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Sarkhel R, Priyadarsini S, Mahawar M. Nutrient limitation and oxidative stress induce the promoter of acetate operon in Salmonella Typhimurium. Arch Microbiol 2024; 206:126. [PMID: 38411730 DOI: 10.1007/s00203-024-03863-2] [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: 12/22/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Glyoxylate shunt is an important pathway for microorganisms to survive under multiple stresses. One of its enzymes, malate synthase (encoded by aceB gene), has been widely speculated for its contribution to both the pathogenesis and virulence of various microorganisms. We have previously demonstrated that malate synthase (MS) is required for the growth of Salmonella Typhimurium (S. Typhimurium) under carbon starvation and survival under oxidative stress conditions. The aceB gene is encoded by the acetate operon in S. Typhimurium. We attempted to study the activity of acetate promoter under both the starvation and oxidative stress conditions in a heterologous system. The lac promoter of the pUC19 plasmid was substituted with the putative promoter sequence of the acetate operon of S. Typhimurium upstream to the lacZ gene and transformed the vector construct into E. coli NEBα cells. The transformed cells were subjected to the stress conditions mentioned above. We observed a fourfold increase in the β-galactosidase activity in these cells resulting from the upregulation of the lacZ gene in the stationary phase of cell growth (nutrient deprived) as compared to the mid-log phase. Following exposure of stationary phase cells to hypochlorite-induced oxidative stress, we further observed a 1.6-fold increase in β galactosidase activity. These data suggest the induction of promoter activity of the acetate operon under carbon starvation and oxidative stress conditions. Thus, these observations corroborate our previous findings regarding the upregulation of aceB expression under stressful environments.
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Affiliation(s)
- Ratanti Sarkhel
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Swagatika Priyadarsini
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
- Indian Council of Agricultural Research- National Research Centre on Camel, Bikaner, Rajasthan, India.
| | - Manish Mahawar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
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Zhu J, Jiang X, Guan D, Kang Y, Li L, Cao F, Zhao B, Ma M, Zhao J, Li J. Effects of rehydration on physiological and transcriptional responses of a water-stressed rhizobium. J Microbiol 2022; 60:31-46. [PMID: 34826097 DOI: 10.1007/s12275-022-1325-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023]
Abstract
As a microsymbiont of soybean, Bradyrhizobium japonicum plays an important role in symbiotic nitrogen fixation and sustainable agriculture. However, the survival of B. japonicum cells under water-deplete (e.g., drought) and water-replete (e.g., flood) conditions is a major concern affecting their nitrogen-fixing ability by establishing the symbiotic relationship with the host. In this study, we isolated a water stress tolerant rhizobium from soybean root nodules and tested its survival under water-deplete conditions. The rhizobium was identified as Bradyrhizobium japonicum and named strain 5038. Interestingly, both plate counting and live/dead fluorescence staining assays indicate that a number of viable but non-culturable cells exist in the culture medium upon the rehydration process which could cause dilution stress. Bradyrhizobium japonicum 5038 cells increased production of exopolysaccharide (EPS) and trehalose when dehydrated, suggesting that protective responses were stimulated. As expected, cells reduced their production upon the subsequent rehydration. To examine differential gene expression of B. japonicum 5038 when exposed to water-deplete and subsequent water-replete conditions, whole-genome transcriptional analysis was performed under 10% relative humidity (RH), and subsequent 100% RH, respectively. A total of 462 differentially expressed genes (DEGs, > 2.0-fold) were identified under the 10% RH condition, while 3,776 genes showed differential expression during the subsequent rehydration (100% RH) process. Genes involved in signal transduction, inorganic ion transport, energy production and metabolisms of carbohydrates, amino acids, and lipids were far more up-regulated than down-regulated in the 10% RH condition. Notably, trehalose biosynthetic genes (otsAB, treS, and treYZ), genes ligD, oprB, and a sigma factor rpoH were significantly induced by 10% RH. Under the subsequent 100% RH condition, genes involved in transcription, translation, cell membrane regulation, replication and repair, and protein processing were highly up-regulated. Interestingly, most of 10%-RH inducible genes displayed rehydration-repressed, except three genes encoding heat shock (Hsp20) proteins. Therefore, this study provides molecular evidence for the switch of gene expression of B. japonicum cells when encountered the opposite water availability from water-deplete to water-replete conditions.
