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Kong D, Ye Z, Dai M, Ma B, Tan X. Light Intensity Modulates the Functional Composition of Leaf Metabolite Groups and Phyllosphere Prokaryotic Community in Garden Lettuce ( Lactuca sativa L.) Plants at the Vegetative Stage. Int J Mol Sci 2024; 25:1451. [PMID: 38338730 PMCID: PMC10855689 DOI: 10.3390/ijms25031451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 02/12/2024] Open
Abstract
Light intensity primarily drives plant growth and morphogenesis, whereas the ecological impact of light intensity on the phyllosphere (leaf surface and endosphere) microbiome is poorly understood. In this study, garden lettuce (Lactuca sativa L.) plants were grown under low, medium, and high light intensities. High light intensity remarkably induced the leaf contents of soluble proteins and chlorophylls, whereas it reduced the contents of leaf nitrate. In comparison, medium light intensity exhibited the highest contents of soluble sugar, cellulose, and free amino acids. Meanwhile, light intensity resulted in significant changes in the composition of functional genes but not in the taxonomic compositions of the prokaryotic community (bacteria and archaea) in the phyllosphere. Notably, garden lettuce plants under high light intensity treatment harbored more sulfur-cycling mdh and carbon-cycling glyA genes than under low light intensity, both of which were among the 20 most abundant prokaryotic genes in the leaf phyllosphere. Furthermore, the correlations between prokaryotic functional genes and lettuce leaf metabolite groups were examined to disclose their interactions under varying light intensities. The relative abundance of the mdh gene was positively correlated with leaf total chlorophyll content but negatively correlated with leaf nitrate content. In comparison, the relative abundance of the glyA gene was positively correlated with leaf total chlorophyll and carotenoids. Overall, this study revealed that the functional composition of the phyllosphere prokaryotic community and leaf metabolite groups were tightly linked in response to changing light intensities. These findings provided novel insights into the interactions between plants and prokaryotic microbes in indoor farming systems, which will help optimize environmental management in indoor farms and harness beneficial plant-microbe relationships for crop production.
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Affiliation(s)
- Dedong Kong
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (D.K.); (Z.Y.); (M.D.)
| | - Ziran Ye
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (D.K.); (Z.Y.); (M.D.)
| | - Mengdi Dai
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (D.K.); (Z.Y.); (M.D.)
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (D.K.); (Z.Y.); (M.D.)
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2
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Farci D, Sanna C, Medda R, Pintus F, Kalaji HM, Kirkpatrick J, Piano D. Shedding light on the presymbiontic phase of C. arietinum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:224-231. [PMID: 31521050 DOI: 10.1016/j.plaphy.2019.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/08/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
A complex network of symbiotic events between plants and bacteria allows the biosphere to exploit the atmospheric reservoir of molecular nitrogen. In seeds, a series of presymbiotic steps are already identified during imbibition, while interactions between the host and its symbiont begin in the early stages of germination. In the present study, a detailed analysis of the substances' complex delivered by Cicer arietinum seeds during imbibition showed a relevant presence of proteins and amino acids, which, except for cysteine, occurred with the whole proteinogenic pool. The imbibing solution was found to provide essential probiotic properties able to sustain the growth of the specific chickpea symbiont Mesorhizobium ciceri. Moreover, the imbibing solution, behaving as a complete medium, was found to be critically important for the symbiont's attraction, a fact this that is strictly related to the presence of the amino acids glycine, serine, and threonine. Here, the presence of these amino acids is constantly supported by the presence of the enzymes serine hydroxymethyltransferase and formyltetrahydrofolate deformylase, which are both involved in their biosynthesis. The reported findings are discussed in the light of the pivotal role played by the imbibing solution in attracting and sustaining symbiosis between the host and its symbiont.
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Affiliation(s)
- Domenica Farci
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy; White Hill Company, Ciołkowskiego 161, 15-545, Białystok, Poland; Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Nowoursynowska Str. 159, 02776, Warsaw, Poland
| | - Cinzia Sanna
- Laboratory of Pharmaceutical Botany, Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy
| | - Rosaria Medda
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, Italy
| | - Francesca Pintus
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, Italy
| | - Hazem M Kalaji
- White Hill Company, Ciołkowskiego 161, 15-545, Białystok, Poland; Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Nowoursynowska Str. 159, 02776, Warsaw, Poland
| | - Joanna Kirkpatrick
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstraβe 11, 07745, Jena, Germany
| | - Dario Piano
- Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123, Cagliari, Italy; Department of Plant Physiology, Warsaw University of Life Sciences - SGGW, Nowoursynowska Str. 159, 02776, Warsaw, Poland.
