonuclease with unprecedented catalytic features, acting also as gene silencing enzyme.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
- These authors contributed equally to the work as the first authors
| | - Alexandra Peregrina
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- These authors contributed equally to the work as the first authors
| | - Marta Robledo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- These authors contributed equally to the work as the first authors
| | - Rute G. Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Rolf Hilker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Javier Serrania
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Cecilia M. Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - José I. Jiménez-Zurdo
- Grupo de Ecología Genética de la Rizosfera, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), 18008 Granada, Spain
- To whom correspondence should be addressed. Tel: +34 958181600; Fax: +34 958181609;
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30
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Ghosh S, Chatterji D. Two zinc finger proteins from Mycobacterium smegmatis: DNA binding and activation of transcription. Genes Cells 2017. [PMID: 28639742 DOI: 10.1111/gtc.12507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Single zinc finger domain containing proteins are very few in number. Of numerous zinc finger proteins in eukaryotes, only three of them like GAGA, Superman and DNA binding by one finger (Dof) have single zinc finger domain. Although few zinc finger proteins have been described in eubacteria, no protein with single C4 zinc finger has been described in details in anyone of them. In this article, we are describing two novel C-terminal C4 zinc finger proteins-Msmeg_0118 and Msmeg_3613 from Mycobacterium smegmatis. We have named these proteins as Mszfp1 (Mycobacterial Single Zinc Finger Protein 1) and Mszfp2 (Mycobacterial Single Zinc Finger Protein 2). Both the proteins are expressed constitutively, can bind to DNA and regulate transcription. It appears that Mszfp1 and Mszfp2 may activate transcription by interacting with RNA polymerase.
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Affiliation(s)
- Subho Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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31
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AraC-like transcriptional activator CuxR binds c-di-GMP by a PilZ-like mechanism to regulate extracellular polysaccharide production. Proc Natl Acad Sci U S A 2017; 114:E4822-E4831. [PMID: 28559336 DOI: 10.1073/pnas.1702435114] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclic dimeric GMP (c-di-GMP) has emerged as a key regulatory player in the transition between planktonic and sedentary biofilm-associated bacterial lifestyles. It controls a multitude of processes including production of extracellular polysaccharides (EPSs). The PilZ domain, consisting of an N-terminal "RxxxR" motif and a β-barrel domain, represents a prototype c-di-GMP receptor. We identified a class of c-di-GMP-responsive proteins, represented by the AraC-like transcription factor CuxR in plant symbiotic α-proteobacteria. In Sinorhizobium meliloti, CuxR stimulates transcription of an EPS biosynthesis gene cluster at elevated c-di-GMP levels. CuxR consists of a Cupin domain, a helical hairpin, and bipartite helix-turn-helix motif. Although unrelated in sequence, the mode of c-di-GMP binding to CuxR is highly reminiscent to that of PilZ domains. c-di-GMP interacts with a conserved N-terminal RxxxR motif and the Cupin domain, thereby promoting CuxR dimerization and DNA binding. We unravel structure and mechanism of a previously unrecognized c-di-GMP-responsive transcription factor and provide insights into the molecular evolution of c-di-GMP binding to proteins.
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Sandhu P, Akhter Y. Siderophore transport by MmpL5-MmpS5 protein complex in Mycobacterium tuberculosis. J Inorg Biochem 2017; 170:75-84. [DOI: 10.1016/j.jinorgbio.2017.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/27/2016] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
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Acosta-Jurado S, Alias-Villegas C, Navarro-Gómez P, Zehner S, Murdoch PDS, Rodríguez-Carvajal MA, Soto MJ, Ollero FJ, Ruiz-Sainz JE, Göttfert M, Vinardell JM. The Sinorhizobium fredii HH103 MucR1 Global Regulator Is Connected With the nod Regulon and Is Required for Efficient Symbiosis With Lotus burttii and Glycine max cv. Williams. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:700-712. [PMID: 27482821 DOI: 10.1094/mpmi-06-16-0116-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sinorhizobium fredii HH103 is a rhizobial strain showing a broad host range of nodulation. In addition to the induction of bacterial nodulation genes, transition from a free-living to a symbiotic state requires complex genetic expression changes with the participation of global regulators. We have analyzed the role of the zinc-finger transcriptional regulator MucR1 from S. fredii HH103 under both free-living conditions and symbiosis with two HH103 host plants, Glycine max and Lotus burttii. Inactivation of HH103 mucR1 led to a severe decrease in exopolysaccharide (EPS) biosynthesis but enhanced production of external cyclic glucans (CG). This mutant also showed increased cell aggregation capacity as well as a drastic reduction in nitrogen-fixation capacity with G. max and L. burttii. However, in these two legumes, the number of nodules induced by the mucR1 mutant was significantly increased and decreased, respectively, with respect to the wild-type strain, indicating that MucR1 can differently affect nodulation depending on the host plant. RNA-Seq analysis carried out in the absence and the presence of flavonoids showed that MucR1 controls the expression of hundreds of genes (including some related to EPS production and CG transport), some of them being related to the nod regulon.
