1
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Smercina DN, Evans SE, Friesen ML, Tiemann LK. Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function. FEMS Microbiol Ecol 2021; 96:5920613. [PMID: 33038234 DOI: 10.1093/femsec/fiaa208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/08/2020] [Indexed: 02/02/2023] Open
Abstract
Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear. In this study, we assess structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites. ANF rates were variable and often unexpectedly high, sometimes 10× greater than reported in the literature, and did not respond in repeatable ways to long-term or short-term N. We found few impacts of N addition on root-associated diazotrophic community structure or membership. Instead, we found a very consistent root-associated diazotrophic community even though switchgrass seeds were germinated in soil from field sites with distinct diazotrophic communities. Ultimately, this work demonstrates that root-associated diazotrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazotrophic community by switchgrass roots.
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Affiliation(s)
- Darian N Smercina
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Sarah E Evans
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lisa K Tiemann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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2
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Fernández N, Cabrera JJ, Varadarajan AR, Lutz S, Ledermann R, Roschitzki B, Eberl L, Bedmar EJ, Fischer HM, Pessi G, Ahrens CH, Mesa S. An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens. Front Microbiol 2019; 10:924. [PMID: 31134003 PMCID: PMC6515984 DOI: 10.3389/fmicb.2019.00924] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 01/31/2023] Open
Abstract
The adaptation of rhizobia from the free-living state in soil to the endosymbiotic state comprises several physiological changes in order to cope with the extremely low oxygen availability (microoxia) within nodules. To uncover cellular functions required for bacterial adaptation to microoxia directly at the protein level, we applied a systems biology approach on the key rhizobial model and soybean endosymbiont Bradyrhizobium diazoefficiens USDA 110 (formerly B. japonicum USDA 110). As a first step, the complete genome of B. diazoefficiens 110spc4, the model strain used in most prior functional genomics studies, was sequenced revealing a deletion of a ~202 kb fragment harboring 223 genes and several additional differences, compared to strain USDA 110. Importantly, the deletion strain showed no significantly different phenotype during symbiosis with several host plants, reinforcing the value of previous OMICS studies. We next performed shotgun proteomics and detected 2,900 and 2,826 proteins in oxically and microoxically grown cells, respectively, largely expanding our knowledge about the inventory of rhizobial proteins expressed in microoxia. A set of 62 proteins was significantly induced under microoxic conditions, including the two nitrogenase subunits NifDK, the nitrogenase reductase NifH, and several subunits of the high-affinity terminal cbb3 oxidase (FixNOQP) required for bacterial respiration inside nodules. Integration with the previously defined microoxia-induced transcriptome uncovered a set of 639 genes or proteins uniquely expressed in microoxia. Finally, besides providing proteogenomic evidence for novelties, we also identified proteins with a regulation similar to that of FixK2: transcript levels of these protein-coding genes were significantly induced, while the corresponding protein abundance remained unchanged or was down-regulated. This suggested that, apart from fixK2, additional B. diazoefficiens genes might be under microoxia-specific post-transcriptional control. This hypothesis was indeed confirmed for several targets (HemA, HemB, and ClpA) by immunoblot analysis.
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Affiliation(s)
- Noemí Fernández
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Adithi R Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland.,Department of Health Sciences and Technology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | | | - Bernd Roschitzki
- Functional Genomics Center Zurich, ETH & UZH Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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3
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Sankari S, O'Brian MR. The Bradyrhizobium japonicum Ferrous Iron Transporter FeoAB Is Required for Ferric Iron Utilization in Free Living Aerobic Cells and for Symbiosis. J Biol Chem 2016; 291:15653-62. [PMID: 27288412 PMCID: PMC4957049 DOI: 10.1074/jbc.m116.734129] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/07/2016] [Indexed: 01/02/2023] Open
Abstract
The bacterium Bradyrhizobium japonicum USDA110 does not synthesize siderophores for iron utilization in aerobic environments, and the mechanism of iron uptake within symbiotic soybean root nodules is unknown. An mbfA bfr double mutant defective in iron export and storage activities cannot grow aerobically in very high iron medium. Here, we found that this phenotype was suppressed by loss of function mutations in the feoAB operon encoding ferrous (Fe(2+)) iron uptake proteins. Expression of the feoAB operon genes was elevated under iron limitation, but mutants defective in either gene were unable to grow aerobically over a wide external ferric (Fe(3+)) iron (FeCl3) concentration range. Thus, FeoAB accommodates iron acquisition under iron limited and iron replete conditions. Incorporation of radiolabel from either (55)Fe(2+) or (59)Fe(3+) into cells was severely defective in the feoA and feoB strains, suggesting Fe(3+) reduction to Fe(2+) prior to traversal across the cytoplasmic membrane by FeoAB. The feoA or feoB deletion strains elicited small, ineffective nodules on soybean roots, containing few bacteria and lacking nitrogen fixation activity. A feoA(E40K) mutant contained partial iron uptake activity in culture that supported normal growth and established an effective symbiosis. The feoA(E40K) strain had partial iron uptake activity in situ within nodules and in isolated cells, indicating that FeoAB is the iron transporter in symbiosis. We conclude that FeoAB supports iron acquisition under limited conditions of soil and in the iron-rich environment of a symbiotic nodule.