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3
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Faruque OM, Miwa H, Yasuda M, Fujii Y, Kaneko T, Sato S, Okazaki S. Identification of Bradyrhizobium elkanii Genes Involved in Incompatibility with Soybean Plants Carrying the Rj4 Allele. Appl Environ Microbiol 2015; 81:6710-7. [PMID: 26187957 PMCID: PMC4561682 DOI: 10.1128/aem.01942-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/13/2015] [Indexed: 11/20/2022] Open
Abstract
Symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. While these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. The formation of nodules in soybean plants (Glycine max) is controlled by several host genes, which are referred to as Rj genes. The soybean cultivar BARC2 carries the Rj4 gene, which restricts nodulation by specific strains, including Bradyrhizobium elkanii USDA61. Here we employed transposon mutagenesis to identify the genetic locus in USDA61 that determines incompatibility with soybean varieties carrying the Rj4 allele. Introduction of the Tn5 transposon into USDA61 resulted in the formation of nitrogen fixation nodules on the roots of soybean cultivar BARC2 (Rj4 Rj4). Sequencing analysis of the sequence flanking the Tn5 insertion revealed that six genes encoding a putative histidine kinase, transcriptional regulator, DNA-binding transcriptional activator, helix-turn-helix-type transcriptional regulator, phage shock protein, and cysteine protease were disrupted. The cysteine protease mutant had a high degree of similarity with the type 3 effector protein XopD of Xanthomonas campestris. Our findings shed light on the diverse and complicated mechanisms that underlie these highly host-specific interactions and indicate the involvement of a type 3 effector in Rj4 nodulation restriction, suggesting that Rj4 incompatibility is partly mediated by effector-triggered immunity.
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Affiliation(s)
- Omar M Faruque
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hiroki Miwa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Michiko Yasuda
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yoshiharu Fujii
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Takakazu Kaneko
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Shin Okazaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
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4
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Zhang XX, Guo HJ, Wang R, Sui XH, Zhang YM, Wang ET, Tian CF, Chen WX. Genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island. Appl Environ Microbiol 2014; 80:3181-90. [PMID: 24632260 PMCID: PMC4018923 DOI: 10.1128/aem.00044-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/07/2014] [Indexed: 01/26/2023] Open
Abstract
The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island ("island" genes; nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense, Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, or Bradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.
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Affiliation(s)
- Xing Xing Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Hui Juan Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Rui Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
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5
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Lorio JC, Kim WS, Krishnan AH, Krishnan HB. Disruption of the glycine cleavage system enables Sinorhizobium fredii USDA257 to form nitrogen-fixing nodules on agronomically improved North American soybean cultivars. Appl Environ Microbiol 2010; 76:4185-93. [PMID: 20453144 PMCID: PMC2897462 DOI: 10.1128/aem.00437-10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 04/26/2010] [Indexed: 11/20/2022] Open
Abstract
The symbiosis between Sinorhizobium fredii USDA257 and soybean [Glycine max (L.) Merr.] exhibits a high degree of cultivar specificity. USDA257 nodulates primitive soybean cultivars but fails to nodulate agronomically improved cultivars such as McCall. In this study we provide evidence for the involvement of a new genetic locus that controls soybean cultivar specificity. This locus was identified in USDA257 by Tn5 transposon mutagenesis followed by nodulation screening on McCall soybean. We have cloned the region corresponding to the site of Tn5 insertion and found that it lies within a 1.5-kb EcoRI fragment. DNA sequence analysis of this fragment and an adjacent 4.4-kb region identified an operon made up of three open reading frames encoding proteins of deduced molecular masses of 41, 13, and 104 kDa, respectively. These proteins revealed significant amino acid homology to glycine cleavage (gcv) system T, H, and P proteins of Escherichia coli and other organisms. Southern blot analysis revealed the presence of similar sequences in diverse rhizobia. Measurement of beta-galactosidase activity of a USDA257 strain containing a transcriptional fusion of gcvT promoter sequences to the lacZ gene revealed that the USDA257 gcvTHP operon was inducible by glycine. Inactivation of either gcvT or gcvP of USDA257 enabled the mutant to nodulate several agronomically improved North American soybean cultivars. These nodules revealed anatomical features typical of determinate nodules, with numerous bacteroids within the infected cells. Unlike for the previously characterized soybean cultivar specificity locus nolBTUVW, inactivation of the gcv locus had no discernible effect on the secretion of nodulation outer proteins of USDA257.
