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Mejía L, Espinosa-Mata E, Freire AL, Zapata S, González-Candelas F. Listeria monocytogenes, a silent foodborne pathogen in Ecuador. Front Microbiol 2023; 14:1278860. [PMID: 38179446 PMCID: PMC10764610 DOI: 10.3389/fmicb.2023.1278860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024] Open
Abstract
Listeria monocytogenes is a foodborne pathogen that can produce serious, even fatal, infections. Among other foods, it can be found in unpasteurized dairy and ready-to-eat products. Surveillance of L. monocytogenes is of great interest since sources of infection are difficult to determine due to the long incubation period, and because the symptoms of listeriosis are similar to other diseases. We performed a genomic study of L. monocytogenes isolated from fresh cheeses and clinical samples from Ecuador. Sixty-five isolates were evaluated and sequenced, 14 isolates from cheese samples and 20 from clinical listeriosis cases from the National Institute of National Institute of Public Health Research, and 31 isolates from artisanal cheese samples from 8 provinces. All isolates exhibited heterogeneous patterns of the presence of pathogenicity islands. All isolates exhibited at least 4 genes from LIPI-1, but all references (26 L. monocytogenes closed genomes available in the NCBI database) showed the complete island, which encompasses 5 genes but is present in only two Ecuadorian isolates. Most isolates lacked gene actA. Genes from LIPI-2 were absent in all isolates. LIPI-3 and LIPI-4 were present in only a few references and isolates. With respect to the stress survival islets, our samples either presented SSI-1 or SSI-F2365, except for one isolate that presented SSI-F2365 and also one gene from SSI-1. None of the samples presented SSI-2. The predominant ST (sequence type) was ST2 (84.62% 55/65), and the only ST found in food (93.33% 42/45) and clinical samples (65% 13/20). Isolates were not grouped according to their sampling origin, date, or place in a phylogenetic tree obtained from the core alignment. The presence of ST2 in food and clinical samples, with high genomic similarity, suggests a foodborne infection risk linked to the consumption of fresh cheeses in Ecuador.
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Affiliation(s)
- Lorena Mejía
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Valencia, Spain
| | - Estefanía Espinosa-Mata
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Ana Lucía Freire
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sonia Zapata
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Valencia, Spain
- CIBER (Centro de Investigación Biomédica en Red) in Epidemiology and Public Health, Valencia, Spain
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2
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Taboada-Castro H, Gil J, Gómez-Caudillo L, Escorcia-Rodríguez JM, Freyre-González JA, Encarnación-Guevara S. Rhizobium etli CFN42 proteomes showed isoenzymes in free-living and symbiosis with a different transcriptional regulation inferred from a transcriptional regulatory network. Front Microbiol 2022; 13:947678. [PMID: 36312930 PMCID: PMC9611204 DOI: 10.3389/fmicb.2022.947678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
A comparative proteomic study at 6 h of growth in minimal medium (MM) and bacteroids at 18 days of symbiosis of Rhizobium etli CFN42 with the Phaseolus vulgaris leguminous plant was performed. A gene ontology classification of proteins in MM and bacteroid, showed 31 and 10 pathways with higher or equal than 30 and 20% of proteins with respect to genome content per pathway, respectively. These pathways were for energy and environmental compound metabolism, contributing to understand how Rhizobium is adapted to the different conditions. Metabolic maps based on orthology of the protein profiles, showed 101 and 74 functional homologous proteins in the MM and bacteroid profiles, respectively, which were grouped in 34 different isoenzymes showing a great impact in metabolism by covering 60 metabolic pathways in MM and symbiosis. Taking advantage of co-expression of transcriptional regulators (TF’s) in the profiles, by selection of genes whose matrices were clustered with matrices of TF’s, Transcriptional Regulatory networks (TRN´s) were deduced by the first time for these metabolic stages. In these clustered TF-MM and clustered TF-bacteroid networks, containing 654 and 246 proteins, including 93 and 46 TFs, respectively, showing valuable information of the TF’s and their regulated genes with high stringency. Isoenzymes were specific for adaptation to the different conditions and a different transcriptional regulation for MM and bacteroid was deduced. The parameters of the TRNs of these expected biological networks and biological networks of E. coli and B. subtilis segregate from the random theoretical networks. These are useful data to design experiments on TF gene–target relationships for bases to construct a TRN.