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Affiliation(s)
- Sebastián Acosta-Jurado
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Cynthia Alias-Villegas
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Pilar Navarro-Gómez
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Susanne Zehner
- 2 Technische Universität Dresden, Institut für Genetik, Helmholtzstrasse 10, 01062 Dresden, Germany
| | | | - Miguel A Rodríguez-Carvajal
- 4 Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Calle Profesor García González 1, C. P. 41012, Sevilla, Spain, and
| | - María J Soto
- 5 Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Francisco-Javier Ollero
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - José E Ruiz-Sainz
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
| | - Michael Göttfert
- 2 Technische Universität Dresden, Institut für Genetik, Helmholtzstrasse 10, 01062 Dresden, Germany
| | - José-María Vinardell
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, C.P. 41012, Sevilla, Spain
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Krol E, Klaner C, Gnau P, Kaever V, Essen LO, Becker A. Cyclic mononucleotide- and Clr-dependent gene regulation in Sinorhizobium meliloti. MICROBIOLOGY-SGM 2016; 162:1840-1856. [PMID: 27535558 DOI: 10.1099/mic.0.000356] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To identify physiological processes affected by cAMP in the plant-symbiotic nitrogen-fixing α-proteobacterium Sinorhizobium meliloti Rm2011, cAMP levels were artificially increased by overexpression of its cognate adenylate/guanylate cyclase gene cyaJ. This resulted in high accumulation of cAMP in the culture supernatant, decreased swimming motility and increased production of succinoglycan, an exopolysaccharide involved in host invasion. Weaker, similar phenotypic changes were induced by overexpression of cyaB and cyaG1. Effects on swimming motility and succinoglycan production were partially dependent on clr encoding a cyclic AMP receptor-like protein. Transcriptome profiling of an cyaJ-overexpressing strain identified 72 upregulated and 82 downregulated genes. A considerable number of upregulated genes are related to polysaccharide biosynthesis and osmotic stress response. These included succinoglycan biosynthesis genes, genes of the putative polysaccharide synthesis nodP2-exoF3 cluster and feuN, the first gene of the operon encoding the FeuNPQ regulatory system. Downregulated genes were mostly related to respiration, central metabolism and swimming motility. Promoter-probe studies in the presence of externally added cAMP revealed 18 novel Clr-cAMP-regulated genes. Moreover, the addition of cGMP into the growth medium also promoted clr-dependent gene regulation. In vitro binding of Clr-cAMP and Clr-cGMP to the promoter regions of SMc02178, SMb20906,SMc04190, SMc00925, SMc01136 and cyaF2 required the DNA motif (A/C/T)GT(T/C)(T/C/A)C (N4) G(G/A)(T/A)ACA. Furthermore, SMc02178, SMb20906,SMc04190and SMc00653 promoters were activated by Clr-cAMP/cGMP in Escherichia coli as heterologous host. These findings suggest direct activation of these 7 genes by Clr-cAMP/cGMP.
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Affiliation(s)
- Elizaveta Krol
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Christina Klaner
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Petra Gnau
- Faculty of Chemistry and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Lars-Oliver Essen
- Faculty of Chemistry and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Anke Becker
- Faculty of Biology and LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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Jiao J, Wu LJ, Zhang B, Hu Y, Li Y, Zhang XX, Guo HJ, Liu LX, Chen WX, Zhang Z, Tian CF. MucR Is Required for Transcriptional Activation of Conserved Ion Transporters to Support Nitrogen Fixation of Sinorhizobium fredii in Soybean Nodules. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:352-61. [PMID: 26883490 DOI: 10.1094/mpmi-01-16-0019-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To achieve effective symbiosis with legume, rhizobia should fine-tune their background regulation network in addition to activating key genes involved in nodulation (nod) and nitrogen fixation (nif). Here, we report that an ancestral zinc finger regulator, MucR1, other than its paralog, MucR2, carrying a frameshift mutation, is essential for supporting nitrogen fixation of Sinorhizobium fredii CCBAU45436 within soybean nodules. In contrast to the chromosomal mucR1, mucR2 is located on symbiosis plasmid, indicating its horizontal transfer potential. A MucR2 homolog lacking the frameshift mutation, such as the one from S. fredii NGR234, can complement phenotypic defects of the mucR1 mutant of CCBAU45436. RNA-seq analysis revealed that the MucR1 regulon of CCBAU45436 within nodules exhibits significant difference compared with that of free-living cells. MucR1 is required for active expression of transporters for phosphate, zinc, and elements essential for nitrogenase activity (iron, molybdenum, and sulfur) in nodules but is dispensable for transcription of key genes (nif/fix) involved in nitrogen fixation. Further reverse genetics suggests that S. fredii uses high-affinity transporters to meet the demand for zinc and phosphate within nodules. These findings, together with the horizontal transfer potential of the mucR homolog, imply an intriguing evolutionary role of this ancestral regulator in supporting nitrogen fixation.