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Affiliation(s)
- Siva Sankari
- From the Department of Biochemistry, State University of New York, Buffalo, New York 14214
| | - Mark R O'Brian
- From the Department of Biochemistry, State University of New York, Buffalo, New York 14214
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4
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Bassarab S, Schenk SU, Werner D. Fatty Acid Composition of the Peribacteroid Membrane and the ER in Nodules ofGlycine maxVaries after Infection by Different Strains of the MicrosymbiontBradyrhizobiumjaponicum. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1989.tb00094.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Wu S, Li X, Yu J, Wang Q. Increased hydrogen production in co-culture of Chlamydomonas reinhardtii and Bradyrhizobium japonicum. BIORESOURCE TECHNOLOGY 2012; 123:184-8. [PMID: 22940317 DOI: 10.1016/j.biortech.2012.07.055] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 06/04/2012] [Accepted: 07/16/2012] [Indexed: 05/26/2023]
Abstract
Co-cultivation of Bradyrhizobium japonicum with Chlamydomonas reinhardtii strain cc849 or the transgenic strain lba, which was hetero-expressed the gene of the soybean leghemoglobin apoprotein Lba in chloroplasts of the strain cc849, in Tris-acetate-phosphate (TAP) or TAP-sulfur free media, improved H(2) yield. H(2) production was 14 times and growth was 26% higher when strain lba and B. japonicum were co-cultured, as compared with cultivation of the algal strain alone under the same conditions. The increase in respiration rate or fast O(2) consumption by about 8 times in the co-cultures was the major reason for the improvement.
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Affiliation(s)
- Shuangxiu Wu
- The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China.
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6
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Schumpp O, Crèvecoeur M, Broughton WJ, Deakin WJ. Delayed maturation of nodules reduces symbiotic effectiveness of the Lotus japonicus-Rhizobium sp. NGR234 interaction. JOURNAL OF EXPERIMENTAL BOTANY 2008; 60:581-90. [PMID: 19060298 PMCID: PMC2651464 DOI: 10.1093/jxb/ern302] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 10/24/2008] [Accepted: 10/31/2008] [Indexed: 05/24/2023]
Abstract
Lotus japonicus, a model legume, develops an efficient, nitrogen-fixing symbiosis with Mesorhizobium loti that promotes plant growth. Lotus japonicus also forms functional nodules with Rhizobium sp. NGR234 and R. etli. Yet, in a plant defence-like reaction, nodules induced by R. etli quickly degenerate, thus limiting plant growth. In contrast, nodules containing NGR234 are long-lasting. It was found that NGR234 initiates nodule formation in a similar way to M. loti MAFF303099, but that the nodules which develop on eleven L. japonicus ecotypes are less efficient in fixing nitrogen. Detailed examination of nodulation of L. japonicus cultivar MG-20 revealed that symbiosomes formed four weeks after inoculation by NGR234 are enlarged in comparison with MAFF303099 and contain multiple bacteroids. Nevertheless, nodules formed by NGR234 fix sufficient nitrogen to avoid rejection by the plant. With time, these nodules develop into fully efficient organs containing bacteroids tightly enclosed in symbiosome membranes, just like those formed by M. loti MAFF303099. This work demonstrates the usefulness of using the well-characterized micro-symbiont NGR234 to study symbiotic signal exchange in the later stages of rhizobia-legume symbioses, especially given the large range of bacterial (NGR234) and plant (L. japonicus) mutants that are available.
