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Hemkemeyer M, Schwalb SA, Heinze S, Joergensen RG, Wichern F. Functions of elements in soil microorganisms. Microbiol Res 2021; 252:126832. [PMID: 34508963 DOI: 10.1016/j.micres.2021.126832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
The soil microbial community fulfils various functions, such as nutrient cycling and carbon (C) sequestration, therefore contributing to maintenance of soil fertility and mitigation of global warming. In this context, a major focus of research has been on C, nitrogen (N) and phosphorus (P) cycling. However, from aquatic and other environments, it is well known that other elements beyond C, N, and P are essential for microbial functioning. Nonetheless, for soil microorganisms this knowledge has not yet been synthesised. To gain a better mechanistic understanding of microbial processes in soil systems, we aimed at summarising the current knowledge on the function of a range of essential or beneficial elements, which may affect the efficiency of microbial processes in soil. This knowledge is discussed in the context of microbial driven nutrient and C cycling. Our findings may support future investigations and data evaluation, where other elements than C, N, and P affect microbial processes.
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Affiliation(s)
- Michael Hemkemeyer
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany.
| | - Sanja A Schwalb
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
| | - Stefanie Heinze
- Department of Soil Science & Soil Ecology, Ruhr-University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Rainer Georg Joergensen
- Department of Soil Biology and Plant Nutrition, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Florian Wichern
- Department of Soil Science and Plant Nutrition, Institute of Biogenic Resources in Sustainable Food Systems - From Farm to Function, Rhine-Waal University of Applied Sciences, Marie-Curie-Str. 1, 47533 Kleve, Germany
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2
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New insights into Nod factor biosynthesis: Analyses of chitooligomers and lipo-chitooligomers of Rhizobium sp. IRBG74 mutants. Carbohydr Res 2016; 434:83-93. [PMID: 27623438 PMCID: PMC5080398 DOI: 10.1016/j.carres.2016.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 07/30/2016] [Accepted: 08/01/2016] [Indexed: 11/30/2022]
Abstract
Soil-dwelling, nitrogen-fixing rhizobia signal their presence to legume hosts by secreting lipo-chitooligomers (LCOs) that are decorated with a variety of chemical substituents. It has long been assumed, but never empirically shown, that the LCO backbone is synthesized first by NodC, NodB, and NodA, followed by addition of one or more substituents by other Nod proteins. By analyzing a collection of in-frame deletion mutants of key nod genes in the bacterium Rhizobium sp. IRBG74 by mass spectrometry, we were able to shed light on the possible substitution order of LCO decorations, and we discovered that the prevailing view is probably erroneous. We found that most substituents could be transferred to a short chitin backbone prior to acylation by NodA, which is probably one of the last steps in LCO biosynthesis. The existence of substituted, short chitin oligomers offers new insights into symbiotic plant–microbe signaling. Rhizobia produce chemically substituted, short chitooligomers (COs). Deacetylation of the non-reducing GlcNAc is necessary for most substitutions. Acylation may be one of the last steps in the biosynthesis of rhizobial lipo-chitooligosaccharides (LCOs).
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3
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Davis-Richardson AG, Russell JT, Dias R, McKinlay AJ, Canepa R, Fagen JR, Rusoff KT, Drew JC, Kolaczkowski B, Emerich DW, Triplett EW. Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N2-Fixing Symbiosis. Front Microbiol 2016; 7:518. [PMID: 27148207 PMCID: PMC4840208 DOI: 10.3389/fmicb.2016.00518] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/29/2016] [Indexed: 11/16/2022] Open
Abstract
Very little is known about the role of epigenetics in the differentiation of a bacterium from the free-living to the symbiotic state. Here genome-wide analysis of DNA methylation changes between these states is described using the model of symbiosis between soybean and its root nodule-forming, nitrogen-fixing symbiont, Bradyrhizobium diazoefficiens. PacBio resequencing of the B. diazoefficiens genome from both states revealed 43,061 sites recognized by five motifs with the potential to be methylated genome-wide. Of those sites, 3276 changed methylation states in 2921 genes or 35.5% of all genes in the genome. Over 10% of the methylation changes occurred within the symbiosis island that comprises 7.4% of the genome. The CCTTGAG motif was methylated only during symbiosis with 1361 adenosines methylated among the 1700 possible sites. Another 89 genes within the symbiotic island and 768 genes throughout the genome were found to have methylation and significant expression changes during symbiotic development. Of those, nine known symbiosis genes involved in all phases of symbiotic development including early infection events, nodule development, and nitrogenase production. These associations between methylation and expression changes in many B. diazoefficiens genes suggest an important role of the epigenome in bacterial differentiation to the symbiotic state.