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Affiliation(s)
- Jian Jiao
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Li Juan Wu
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Biliang Zhang
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yue Hu
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Yan Li
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Xing Xing Zhang
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Hui Juan Guo
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Li Xue Liu
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Ziding Zhang
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- 1 State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- 2 Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China; and
- 3 Rhizobium Research Center, China Agricultural University, Beijing, China
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Scharf BE, Hynes MF, Alexandre GM. Chemotaxis signaling systems in model beneficial plant-bacteria associations. PLANT MOLECULAR BIOLOGY 2016; 90:549-59. [PMID: 26797793 DOI: 10.1007/s11103-016-0432-4] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/04/2016] [Indexed: 05/07/2023]
Abstract
Beneficial plant-microbe associations play critical roles in plant health. Bacterial chemotaxis provides a competitive advantage to motile flagellated bacteria in colonization of plant root surfaces, which is a prerequisite for the establishment of beneficial associations. Chemotaxis signaling enables motile soil bacteria to sense and respond to gradients of chemical compounds released by plant roots. This process allows bacteria to actively swim towards plant roots and is thus critical for competitive root surface colonization. The complete genome sequences of several plant-associated bacterial species indicate the presence of multiple chemotaxis systems and a large number of chemoreceptors. Further, most soil bacteria are motile and capable of chemotaxis, and chemotaxis-encoding genes are enriched in the bacteria found in the rhizosphere compared to the bulk soil. This review compares the architecture and diversity of chemotaxis signaling systems in model beneficial plant-associated bacteria and discusses their relevance to the rhizosphere lifestyle. While it is unclear how controlling chemotaxis via multiple parallel chemotaxis systems provides a competitive advantage to certain bacterial species, the presence of a larger number of chemoreceptors is likely to contribute to the ability of motile bacteria to survive in the soil and to compete for root surface colonization.
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Affiliation(s)
- Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Gladys M Alexandre
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle. J Bacteriol 2016; 198:1149-59. [PMID: 26833409 DOI: 10.1128/jb.00896-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/24/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The dimorphic alphaproteobacterium Prosthecomicrobium hirschii has both short-stalked and long-stalked morphotypes. Notably, these morphologies do not arise from transitions in a cell cycle. Instead, the maternal cell morphology is typically reproduced in daughter cells, which results in microcolonies of a single cell type. In this work, we further characterized the short-stalked cells and found that these cells have a Caulobacter-like life cycle in which cell division leads to the generation of two morphologically distinct daughter cells. Using a microfluidic device and total internal reflection fluorescence (TIRF) microscopy, we observed that motile short-stalked cells attach to a surface by means of a polar adhesin. Cells attached at their poles elongate and ultimately release motile daughter cells. Robust biofilm growth occurs in the microfluidic device, enabling the collection of synchronous motile cells and downstream analysis of cell growth and attachment. Analysis of a draft P. hirschii genome sequence indicates the presence of CtrA-dependent cell cycle regulation. This characterization of P. hirschii will enable future studies on the mechanisms underlying complex morphologies and polymorphic cell cycles. IMPORTANCE Bacterial cell shape plays a critical role in regulating important behaviors, such as attachment to surfaces, motility, predation, and cellular differentiation; however, most studies on these behaviors focus on bacteria with relatively simple morphologies, such as rods and spheres. Notably, complex morphologies abound throughout the bacteria, with striking examples, such as P. hirschii, found within the stalked Alphaproteobacteria. P. hirschii is an outstanding candidate for studies of complex morphology generation and polymorphic cell cycles. Here, the cell cycle and genome of P. hirschii are characterized. This work sets the stage for future studies of the impact of complex cell shapes on bacterial behaviors.
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Rachwał K, Matczyńska E, Janczarek M. Transcriptome profiling of a Rhizobium leguminosarum bv. trifolii rosR mutant reveals the role of the transcriptional regulator RosR in motility, synthesis of cell-surface components, and other cellular processes. BMC Genomics 2015; 16:1111. [PMID: 26715155 PMCID: PMC4696191 DOI: 10.1186/s12864-015-2332-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022] Open
Abstract
Background Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing a symbiotic relationship with red clover (Trifolium pratense). The presence of surface polysaccharides and other extracellular components as well as motility and competitiveness are essential traits for both adaptation of this bacterium to changing environmental conditions and successful infection of host plant roots. The R. leguminosarum bv. trifolii rosR gene encodes a protein belonging to the family of Ros/MucR transcriptional regulators, which contain a Cys2His2-type zinc-finger motif and are involved in the regulation of exopolysaccharide synthesis in several rhizobial species. Previously, it was established that a mutation in the rosR gene significantly decreased exopolysaccharide synthesis, increased bacterial sensitivity to some stress factors, and negatively affected infection of clover roots. Results RNA-Seq analysis performed for the R. leguminosarum bv. trifolii wild-type strain Rt24.2 and its derivative Rt2472 carrying a rosR mutation identified a large number of genes which were differentially expressed in these two backgrounds. A considerable majority of these genes were up-regulated in the mutant (63.22 %), indicating that RosR functions mainly as a repressor. Transcriptome profiling of the rosR mutant revealed a role of this regulator in several cellular processes, including the synthesis of cell-surface components and polysaccharides, motility, and bacterial metabolism. Moreover, it was established that the Rt2472 strain was characterized by a longer generation time and showed an increased aggregation ability, but was impaired in motility as a result of considerably reduced flagellation of its cells. Conclusions The comparative transcriptome analysis of R. leguminosarum bv. trifolii wild-type Rt24.2 and the Rt2472 mutant identified a set of genes belonging to the RosR regulon and confirmed the important role of RosR in the regulatory network. The data obtained in this study indicate that this protein affects several cellular processes and plays an important role in bacterial adaptation to environmental conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2332-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kamila Rachwał
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Ewa Matczyńska
- Department of Mathematics and Computer Science, Institute of Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348, Cracow, Poland.,Genomed SA, Ponczowa 12, 02-971, Warsaw, Poland
| | - Monika Janczarek
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland.