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Affiliation(s)
| | - Michèle Crèvecoeur
- Département de Botanique et de Biologie Végétale, Université de Genève, 30 Quai Ernest-Ansermet, Sciences III, CH-1211 Genève 4, Switzerland
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7
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Abstract
Eukaryotic organisms do not fix nitrogen. Animals generally have no need to do so because of their complex food-acquisition and waste-disposal systems. Plants, by using carbon polymers for structural purposes, minimize their need for nitrogen. When very nitrogen-limited, to enter into symbiosis with nitrogen-fixing microorganisms may be the most controllable method for eukaryotes to obtain fixed nitrogen. Filamentous, heterocystous nitrogen-fixing cyanobacteria may be better adapted to a free-living than to a symbiotic existence, because of their complexity. In symbioses, their photosynthetic machinery becomes redundant and the need to differentiate heterocysts as well as derepress
nif
genes may be a disadvantage. This could in part account for the greater success of symbioses involving the structurally simpler genera
Frankia
,
Rhizobium
and
Bradyrhizobium
. Nitrogen fixation by legume nodules can be controlled by varying the oxygen supply. This control may be effected by a variable diffusion resistance, enabling oxygen required for ATP synthesis to be matched to available photosynthate. Such a resistance, which is probably located in the nodule cortex, may also be used to reduce nitrogen fixation in the presence of combined nitrogen and could also facilitate rapid responses to other forms of stress. Alternative resistances to gaseous diffusion may operate when water supplies are restricted.
Rhizobium
and
Bradyrhizobium
follow different patterns of differentiation into nitrogen-fixing bacteroids. These patterns are coupled with retention or loss of viability and with significant or no natural enrichment of the bacteroids with
15
N respectively. The basic patterns of each type are subject to host-modification. Recent studies on structures of primitive legume nodules show some parallels both with actinorhizas and with nodules on
Parasponia
induced by
Bradyrhizobium
. In particular, distribution of rhizobia in nodule tissues is intercellular and infection threads are formed only when bacteria ‘enter’ host cells; there is no intracellular ‘bacteroid’ stage. These threads are retained in the active nitrogen-fixing cells. Many legumes and some actinorhizas are not infected via root hairs. Therefore two of the stages often considered typical of the development of effective legume nodules, i.e. ‘release’ of bacteria into vesicles bounded by peribacteroid membrane and infection through root hairs, can be omitted; these omissions may be of use in attempts to transfer nodulating ability to new genera.
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8
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Wiggli M, Cornacchia L, Saegesser R, Bachofen R, Ghosh R. Characterization of Rhodospirillum rubrum ST2. A new Tn5-induced carotenoid-less mutant for functional studies. Microbiol Res 1996. [DOI: 10.1016/s0944-5013(96)80056-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Abstract
Soil bacteria of the genera Azorhizobium, Bradyrhizobium, and Rhizobium are collectively termed rhizobia. They share the ability to penetrate legume roots and elicit morphological responses that lead to the appearance of nodules. Bacteria within these symbiotic structures fix atmosphere nitrogen and thus are of immense ecological and agricultural significance. Although modern genetic analysis of rhizobia began less than 20 years ago, dozens of nodulation genes have now been identified, some in multiple species of rhizobia. These genetic advances have led to the discovery of a host surveillance system encoded by nodD and to the identification of Nod factor signals. These derivatives of oligochitin are synthesized by the protein products of nodABC, nodFE, NodPQ, and other nodulation genes; they provoke symbiotic responses on the part of the host and have generated immense interest in recent years. The symbiotic functions of other nodulation genes are nonetheless uncertain, and there remain significant gaps in our knowledge of several large groups of rhizobia with interesting biological properties. This review focuses on the nodulation genes of rhizobia, with particular emphasis on the concept of biological specificity of symbiosis with legume host plants.