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Affiliation(s)
- Austin G Davis-Richardson
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Jordan T Russell
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Raquel Dias
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Andrew J McKinlay
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Ronald Canepa
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Jennie R Fagen
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Kristin T Rusoff
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Jennifer C Drew
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - Bryan Kolaczkowski
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
| | - David W Emerich
- Biochemistry Department, University of Missouri Columbia, MO, USA
| | - Eric W Triplett
- Microbiology and Cell Science Department, Institute of Food and Agricultural Sciences, University of Florida Gainesville, FL, USA
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4
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Shuguo H, Wei Z, Chao Z, Daoji W. One-step expression and tyrosine O-sulfonation of Ax21 in Escherichia coli. Appl Biochem Biotechnol 2012; 166:1368-79. [PMID: 22249854 DOI: 10.1007/s12010-011-9525-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/26/2011] [Indexed: 11/25/2022]
Abstract
Ax21 (activator of Xa21-mediated immunity), a pathogen-associated molecular pattern secreted by Xanthomonas oryzae pv. oryzae, can be perceived by a membrane-located pattern recognition receptor Xa21 and triggered immune responses in rice. An Ax21-derived peptide (17-amino acid) containing a sulfated tyrosine-22 (axY(S)22) is sufficient for Ax21 activity. Here, we expressed Ax21 and O-sulfated its tyrosine-22 through coexpressing a putative tyrosine sulfotransferase, raxST, and two other genes involved in the synthesis of 3'-phosphoadenosine 5'-phosphosulfate in Escherichia coli BL21 (DE3). The sulfated Ax21 fused with a histidine tag in its N-terminus was extracted and bound onto a Ni-NTA agarose and then cleaved with Factor Xa and CNBr in turn. Δax21Y(S)22, a 36-amino acid peptide covering axY(S)22 in the lysate supernatant, was finally yielded after ultrafiltration. The purified peptide was further verified by Tricine-SDS-PAGE and isoelectrofocusing electrophoresis. Lesion length analysis, reactive oxygen species production, and mitogen-activated protein kinase (MAPK) activation of rice leaves inoculated with Δax21Y(S)22 confirmed the activity of the sulfated peptide. Overall, this study successfully established an efficient system for expression and purification of a sulfated peptide. In addition, the sulfotransferase activity of RaxST was confirmed for the first time.
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Affiliation(s)
- Hou Shuguo
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, China.
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5
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The Role of Diffusible Signals in the Establishment of Rhizobial and Mycorrhizal Symbioses. SIGNALING AND COMMUNICATION IN PLANT SYMBIOSIS 2012. [DOI: 10.1007/978-3-642-20966-6_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Steenkamp ET, Stepkowski T, Przymusiak A, Botha WJ, Law IJ. Cowpea and peanut in southern Africa are nodulated by diverse Bradyrhizobium strains harboring nodulation genes that belong to the large pantropical clade common in Africa. Mol Phylogenet Evol 2008; 48:1131-44. [PMID: 18539053 DOI: 10.1016/j.ympev.2008.04.032] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 04/13/2008] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
Abstract
Cowpea (Vigna unguiculata) and peanut (Arachis hypogaea) in southern Africa are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the identity of these bacteria, a collection of 22 isolates originating from the root nodules of both hosts in Botswana and South Africa was investigated using the combined sequences for the core genome genes rrs, recA, and glnII. These data separated the majority of the isolates into one of three unique lineages that most likely represent novel Bradyrhizobium species. Some isolates were also conspecific with B. yuanmingense and with B. elkanii, although none grouped with B. japonicum, B. canariense or B. liaoningense. To study the evolution of nodulation genes in these bacteria, the common nodulation gene, nodA, and host-specific nodulation genes, nodZ, noeE, and noeI, were analyzed. The nodA phylogeny showed that the cowpea and peanut Bradyrhizobium isolates represent various locally adapted groups or ecotypes that form part of Clade III of the seven known BradyrhizobiumnodA clades. This large and highly diverse clade comprises all strains from sub-Saharan Africa, as well as some originating from the Americas, Australia, Indonesia, China and Japan. Some similar groupings were supported by the other nodulation genes, although the overall phylogenies for the nodulation genes were incongruent with that inferred from the core genome genes, suggesting that horizontal gene transfer significantly influences the evolution of cowpea and peanut root-nodule bacteria. Furthermore, identification of the nodZ, noeI, and noeE genes in the isolates tested indicates that African Bradyrhizobium species may produce highly decorated nodulation factors, which potentially represent an important adaptation enabling nodulation of a great variety of legumes inhabiting the African continent.