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Baumgardt K, Šmídová K, Rahn H, Lochnit G, Robledo M, Evguenieva-Hackenberg E. The stress-related, rhizobial small RNA RcsR1 destabilizes the autoinducer synthase encoding mRNA sinI in Sinorhizobium meliloti. RNA Biol 2015; 13:486-99. [PMID: 26588798 PMCID: PMC4962803 DOI: 10.1080/15476286.2015.1110673] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Quorum sensing is a cell density-dependent communication system of bacteria relying on autoinducer molecules. During the analysis of the post-transcriptional regulation of quorum sensing in the nitrogen fixing plant symbiont Sinorhizobium meliloti, we predicted and verified a direct interaction between the 5'-UTR of sinI mRNA encoding the autoinducer synthase and a small RNA (sRNA), which we named RcsR1. In vitro, RcsR1 prevented cleavage in the 5'-UTR of sinI by RNase E and impaired sinI translation. In line with low ribosomal occupancy and transcript destabilization upon binding of RcsR1 to sinI, overproduction of RcsR1 in S. meliloti resulted in lower level and shorter half-life of sinI mRNA, and in decreased autoinducer amount. Although RcsR1 can influence quorum sensing via sinI, its level did not vary at different cell densities, but decreased under salt stress and increased at low temperature. We found that RcsR1 and its stress-related expression pattern, but not the interaction with sinI homologs, are conserved in Sinorhizobium, Rhizobium and Agrobacterium. Consistently, overproduction of RcsR1 in S. meliloti and Agrobacterium tumefaciens inhibited growth at high salinity. We identified conserved targets of RcsR1 and showed that most conserved interactions and the effect on growth under salt stress are mediated by the first stem-loop of RcsR1, while its central part is responsible for the species-specific interaction with sinI. We conclude that RcsR1 is an ancient, stress-related riboregulator in rhizobia and propose that it links stress responses to quorum sensing in S. meliloti.
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Affiliation(s)
- Kathrin Baumgardt
- a Institute for Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring Giessen , Germany
| | - Klára Šmídová
- a Institute for Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring Giessen , Germany.,b Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Studnickova 7, Prague 2, and Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Bioinformatics, Videnska Prague 4 , Czech Republic
| | - Helen Rahn
- a Institute for Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring Giessen , Germany
| | - Günter Lochnit
- c Institute of Biochemistry, Friedrichstraße Giessen , Germany
| | - Marta Robledo
- d LOEWE Center for Synthetic Microbiology and Department of Biology, Hans-Meerwein-Straße Marburg , Germany
| | - Elena Evguenieva-Hackenberg
- a Institute for Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring Giessen , Germany
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Cyclic Di-GMP Regulates Multiple Cellular Functions in the Symbiotic Alphaproteobacterium Sinorhizobium meliloti. J Bacteriol 2015; 198:521-35. [PMID: 26574513 DOI: 10.1128/jb.00795-15] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/09/2015] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Sinorhizobium meliloti undergoes major lifestyle changes between planktonic states, biofilm formation, and symbiosis with leguminous plant hosts. In many bacteria, the second messenger 3',5'-cyclic di-GMP (c-di-GMP, or cdG) promotes a sessile lifestyle by regulating a plethora of processes involved in biofilm formation, including motility and biosynthesis of exopolysaccharides (EPS). Here, we systematically investigated the role of cdG in S. meliloti Rm2011 encoding 22 proteins putatively associated with cdG synthesis, degradation, or binding. Single mutations in 21 of these genes did not cause evident changes in biofilm formation, motility, or EPS biosynthesis. In contrast, manipulation of cdG levels by overproducing endogenous or heterologous diguanylate cyclases (DGCs) or phosphodiesterases (PDEs) affected these processes and accumulation of N-Acyl-homoserine lactones in the culture supernatant. Specifically, individual overexpression of the S. meliloti genes pleD, SMb20523, SMb20447, SMc01464, and SMc03178 encoding putative DGCs and of SMb21517 encoding a single-domain PDE protein had an impact and resulted in increased levels of cdG. Compared to the wild type, an S. meliloti strain that did not produce detectable levels of cdG (cdG(0)) was more sensitive to acid stress. However, it was symbiotically potent, unaffected in motility, and only slightly reduced in biofilm formation. The SMc01790-SMc01796 locus, homologous to the Agrobacterium tumefaciens uppABCDEF cluster governing biosynthesis of a unipolarly localized polysaccharide, was found to be required for cdG-stimulated biofilm formation, while the single-domain PilZ protein McrA was identified as a cdG receptor protein involved in regulation of motility. IMPORTANCE We present the first systematic genome-wide investigation of the role of 3',5'-cyclic di-GMP (c-di-GMP, or cdG) in regulation of motility, biosynthesis of exopolysaccharides, biofilm formation, quorum sensing, and symbiosis in a symbiotic alpha-rhizobial species. Phenotypes of an S. meliloti strain unable to produce cdG (cdG(0)) demonstrated that this second messenger is not essential for root nodule symbiosis but may contribute to acid tolerance. Our data further suggest that enhanced levels of cdG promote sessility of S. meliloti and uncovered a single-domain PilZ protein as regulator of motility.
