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Kudjordjie EN, Sapkota R, Steffensen SK, Fomsgaard IS, Nicolaisen M. Maize synthesized benzoxazinoids affect the host associated microbiome. Microbiome 2019; 7:59. [PMID: 30975184 DOI: 10.1186/s40168-019-0677-677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/28/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Plants actively shape their associated microbial communities by synthesizing bio-active substances. Plant secondary metabolites are known for their signaling and plant defense functions, yet little is known about their overall effect on the plant microbiome. In this work, we studied the effects of benzoxazinoids (BXs), a group of secondary metabolites present in maize, on the host-associated microbial structure. Using BX knock-out mutants and their W22 parental lines, we employed 16S and ITS2 rRNA gene amplicon analysis to characterize the maize microbiome at early growth stages. RESULTS Rhizo-box experiment showed that BXs affected microbial communities not only in roots and shoots, but also in the rhizosphere. Fungal richness in roots was more affected by BXs than root bacterial richness. Maize genotype (BX mutants and their parental lines) as well as plant age explained both fungal and bacterial community structure. Genotypic effect on microbial communities was stronger in roots than in rhizosphere. Diverse, but specific, microbial taxa were affected by BX in both roots and shoots, for instance, many plant pathogens were negatively correlated to BX content. In addition, a co-occurrence analysis of the root microbiome revealed that BXs affected specific groups of the microbiome. CONCLUSIONS This study provides insights into the role of BXs for microbial community assembly in the rhizosphere and in roots and shoots. Coupling the quantification of BX metabolites with bacterial and fungal communities, we were able to suggest a gatekeeper role of BX by showing its correlation with specific microbial taxa and thus providing insights into effects on specific fungal and bacterial taxa in maize roots and shoots. Root microbial co-occurrence networks revealed that BXs affect specific microbial clusters.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Rumakanta Sapkota
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Stine K Steffensen
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Inge S Fomsgaard
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Nicolaisen
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark.
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Kudjordjie EN, Sapkota R, Steffensen SK, Fomsgaard IS, Nicolaisen M. Maize synthesized benzoxazinoids affect the host associated microbiome. Microbiome 2019; 7:59. [PMID: 30975184 PMCID: PMC6460791 DOI: 10.1186/s40168-019-0677-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/28/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plants actively shape their associated microbial communities by synthesizing bio-active substances. Plant secondary metabolites are known for their signaling and plant defense functions, yet little is known about their overall effect on the plant microbiome. In this work, we studied the effects of benzoxazinoids (BXs), a group of secondary metabolites present in maize, on the host-associated microbial structure. Using BX knock-out mutants and their W22 parental lines, we employed 16S and ITS2 rRNA gene amplicon analysis to characterize the maize microbiome at early growth stages. RESULTS Rhizo-box experiment showed that BXs affected microbial communities not only in roots and shoots, but also in the rhizosphere. Fungal richness in roots was more affected by BXs than root bacterial richness. Maize genotype (BX mutants and their parental lines) as well as plant age explained both fungal and bacterial community structure. Genotypic effect on microbial communities was stronger in roots than in rhizosphere. Diverse, but specific, microbial taxa were affected by BX in both roots and shoots, for instance, many plant pathogens were negatively correlated to BX content. In addition, a co-occurrence analysis of the root microbiome revealed that BXs affected specific groups of the microbiome. CONCLUSIONS This study provides insights into the role of BXs for microbial community assembly in the rhizosphere and in roots and shoots. Coupling the quantification of BX metabolites with bacterial and fungal communities, we were able to suggest a gatekeeper role of BX by showing its correlation with specific microbial taxa and thus providing insights into effects on specific fungal and bacterial taxa in maize roots and shoots. Root microbial co-occurrence networks revealed that BXs affect specific microbial clusters.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Rumakanta Sapkota
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Stine K. Steffensen
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Inge S. Fomsgaard
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Mogens Nicolaisen
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
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Semashko TA, Arzamasov AA, Fisunov GY, Govorun VM. Transcription profiling data set of different states of Mycoplasma gallisepticum. Genom Data 2016; 11:49-54. [PMID: 27942460 PMCID: PMC5137179 DOI: 10.1016/j.gdata.2016.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 12/01/2022]
Abstract
Mycoplasma gallisepticum belongs to class Mollicutes and causes chronic respiratory disease in birds. It has a reduced genome, lack of cell wall and many metabolic pathways, and also easy to culture and non-pathogenic to humans. Aforementioned made it is a convenient model for studying of systems biology of minimal cell. Studying the transcriptomic level of M. gallisepticum is interesting for both understanding of common principles of transcription regulation of minimal cell and response to definite influence for pathogen bacteria. For rapid investigation of gene expression we developed microarray design including 3366 probes for 678 genes. They included 665 protein coding sequences and 13 antisense RNAs from 816 genes and 17 ncRNAs present in Mycoplasma gallisepticum. The study was performed on Agilent one-color microarray with custom design and random-T7 polymerase primer for cDNA synthesis. Here we present the data for transcription profiling of M. gallisepticum under different types of exposures: genetic knock-out mutants, cell culture exposed to sublethal concentrations of antibiotics and well-characterized heat stress effect. Mutants have transposon insertion to hypothetical membrane protein, lactate dehydrogenase, helicase with unknown function, 1-deoxy-d-xylulose 5-phosphate reductoisomerase or potential sigma factor. For inhibition of important cell systems, treatment with carbonyl cyanide m-chlorophenylhydrazone (CCCP), novobiocin or tetracycline were chosen. Data are available via NCBI Gene Expression Omnibus (GEO) with the accession number GSE85777 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85777)
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Affiliation(s)