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Affiliation(s)
- Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa.
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Townsend GE, Keating DH. Identification and characterization of KpsS, a novel polysaccharide sulphotransferase in Mesorhizobium loti. Mol Microbiol 2008; 68:1149-64. [PMID: 18430142 DOI: 10.1111/j.1365-2958.2008.06215.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plants enter into symbiotic relationships with bacteria that allow survival in nutrient-limiting environments. The bacterium Mesorhizobium loti enters into a symbiosis with the legume host, Lotus japonicus, which results in the formation of novel plant structures called root nodules. The bacteria colonize the nodules, and are internalized into the cytoplasm of the plant cells, where they reduce molecular dinitrogen for the plant. Symbiosis between M. loti and L. japonicus requires bacterial synthesis of secreted and cell-surface polysaccharides. We previously reported the identification of an unusual sulphate-modified form of capsular polysaccharide (KPS) in M. loti. To better understand the physiological function of sulphated KPS, we isolated the sulphotransferase responsible for KPS sulphation from M. loti extracts, determined its amino acid sequence and identified the corresponding M. loti open reading frame, mll7563 (which we have named kpsS). We demonstrated that partially purified KpsS functions as a fucosyl sulphotransferase in vitro. Furthermore, mutants deficient for this gene exhibit a lack of KPS sulphation and a decreased rate of nodule formation on L. japonicus. Interestingly, the kpsS gene product shares no significant amino acid similarity with previously identified sulphotransferases, but exhibited sequence identity to open reading frames of unknown function in diverse bacteria that interact with eukaryotes.
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Affiliation(s)
- Guy E Townsend
- Department of Microbiology and Immunology, Loyola University, Chicago, IL, USA
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8
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Del Papa MF, Pistorio M, Draghi WO, Lozano MJ, Giusti MA, Medina C, van Dillewijn P, Martínez-Abarca F, Moron Flores B, Ruiz-Sainz JE, Megías M, Pühler A, Niehaus K, Toro N, Lagares A. Identification and characterization of a nodH ortholog from the alfalfa-nodulating Or191-like rhizobia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:138-45. [PMID: 17313165 DOI: 10.1094/mpmi-20-2-0138] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nodulation of Medicago sativa (alfalfa) is known to be restricted to Sinorhizobium meliloti and a few other rhizobia that include the poorly characterized isolates related to Rhizobium sp. strain Or191. Distinctive features of the symbiosis between alfalfa and S. meliloti are the marked specificity from the plant to the bacteria and the strict requirement for the presence of sulfated lipochitooligosaccharides (Nod factors [NFs]) at its reducing end. Here, we present evidence of the presence of a functional nodH-encoded NF sulfotransferase in the Or191-like rhizobia. The nodH gene, present in single copy, maps to a high molecular weight megaplasmid. As in S. meliloti, a nodF homolog was identified immediately upstream of nodH that was transcribed in the opposite direction (local synteny). This novel nodH ortholog was cloned and shown to restore both NF sulfation and the Nif+Fix+ phenotypes when introduced into an S. meliloti nodH mutant. Unexpectedly, however, nodH disruption in the Or191-like bacteria did not abolish their ability to nodulate alfalfa, resulting instead in a severely delayed nodulation. In agreement with evidence from other authors, the nodH sequence analysis strongly supports the idea that the Or191-like rhizobia most likely represent a genetic mosaic resulting from the horizontal transfer of symbiotic genes from a sinorhizobial megaplasmid to a not yet clearly identified ancestor.