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Malgieri G, Palmieri M, Russo L, Fattorusso R, Pedone PV, Isernia C. The prokaryotic zinc-finger: structure, function and comparison with the eukaryotic counterpart. FEBS J 2015; 282:4480-96. [PMID: 26365095 DOI: 10.1111/febs.13503] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/23/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Classical zinc finger (ZF) domains were thought to be confined to the eukaryotic kingdom until the transcriptional regulator Ros protein was identified in Agrobacterium tumefaciens. The Ros Cys2 His2 ZF binds DNA in a peculiar mode and folds in a domain significantly larger than its eukaryotic counterpart consisting of 58 amino acids (the 9-66 region) arranged in a βββαα topology, and stabilized by a conserved, extensive, 15-residue hydrophobic core. The prokaryotic ZF domain, then, shows some intriguing new features that make it interestingly different from its eukaryotic counterpart. This review will focus on the prokaryotic ZFs, summarizing and discussing differences and analogies with the eukaryotic domains and providing important insights into their structure/function relationships.
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Affiliation(s)
- Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Maddalena Palmieri
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, II University of Naples, Caserta, Italy.,Interuniversity Research Centre on Bioactive Peptides, University of Naples 'Federico II', Naples, Italy
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Bernabéu-Roda L, Calatrava-Morales N, Cuéllar V, Soto MJ. Characterization of surface motility in Sinorhizobium meliloti: regulation and role in symbiosis. Symbiosis 2015. [DOI: 10.1007/s13199-015-0340-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Heavner ME, Qiu WG, Cheng HP. Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales. PLoS One 2015; 10:e0135655. [PMID: 26309130 PMCID: PMC4550343 DOI: 10.1371/journal.pone.0135655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/23/2015] [Indexed: 11/18/2022] Open
Abstract
Both bacterial symbionts and pathogens rely on their host-sensing mechanisms to activate the biosynthetic pathways necessary for their invasion into host cells. The Gram-negative bacterium Sinorhizobium meliloti relies on its RSI (ExoR-ExoS-ChvI) Invasion Switch to turn on the production of succinoglycan, an exopolysaccharide required for its host invasion. Recent whole-genome sequencing efforts have uncovered putative components of RSI-like invasion switches in many other symbiotic and pathogenic bacteria. To explore the possibility of the existence of a common invasion switch, we have conducted a phylogenomic survey of orthologous ExoR, ExoS, and ChvI tripartite sets in more than ninety proteobacterial genomes. Our analyses suggest that functional orthologs of the RSI invasion switch co-exist in Rhizobiales, an order characterized by numerous invasive species, but not in the order’s close relatives. Phylogenomic analyses and reconstruction of orthologous sets of the three proteins in Alphaproteobacteria confirm Rhizobiales-specific gene synteny and congruent RSI evolutionary histories. Evolutionary analyses further revealed site-specific substitutions correlated specifically to either animal-bacteria or plant-bacteria associations. Lineage restricted conservation of any one specialized gene is in itself an indication of species adaptation. However, the orthologous phylogenetic co-occurrence of all interacting partners within this single signaling pathway strongly suggests that the development of the RSI switch was a key adaptive mechanism. The RSI invasion switch, originally found in S. meliloti, is a characteristic of the Rhizobiales, and potentially a conserved crucial activation step that may be targeted to control host invasion by pathogenic bacterial species.