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Affiliation(s)
- Julio C. Lorio
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri, Columbia, Missouri 65211
| | - Won-Seok Kim
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri, Columbia, Missouri 65211
| | - Ammulu H. Krishnan
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri, Columbia, Missouri 65211
| | - Hari B. Krishnan
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri, Columbia, Missouri 65211
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6
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Selao TT, Nordlund S, Norén A. Comparative Proteomic Studies in Rhodospirillum rubrum Grown under Different Nitrogen Conditions. J Proteome Res 2008; 7:3267-75. [DOI: 10.1021/pr700771u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tiago T. Selao
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
| | - Stefan Nordlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
| | - Agneta Norén
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Sweden
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7
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Larrainzar E, Wienkoop S, Weckwerth W, Ladrera R, Arrese-Igor C, González EM. Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress. PLANT PHYSIOLOGY 2007; 144:1495-507. [PMID: 17545507 PMCID: PMC1914115 DOI: 10.1104/pp.107.101618] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Drought is one of the environmental factors most affecting crop production. Under drought, symbiotic nitrogen fixation is one of the physiological processes to first show stress responses in nodulated legumes. This inhibition process involves a number of factors whose interactions are not yet understood. This work aims to further understand changes occurring in nodules under drought stress from a proteomic perspective. Drought was imposed on Medicago truncatula 'Jemalong A17' plants grown in symbiosis with Sinorhizobium meliloti strain 2011. Changes at the protein level were analyzed using a nongel approach based on liquid chromatography coupled to tandem mass spectrometry. Due to the complexity of nodule tissue, the separation of plant and bacteroid fractions in M. truncatula root nodules was first checked with the aim of minimizing cross contamination between the fractions. Second, the protein plant fraction of M. truncatula nodules was profiled, leading to the identification of 377 plant proteins, the largest description of the plant nodule proteome so far. Third, both symbiotic partners were independently analyzed for quantitative differences at the protein level during drought stress. Multivariate data mining allowed for the classification of proteins sets that were involved in drought stress responses. The isolation of the nodule plant and bacteroid protein fractions enabled the independent analysis of the response of both counterparts, gaining further understanding of how each symbiotic member is distinctly affected at the protein level under a water-deficit situation.
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Affiliation(s)
- Estíbaliz Larrainzar
- Departamento de Ciencias del Medio Natural, Universidad Pública de Navarra, Pamplona, Navarra, Spain
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8
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Chistoserdova L, Chen SW, Lapidus A, Lidstrom ME. Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol 2003; 185:2980-7. [PMID: 12730156 PMCID: PMC154073 DOI: 10.1128/jb.185.10.2980-2987.2003] [Citation(s) in RCA: 225] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-2125, USA
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9
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Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD, Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS, Weaver JE, Webby RJ, De Bruijn FJ, Ronson CW. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol 2002; 184:3086-95. [PMID: 12003951 PMCID: PMC135072 DOI: 10.1128/jb.184.11.3086-3095.2002] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mesorhizobium loti strain R7A symbiosis island is a 502-kb chromosomally integrated element which transfers to nonsymbiotic mesorhizobia in the environment, converting them to Lotus symbionts. It integrates into a phenylalanine tRNA gene in a process mediated by a P4-type integrase encoded at the left end of the element. We have determined the nucleotide sequence of the island and compared its deduced genetic complement with that reported for the 611-kb putative symbiosis island of M. loti strain MAFF303099. The two islands share 248 kb of DNA, with multiple deletions and insertions of up to 168 kb interrupting highly conserved colinear DNA regions in the two strains. The shared DNA regions contain all the genes likely to be required for Nod factor synthesis, nitrogen fixation, and island transfer. Transfer genes include a trb operon and a cluster of potential tra genes which are also present on the strain MAFF303099 plasmid pMLb. The island lacks plasmid replication genes, suggesting that it is a site-specific conjugative transposon. The R7A island encodes a type IV secretion system with strong similarity to the vir pilus from Agrobacterium tumefaciens that is deleted from MAFF303099, which in turn encodes a type III secretion system not found on the R7A island. The 414 genes on the R7A island also include putative regulatory genes, transport genes, and an array of metabolic genes. Most of the unique hypothetical genes on the R7A island are strain-specific and clustered, suggesting that they may represent other acquired genetic elements rather than symbiotically relevant DNA.
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Affiliation(s)
- John T Sullivan
- Department of Microbiology, University of Otago, Dunedin, New Zealand
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10
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Ferraioli S, Tatè R, Cermola M, Favre R, Iaccarino M, Patriarca EJ. Auxotrophic mutant strains of Rhizobium etli reveal new nodule development phenotypes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2002; 15:501-510. [PMID: 12036281 DOI: 10.1094/mpmi.2002.15.5.501] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We report here the isolation and characterization of amino acid-requiring mutant strains of Rhizobium etli. We observe that the phenotype of most mutations, even when causing a strict auxotrophy, is overcome by cross-feeding from the host plant Phaseolus vulgaris, thereby allowing bacterial production of Nod factors and, consequently, nodule induction. Conversely, light and electron microscopy analysis reveals that the nodules induced by all mutants, including those with normal external morphology, are halted or strongly altered at intermediate or late stages of development. Moreover, some mutants induce nodules that display novel symbiotic phenotypes, such as specific alterations of the invaded cells or the presence of a reduced number of abnormally shaped uninvaded cells. Other mutants induce nodules showing an early and vast necrosis of the central tissue, a phenotype not previously observed in bean nodules, not even in nodules induced by a Fix- mutant. These observations indicate that amino acid auxotrophs represent a powerful tool to study the development of globose determinate-type nodules and emphasize the importance of establishing their histology and cytology before considerations of metabolic exchange are made.