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Affiliation(s)
- Hermenegildo Taboada-Castro
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Jeovanis Gil
- Division of Oncology, Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Lund, Sweden
| | - Leopoldo Gómez-Caudillo
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
| | - Juan Miguel Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Julio Augusto Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Sergio Encarnación-Guevara
- Proteomics Laboratory, Program of Functional Genomics of Prokaryotes, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos, Mexico
- *Correspondence: Sergio Encarnacion Guevara,
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Hooykaas MJG, Hooykaas PJJ. Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid. BMC Microbiol 2021; 21:295. [PMID: 34711172 PMCID: PMC8554961 DOI: 10.1186/s12866-021-02358-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/06/2021] [Indexed: 01/18/2023] Open
Abstract
Background The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7012 genes (6948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in ridéopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02358-0.
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Rejili M, BenAbderrahim MA, Mars M, Sherrier JD. Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties. FEMS Microbiol Lett 2020; 367:5838745. [DOI: 10.1093/femsle/fnaa084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/17/2020] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
Phylogenetically diverse rhizobial strains endemic to Tunisia were isolated from symbiotic nodules of Lotus creticus, growing in different arid extremophile geographical regions of Tunisia, and speciated using multiloci-phylogenetic analysis as Neorhizobium huautlense (LCK33, LCK35, LCO42 and LCO49), Ensifer numidicus (LCD22, LCD25, LCK22 and LCK25), Ensifer meliloti (LCK8, LCK9 and LCK12) and Mesorhizobium camelthorni (LCD11, LCD13, LCD31 and LCD33). In addition, phylogenetic analyses revealed eight additional strains with previously undescribed chromosomal lineages within the genera Ensifer (LCF5, LCF6 and LCF8),Rhizobium (LCF11, LCF12 and LCF14) and Mesorhizobium (LCF16 and LCF19). Analysis using the nodC gene identified five symbiovar groups, four of which were already known. The remaining group composed of two strains (LCD11 and LCD33) represented a new symbiovar of Mesorhizobium camelthorni, which we propose designating as sv. hedysari. Interestingly, we report that soil properties drive and structure the symbiosis of L. creticus and its rhizobia.
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Affiliation(s)
- Mokhtar Rejili
- Research Laboratory Biodiversity & Valorization of Arid Areas Bioressources (BVBAA) - Faculty of Sciences of Gabes, Erriadh-Zrig, 6072-Tunisia
| | - Mohamed Ali BenAbderrahim
- Laboratoire d'Aridocultures et des Cultures Oasiennes, Institut des Régions Arides, 6051 Gabès, Tunisia
| | - Mohamed Mars
- Research Laboratory Biodiversity & Valorization of Arid Areas Bioressources (BVBAA) - Faculty of Sciences of Gabes, Erriadh-Zrig, 6072-Tunisia
| | - Janine Darla Sherrier
- Department of Crop & Soil Sciences, University of Georgia, 3111 Miller Plant Sci, 120 Carlton St., Athens, GA 30602, USA
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López-Sámano M, Beltrán LFLA, Sánchez-Thomas R, Dávalos A, Villaseñor T, García-García JD, García-de Los Santos A. A novel way to synthesize pantothenate in bacteria involves β-alanine synthase present in uracil degradation pathway. Microbiologyopen 2020; 9:e1006. [PMID: 32112625 PMCID: PMC7142369 DOI: 10.1002/mbo3.1006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/05/2020] [Accepted: 01/15/2020] [Indexed: 11/07/2022] Open
Abstract
Pantothenate is an indispensable vitamin precursor of the synthesis of coenzyme A (CoA), a key metabolite required in over 100 metabolic reactions. β-Alanine (β-ala) is an indispensable component of pantothenate. Due to the metabolic relevance of this pathway, we assumed that orthologous genes for ß-alanine synthesis would be present in the genomes of bacteria, archaea, and eukaryotes. However, comparative genomic studies revealed that orthologous gene replacement and loss of synteny occur at high frequency in panD genes. We have previously reported the atypical plasmid-encoded location of the pantothenate pathway genes panC and panB (two copies) in R. etli CFN42. This study also revealed the unexpected absence of a panD gene encoding the aspartate decarboxylase enzyme (ADC), required for the synthesis of β-ala. The aim of this study was to identify the source of β-alanine in Rhizobium etli CFN42. In this study, we present a bioinformatic analysis and an experimental validation demonstrating that the source of β-ala in this R. etli comes from β-alanine synthase, the last enzyme of the uracil degradation pathway.