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Affiliation(s)
- Jie Zhu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China.
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Yaowei Kang
- Life Sciences College of Zhaoqing University, Zhaoqing, 526061, P. R. China
| | - Li Li
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Ji Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China.
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, P. R. China.
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Singh CK, Singh D, Taunk J, Chaudhary P, Tomar RSS, Chandra S, Singh D, Pal M, Konjengbam NS, Singh MP, Singh Sengar R, Sarker A. Comparative Inter- and IntraSpecies Transcriptomics Revealed Key Differential Pathways Associated With Aluminium Stress Tolerance in Lentil. FRONTIERS IN PLANT SCIENCE 2021; 12:693630. [PMID: 34531881 PMCID: PMC8438445 DOI: 10.3389/fpls.2021.693630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/30/2021] [Indexed: 05/28/2023]
Abstract
Aluminium stress causes plant growth retardation and engenders productivity loss under acidic soil conditions. This study accentuates morpho-physiological and molecular bases of aluminium (Al) tolerance within and between wild (ILWL-15) and cultivated (L-4602 and BM-4) lentil species. Morpho-physiological studies revealed better cyto-morphology of tolerant genotypes over sensitive under Al3+ stress conditions. Mitotic lesions were observed in root cells under these conditions. Transcriptome analysis under Al3+ stress revealed 30,158 specifically up-regulated genes in different comparison groups showing contigs between 15,305 and 18,861 bp. In tolerant genotypes, top up-regulated differentially expressed genes (DEGs) were found to be involved in organic acid synthesis and exudation, production of antioxidants, callose synthesis, protein degradation, and phytohormone- and calcium-mediated signalling under stress conditions. DEGs associated with epigenetic regulation and Al3+ sequestration inside vacuole were specifically upregulated in wild and cultivars, respectively. Based on assembled unigenes, an average of 6,645.7 simple sequence repeats (SSRs) and 14,953.7 high-quality single nucleotide polymorphisms (SNPs) were spotted. By quantitative real-time polymerase chain reaction (qRT-PCR), 12 selected genes were validated. Gene ontology (GO) annotation revealed a total of 8,757 GO terms in three categories, viz., molecular, biological, and cellular processes. Kyoto Encyclopaedia of Genes and Genomes pathway scanning also revealed another probable pathway pertaining to metacaspase-1,-4, and -9 for programmed cell death under Al-stress conditions. This investigation reveals key inter- and intraspecies metabolic pathways associated with Al-stress tolerance in lentil species that can be utilised in designing future breeding programmes to improve lentil and related species towards Al3+ stress.
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Affiliation(s)
- Chandan Kumar Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Dharmendra Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Jyoti Taunk
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Priya Chaudhary
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Shivani Chandra
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University—Imphal, Umiam, India
| | - M. Premjit Singh
- College of Agriculture, Central Agricultural University—Imphal, Iroisemba, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut, India
| | - Ashutosh Sarker
- International Center for Agriculture Research in the Dry Areas, New Delhi, India
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Park C, Shin B, Kim W, Cheong H, Park S, Park W. Comparative genomics of wild-type and laboratory-evolved biofilm-overproducing Deinococcus metallilatus strains. Microb Genom 2020; 6. [PMID: 33147125 PMCID: PMC8116681 DOI: 10.1099/mgen.0.000464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deinococcus metallilatus MA1002 was exposed to ultraviolet radiation to generate mutants with enhanced biofilm production. Two strains (nos 5 and 6) were then selected based on their high biofilm formation, as well as their possession of higher concentrations of extracellular matrix components (eDNA, protein and saccharides) than the wild-type (WT). Genomic sequencing revealed the presence of large genome deletions in a secondary chromosome in the mutants. Expression analyses of the WT and mutant strains indicated the upregulation of genes associated with exopolysaccharide synthesis and stress response. The mutant strains showed high mortality in glucose-supplemented (TYG) medium; however, cell death and biofilm formation were not increased in mutant cells grown under acetate- or glyoxylate-added media, suggesting that metabolic toxicity during glucose metabolism induced a high rate of cell death but improved biofilm formation in mutant strains. In damaged cells, eDNAs contributed to the enhanced biofilm formation of D. metallilatus.