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Affiliation(s)
- Simona Ferraioli
- International Institute of Genetics and Biophysics, C.N.R., Naples, Italy
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11
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Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci U S A 2001; 98:9883-8. [PMID: 11481432 PMCID: PMC55547 DOI: 10.1073/pnas.161294798] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti contains three replicons: pSymA, pSymB, and the chromosome. We report here the complete 1,354,226-nt sequence of pSymA. In addition to a large fraction of the genes known to be specifically involved in symbiosis, pSymA contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.
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Affiliation(s)
- M J Barnett
- Department of Biological Sciences, and Howard Hughes Medical Institute, Stanford University, CA 94305, USA
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12
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Barloy-Hubler F, Capela D, Barnett MJ, Kalman S, Federspiel NA, Long SR, Galibert F. High-resolution physical map of the Sinorhizobium meliloti 1021 pSyma megaplasmid. J Bacteriol 2000; 182:1185-9. [PMID: 10648551 PMCID: PMC94401 DOI: 10.1128/jb.182.4.1185-1189.2000] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To facilitate sequencing of the Sinorhizobium meliloti 1021 pSyma megaplasmid, a high-resolution map was constructed by ordering 113 overlapping bacterial artificial chromosome clones with 192 markers. The 157 anonymous sequence tagged site markers (81,072 bases) reveal hypothetical functions encoded by the replicon.
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Affiliation(s)
- F Barloy-Hubler
- Laboratoire de Recombinaisons Génétiques UPR41-CNRS, Faculté de Médecine, F-35043 Rennes Cedex, France
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13
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Hong MC, Wu ML, Chang MC. Cloning and complete nucleotide sequence of Acinetobacter radioresistens CMC-1 AglyA gene encoding serine hydroxymethyltransferase. FEMS Microbiol Lett 1999; 170:413-8. [PMID: 9933935 DOI: 10.1111/j.1574-6968.1999.tb13402.x] [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: 11/29/2022] Open
Abstract
A gene (AglyA) encoding serine hydroxymethyltransferase of Acinetobacter radioresistens CMC-1 was cloned and sequenced. Nucleotide sequence analysis of AglyA predicted a single open reading frame (ORF) of 1251 bp encoding a 417-amino acid polypeptide. Two putative MetR-like binding sites (5'-TGAAACATGAGCT) and (5'-TGAGCAAAGTTCA), centered at bp -123 and -95 relative to the +1 translation start site were found, which have six out of nine and eight out of nine nucleotides that match to the consensus sequence of Escherichia coli (5'-TGAANNT/ANNTTCA), respectively. The enzyme also showed a high level of homology to other sources of serine hydroxymethyltransferase proteins.
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Affiliation(s)
- M C Hong
- Department of Biochemistry, Medical College, National Cheng Kung University, Tainan, Taiwan
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14
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Jagath JR, Sharma B, Rao NA, Savithri HS. The role of His-134, -147, and -150 residues in subunit assembly, cofactor binding, and catalysis of sheep liver cytosolic serine hydroxymethyltransferase. J Biol Chem 1997; 272:24355-62. [PMID: 9305893 DOI: 10.1074/jbc.272.39.24355] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In an attempt to unravel the role of conserved histidine residues in the structure-function of sheep liver cytosolic serine hydroxymethyltransferase (SHMT), three site-specific mutants (H134N, H147N, and H150N) were constructed and expressed. H134N and H147N SHMTs had Km values for L-serine, L-allo-threonine and beta-phenylserine similar to that of wild type enzyme, although the kcat values were markedly decreased. H134N SHMT was obtained in a dimeric form with only 6% of bound pyridoxal 5'-phosphate (PLP) compared with the wild type enzyme. Increasing concentrations of PLP (up to 500 microM) enhanced the enzyme activity without changing its oligomeric structure, indicating that His-134 may be involved in dimer-dimer interactions. H147N SHMT was obtained in a tetrameric form but with very little PLP (3%) bound to it, suggesting that this residue was probably involved in cofactor binding. Unlike the wild type enzyme, the cofactor could be easily removed by dialysis from H147N SHMT, and the apoenzyme thus formed was present predominantly in the dimeric form, indicating that PLP binding is at the dimer-dimer interface. H150N SHMT was obtained in a tetrameric form with bound PLP. However, the mutant had very little enzyme activity (<2%). The kcat/Km values for L-serine, L-allo-threonine and beta-phenylserine were 80-, 56-, and 33-fold less compared with wild type enzyme. Unlike the wild type enzyme, it failed to form the characteristic quinonoid intermediate and was unable to carry out the exchange of 2-S proton from glycine in the presence of H4-folate. However, it could form an external aldimine with serine and glycine. The wild type and the mutant enzyme had similar Kd values for serine and glycine. These results suggest that His-150 may be the base that abstracts the alpha-proton of the substrate, leading to formation of the quinonoid intermediate in the reaction catalyzed by SHMT.