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Affiliation(s)
- Mariana López-Sámano
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, México
| | | | - Rosina Sánchez-Thomas
- Departamento de Bioquímica, Instituto Nacional de Cardiología "Ignacio Chávez", Tlalpan, México
| | - Araceli Dávalos
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, México
| | - Tomás Villaseñor
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, UNAM, Cuernavaca, México
| | | | - Alejandro García-de Los Santos
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, México
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Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A. Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes. Front Microbiol 2019; 10:2896. [PMID: 31921071 PMCID: PMC6928123 DOI: 10.3389/fmicb.2019.02896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/02/2019] [Indexed: 01/02/2023] Open
Abstract
Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.
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Affiliation(s)
- Jayanti Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Barnan K. Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Pal Sarkar
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Vivek Roy
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Ayon Pal
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
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7
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Bañuelos-Vazquez LA, Torres Tejerizo G, Cervantes-De La Luz L, Girard L, Romero D, Brom S. Conjugative transfer between Rhizobium etli endosymbionts inside the root nodule. Environ Microbiol 2019; 21:3430-3441. [PMID: 31037804 DOI: 10.1111/1462-2920.14645] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/05/2019] [Accepted: 04/26/2019] [Indexed: 11/30/2022]
Abstract
Since the discovery that biological nitrogen fixation ensues in nodules resulting from the interaction of rhizobia with legumes, nodules were thought to be exclusive for hosting nitrogen-fixing and plant growth promoting bacteria. In this work, we uncover a novel function of nodules, as a niche permissive to acquisition of plasmids via conjugative transfer. We used Rhizobium etli CFN42, which nodulates Phaseolus vulgaris. The genome of R. etli CFN42 contains a chromosome and six plasmids. pRet42a is a conjugative plasmid regulated by Quorum-Sensing (QS), and pRet42d is the symbiotic plasmid. Here, using confocal microscopy and flow cytometry, we show that pRet42a transfers on the root's surface, and unexpectedly, inside the nodules. Conjugation still took place inside nodules, even when it was restricted on the plant surface by placing the QS traI regulator under the promoter of the nitrogenase gene, which is only expressed inside the nodules, or by inhibiting the QS transcriptional induction of transfer genes with a traM antiactivator on an unstable vector maintained on the plant surface and lost inside the nodules. These results conclusively confirm the occurrence of conjugation in these structures, defining them as a protected environment for bacterial diversification.