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Affiliation(s)
- S G Pueppke
- Department of Plant Pathology, University of Missouri, Columbia, MO 65211, USA
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10
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Chun JY, Sexton GL, Roth LE, Stacey G. Identification and characterization of a novel Bradyrhizobium japonicum gene involved in host-specific nitrogen fixation. J Bacteriol 1994; 176:6717-29. [PMID: 7961425 PMCID: PMC197029 DOI: 10.1128/jb.176.21.6717-6729.1994] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
To understand the genetic mechanism of host specificity in the interaction between rhizobia and their hosts, it is important to identify genes that influence both early and late steps in symbiotic development. This paper focuses on the little-understood genetics of host-specific nitrogen fixation. A deletion mutant of Bradyrhizobium japonicum, strain NAD163, was found to induce effective, nitrogen-fixing nodules on soybean and siratro plants but produced ineffective nodules on cowpea plants. Additional transposon and deletion mutants defined a small region that conferred this phenotype, and this region was sequenced to identify two putative open reading frames (ORFs). Data indicate that only one of these ORFs is detectable in bacteroids. This ORF was termed hsfA, with a predicted protein product of 11 kDa. The transcriptional start site of hsfA was determined and found to coincide with a predicted RpoN-dependent promoter. Microscopic studies of nodules induced by the wild type and hsfA mutants on cowpea and soybean plants indicate that the cowpea mutant nodules are slow to develop. The data indicate that hsfA appears to play a crucial role in bacteroid development on cowpea but does not appear to be essential for nitrogen fixation on the other hosts tested.
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Affiliation(s)
- J Y Chun
- Center for Legume Research, Graduate Program of Plant Physiology and Genetics, Department of Zoology, and Department of Microbiology and Graduate Program of Ecology, University of Tennessee, Knoxville 37996
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11
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Bradburne JA, Mathis JN, Israel DW. nifGene expression in a Nif +, Fix âBradyrhizobium japanicumvariant. FEMS Microbiol Lett 1994. [DOI: 10.1111/j.1574-6968.1994.tb07206.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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12
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Thöny-Meyer L, Ritz D, Hennecke H. Cytochrome c biogenesis in bacteria: a possible pathway begins to emerge. Mol Microbiol 1994; 12:1-9. [PMID: 8057830 DOI: 10.1111/j.1365-2958.1994.tb00988.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cytochrome c biogenesis describes the posttranslational pathway for the conversion of pre-apocytochrome c into the mature holocytochrome c. It involves an unknown number of consecutive biochemical steps, including translocation of the precursor polypeptide and haem into the periplasm and the covalent linkage between these two molecules. Genetic and molecular analysis of several bacterial mutants suggest that at least eight genes contribute to this process. In this review we summarize the present knowledge of the cytochrome c maturation pathway in bacteria and propose a model in which certain genes and their products are attributed to specific functions.
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Affiliation(s)
- L Thöny-Meyer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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13
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Studer D, Hennecke H, Müller M. High-pressure freezing of soybean nodules leads to an improved preservation of ultrastructure. PLANTA 1992; 188:155-163. [PMID: 24178251 DOI: 10.1007/bf00216809] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/21/1992] [Indexed: 06/02/2023]
Abstract
High-pressure freezing of chemically untreated nodules of soybean (Glycine max (L.) Merr.), in sharp contrast to chemical fixation and prefixation, appears to preserve the ultrastructure close to the native state. This is supported by the observation that the peribacteroid membrane of high-pressure-frozen samples is tightly wrapped around the bacteroids, a finding that is fully consistent with the current views on the physiology of oxygen and metabolite transport between plant cytosol and bacteroids. In soybean root nodules, the plant tissue and the enclosed bacteria are so dissimilar that conventional aldehyde-fixation procedures are unable to preserve the overall native ultrastructure. This was demonstrated by high-pressure freezing of nodules that had been pre-fixed in glutaraldehyde at various buffer molalities: no buffer strength tested preserved all ultrastructural aspects that could be seen after high-pressure freezing of chemically untreated nodules.