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Affiliation(s)
- J R Jagath
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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15
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Thöny-Meyer L, Künzler P. The Bradyrhizobium japonicum aconitase gene (acnA) is important for free-living growth but not for an effective root nodule symbiosis. J Bacteriol 1996; 178:6166-72. [PMID: 8892815 PMCID: PMC178486 DOI: 10.1128/jb.178.21.6166-6172.1996] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Bradyrhizobium japonicum acnA gene encoding the tricarboxylic acid cycle enzyme aconitase was cloned and characterized. The gene was mapped immediately upstream of the cytochrome c biogenesis gene cycV and found to be transcribed in the opposite direction. The nucleotide sequence of acnA was determined; the derived amino acid sequence shared a significant similarity with bacterial aconitases and with the human iron-responsive-element-binding protein. The level of expression of the acnA gene under aerobic growth conditions was 10-fold higher than that under anaerobic conditions. The start of transcription was mapped by primer extension experiments, and the putative promoter was found to contain a typical -10 but no -35 consensus sequence for a sigma70-type RNA polymerase. A 5' deletion removing all but 19 nucleotides upstream of the start of transcription completely abolished gene expression. An acnA mutant was constructed by gene disruption, and the mutant phenotype was characterized. Growth of the mutant was severely affected and could not be corrected by the addition of glutamate as a supplement. Although aconitase activity in free-living cells was decreased by more than 70%, the ability of the mutant to establish an effective root nodule symbiosis with soybean plants was not affected. This suggested either the existence of a second aconitase or the compensation for the mutant defect by symbiosis-specific metabolites synthesized in the root nodules.
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Affiliation(s)
- L Thöny-Meyer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, Zürich, Switzerland.
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16
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17
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Chistoserdova LV, Lidstrom ME. Genetics of the serine cycle in Methylobacterium extorquens AM1: cloning, sequence, mutation, and physiological effect of glyA, the gene for serine hydroxymethyltransferase. J Bacteriol 1994; 176:6759-62. [PMID: 7961431 PMCID: PMC197035 DOI: 10.1128/jb.176.21.6759-6762.1994] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The gene (glyA) of Methylobacterium extorquens AM1 encoding serine hydroxymethyltransferase (SHMT), one of the key enzymes of the serine cycle for C1 assimilation, was isolated by using a synthetic oligonucleotide with a sequence based on amino acid sequence conserved in SHMTs from different sources. The amino acid sequence deduced from the gene revealed high similarity to those of known SHMTs. The cloned gene was inactivated by insertion of a kanamycin resistance gene, and recombination of this insertion derivative with the wild-type gene produced an SHMT null mutant. Surprisingly, this mutant had lost its ability to grow on C1 as well as on C2 compounds but was still able to grow on succinate. The DNA fragment containing glyA was shown not to be linked with fragments carrying serine cycle genes identified earlier, making it the fourth chromosomal region of M. extorquens AM1 to be indicated as being involved in C1 assimilation.
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Affiliation(s)
- L V Chistoserdova
- W.M. Keck Laboratories 138-78, California Institute of Technology, Pasadena 91125
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18
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Abstract
This review presents a comparison between the complex genetic regulatory networks that control nitrogen fixation in three representative rhizobial species, Rhizobium meliloti, Bradyrhizobium japonicum, and Azorhizobium caulinodans. Transcription of nitrogen fixation genes (nif and fix genes) in these bacteria is induced primarily by low-oxygen conditions. Low-oxygen sensing and transmission of this signal to the level of nif and fix gene expression involve at least five regulatory proteins, FixL, FixJ, FixK, NifA, and RpoN (sigma 54). The characteristic features of these proteins and their functions within species-specific regulatory pathways are described. Oxygen interferes with the activities of two transcriptional activators, FixJ and NifA. FixJ activity is modulated via phosphorylation-dephosphorylation by the cognate sensor hemoprotein FixL. In addition to the oxygen responsiveness of the NifA protein, synthesis of NifA is oxygen regulated at the level of transcription. This type of control includes FixLJ in R. meliloti and FixLJ-FixK in A. caulinodans or is brought about by autoregulation in B. japonicum. NifA, in concert with sigma 54 RNA polymerase, activates transcription from -24/-12-type promoters associated with nif and fix genes and additional genes that are not directly involved in nitrogen fixation. The FixK proteins constitute a subgroup of the Crp-Fnr family of bacterial regulators. Although the involvement of FixLJ and FixK in nifA regulation is remarkably different in the three rhizobial species discussed here, they constitute a regulatory cascade that uniformly controls the expression of genes (fixNOQP) encoding a distinct cytochrome oxidase complex probably required for bacterial respiration under low-oxygen conditions. In B. japonicum, the FixLJ-FixK cascade also controls genes for nitrate respiration and for one of two sigma 54 proteins.