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Affiliation(s)
- Mary Ellen Heavner
- Biochemistry Program, The Graduate Center, City University of New York, New York, New York, United States of America
| | - Wei-Gang Qiu
- Biological Sciences Department, Hunter College, City University of New York, New York, New York, United States of America
| | - Hai-Ping Cheng
- Biochemistry Program, The Graduate Center, City University of New York, New York, New York, United States of America
- Biological Sciences Department, Lehman College, City University of New York, Bronx, New York, United States of America
- * E-mail:
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A stress-induced small RNA modulates alpha-rhizobial cell cycle progression. PLoS Genet 2015; 11:e1005153. [PMID: 25923724 PMCID: PMC4414408 DOI: 10.1371/journal.pgen.1005153] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 03/18/2015] [Indexed: 01/22/2023] Open
Abstract
Mechanisms adjusting replication initiation and cell cycle progression in response to environmental conditions are crucial for microbial survival. Functional characterization of the trans-encoded small non-coding RNA (trans-sRNA) EcpR1 in the plant-symbiotic alpha-proteobacterium Sinorhizobium meliloti revealed a role of this class of riboregulators in modulation of cell cycle regulation. EcpR1 is broadly conserved in at least five families of the Rhizobiales and is predicted to form a stable structure with two defined stem-loop domains. In S. meliloti, this trans-sRNA is encoded downstream of the divK-pleD operon. ecpR1 belongs to the stringent response regulon, and its expression was induced by various stress factors and in stationary phase. Induced EcpR1 overproduction led to cell elongation and increased DNA content, while deletion of ecpR1 resulted in reduced competitiveness. Computationally predicted EcpR1 targets were enriched with cell cycle-related mRNAs. Post-transcriptional repression of the cell cycle key regulatory genes gcrA and dnaA mediated by mRNA base-pairing with the strongly conserved loop 1 of EcpR1 was experimentally confirmed by two-plasmid differential gene expression assays and compensatory changes in sRNA and mRNA. Evidence is presented for EcpR1 promoting RNase E-dependent degradation of the dnaA mRNA. We propose that EcpR1 contributes to modulation of cell cycle regulation under detrimental conditions. Microorganisms frequently encounter adverse conditions unfavorable for cell proliferation. They have evolved diverse mechanisms, including transcriptional control and targeted protein degradation, to adjust cell cycle progression in response to environmental cues. Non-coding RNAs are widespread regulators of various cellular processes in all domains of life. In prokaryotes, trans-encoded small non-coding RNAs (trans-sRNAs) contribute to a rapid cellular response to changing environments, but so far have not been directly related to cell cycle regulation. Here, we report the first example of a trans-sRNA (EcpR1) with two experimentally confirmed targets in the core of cell cycle regulation and demonstrate that in the plant-symbiotic alpha-proteobacterium Sinorhizobium meliloti the regulatory mechanism involves base-pairing of this sRNA with the dnaA and gcrA mRNAs. Most trans-sRNAs are restricted to closely related species, but the stress-induced EcpR1 is broadly conserved in the order of Rhizobiales suggesting an evolutionary advantage conferred by ecpR1. It broadens the functional diversity of prokaryotic sRNAs and adds a new regulatory level to the mechanisms that contribute to interlinking stress responses with the cell cycle machinery.
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Charoenpanich P, Soto MJ, Becker A, McIntosh M. Quorum sensing restrains growth and is rapidly inactivated during domestication of Sinorhizobium meliloti. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:373-382. [PMID: 25534533 DOI: 10.1111/1758-2229.12262] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/11/2014] [Indexed: 06/04/2023]
Abstract
Microbial cooperative behaviours, such as quorum sensing (QS), improve survival and this explains their prevalence throughout the microbial world. However, relatively little is known about the mechanisms by which cooperation promotes survival. Furthermore, cooperation typically requires costly contributions, e.g. exopolysaccharides, which are produced from limited resources. Inevitably, cooperation is vulnerable to damaging mutations which results in mutants that are relieved of the burden of contributing but nonetheless benefit from the contributions of their parent. Unless somehow prevented, such mutants may outcompete and replace the parent. The bacterium Sinorhizobium meliloti uses QS to activate the production of copious levels of exopolysaccharide (EPS). Domestication of this bacterium is typified by the appearance of spontaneous mutants incapable of EPS production, which take advantage of EPS production by the parent and outcompete the parent. We found that all of the mutants were defect in QS, implying that loss of QS is a typical consequence of the domestication of this bacterium. This instability was traced to several QS-regulated processes, including a QS-dependent restraint of growth, providing the mutant with a significant growth advantage. A model is proposed whereby QS restrains population growth to prevent overcrowding and prepares the population for the survival of severe conditions.