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Affiliation(s)
- Luis Alfredo Bañuelos-Vazquez
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Gonzalo Torres Tejerizo
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Laura Cervantes-De La Luz
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lourdes Girard
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - David Romero
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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8
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Li X, Wang H, Tong W, Feng L, Wang L, Rahman SU, Wei G, Tao S. Exploring the evolutionary dynamics of Rhizobium plasmids through bipartite network analysis. Environ Microbiol 2019; 22:934-951. [PMID: 31361937 DOI: 10.1111/1462-2920.14762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 07/25/2019] [Indexed: 10/26/2022]
Abstract
The genus Rhizobium usually has a multipartite genome architecture with a chromosome and several plasmids, making these bacteria a perfect candidate for plasmid biology studies. As there are no universally shared genes among typical plasmids, network analyses can complement traditional phylogenetics in a broad-scale study of plasmid evolution. Here, we present an exhaustive analysis of 216 plasmids from 49 complete genomes of Rhizobium by constructing a bipartite network that consists of two classes of nodes, the plasmids and homologous protein families that connect them. Dissection of the network using a hierarchical clustering strategy reveals extensive variety, with 34 homologous plasmid clusters. Four large clusters including one cluster of symbiotic plasmids and two clusters of chromids carrying some truly essential genes are widely distributed among Rhizobium. In contrast, the other clusters are quite small and rare. Symbiotic clusters and rare accessory clusters are exogenetic and do not appear to have co-evolved with the common accessory clusters; the latter ones have a large coding potential and functional complementarity for different lifestyles in Rhizobium. The bipartite network also provides preliminary evidence of Rhizobium plasmid variation and formation including genetic exchange, plasmid fusion and fission, exogenetic plasmid transfer, host plant selection, and environmental adaptation.
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Affiliation(s)
- Xiangchen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenjun Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Li Feng
- College of Enology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lina Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Siddiq Ur Rahman
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa, 27200, Pakistan
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, China
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9
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Checcucci A, diCenzo GC, Ghini V, Bazzicalupo M, Becker A, Decorosi F, Döhlemann J, Fagorzi C, Finan TM, Fondi M, Luchinat C, Turano P, Vignolini T, Viti C, Mengoni A. Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti. ACS Synth Biol 2018; 7:2365-2378. [PMID: 30223644 DOI: 10.1021/acssynbio.8b00158] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.
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Affiliation(s)
- Alice Checcucci
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - George C. diCenzo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Veronica Ghini
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Marco Bazzicalupo
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Anke Becker
- LOEWE − Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Francesca Decorosi
- Department of Agri-food Production and Environmental Science, University of Florence, 50019 Florence, Italy
| | | | - Camilla Fagorzi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Marco Fondi
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
- CERM and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Paola Turano
- CERM & CIRMMP, University of Florence, 50019 Sesto Fiorentino, Italy
- CERM and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Tiziano Vignolini
- European Laboratory for Non-Linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
| | - Carlo Viti
- Department of Agri-food Production and Environmental Science, University of Florence, 50019 Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
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Boyd BM, Allen JM, Nguyen NP, Vachaspati P, Quicksall ZS, Warnow T, Mugisha L, Johnson KP, Reed DL. Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice. Mol Biol Evol 2017; 34:1743-1757. [PMID: 28419279 PMCID: PMC5455983 DOI: 10.1093/molbev/msx117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement. Examination of the highly reduced symbiont genomes (0.53–0.57 Mb) reveals much of the genomes are dedicated to vitamin synthesis. This is unchanged in the smallest symbiont genome and one that appears to have been reorganized. Specifically, symbionts from human lice, chimpanzee lice, and gorilla lice carry a small plasmid that encodes synthesis of vitamin B5, a vitamin critical to the bacteria-louse symbiosis. This plasmid is absent in an old world monkey louse symbiont, where this pathway is on its primary chromosome. This suggests the unique genomic configuration brought about by the plasmid is not essential for symbiosis, but once obtained, it has persisted for up to 25 My. We also find evidence that human, chimpanzee, and gorilla louse endosymbionts have lost a pathway for synthesis of vitamin B1, whereas the monkey louse symbiont has retained this pathway. It is unclear whether these changes are adaptive, but they may point to evolutionary responses of louse symbionts to shifts in primate biology.
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Affiliation(s)
- Bret M Boyd
- Department of Entomology, University of Georgia Athens, Athens, GA.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL.,Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - Nam-Phuong Nguyen
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA
| | - Pranjal Vachaspati
- Department of Computer Science and Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL
| | | | - Tandy Warnow
- Department of Computer Science and Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL
| | - Lawrence Mugisha
- Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda.,College of Veterinary Medicine, Animal Resources & Biosecurity (COVAB), Makerere University, Kampala, Uganda
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL
| | - David L Reed
- Florida Museum of Natural History, University of Florida, Gainesville, FL
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11
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diCenzo GC, Finan TM. The Divided Bacterial Genome: Structure, Function, and Evolution. Microbiol Mol Biol Rev 2017; 81:e00019-17. [PMID: 28794225 PMCID: PMC5584315 DOI: 10.1128/mmbr.00019-17] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.