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Affiliation(s)
- H M Fischer
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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19
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Newman JD, Diebold RJ, Schultz BW, Noel KD. Infection of soybean and pea nodules by Rhizobium spp. purine auxotrophs in the presence of 5-aminoimidazole-4-carboxamide riboside. J Bacteriol 1994; 176:3286-94. [PMID: 8195084 PMCID: PMC205499 DOI: 10.1128/jb.176.11.3286-3294.1994] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Purine auxotrophs of various Rhizobium species are symbiotically defective, usually unable to initiate or complete the infection process. Earlier studies demonstrated that, in the Rhizobium etli-bean symbiosis, infection by purine auxotrophs is partially restored by supplementation of the plant medium with 5-amino-imidazole-4-carboxamide (AICA) riboside, the unphosphorylated form of the purine biosynthetic intermediate AICAR. The addition of purine to the root environment does not have this effect. In this study, purine auxotrophs of Rhizobium fredii HH303 and Rhizobium leguminosarum 128C56 (bv. viciae) were examined. Nutritional and genetic characterization indicated that each mutant was blocked in purine biosynthesis prior to the production of AICAR. R. fredii HH303 and R. leguminosarum 128C56 appeared to be deficient in AICA riboside transport and/or conversion into AICAR, and the auxotrophs derived from them grew very poorly with AICA riboside as a purine source. All of the auxotrophs elicited poorly developed, uninfected nodules on their appropriate hosts. On peas, addition of AICA riboside or purine to the root environment led to enhanced nodulation; however, infection threads were observed only in the presence of AICA riboside. On soybeans, only AICA riboside was effective in enhancing nodulation and promoting infection. Although AICA riboside supplementation of the auxotrophs led to infection thread development on both hosts, the numbers of bacteria recovered from the nodules were still 2 or more orders of magnitude lower than in fully developed nodules populated by wild-type bacteria. The ability to AICA riboside to promote infection by purine auxotrophs, despite serving as a very poor purine source for these strains, supports the hypothesis that AICAR plays a role in infection other than merely promoting bacterial growth.
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Affiliation(s)
- J D Newman
- Department of Biology, Marquette University, Milwaukee, Wisconsin 53233, USA
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20
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McNeil J, McIntosh E, Taylor B, Zhang F, Tang S, Bognar A. Cloning and molecular characterization of three genes, including two genes encoding serine hydroxymethyltransferases, whose inactivation is required to render yeast auxotrophic for glycine. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37089-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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21
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Usha R, Savithri HS, Rao NA. The primary structure of sheep liver cytosolic serine hydroxymethyltransferase and an analysis of the evolutionary relationships among serine hydroxymethyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1204:75-83. [PMID: 8305478 DOI: 10.1016/0167-4838(94)90035-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The complete amino-acid sequence of sheep liver cytosolic serine hydroxymethyltransferase was determined from an analysis of tryptic, chymotryptic, CNBr and hydroxylamine peptides. Each subunit of sheep liver serine hydroxymethyltransferase consisted of 483 amino-acid residues. A comparison of this sequence with 8 other serine hydroxymethyltransferases revealed that a possible gene duplication event could have occurred after the divergence of animals and fungi. This analysis also showed independent duplication of SHMT genes in Neurospora crassa. At the secondary structural level, all the serine hydroxymethyltransferases belong to the alpha/beta category of proteins. The predicted secondary structure of sheep liver serine hydroxymethyltransferase was similar to that of the observed structure of tryptophan synthase, another pyridoxal 5'-phosphate containing enzyme, suggesting that sheep liver serine hydroxymethyltransferase might have a similar pyridoxal 5'-phosphate binding domain. In addition, a conserved glycine rich region, G L Q G G P, was identified in all the serine hydroxymethyltransferases and could be important in pyridoxal 5'-phosphate binding. A comparison of the cytosolic serine hydroxymethyltransferases from rabbit and sheep liver with other proteins sequenced from both these sources showed that serine hydroxymethyltransferase was a highly conserved protein. It was slightly less conserved than cytochrome c but better conserved than myoglobin, both of which are well known evolutionary markers. C67 and C203 were specifically protected by pyridoxal 5'-phosphate against modification with [14C]iodoacetic acid, while C247 and C261 were buried in the native serine hydroxymethyltransferase. However, the cysteines are not conserved among the various serine hydroxymethyltransferases. The exact role of the cysteines in the reaction catalyzed by serine hydroxymethyltransferase remains to be elucidated.
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Affiliation(s)
- R Usha
- Department of Biochemistry, Indian Institute of Science, Bangalore
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22
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Pascarella S, Schirch V, Bossa F. Similarity between serine hydroxymethyltransferase and other pyridoxal phosphate-dependent enzymes. FEBS Lett 1993; 331:145-9. [PMID: 8405393 DOI: 10.1016/0014-5793(93)80314-k] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A structural homology of the pyridoxal-5'-phosphate (PLP)-dependent enzyme serine hydroxymethyltransferase (SHMT) with aspartate aminotransferase (AAT) is proposed. Although the two sequences are very dissimilar, a reasonable alignment was obtained using the profile analysis method. Sequences of AAT and dialkylglycine decarboxylase (DGD), for which crystal structure data are available, have been aligned on the basis of their structure superposition. A profile was then calculated and SHMT sequence aligned to it. Three of the four residues conserved in all aminotransferases (including the PLP-binding lysine) are matched. A profile search with DGD-AAT-SHMT profile is more selective and sensitive than individual sequence profiles for PLP-dependent enzyme detection. Potential homologies with the eryC1 gene product involved in erythromycin biosynthesis and with amino acid decarboxylases were observed. Homology with AAT will be used as a guideline for planning site-directed mutagenesis experiments on SHMT.