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Affiliation(s)
- Pornsri Charoenpanich
- LOEWE Center for Synthetic Microbiology, Faculty of Biology, University of Marburg, Marburg, Germany
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The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3. J Bacteriol 2015; 197:1792-806. [PMID: 25777671 DOI: 10.1128/jb.02626-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/06/2015] [Indexed: 01/27/2023] Open
Abstract
UNLABELLED In Sinorhizobium meliloti, three NodD transcriptional regulators activate bacterial nodulation (nod) gene expression. NodD1 and NodD2 require plant compounds to activate nod genes. The NodD3 protein does not require exogenous compounds to activate nod gene expression; instead, another transcriptional regulator, SyrM, activates nodD3 expression. In addition, NodD3 can activate syrM expression. SyrM also activates expression of another gene, syrA, which when overexpressed causes a dramatic increase in exopolysaccharide production. In a previous study, we identified more than 200 genes with altered expression in a strain overexpressing nodD3. In this work, we define the transcriptomes of strains overexpressing syrM or syrA. The syrM, nodD3, and syrA overexpression transcriptomes share similar gene expression changes; analyses imply that nodD3 and syrA are the only targets directly activated by SyrM. We propose that most of the gene expression changes observed when nodD3 is overexpressed are due to NodD3 activation of syrM expression, which in turn stimulates SyrM activation of syrA expression. The subsequent increase in SyrA abundance results in broad changes in gene expression, most likely mediated by the ChvI-ExoS-ExoR regulatory circuit. IMPORTANCE Symbioses with bacteria are prevalent across the animal and plant kingdoms. Our system of study, the rhizobium-legume symbiosis (Sinorhizobium meliloti and Medicago spp.), involves specific host-microbe signaling, differentiation in both partners, and metabolic exchange of bacterial fixed nitrogen for host photosynthate. During this complex developmental process, both bacteria and plants undergo profound changes in gene expression. The S. meliloti SyrM-NodD3-SyrA and ChvI-ExoS-ExoR regulatory circuits affect gene expression and are important for optimal symbiosis. In this study, we defined the transcriptomes of S. meliloti overexpressing SyrM or SyrA. In addition to identifying new targets of the SyrM-NodD3-SyrA regulatory circuit, our work further suggests how it is linked to the ChvI-ExoS-ExoR regulatory circuit.
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Schlüter JP, Czuppon P, Schauer O, Pfaffelhuber P, McIntosh M, Becker A. Classification of phenotypic subpopulations in isogenic bacterial cultures by triple promoter probing at single cell level. J Biotechnol 2015; 198:3-14. [PMID: 25661839 DOI: 10.1016/j.jbiotec.2015.01.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/17/2015] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
Phenotypic heterogeneity, defined as the unequal behavior of individuals in an isogenic population, is prevalent in microorganisms. It has a significant impact both on industrial bioprocesses and microbial ecology. We introduce a new versatile reporter system designed for simultaneous monitoring of the activities of three different promoters, where each promoter is fused to a dedicated fluorescent reporter gene (cerulean, mCherry, and mVenus). The compact 3.1 kb triple reporter cassette can either be carried on a replicating plasmid or integrated into the genome avoiding artifacts associated with variation in copy number of plasmid-borne reporter constructs. This construct was applied to monitor promoter activities related to quorum sensing (sinI promoter) and biosynthesis of the exopolysaccharide galactoglucan (wgeA promoter) at single cell level in colonies of the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti growing in a microfluidics system. The T5-promoter served as a constitutive and homogeneously active control promoter indicating cell viability. wgeA promoter activity was heterogeneous over the whole period of colony development, whereas sinI promoter activity passed through a phase of heterogeneity before becoming homogeneous at late stages. Although quorum sensing-dependent regulation is a major factor activating galactoglucan production, activities of both promoters did not correlate at single cell level. We developed a novel mathematical strategy for classification of the gene expression status in cell populations based on the increase in fluorescence over time in each individual. With respect to galactoglucan biosynthesis, cells in the population were classified into non-contributors, weak contributors, and strong contributors.
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Affiliation(s)
- Jan-Philip Schlüter
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, Marburg, Germany
| | - Peter Czuppon
- Department of Mathematical Stochastics, Faculty of Mathematics and Physics, Albert-Ludwigs University Freiburg, Freiburg im Breisgau, Germany
| | - Oliver Schauer
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, Marburg, Germany
| | - Peter Pfaffelhuber
- Department of Mathematical Stochastics, Faculty of Mathematics and Physics, Albert-Ludwigs University Freiburg, Freiburg im Breisgau, Germany
| | - Matthew McIntosh
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, Marburg, Germany.
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-University Marburg, Marburg, Germany.
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Panis G, Murray SR, Viollier PH. Versatility of global transcriptional regulators in alpha-Proteobacteria: from essential cell cycle control to ancillary functions. FEMS Microbiol Rev 2014; 39:120-33. [PMID: 25793963 DOI: 10.1093/femsre/fuu002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recent data indicate that cell cycle transcription in many alpha-Proteobacteria is executed by at least three conserved functional modules in which pairs of antagonistic regulators act jointly, rather than in isolation, to control transcription in S-, G2- or G1-phase. Inactivation of module components often results in pleiotropic defects, ranging from cell death and impaired cell division to fairly benign deficiencies in motility. Expression of module components can follow systemic (cell cycle) or external (nutritional/cell density) cues and may be implemented by auto-regulation, ancillary regulators or other (unknown) mechanisms. Here, we highlight the recent progress in understanding the molecular events and the genetic relationships of the module components in environmental, pathogenic and/or symbiotic alpha-proteobacterial genera. Additionally, we take advantage of the recent genome-wide transcriptional analyses performed in the model alpha-Proteobacterium Caulobacter crescentus to illustrate the complexity of the interactions of the global regulators at selected cell cycle-regulated promoters and we detail the consequences of (mis-)expression when the regulators are absent. This review thus provides the first detailed mechanistic framework for understanding orthologous operational principles acting on cell cycle-regulated promoters in other alpha-Proteobacteria.