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Affiliation(s)
- Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Hoon Cheong
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Soyoon Park
- EMBIOME, Seoho-ro, Gwonseon-gu, Suwon, Gyeonggi 16614, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
- *Correspondence: Woojun Park,
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Zhang X, Ruan Y, Liu W, Chen Q, Gu L, Guo A. Transcriptome Analysis of Gene Expression in Dermacoccus abyssi HZAU 226 under Lysozyme Stress. Microorganisms 2020; 8:microorganisms8050707. [PMID: 32403298 PMCID: PMC7286019 DOI: 10.3390/microorganisms8050707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 12/17/2022] Open
Abstract
Lysozyme acts as a kind of cationic antimicrobial protein and effectively hydrolyzes bacterial peptidoglycan to have a bactericidal effect, which also plays an important role in protecting eggs from microbial contamination. Dermacoccus abyssi HZAU 226, a Gram-positive bacterium isolated from spoiled eggs, has egg white and lysozyme tolerance, but its survival mechanism is unknown, especially from a transcriptomics point of view. In this study, the high lysozyme tolerance of D. abyssi HZAU 226 was characterized by three independent experiments, and then the Illumina RNA-seq was used to compare the transcriptional profiles of this strain in Luria–Bertani (LB) medium with and without 5 mg/mL lysozyme to identify differentially expressed genes (DEGs); 1024 DEGs were identified by expression analysis, including 544 up-regulated genes and 480 down-regulated genes in response to lysozyme treatment. The functional annotation analysis results of DEGs showed that these genes were mainly involved in glutathione biosynthesis and metabolism, ion transport, energy metabolism pathways, and peptidoglycan biosynthesis. This study is the first report of bacterial-related lysozyme RNA-seq, and our results help in understanding the lysozyme-tolerance mechanism of bacteria from a new perspective and provide transcriptome resources for subsequent research in related fields.
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Affiliation(s)
- Xinshuai Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430000, China; (X.Z.); (Y.R.); (W.L.); (Q.C.); (L.G.)
| | - Yao Ruan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430000, China; (X.Z.); (Y.R.); (W.L.); (Q.C.); (L.G.)
| | - Wukang Liu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430000, China; (X.Z.); (Y.R.); (W.L.); (Q.C.); (L.G.)
| | - Qian Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430000, China; (X.Z.); (Y.R.); (W.L.); (Q.C.); (L.G.)
| | - Lihong Gu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430000, China; (X.Z.); (Y.R.); (W.L.); (Q.C.); (L.G.)
| | - Ailing Guo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430000, China; (X.Z.); (Y.R.); (W.L.); (Q.C.); (L.G.)