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Affiliation(s)
- George C diCenzo
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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12
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13
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Huang T, Yu X, Gelbič I, Guan X. RAP-PCR fingerprinting reveals time-dependent expression of development-related genes following differentiation process of Bacillus thuringiensis. Can J Microbiol 2015; 61:683-90. [DOI: 10.1139/cjm-2015-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Gene expression profiles are important data to reveal the functions of genes putatively involved in crucial biological processes. RNA arbitrarily primed polymerase chain reaction (RAP-PCR) and specifically primed reverse transcription polymerase chain reaction (RT-PCR) were combined to screen differentially expressed genes following development of a commercial Bacillus thuringiensis subsp. kurstaki strain 8010 (serotype 3a3b). Six differentially expressed transcripts (RAP1 to RAP6) were obtained. RAP1 encoded a putative triple helix repeat-containing collagen or an exosporium protein H related to spore pathogenicity. RAP2 was homologous to a ClpX protease and an ATP-dependent protease La (LonB), which likely acted as virulence factors. RAP3 was homologous to a beta subunit of propionyl-CoA carboxylase required for the development of Myxococcus xanthus. RAP4 had homology to a quinone oxidoreductase involved in electron transport and ATP formation. RAP5 showed significant homology to a uridine kinase that mediates phosphorylation of uridine and azauridine. RAP6 shared high sequence identity with 3-methyl-2-oxobutanoate-hydroxymethyltransferase (also known as ketopantoate hydroxymethyltransferase or PanB) involved in the operation of the tricarboxylic acid cycle. The findings described here would help to elucidate the molecular mechanisms underlying the differentiation process of B. thuringiensis and unravel novel pathogenic genes.
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Affiliation(s)
- Tianpei Huang
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, People’s Republic of China
- Fujian–Taiwan Joint Center for Ecological Control of Crop Pests, 350002 Fuzhou, Fujian, People’s Republic of China
| | - Xiaomin Yu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, People’s Republic of China
| | - Ivan Gelbič
- Biological Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Xiong Guan
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, People’s Republic of China
- Fujian–Taiwan Joint Center for Ecological Control of Crop Pests, 350002 Fuzhou, Fujian, People’s Republic of China
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14
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Cloning and validation of reference genes for normalization of gene expression studies in pearl millet [Pennisetum glaucum (L.) R. Br.] by quantitative real-time PCR. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.plgene.2015.02.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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López-Fuentes E, Torres-Tejerizo G, Cervantes L, Brom S. Genes encoding conserved hypothetical proteins localized in the conjugative transfer region of plasmid pRet42a from Rhizobium etli CFN42 participate in modulating transfer and affect conjugation from different donors. Front Microbiol 2015; 5:793. [PMID: 25642223 PMCID: PMC4294206 DOI: 10.3389/fmicb.2014.00793] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/23/2014] [Indexed: 11/13/2022] Open
Abstract
Among sequenced genomes, it is common to find a high proportion of genes encoding proteins that cannot be assigned a known function. In bacterial genomes, genes related to a similar function are often located in contiguous regions. The presence of genes encoding conserved hypothetical proteins (chp) in such a region may suggest that they are related to that particular function. Plasmid pRet42a from Rhizobium etli CFN42 is a conjugative plasmid containing a segment of approximately 30 Kb encoding genes involved in conjugative transfer. In addition to genes responsible for Dtr (DNA transfer and replication), Mpf (Mating pair formation) and regulation, it has two chp-encoding genes (RHE_PA00163 and RHE_PA00164) and a transcriptional regulator (RHE_PA00165). RHE_PA00163 encodes an uncharacterized protein conserved in bacteria that presents a COG4634 conserved domain, and RHE_PA00164 encodes an uncharacterized conserved protein with a DUF433 domain of unknown function. RHE_PA00165 presents a HTH_XRE domain, characteristic of DNA-binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Interestingly, genes similar to these are also present in transfer regions of plasmids from other bacteria. To determine if these genes participate in conjugative transfer, we mutagenized them and analyzed their conjugative phenotype. A mutant in RHE_PA00163 showed a slight (10 times) but reproducible increase in transfer frequency from Rhizobium donors, while mutants in RHE_PA00164 and RHE_PA00165 lost their ability to transfer the plasmid from some Agrobacterium donors. Our results indicate that the chp-encoding genes located among conjugation genes are indeed related to this function. However, the participation of RHE_PA00164 and RHE_PA00165 is only revealed under very specific circumstances, and is not perceived when the plasmid is transferred from the original host. RHE_PA00163 seems to be a fine-tuning modulator for conjugative transfer.