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Affiliation(s)
- D Studer
- Laboratorium für Elektronenmikroskopie I, Eidgenössische Technische Hochschule, Schmelzbergstrasse 7, CH-8092, Zürich, Switzerland
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14
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Ebeling S, Kündig C, Hennecke H. Discovery of a rhizobial RNA that is essential for symbiotic root nodule development. J Bacteriol 1991; 173:6373-82. [PMID: 1717438 PMCID: PMC208969 DOI: 10.1128/jb.173.20.6373-6382.1991] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
All of the Azorhizobium, Bradyrhizobium, and Rhizobium genes known to be involved in the development of nitrogen-fixing legume root nodules are genes that code for proteins. Here we report the first exception to this rule: the sra gene; it was discovered during the genetic analysis of a Bradyrhizobium japonicum Tn5 mutant (strain 259) which had a severe deficiency in colonizing soybean nodules. A DNA region as small as 0.56 kb cloned from the parental wild type restored a wild-type phenotype in strain 259 by genetic complementation. The sra gene was located on this fragment, sequenced, and shown to be transcribed into a 213-nucleotide RNA. Results obtained with critical point mutations in the sra gene proved that the transcript was not translated into protein; rather, it appeared to function as an RNA molecule with a certain stem-and-loop secondary structure. We also detected an sra homolog in Rhizobium meliloti which, when cloned and transferred to B. japonicum mutant 259, fully restored symbiotic effectiveness in that strain. We propose several alternative functions for the sra gene product, of which that as a regulatory RNA for gene expression may be the most probable one.
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Affiliation(s)
- S Ebeling
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zurich, Switzerland
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15
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Discovery and sequence analysis of bacterial genes involved in the biogenesis of c-type cytochromes. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(20)89520-9] [Citation(s) in RCA: 127] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Bott M, Bolliger M, Hennecke H. Genetic analysis of the cytochrome c-aa3 branch of the Bradyrhizobium japonicum respiratory chain. Mol Microbiol 1990; 4:2147-57. [PMID: 1965217 DOI: 10.1111/j.1365-2958.1990.tb00576.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Further genetic evidence is provided here that Bradyrhizobium japonicum possesses a mitochondria-like electron-transport pathway: 2[H]----UQ----bc1----c----aa3----O2. Two Tn5-induced mutants, COX122 and COX132, having cytochrome c oxidase-negative phenotypes, were obtained and characterized. Mutant COX122 was defective in a novel gene, named cycM, which was responsible for the synthesis of a c-type cytochrome with an Mr of 20,000 (20K). This 20K cytochrome c appeared to catalyse electron transport from the cytochrome bc1 complex to the aa3-type terminal oxidase and, unlike mitochondrial cytochrome c, was membrane-bound in B. japonicum. The Tn5 insertion of mutant COX132 was localized in coxA, the structural gene for subunit I of cytochrome aa3. This finding also led to the cloning and sequencing of the corresponding wild-type coxA gene that encoded a 541-amino-acid protein with a predicted Mr of 59,247. The CoxA protein shared about 60% sequence identity with the cytochrome aa3 subunit I of mitochondria. The B. japonicum cycM and coxA mutants were able to fix nitrogen in symbiosis with soybean (Fix+). In contrast, mutants described previously which lacked the bc1 complex did not develop into endosymbiotic bacteroids and were thus Fix-. The data suggest that a symbiosis-specific respiratory chain exists in B. japonicum in which the electrons branch off at the bc1 complex.
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Affiliation(s)
- M Bott
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland
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17
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Kannenberg EL, Brewin NJ. Expression of a cell surface antigen from Rhizobium leguminosarum 3841 is regulated by oxygen and pH. J Bacteriol 1989; 171:4543-8. [PMID: 2768181 PMCID: PMC210248 DOI: 10.1128/jb.171.9.4543-4548.1989] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae 3841 was grown in liquid suspension culture to investigate how culture conditions could affect the expression of a developmentally regulated cell surface antigen associated with lipopolysaccharide. The antigen, which is recognized by monoclonal antibody AFRC MAC 203, was expressed when cultures were grown at neutral pH under low-oxygen conditions (less than 7.5% [vol/vol] O2 in the gas phase). Antigen was also expressed in aerobically grown cultures at pH values below 5.3. The nature of the nitrogen and the carbon sources had no effect on antigen expression except by indirect changes on the pH of the culture medium; similarly, growth in 0.3 M NaCl did not result in antigen expression. The induction of MAC 203 antigen by low-oxygen or low-pH culture conditions is discussed in the context of tissue-specific expression within the legume root nodule.