- National Research and Development Center for Egg Processing, Wuhan 430000, China
- Correspondence: ; Tel.: +86-1534-224-1896
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6
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Alternative fate of glyoxylate during acetate and hexadecane metabolism in Acinetobacter oleivorans DR1. Sci Rep 2019; 9:14402. [PMID: 31591464 PMCID: PMC6779741 DOI: 10.1038/s41598-019-50852-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/31/2019] [Indexed: 12/21/2022] Open
Abstract
The glyoxylate shunt (GS), involving isocitrate lyase (encoded by aceA) and malate synthase G (encoded by glcB), is known to play important roles under several conditions including oxidative stress, antibiotic defense, or certain carbon source metabolism (acetate and fatty acids). Comparative growth analyses of wild type (WT), aceA, and glcB null-strains revealed that aceA, but not glcB, is essential for cells to grow on either acetate (1%) or hexadecane (1%) in Acinetobacter oleivorans DR1. Interestingly. the aceA knockout strain was able to grow slower in 0.1% acetate than the parent strain. Northern Blot analysis showed that the expression of aceA was dependent on the concentration of acetate or H2O2, while glcB was constitutively expressed. Up-regulation of stress response-related genes and down-regulation of main carbon metabolism-participating genes in a ΔaceA mutant, compared to that in the parent strain, suggested that an ΔaceA mutant is susceptible to acetate toxicity, but grows slowly in 0.1% acetate. However, a ΔglcB mutant showed no growth defect in acetate or hexadecane and no susceptibility to H2O2, suggesting the presence of an alternative pathway to eliminate glyoxylate toxicity. A lactate dehydrogenase (LDH, encoded by a ldh) could possibly mediate the conversion from glyoxylate to oxalate based on our RNA-seq profiles. Oxalate production during hexadecane degradation and impaired growth of a ΔldhΔglcB double mutant in both acetate and hexadecane-supplemented media suggested that LDH is a potential detoxifying enzyme for glyoxylate. Our constructed LDH-overexpressing Escherichia coli strain also showed an important role of LDH under lactate, acetate, and glyoxylate metabolisms. The LDH-overexpressing E. coli strain, but not wild type strain, produced oxalate under glyoxylate condition. In conclusion, the GS is a main player, but alternative glyoxylate pathways exist during acetate and hexadecane metabolism in A. oleivorans DR1.
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Rodríguez-Andrade O, Corral-Lugo A, Morales-García YE, Quintero-Hernández V, Rivera-Urbalejo AP, Molina-Romero D, Martínez-Contreras RD, Bernal P, Muñoz-Rojas J. Identification of Klebsiella Variicola T29A Genes Involved In Tolerance To Desiccation. Open Microbiol J 2019. [DOI: 10.2174/1874285801913010256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Introduction:Several plant-beneficial bacteria have the capability to promote the growth of plants through different mechanisms. The survival of such bacteria could be affected by environmental abiotic factors compromising their capabilities of phytostimulation. One of the limiting abiotic factors is low water availability.Materials and Methods:In extreme cases, bacterial cells can suffer desiccation, which triggers harmful effects on cells. Bacteria tolerant to desiccation have developed different strategies to cope with these conditions; however, the genes involved in these processes have not been sufficiently explored.Klebsiella variicolaT29A is a beneficial bacterial strain that promotes the growth of corn plants and is highly tolerant to desiccation. In the present work, we investigated genes involved in desiccation tolerance.Results & Discussion:As a result, a library of 8974 mutants of this bacterial strain was generated by random mutagenesis with mini-Tn5 transposon, and mutants that lost the capability to tolerate desiccation were selected. We found 14 sensitive mutants; those with the lowest bacterial survival rate contained mini-Tn5 transposon inserted into genes encoding a protein domain related to BetR, putative secretion ATPase and dihydroorotase. The mutant in the betR gene had the lowest survival; therefore, the mutagenized gene was validated using specific amplification and sequencing.Conclusion:Trans complementation with the wild-type gene improved the survival of the mutant under desiccation conditions, showing that this gene is a determinant for the survival ofK. variicolaT29A under desiccation conditions.