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Affiliation(s)
- Eunice López-Fuentes
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Gonzalo Torres-Tejerizo
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Laura Cervantes
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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Saraiva KDC, Fernandes de Melo D, Morais VD, Vasconcelos IM, Costa JH. Selection of suitable soybean EF1α genes as internal controls for real-time PCR analyses of tissues during plant development and under stress conditions. PLANT CELL REPORTS 2014; 33:1453-65. [PMID: 24820128 DOI: 10.1007/s00299-014-1628-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE The EF1α genes were stable in the large majority of soybean tissues during development and in specific tissues/conditions under stress. Quantitative real-time PCR (qPCR) analysis strongly depends on transcript normalization using stable reference genes. Reference genes are generally encoded by multigene families and are used in qPCR normalization; however, little effort has been made to verify the stability of different gene members within a family. Here, the expression stability of members of the soybean EF1α gene family (named EF1α 1a1, 1a2, 1b, 2a, 2b and 3) was evaluated in different tissues during plant development and stress exposure (SA and PEG). Four genes (UKN1, SKIP 16, EF1β and MTP) already established as stably expressed were also used in the comparative analysis. GeNorm analyses revealed different combinations of reference genes as stable in soybean tissues during development. The EF1α genes were the most stable in cotyledons (EF1α 3 and EF1α 1b), epicotyls (EF1α 1a2, EF1α 2b and EF1α 1a1), hypocotyls (EF1α 1a1 and EF1β), pods (EF1α 2a and EF1α 2b) and roots (EF1α 2a and UKN1) and less stable in tissues such as trifoliate and unifoliate leaves and germinating seeds. Under stress conditions, no suitable combination including only EF1α genes was found; however, some genes were relatively stable in leaves (EF1α 1a2) and roots (EF1α 1a1) treated with SA as well as in roots treated with PEG (EF1α 2b). EF1α 2a was the most stably expressed EF1α gene in all soybean tissues under stress. Taken together, our data provide guidelines for the selection of EF1α genes for use as reference genes in qPCR expression analyses during plant development and under stress conditions.