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Affiliation(s)
- M F Del Papa
- Instituto de Bioquímica y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900) La Plata, Argentina
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9
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Williams SJ, Davies GJ. A master of its sulfate. Nat Struct Mol Biol 2004; 11:686-7. [PMID: 15280877 DOI: 10.1038/nsmb0804-686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Mougous JD, Green RE, Williams SJ, Brenner SE, Bertozzi CR. Sulfotransferases and sulfatases in mycobacteria. CHEMISTRY & BIOLOGY 2002; 9:767-76. [PMID: 12144918 DOI: 10.1016/s1074-5521(02)00175-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Analysis of the genomes of M. tuberculosis, M. leprae, M. smegmatis, and M. avium has revealed a large family of genes homologous to known sulfotransferases. Despite reports detailing a suite of sulfated glycolipids in many mycobacteria, a corresponding family of sulfotransferase genes remains uncharacterized. Here, a sequence-based analysis of newly discovered mycobacterial sulfotransferase genes, named stf1-stf10, is presented. Interestingly, two sulfotransferase genes are highly similar to mammalian sulfotransferases, increasing the list of mycobacterial eukaryotic-like protein families. The sulfotransferases join an equally complex family of mycobacterial sulfatases: a large family of sulfatase genes has been found in all of the mycobacterial genomes examined. As sulfated molecules are common mediators of cell-cell interactions, the sulfotransferases and sulfatases may be involved in regulating host-pathogen interactions.
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Affiliation(s)
- Joseph D Mougous
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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11
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Southwick AM, Wang LX, Long SR, Lee YC. Activity of Sinorhizobium meliloti NodAB and NodH enzymes on thiochitooligosaccharides. J Bacteriol 2002; 184:4039-43. [PMID: 12081977 PMCID: PMC135183 DOI: 10.1128/jb.184.14.4039-4043.2002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobium bacteria synthesize signal molecules called Nod factors that elicit responses in the legume root during nodulation. Nod factors, modified N-acylated beta-(1,4)-N-acetylglucosamine, are synthesized by the nodulation (nod) gene products. We tested the ability of three Sinorhizobium meliloti nod gene products to modify Nod factor analogs with thio linkages instead of O-glycosidic bonds in the oligosaccharide backbone.
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Affiliation(s)
- Audrey M Southwick
- Department of Biological Sciences, Stanford University, California 94305-5020, USA
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12
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Rivera-Marrero CA, Ritzenthaler JD, Newburn SA, Roman J, Cummings RD. Molecular cloning and expression of a novel glycolipid sulfotransferase in Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2002; 148:783-792. [PMID: 11882713 DOI: 10.1099/00221287-148-3-783] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sulfated trehalose glycolipids are among the most characteristic cell wall molecules of virulent strains of Mycobacterium tuberculosis. They comprise a family of trehalose-2-sulfate esters with an array of acyl fatty acids at various positions of the trehalose moiety. Although their structure has been well characterized, most of the enzymes involved in their biosynthesis, such as sulfotransferases, are unknown. It is demonstrated here by metabolic labelling with 35S abundant incorporation into sulfolipids of M. tuberculosis strains, in comparison to Mycobacterium avium, Mycobacterium bovis BCG and Mycobacterium smegmatis. The most abundant sulfolipid, sulfolipid I, is present in virulent strains H37Rv and Erdman, but absent in attenuated H37Ra. Sulfotransferase assays with the donor substrate 3'-phosphoadenosine-5'-[35S]phosphosulfonate and whole cell lysates of H37Ra resulted in the synthesis of four major sulfolipids (I, II, IV and VI). A search for sulfotransferase gene sequences in M. tuberculosis yielded gene Rv1373, a 981 bp gene slightly homologous (24% identity) to eukaryotic aryl-sulfotransferases. Rv1373 was cloned by PCR and expressed as a 39 kDa recombinant his-tagged protein. The recombinant M. tuberculosis aryl-sulfotransferase exhibited activity towards the cerebroside glycolipids glucosyl- and galactosylceramide. No activity was detected with sulfatide (3'-sulfated galactosylceramide), suggesting that sulfation of galactosylceramide may occur at C-3 of the galactose. Treatment of sulfated products with ceramide glycanase resulted in the release of 35S-labelled material showing that sulfation was at the saccharide moiety (galactose or glucose) of the ceramide. Assays with the M. tuberculosis aryl-sulfotransferase and total H37Ra glycolipids showed one major product corresponding to sulfolipid IV. These results demonstrate that Rv1373 encodes a novel glycolipid sulfotransferase with activity towards typical ceramide glycolipids and mycobacterial trehalose glycolipids.