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Ren B, Wang X, Duan J, Ma J. Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation. Science 2019; 365:919-922. [PMID: 31346137 DOI: 10.1126/science.aav8907] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/22/2019] [Accepted: 07/10/2019] [Indexed: 12/20/2022]
Abstract
Rhizobial infection and root nodule formation in legumes require recognition of signal molecules produced by the bacteria and their hosts. Here, we show that rhizobial transfer RNA (tRNA)-derived small RNA fragments (tRFs) are signal molecules that modulate host nodulation. Three families of rhizobial tRFs were confirmed to regulate host genes associated with nodule initiation and development through hijacking the host RNA-interference machinery that involves ARGONAUTE 1. Silencing individual tRFs with the use of short tandem target mimics or by overexpressing their targets represses root hair curling and nodule formation, whereas repressing these targets with artificial microRNAs identical to the respective tRFs or mutating these targets with CRISPR-Cas9 promotes nodulation. Our findings thus uncover a bacterial small RNA-mediated mechanism for prokaryote-eukaryote interaction and may pave the way for enhancing nodulation efficiency in legumes.
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MESH Headings
- Argonaute Proteins/genetics
- Bradyrhizobium/genetics
- Bradyrhizobium/physiology
- CRISPR-Cas Systems
- Gene Expression Regulation, Plant
- Host Microbial Interactions/genetics
- Nitrogen Fixation
- Nucleic Acid Conformation
- Plant Proteins/genetics
- Plant Root Nodulation/genetics
- Plant Roots/metabolism
- Plant Roots/microbiology
- RNA Interference
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/physiology
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/physiology
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/physiology
- Glycine max/genetics
- Glycine max/metabolism
- Glycine max/microbiology
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Affiliation(s)
- Bo Ren
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Jingbo Duan
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
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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: 19] [Impact Index Per Article: 3.8] [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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Ghedira K, Harigua-Souiai E, Ben Hamda C, Fournier P, Pujic P, Guesmi S, Guizani I, Miotello G, Armengaud J, Normand P, Sghaier H. The PEG-responding desiccome of the alder microsymbiont Frankia alni. Sci Rep 2018; 8:759. [PMID: 29335550 PMCID: PMC5768760 DOI: 10.1038/s41598-017-18839-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/05/2017] [Indexed: 01/22/2023] Open
Abstract
Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.
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Affiliation(s)
- Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
- Université de Carthage, Faculté des Sciences de Bizerte, Tunis, 7021, Tunisia
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France
| | - Sihem Guesmi
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- National Agronomy Institute (INAT), Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology - LR11IPT04, Institut Pasteur de Tunis, Université de Tunis el Manar, Tunis, 1002, Tunisia
| | - Guylaine Miotello
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207, Bagnols sur Cèze, France
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, Lyon; CNRS, UMR 5557, Ecologie Microbienne, UMR1418, INRA, 69622 Cedex, Villeurbanne, France.
| | - Haïtham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, 2020, Tunisia
- Associated with Laboratory "Biotechnology and Nuclear Technology" (LR16CNSTN01) & Laboratory "Biotechnology and Bio-Geo Resources Valorization" (LR11ES31), Sidi Thabet Technopark, 2020, Tunisia
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Requirement of the isocitrate lyase gene ICL1 for VPS41-mediated starvation response in Cryptococcus neoformans. J Microbiol 2016; 54:487-91. [PMID: 27350614 DOI: 10.1007/s12275-016-6177-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Cryptococcus neoformans is a major cause of fungal meningitis in individuals with impaired immunity. Our previous studies have shown that the VPS41 gene plays a critical role in the survival of Cryptococcus neoformans under nitrogen starvation; however, the molecular mechanisms underlying VPS41-mediated starvation response remain to be elucidated. In the present study, we show that, under nitrogen starvation, VPS41 strongly enhanced ICL1 expression in C. neoformans and that overexpression of ICL1 in the vps41 mutant dramatically suppressed its defects in starvation response due to the loss of VPS41 function. Moreover, targeted deletion of ICL1 resulted in a dramatic decline in viability of C. neoformans cells under nitrogen deprivation. Taken together, our data suggest a model in which VPS41 up-regulates ICL1 expression, directly or indirectly, to promote survival of C. neoformans under nitrogen starvation.
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