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Affiliation(s)
- Gaël Panis
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Sean R Murray
- Department of Biology, Center for Cancer and Developmental Biology, Interdisciplinary Research Institute for the Sciences, California State University Northridge, 18111 Nordhoff Street, Northridge, CA 91330-8303, USA
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine/CMU, University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
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Krol E, Becker A. Rhizobial homologs of the fatty acid transporter FadL facilitate perception of long-chain acyl-homoserine lactone signals. Proc Natl Acad Sci U S A 2014; 111:10702-7. [PMID: 25002473 PMCID: PMC4115515 DOI: 10.1073/pnas.1404929111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quorum sensing (QS) using N-acyl homoserine lactones (AHLs) as signal molecules is a common strategy used by diverse Gram-negative bacteria. A widespread mechanism of AHL sensing involves binding of these molecules by cytosolic LuxR-type transcriptional regulators, which requires uptake of external AHLs. The outer membrane is supposed to be an efficient barrier for diffusion of long-chain AHLs. Here we report evidence that in Sinorhizobium meliloti, sensing of AHLs with acyl chains composed of 14 or more carbons is facilitated by the outer membrane protein FadLSm, a homolog of the Escherichia coli FadLEc long-chain fatty acid transporter. The effect of fadLSm on AHL sensing was more prominent for longer and more hydrophobic signal molecules. Using reporter gene fusions to QS target genes, we found that fadLSm increased AHL sensitivity and accelerated the course of QS. In contrast to FadLEc, FadLSm did not support uptake of oleic acid, but did contribute to growth on palmitoleic acid. FadLSm homologs from related symbiotic α-rhizobia and the plant pathogen Agrobacterium tumefaciens differed in their ability to facilitate long-chain AHL sensing or to support growth on oleic acid. FadLAt was found to be ineffective toward long-chain AHLs. We obtained evidence that the predicted extracellular loop 5 of FadLSm and further α-rhizobial FadL proteins contains determinants of specificity to long-chain AHLs. Replacement of a part of loop 5 by the corresponding region from α-rhizobial FadL proteins transferred sensitivity for long-chain AHLs to FadLAt.
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Affiliation(s)
- Elizaveta Krol
- LOEWE Center for Synthetic Microbiology, Department of Biology, Philipps-University Marburg, 35032 Marburg, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, Department of Biology, Philipps-University Marburg, 35032 Marburg, Germany
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50
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Fumeaux C, Radhakrishnan SK, Ardissone S, Théraulaz L, Frandi A, Martins D, Nesper J, Abel S, Jenal U, Viollier PH. Cell cycle transition from S-phase to G1 in Caulobacter is mediated by ancestral virulence regulators. Nat Commun 2014; 5:4081. [PMID: 24939058 PMCID: PMC4083442 DOI: 10.1038/ncomms5081] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 05/09/2014] [Indexed: 11/10/2022] Open
Abstract
Zinc-finger domain transcriptional regulators regulate a myriad of functions in eukaryotes. Interestingly, ancestral versions (MucR) from Alpha-proteobacteria control bacterial virulence/symbiosis. Whether virulence regulators can also control cell cycle transcription is unknown. Here we report that MucR proteins implement a hitherto elusive primordial S→G1 transcriptional switch. After charting G1-specific promoters in the cell cycle model Caulobacter crescentus by comparative ChIP-seq, we use one such promoter as genetic proxy to unearth two MucR paralogs, MucR1/2, as constituents of a quadripartite and homeostatic regulatory module directing the S→G1 transcriptional switch. Surprisingly, MucR orthologues that regulate virulence and symbiosis gene transcription in Brucella, Agrobacterium or Sinorhizobium support this S→G1 switch in Caulobacter. Pan-genomic ChIP-seq analyses in Sinorhizobium and Caulobacter show that this module indeed targets orthologous genes. We propose that MucR proteins and possibly other virulence regulators primarily control bacterial cell cycle (G1-phase) transcription, rendering expression of target (virulence) genes periodic and in tune with the cell cycle. The bacterium Caulobacter crescentus divides asymmetrically to generate a replicative stalk cell and a quiescent swarmer cell. Fumeaux et al. show that MucR zinc-finger transcription factors, which regulate virulence in other species, also control re-entry into quiescence in Caulobacter.
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Affiliation(s)
- Coralie Fumeaux
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Sunish Kumar Radhakrishnan
- 1] Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland [2]
| | - Silvia Ardissone
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Laurence Théraulaz
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Antonio Frandi
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Daniel Martins
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
| | - Jutta Nesper
- Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Sören Abel
- 1] Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland [2]
| | - Urs Jenal
- Biozentrum of the University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Patrick H Viollier
- Department Microbiology and Molecular Medicine, Faculty of Medicine/CMU, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Rue Michel Servet 1, 1211 Genève 4, Switzerland
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