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Affiliation(s)
- S Pascarella
- Dipartimento di Scienze Biochimiche A Rossi Fanelli, Università La Sapienza, Roma, Italy
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23
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Jones CE, Brook JM, Buck D, Abell C, Smith AG. Cloning and sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme. J Bacteriol 1993; 175:2125-30. [PMID: 8096212 PMCID: PMC204323 DOI: 10.1128/jb.175.7.2125-2130.1993] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The panB gene from Escherichia coli, encoding the first enzyme of the pantothenate biosynthesis pathway, ketopantoate hydroxymethyltransferase (KPHMT), has been isolated by functional complementation of a panB mutant strain with an E. coli genomic library. The gene is 792 bp long, encoding a protein of 264 amino acids with a predicted M(r) of 28,179. The identity of the gene product as ketopantoate hydroxymethyltransferase was confirmed by purification of the enzyme protein, which was overexpressed approximately 50-fold in the mutant harboring the gene on a high-copy-number plasmid. The N-terminal amino acid sequence of the purified protein was found to be identical to that predicted from the gene sequence, as was its mass, determined by electrospray mass spectrometry. Upstream of the panB gene is an incomplete open reading frame encoding a protein of 220 amino acids, which shares sequence similarity to fimbrial precursor proteins from other bacteria. Northern (RNA) analysis showed that the panB gene is likely to be cotranscribed with at least one other gene but that this is not the putative fimbrial protein, since no transcripts for this gene could be detected.
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Affiliation(s)
- C E Jones
- Department of Plant Sciences, University of Cambridge, England
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24
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Miyata A, Yoshida T, Yamaguchi K, Yokoyama C, Tanabe T, Toh H, Mitsunaga T, Izumi Y. Molecular cloning and expression of the gene for serine hydroxymethyltransferase from an obligate methylotroph Hyphomicrobium methylovorum GM2. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 212:745-50. [PMID: 8462546 DOI: 10.1111/j.1432-1033.1993.tb17713.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The gene encoding serine hydroxymethyltransferase (SHMT), one of the key enzymes of the one-carbon-compound assimilation of a methylotroph, Hyphomicrobium methylovorum GM2, and its flanking regions were isolated using a DNA fragment encoding Escherichia coli SHMT as a probe. Nucleotide sequencing of the recombinant plasmids revealed the SHMT gene codes for the 434-amino-acid protein with a calculated molecular mass of 46,068 Da. The amino-acid sequence of the enzyme showed identity to the sequences of the enzymes from E. coli (55%) and rabbit liver (44%). The recombinant plasmid, which was constructed by ligation of the cloned gene and an expression vector pKK223-3, was introduced to an SHMT-deficient E. coli mutant ME5427 (glyA-). The transformed E. coli cells expressed SHMT, which was immunologically and enzymologically indistinguishable from the enzyme isolated from H. methylovorum GM2.
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Affiliation(s)
- A Miyata
- Department of Pharmacology, National Cardiovascular Center Research Institute, Osaka, Japan
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25
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Kündig C, Hennecke H, Göttfert M. Correlated physical and genetic map of the Bradyrhizobium japonicum 110 genome. J Bacteriol 1993; 175:613-22. [PMID: 8423135 PMCID: PMC196196 DOI: 10.1128/jb.175.3.613-622.1993] [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: 01/30/2023] Open
Abstract
We describe a compilation of 79 known genes of Bradyrhizobium japonicum 110, 63 of which were placed on a correlated physical and genetic map of the chromosome. Genomic DNA was restricted with enzymes PacI, PmeI, and SwaI, which yielded two, five, and nine fragments, respectively. Linkage of some of the fragments was established by performing Southern blot hybridization experiments. For probes we used isolated, labelled fragments that were produced either by PmeI or by SwaI. Genes were mapped on individual restriction fragments by performing gene-directed mutagenesis. The principle of this method was to introduce recognition sites for all three restriction enzymes mentioned above into or very near the desired gene loci. Pulsed-field gel electrophoresis of restricted mutant DNA then resulted in an altered fragment pattern compared with wild-type DNA. This allowed us to identify overlapping fragments and to determine the exact position of any selected gene locus. The technique was limited only by the accuracy of the fragment size estimates. After linkage of all of the restriction fragments we concluded that the B. japonicum genome consists of a single, circular chromosome that is approximately 8,700 kb long. Genes directly concerned with nodulation and symbiotic nitrogen fixation are clustered in a chromosomal section that is about 380 kb long.