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18
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Thöny B, Anthamatten D, Hennecke H. Dual control of the Bradyrhizobium japonicum symbiotic nitrogen fixation regulatory operon fixR nifA: analysis of cis- and trans-acting elements. J Bacteriol 1989; 171:4162-9. [PMID: 2753853 PMCID: PMC210186 DOI: 10.1128/jb.171.8.4162-4169.1989] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Aerobic expression of the fixR nifA operon in Bradyrhizobium japonicum was shown to depend on a cis-acting, promoter-upstream DNA sequence located between the -24/-12 promoter and position -86 relative to the transcription start site. An adenine at position -66 was essential for maximal expression. A chromosomal deletion of the upstream activator sequence (UAS) led to a symbiotically defective phenotype which was typical of nifA mutants. B. japonicum crude extracts contained a protein that bound to the UAS. By using chromosomally integrated fixR-lacZ fusions, the level of expression of the fixR nifA operon was found to be fivefold higher under reduced oxygen tension than under aerobiosis. This increase was due to autoactivation by the NifA protein and was partly independent of the UAS. Based on these data, we propose a model for the regulation of nitrogen fixation genes in B. japonicum that involves dual positive control of the fixR nifA operon. At high oxygen concentrations, the operon is expressed at a moderate level, subject to activation by the binding of a trans-acting factor to the UAS. Under such conditions, the nifA gene product is known to be inactive. At very low oxygen concentrations--a condition favorable to NifA activity--the NifA protein is the trans-acting factor which (i) enhances the level of fixR nifA expression (and hence its own synthesis) and (ii) activates other nif and fix genes.
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Affiliation(s)
- B Thöny
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zurich, Switzerland
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Thöny-Meyer L, Stax D, Hennecke H. An unusual gene cluster for the cytochrome bc1 complex in Bradyrhizobium japonicum and its requirement for effective root nodule symbiosis. Cell 1989; 57:683-97. [PMID: 2541921 DOI: 10.1016/0092-8674(89)90137-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Two adjacent genes in Bradyrhizobium japonicum, fbcF and fbcH, encode the Rieske iron sulfur protein and cytochromes b and c1, characteristic constituents of the respiratory complex III. Remarkably, fbcH is a single gene of which the 5' half codes for cytochrome b and the 3' half codes for cytochrome c1. Experimental evidence suggests that a large FbcH precursor is posttranslationally processed into the two proteins. B. japonicum fbcF and fbcH insertion mutants grow aerobically but are unable to fix nitrogen in root nodule symbiosis with soybean. Thus, fbcF and fbcH are symbiotically essential. We propose that B. japonicum makes use of a cytochrome bc1-containing respiratory chain on its way to become a microaerobic endosymbiont, whereas under aerobiosis, respiration can occur by a bc1-independent pathway.
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Affiliation(s)
- L Thöny-Meyer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland
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20
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Mellor RB, Garbers C, Werner D. Peribacteroid membrane nodulin gene induction by Bradyrhizobium japonicum mutants. PLANT MOLECULAR BIOLOGY 1989; 12:307-315. [PMID: 24272866 DOI: 10.1007/bf00043208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/1988] [Accepted: 12/13/1988] [Indexed: 06/02/2023]
Abstract
Seventeen translation products from Glycine max root mRNA precipitated with antiserum prepared against a peribacteroid membrane preparation from effective root nodules. Messenger RNA from fix (+) nodules coded for these 17 products plus 7 other nodule-specific polypeptides which bound to the antiserum. Of these 7 nodulins only 4 were present when nodules were infected with Bradyrhizobium japonicum 110 rif 15 2960, which induces the plant to produce 'empty' peribacteroid membranes. In nodules infected with B. japonicum strains inducing either very short-lived or defective peribacteroid membrane, only 5 or 6, respectively, of these nodulins could be detected.From these results we hypothesize that the microsymbiont is responsible for the production of at least 4 different signals leading to peribacteriod membrane formation by the plant.