- Tatiana A Semashko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Alexander A Arzamasov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Gleb Y Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vadim M Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russian Federation
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Zhang Y, Navarro E, Cánovas-Márquez JT, Almagro L, Chen H, Chen YQ, Zhang H, Torres-Martínez S, Chen W, Garre V. A new regulatory mechanism controlling carotenogenesis in the fungus Mucor circinelloides as a target to generate β-carotene over-producing strains by genetic engineering. Microb Cell Fact 2016; 15:99. [PMID: 27266994 PMCID: PMC4897934 DOI: 10.1186/s12934-016-0493-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/23/2016] [Indexed: 12/13/2022] Open
Abstract
Background Carotenoids are natural pigments with antioxidant properties that have important functions in human physiology and must be supplied through the diet. They also have important industrial applications as food colourants, animal feed additives and nutraceuticals. Some of them, such as β-carotene, are produced on an industrial scale with the use of microorganisms, including fungi. The mucoral Blakeslea trispora is used by the industry to produce β-carotene, although optimisation of production by molecular genetic engineering is unfeasible. However, the phylogenetically closely related Mucor circinelloides, which is also able to accumulate β-carotene, possesses a vast collection of genetic tools with which to manipulate its genome. Results This work combines classical forward and modern reverse genetic techniques to deepen the regulation of carotenoid synthesis and generate candidate strains for biotechnological production of β-carotene. Mutagenesis followed by screening for mutants with altered colour in the dark and/or in light led to the isolation of 26 mutants that, together with eight previously isolated mutants, have been analysed in this work. Although most of the mutants harboured mutations in known structural and regulatory carotenogenic genes, eight of them lacked mutations in those genes. Whole-genome sequencing of six of these strains revealed the presence of many mutations throughout their genomes, which makes identification of the mutation that produced the phenotype difficult. However, deletion of the crgA gene, a well-known repressor of carotenoid biosynthesis in M. circinelloides, in two mutants (MU206 and MU218) with high levels of β-carotene resulted in a further increase in β-carotene content to differing extents with respect to the crgA single-null strain; in particular, one strain derived from MU218 was able to accumulate up to 4 mg/g of β-carotene. The additive effect of crgA deletion and the mutations present in MU218 suggests the existence of a previously unknown regulatory mechanism that represses carotenoid biosynthesis independently and in parallel to crgA. Conclusions The use of a mucoral model such as M. circinelloides can allow the identification of the regulatory mechanisms that control carotenoid biosynthesis, which can then be manipulated to generate tailored strains of biotechnological interest. Mutants in the repressor crgA and in the newly identified regulatory mechanism generated in this work accumulate high levels of β-carotene and are candidates for further improvements in biotechnological β-carotene production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0493-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingtong Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Eusebio Navarro
- Departamento de Genética y Microbiología (Associate Unit to IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - José T Cánovas-Márquez
- Departamento de Genética y Microbiología (Associate Unit to IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Lorena Almagro
- Department of Plant Biology, Faculty of Biology, University of Murcia, Campus de Espinardo, 30100, Murcia, Spain
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Santiago Torres-Martínez
- Departamento de Genética y Microbiología (Associate Unit to IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China.
| | - Victoriano Garre
- Departamento de Genética y Microbiología (Associate Unit to IQFR-CSIC), Facultad de Biología, Universidad de Murcia, 30100, Murcia, Spain.
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Dragićević M, Todorović S, Bogdanović M, Filipović B, Mišić D, Simonović A. Knockout mutants as a tool to identify the subunit composition of Arabidopsis glutamine synthetase isoforms. Plant Physiol Biochem 2014; 79:1-9. [PMID: 24657507 DOI: 10.1016/j.plaphy.2014.02.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/25/2014] [Indexed: 06/03/2023]
Abstract
Glutamine synthetase (GS) is a key enzyme in nitrogen assimilation, which catalyzes the formation of glutamine from ammonia and glutamate. Plant GS isoforms are multimeric enzymes, recently shown to be decamers. The Arabidopsis genome encodes five cytosolic (GS1) proteins labeled as GLN1;1 through GLN1;5 and one chloroplastic (GS2) isoform, GLN2;0. However, as many as 11 GS activity bands were resolved from different Arabidopsis tissues by Native PAGE and activity staining. Western analysis showed that all 11 isoforms are composed exclusively of 40 kDa GS1 subunits. Of five GS1 genes, only GLN1;1, GLN1;2 and GLN1;3 transcripts accumulated to significant levels in vegetative tissues, indicating that only subunits encoded by these three genes produce the 11-band zymogram. Even though the GS2 gene also had significant expression, the corresponding activity was not detected, probably due to inactivation. To resolve the subunit composition of 11 active GS1 isoforms, homozygous knockout mutants deficient in the expression of different GS1 genes were selected from the progeny of T-DNA insertional SALK and SAIL lines. Comparison of GS isoenzyme patterns of the selected GS1 knockout mutants indicated that all of the detected isoforms consist of varying proportions of GLN1;1, GLN1;2 and GLN1;3 subunits, and that GLN1;1 and GLN1;3, as well as GLN1;2 and GLN1;3 and possibly GLN1;1 and GLN1;2 proteins combine in all proportions to form active homo- and heterodecamers.
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Affiliation(s)
- Milan Dragićević
- Institute for Biological Research "Siniša Stanković", Department for Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia.
| | - Slađana Todorović
- Institute for Biological Research "Siniša Stanković", Department for Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia.
| | - Milica Bogdanović
- Institute for Biological Research "Siniša Stanković", Department for Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia.
| | - Biljana Filipović
- Institute for Biological Research "Siniša Stanković", Department for Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia.
| | - Danijela Mišić
- Institute for Biological Research "Siniša Stanković", Department for Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia.
| | - Ana Simonović
- Institute for Biological Research "Siniša Stanković", Department for Plant Physiology, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia.
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