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Affiliation(s)
- Carlos A Rivera-Marrero
- Department of Medicine, Pulmonary and Critical Care Division, Atlanta VA Medical Center, Emory University School of Medicine, Room 12C 106, 1670 Clairmont Rd, Decatur, GA 30033, USA1
| | - Jeffrey D Ritzenthaler
- Department of Medicine, Pulmonary and Critical Care Division, Atlanta VA Medical Center, Emory University School of Medicine, Room 12C 106, 1670 Clairmont Rd, Decatur, GA 30033, USA1
| | - Sarah A Newburn
- Department of Medicine, Pulmonary and Critical Care Division, Atlanta VA Medical Center, Emory University School of Medicine, Room 12C 106, 1670 Clairmont Rd, Decatur, GA 30033, USA1
| | - Jesse Roman
- Department of Medicine, Pulmonary and Critical Care Division, Atlanta VA Medical Center, Emory University School of Medicine, Room 12C 106, 1670 Clairmont Rd, Decatur, GA 30033, USA1
| | - Richard D Cummings
- Department of Biochemistry and Molecular Biology, Oklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA2
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Manyani H, Sousa C, Soria Díaz ME, Gil-Serrano A, Megías M. Regulation of nod factor sulphation genes in Rhizobium tropici CIAT899. Can J Microbiol 2001; 47:574-9. [PMID: 11467733 DOI: 10.1139/w01-032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rhizobium tropici CIAT899 is a tropical symbiont able to nodulate various legumes such as Leucaena, Phaseolus, and Macroptilium. Broad host range of this species is related to its Nod factors wide spectrum. R. tropici contains Nod factors sulphation nod genes, nodHPQ genes, which control nodulation efficiency in Leucaena. To study nodHPQ regulation, we carried out different interposon insertions in its upstream region. One of these generated interruptions, nodI mutant produced nonsulphated Nod factors suggesting a possible dependence of these genes on nodI upstream region. Moreover, analysis results of lacZ transcriptional fusions with these genes in symbiotic plasmid showed dependence of these genes on NodD protein. In order to determine nodHPQ organization, we studied the effect of interposon insertion upstream of each lacZ transcriptional fusion, and the data obtained was used to indicate that nodHPQ belong to the nodABCSUIJ operon. However, comparison between nodP::lacZ beta-galactosidase activity in the symbiotic plasmid and in the pHM500 plasmid (containing nodHPQ genes) suggested constitutive expression in free living, and flavonoid inducible expression in symbiotic conditions. Constitutive nodHPQ expression may play a role in bacterial house-keeping metabolism. On the other hand, the transference of R. tropici nodHPQ genes to other rhizobia that do not present sulphated substitutions demonstrated that NodH protein sulphotransference is specific to C6 at the reducing end.
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Affiliation(s)
- H Manyani
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Spain
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Göttfert M, Röthlisberger S, Kündig C, Beck C, Marty R, Hennecke H. Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J Bacteriol 2001; 183:1405-12. [PMID: 11157954 PMCID: PMC95015 DOI: 10.1128/jb.183.4.1405-1412.2001] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The physical and genetic map of the Bradyrhizobium japonicum chromosome revealed that nitrogen fixation and nodulation genes are clustered. Because of the complex interactions between the bacterium and the plant, we expected this chromosomal sector to contain additional genes that are involved in the maintenance of an efficient symbiosis. Therefore, we determined the nucleotide sequence of a 410-kb region. The overall G+C nucleotide content was 59.1%. Using a minimum gene length of 150 nucleotides, 388 open reading frames (ORFs) were selected as coding regions. Thirty-five percent of the predicted proteins showed similarity to proteins of rhizobia. Sixteen percent were similar only to proteins of other bacteria. No database match was found for 29%. Repetitive DNA sequence-derived ORFs accounted for the rest. The sequenced region contained all nitrogen fixation genes and, apart from nodM, all nodulation genes that were known to exist in B. japonicum. We found several genes that seem to encode transport systems for ferric citrate, molybdate, or carbon sources. Some of them are preceded by -24/-12 promoter elements. A number of putative outer membrane proteins and cell wall-modifying enzymes as well as a type III secretion system might be involved in the interaction with the host.