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Affiliation(s)
- R B Mellor
- Botanisches Institut, Fachbereich Biologie der Philipps-Universität Marburg, D-3550, Marburg, Federal Republic of Germany
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21
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Cloning of a DNA region from Bradyrhizobium japonicum encoding pleiotropic functions in heme metabolism and respiration. Arch Microbiol 1989. [DOI: 10.1007/bf00413131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Göttfert M, Lamb JW, Gasser R, Semenza J, Hennecke H. Mutational analysis of the Bradyrhizobium japonicum common nod genes and further nod box-linked genomic DNA regions. MOLECULAR & GENERAL GENETICS : MGG 1989; 215:407-15. [PMID: 2710106 DOI: 10.1007/bf00427037] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
By insertional and deletional marker replacement mutagenesis the common nod region of Bradyrhizobium japonicum was examined for the presence of additional, essential nodulation genes. An open reading frame located in the 800 bp large intergenic region between nodD1 and nodA did not appear to be essential for nodulation of soybean. Furthermore, a strain with a deletion of the nodI- and nodJ-like genes downstream of nodC had a Nod+ phenotype. A mutant with a 1.7 kb deletion immediately downstream of nodD1 considerably delayed the onset of nodulation. This region carried a second copy of nodD (nodD2). A nodD1-nodD2 double mutant had a similar phenotype to the nodD2 mutant. Using a 22-mer oligonucleotide probe partially identical to the nod box sequence, a total of six hybridizing regions were identified in B. japonicum genomic DNA and isolated from a cosmid library. Sequencing of the hybridizing regions revealed that at least three of them represented true nod box sequences whereas the others showed considerable deviations from the consensus sequence. One of the three nod box sequences was the one known to be associated with nodA, whereas the other two were located 60 to 70 kb away from nif cluster I. A deletion of one of these two sequences plus adjacent DNA material (mutant delta 308) led to a reduced nodulation on Vigna radiata but not on soybean. Thus, this region is probably involved in the determination of host specificity.
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Affiliation(s)
- M Göttfert
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland
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23
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Inhibition of Bradyrhizobium japonicum nifA-dependent nif gene activation by oxygen occurs at the NifA protein level and is irreversible. Arch Microbiol 1989. [DOI: 10.1007/bf00413129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Werner D, Mörschel E, Garbers C, Bassarab S, Mellor RB. Particle density and protein composition of the peribacteroid membrane from soybean root nodules is affected by mutation in the microsymbiont Bradyrhizobium japonicum. PLANTA 1988; 174:263-270. [PMID: 24221484 DOI: 10.1007/bf00394780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/1987] [Accepted: 10/19/1987] [Indexed: 06/02/2023]
Abstract
Particle frequency of the peribacteroid membrane (PBM) from nodules of Glycine max (L.) Merr. cv. Maple Arrow infected with Bradyrhizobium japonicum 61-A-101 (wild-type strain) was determined by freeze-fracturing to be about 2200·μm(-2) in the protoplasmic fracture face and 700·μm(-2) in the exoplasmic fracture face. In membranes isolated from nodules infected with the mutant RH 31-Marburg of B. japonicum, the particle frequency was similar in both fracture faces with 1200-1300 particles·μm(-2). Analysis of particlesize distribution on peribacteroid membranes showed a loss, especially of particle sizes larger than 11 nm, in the mutant-infected nodules. Two-dimensional gel electrophoresis (isoelectric focussing and sodium dodecyl sulfate-polyacrylamide) showed 27 different polypeptides in the PBM from nodules infected with the wild-type strain, four of which were absent from the PBM of nodules infected with the mutant RH 31-Marburg, which also exhibited one extra small-molecular-weight polypeptide. At least 14 of the 27 polypeptides in the PBM from the wild-type-infected nodule were glycoproteins. In three of these glycoproteins, post-translational modifications were either lacking or different when the membrane was derived from mutant-infected nodules.
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Affiliation(s)
- D Werner
- Botanisches Institut, Fachbereich Biologie der Philipps-Universität Marburg, Karl v. Frischstrasse, D-355, Marburg-L, Federal Republic of Germany
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Abstract
The transcriptional start site of the Bradyrhizobium japonicum fixBC operon was identified by nuclease S1 mapping. It was located approximately 700 base pairs upstream of fixB and was preceded by a promoter sequence that showed strong homology to the B. japonicum fixA promoter and thus to the general nif consensus promoter sequence. Further transcript mapping experiments revealed that fixA and fixBC transcription in B. japonicum strictly depended on the presence of the regulatory gene nifA and on low oxygen partial pressure. Consistent with these data, chromosomally integrated fixA- and fixB-lacZ fusions expressed beta-galactosidase activity only in the wild type but not in a nifA mutant and only under microaerobic but not aerobic growth conditions. The presence of nifA accounted for a 19-fold and 44-fold activation of the fixA and fixB promoters, respectively. These results show that the fixA and fixBC genes are regulated in a way similar to that of the nitrogenase genes nifH and nifDK. A very peculiar finding was that the fixA and fixB promoters, when they were located on plasmids, could hardly be activated by the NifA protein, irrespective of whether this was tested in Escherichia coli or B. japonicum backgrounds. This is in clear contrast to the situation with nifH and nifD promoters.