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Affiliation(s)
- C Kündig
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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26
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Characterization of the formate (for) locus, which encodes the cytosolic serine hydroxymethyltransferase of Neurospora crassa. Mol Cell Biol 1992. [PMID: 1532227 DOI: 10.1128/mcb.12.4.1412] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT) occupies a central position in one-carbon (C1) metabolism, catalyzing the reaction of serine and tetrahydrofolate to yield glycine and 5,10-methylenetetrahydrofolate. Methylenetetrahydrofolate serves as a donor of C1 units for the synthesis of numerous compounds, including purines, thymidylate, lipids, and methionine. We provide evidence that the formate (for) locus of Neurospora crassa encodes cytosolic SHMT. The for+ gene was localized to a 2.8-kb BglII fragment by complementation (restoration to formate-independent growth) of a strain carrying a recessive for allele, which confers a growth requirement for formate. The for+ gene encodes a polypeptide of 479 amino acids which shows significant similarity to amino acid sequences of SHMT from bacterial and mammalian sources (47 and 60% amino acid identity, respectively). The for+ mRNA has several different start and stop sites. The abundance of for+ mRNA increased in response to amino acid imbalance induced by glycine supplementation, suggesting regulation by the N. crassa cross-pathway control system, which is analogous to general amino acid control in Saccharomyces cerevisiae. This was confirmed by documenting that for+ expression increased in response to histidine limitation (induced by 3-amino-1,2,4-triazole) and that this response was dependent on the presence of a functional cross-pathway control-1 (cpc-1) gene, which encodes CPC1, a positively acting transcription factor. There are at least five potential CPC1 binding sites upstream of the for+ transcriptional start, as well as one that exactly matches the consensus CPC1 binding site in the first intron of the for+ gene.
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27
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McClung CR, Davis CR, Page KM, Denome SA. Characterization of the formate (for) locus, which encodes the cytosolic serine hydroxymethyltransferase of Neurospora crassa. Mol Cell Biol 1992; 12:1412-21. [PMID: 1532227 PMCID: PMC369582 DOI: 10.1128/mcb.12.4.1412-1421.1992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Serine hydroxymethyltransferase (SHMT) occupies a central position in one-carbon (C1) metabolism, catalyzing the reaction of serine and tetrahydrofolate to yield glycine and 5,10-methylenetetrahydrofolate. Methylenetetrahydrofolate serves as a donor of C1 units for the synthesis of numerous compounds, including purines, thymidylate, lipids, and methionine. We provide evidence that the formate (for) locus of Neurospora crassa encodes cytosolic SHMT. The for+ gene was localized to a 2.8-kb BglII fragment by complementation (restoration to formate-independent growth) of a strain carrying a recessive for allele, which confers a growth requirement for formate. The for+ gene encodes a polypeptide of 479 amino acids which shows significant similarity to amino acid sequences of SHMT from bacterial and mammalian sources (47 and 60% amino acid identity, respectively). The for+ mRNA has several different start and stop sites. The abundance of for+ mRNA increased in response to amino acid imbalance induced by glycine supplementation, suggesting regulation by the N. crassa cross-pathway control system, which is analogous to general amino acid control in Saccharomyces cerevisiae. This was confirmed by documenting that for+ expression increased in response to histidine limitation (induced by 3-amino-1,2,4-triazole) and that this response was dependent on the presence of a functional cross-pathway control-1 (cpc-1) gene, which encodes CPC1, a positively acting transcription factor. There are at least five potential CPC1 binding sites upstream of the for+ transcriptional start, as well as one that exactly matches the consensus CPC1 binding site in the first intron of the for+ gene.
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Affiliation(s)
- C R McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
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28
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New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1992; 20:1173-9. [PMID: 1549508 PMCID: PMC312152 DOI: 10.1093/nar/20.5.1173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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29
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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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30
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Ramseier TM, Göttfert M. Codon usage and G + C content in Bradyrhizobium japonicum genes are not uniform. Arch Microbiol 1991; 156:270-6. [PMID: 1793334 DOI: 10.1007/bf00262997] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To date, the sequences of 45 Bradyrhizobium japonicum genes are known. This provides sufficient information to determine their codon usage and G + C content. Surprisingly, B. japonicum nodulation and NifA-regulated genes were found to have a less biased codon usage and a lower G + C content than genes not belonging to these two groups. Thus, the coding regions of nodulation genes and NifA-regulated genes could hardly be identified in codon preference plots whereas this was not difficult with other genes. The codon frequency table of the highly biased genes was used in a codon preference plot to analyze the RSRj alpha 9 sequence which is an insertion sequence (IS)-like element. The plot helped identify a new open reading frame (ORF355) that escaped previous detection because of two sequencing errors. These were now corrected. The deduced gene product of ORF355 in RSRj alpha 9 showed extensive similarity to a putative protein encoded by an ORF in the T-DNA of Agrobacterium rhizogenes. The DNA sequences bordering both ORFs showed inverted repeats and potential target site duplications which supported the assumption that they were IS-like elements.
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Affiliation(s)
- T M Ramseier
- Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland
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