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Affiliation(s)
- M Göttfert
- Institut für Genetik, Technische Universität Dresden, D-01062 Dresden, Germany.
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15
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Abstract
Eukaryotes often form symbioses with microorganisms. Among these, associations between plants and nitrogen-fixing bacteria are responsible for the nitrogen input into various ecological niches. Plants of many different families have evolved the capacity to develop root or stem nodules with diverse genera of soil bacteria. Of these, symbioses between legumes and rhizobia (Azorhizobium, Bradyrhizobium, Mesorhizobium, and Rhizobium) are the most important from an agricultural perspective. Nitrogen-fixing nodules arise when symbiotic rhizobia penetrate their hosts in a strictly controlled and coordinated manner. Molecular codes are exchanged between the symbionts in the rhizosphere to select compatible rhizobia from pathogens. Entry into the plant is restricted to bacteria that have the "keys" to a succession of legume "doors". Some symbionts intimately associate with many different partners (and are thus promiscuous), while others are more selective and have a narrow host range. For historical reasons, narrow host range has been more intensively investigated than promiscuity. In our view, this has given a false impression of specificity in legume-Rhizobium associations. Rather, we suggest that restricted host ranges are limited to specific niches and represent specialization of widespread and more ancestral promiscuous symbioses. Here we analyze the molecular mechanisms governing symbiotic promiscuity in rhizobia and show that it is controlled by a number of molecular keys.
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Affiliation(s)
- X Perret
- Laboratoire de Biologie Moléculaire des Plantes Supérieures, Université de Genève, 1292 Chambésy/Geneva, Switzerland
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16
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Berck S, Perret X, Quesada-Vincens D, Promé J, Broughton WJ, Jabbouri S. NolL of Rhizobium sp. strain NGR234 is required for O-acetyltransferase activity. J Bacteriol 1999; 181:957-64. [PMID: 9922261 PMCID: PMC93464 DOI: 10.1128/jb.181.3.957-964.1999] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Following (iso)flavonoid induction, nodulation genes of the symbiotic nitrogen-fixing bacterium Rhizobium sp. strain NGR234 elaborate a large family of lipooligosaccharidic Nod factors (NodNGR factors). When secreted into the rhizosphere of compatible legumes, these signal molecules initiate root hair deformation and nodule development. The nonreducing glucosamine residue of NodNGR factors are N acylated, N methylated, and mono- or biscarbamoylated, while position C-6 of the reducing extremity is fucosylated. This fucose residue is normally 2-O methylated and either sulfated or acetylated. Here we present an analysis of all acetylated NodNGR factors, which clearly shows that the acetate group may occupy position C-3 or C-4 of the fucose moiety. Disruption of the flavonoid-inducible nolL gene, which is preceded by a nod box, results in the synthesis of NodNGR factors that lack the 3-O- or 4-O-acetate groups. Interestingly, the nodulation capacity of the mutant NGROmeganolL is not impaired, whereas introduction of the nod box::nolL construct into the related strain Rhizobium fredii USDA257 extends the host range of this bacterium to Calopogonium caeruleum, Leucaena leucocephala, and Lotus halophilus. Nod factors produced by a USDA257(pnolL) transconjugant were also acetylated. The nod box::nolL construct was also introduced into ANU265 (NGR234 cured of its symbiotic plasmid), along with extra copies of the nodD1 gene. When permeabilized, these cells possessed acetyltransferase activity, although crude extracts did not.
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Affiliation(s)
- S Berck
- Laboratoire de Biologie Moléculaire des Plantes Supérieures, Université de Genève, 1292 Chambésy, Geneva, Switzerland
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Bowman KG, Bertozzi CR. Carbohydrate sulfotransferases: mediators of extracellular communication. CHEMISTRY & BIOLOGY 1999; 6:R9-R22. [PMID: 9889154 DOI: 10.1016/s1074-5521(99)80014-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Sulfated carbohydrates mediate diverse extracellular recognition events in both normal and pathological processes. The sulfotransferases that generate specific carbohydrate 'sulfoforms' have recently been recognized as key modulators of these processes and therefore represent potential therapeutic targets.
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Affiliation(s)
- K G Bowman
- Department of Chemistry, University of California, Berkeley 94720, USA
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