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Affiliation(s)
- M Gubler
- Mikrobiologisches Institut, ETH-Zentrum, Zürich, Switzerland
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Fischer HM, Hennecke H. Direct response of Bradyrhizobium japonicum nifA-mediated nif gene regulation to cellular oxygen status. MOLECULAR & GENERAL GENETICS : MGG 1987; 209:621-6. [PMID: 17193716 DOI: 10.1007/bf00331174] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The nifA genes of Klebsiella pneumoniae and Bradyrhizobium japonicum were constitutively expressed from the pBR329-derived chloramphenicol resistance promoter. The inserts of these nifA plasmid constructs were devoid of any other intact flanking genes. The nifA genes thus expressed led to a marked activation of a B. japonicum nifD-lacZ fusion under microaerobic conditions. Under aerobic growth conditions, however, activation was mediated only by the K. pneumoniae nifA gene but not by the B. japonicum nifA gene. This selective effect was observed in both the Escherichia coli as well as the B. japonicum backgrounds. Several lines of evidence suggest that in these experiments oxygen adversely affects B. japonicum nifA-dependent nif gene regulation at the post-transcriptional level, probably even at the post-translational level, and that this effect does not require a nifL-like gene. Models are proposed in which oxygen inhibits the B. japonicum NifA protein either directly or indirectly via other cellular components involved in general protein oxidation pathways.
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Affiliation(s)
- H M Fischer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Universitätstrasse 2, CH-8092 Zürich, Switzerland
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McDermott TR, Graham PH, Brandwein DH. Viability of Bradyrhizobium japonicum bacteriods. Arch Microbiol 1987. [DOI: 10.1007/bf00425356] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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O'Brian MR, Kirshbom PM, Maier RJ. Tn5-induced cytochrome mutants of Bradyrhizobium japonicum: effects of the mutations on cells grown symbiotically and in culture. J Bacteriol 1987; 169:1089-94. [PMID: 3029019 PMCID: PMC211904 DOI: 10.1128/jb.169.3.1089-1094.1987] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Two Bradyrhizobium japonicum cytochrome mutants were obtained by Tn5 mutagenesis of strain LO and were characterized in free-living cultures and in symbiosis in soybean root nodules. One mutant strain, LO501, expressed no cytochrome aa3 in culture; it had wild-type levels of succinate oxidase activity but could not oxidize NADH or N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD). The cytochrome content of LO501 root nodule bacteroids was nearly identical to that of the wild type, but the mutant expressed over fourfold more bacteroid cytochrome c oxidase activity than was found in strain LO. The Tn5 insertion of the second mutant, LO505, had a pleiotropic effect; this strain was missing cytochromes c and aa3 in culture and had a diminished amount of cytochrome b as well. The oxidations of TMPD, NADH, and succinate by cultured LO505 cells were very similar to those by the cytochrome aa3 mutant LO501, supporting the conclusion that cytochromes c and aa3 are part of the same branch of the electron transport system. Nodules formed from the symbiosis of strain LO505 with soybean contained no detectable amount of leghemoglobin and had no N2 fixation activity. LO505 bacteroids were cytochrome deficient but contained nearly wild-type levels of bacteroid cytochrome c oxidase activity. The absence of leghemoglobin and the diminished bacterial cytochrome content in nodules from strain LO505 suggest that this mutant may be deficient in some aspect of heme biosynthesis.
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NIF, FIX and NOD Gene Clusters in Bradyrhizobium Japonicum, and NifA-Mediated Control of Symbiotic Nitrogen Fixation. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/978-94-009-4482-4_48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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30
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