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Affiliation(s)
- Kátia D C Saraiva
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Campus do Pici, Cx., Postal 6033, Fortaleza, Ceará, 60451-970, Brazil
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Stasiak G, Mazur A, Wielbo J, Marczak M, Zebracki K, Koper P, Skorupska A. Functional relationships between plasmids and their significance for metabolism and symbiotic performance of Rhizobium leguminosarum bv. trifolii. J Appl Genet 2014; 55:515-27. [PMID: 24839164 PMCID: PMC4185100 DOI: 10.1007/s13353-014-0220-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/11/2014] [Accepted: 04/30/2014] [Indexed: 12/31/2022]
Abstract
Rhizobium leguminosarum bv. trifolii TA1 (RtTA1) is a soil bacterium establishing a highly specific symbiotic relationship with clover, which is based on the exchange of molecular signals between the host plant and the microsymbiont. The RtTA1 genome is large and multipartite, composed of a chromosome and four plasmids, which comprise approximately 65 % and 35 % of the total genome, respectively. Extrachromosomal replicons were previously shown to confer significant metabolic versatility to bacteria, which is important for their adaptation in the soil and nodulation competitiveness. To investigate the contribution of individual RtTA1 plasmids to the overall cell phenotype, metabolic properties and symbiotic performance, a transposon-based elimination strategy was employed. RtTA1 derivatives cured of pRleTA1b or pRleTA1d and deleted in pRleTA1a were obtained. In contrast to the in silico predictions of pRleTA1b and pRleTA1d, which were described as chromid-like replicons, both appeared to be completely curable. On the other hand, for pRleTA1a (symbiotic plasmid) and pRleTA1c, which were proposed to be unessential for RtTA1 viability, it was not possible to eliminate them at all (pRleTA1c) or entirely (pRleTA1a). Analyses of the phenotypic traits of the RtTA1 derivatives obtained revealed the functional significance of individual plasmids and their indispensability for growth, certain metabolic pathways, production of surface polysaccharides, autoaggregation, biofilm formation, motility and symbiotic performance. Moreover, the results allow us to suggest broad functional cooperation among the plasmids in shaping the phenotypic properties and symbiotic capabilities of rhizobia.
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Affiliation(s)
- Grażyna Stasiak
- Department of Genetics and Microbiology, Maria-Curie Skłodowska University, 19 Akademicka St., 20-033, Lublin, Poland
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Abstract
Rhizobia are bacteria in the α-proteobacterial genera Rhizobium, Sinorhizobium, Mesorhizobium, Azorhizobium and Bradyrhizobium that reduce (fix) atmospheric nitrogen in symbiotic association with a compatible host plant. In free-living and/or symbiotically associated rhizobia, amino acids may, in addition to their incorporation into proteins, serve as carbon, nitrogen or sulfur sources, signals of cellular nitrogen status and precursors of important metabolites. Depending on the rhizobia-host plant combination, microsymbiont amino acid metabolism (biosynthesis, transport and/or degradation) is often crucial to the establishment and maintenance of an effective nitrogen-fixing symbiosis and is intimately interconnected with the metabolism of the plant. This review summarizes past findings and current research directions in rhizobial amino acid metabolism and evaluates the genetic, biochemical and genome expression studies from which these are derived. Specific sections deal with the regulation of rhizobial amino acid metabolism, amino acid transport, and finally the symbiotic roles of individual amino acids in different plant-rhizobia combinations.
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Dziewit L, Czarnecki J, Wibberg D, Radlinska M, Mrozek P, Szymczak M, Schlüter A, Pühler A, Bartosik D. Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids. BMC Genomics 2014; 15:124. [PMID: 24517536 PMCID: PMC3925955 DOI: 10.1186/1471-2164-15-124] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/07/2014] [Indexed: 11/10/2022] Open
Abstract
Background Paracoccus aminophilus JCM 7686 is a methylotrophic α-Proteobacterium capable of utilizing reduced one-carbon compounds as sole carbon and energy source for growth, including toxic N,N-dimethylformamide, formamide, methanol, and methylamines, which are widely used in the industry. P. aminophilus JCM 7686, as many other Paracoccus spp., possesses a genome representing a multipartite structure, in which the genomic information is split between various replicons, including chromids, essential plasmid-like replicons, with properties of both chromosomes and plasmids. In this study, whole-genome sequencing and functional genomics approaches were applied to investigate P. aminophilus genome information. Results The P. aminophilus JCM 7686 genome has a multipartite structure, composed of a single circular chromosome and eight additional replicons ranging in size between 5.6 and 438.1 kb. Functional analyses revealed that two of the replicons, pAMI5 and pAMI6, are essential for host viability, therefore they should be considered as chromids. Both replicons carry housekeeping genes, e.g. responsible for de novo NAD biosynthesis and ammonium transport. Other mobile genetic elements have also been identified, including 20 insertion sequences, 4 transposons and 10 prophage regions, one of which represents a novel, functional serine recombinase-encoding bacteriophage, ϕPam-6. Moreover, in silico analyses allowed us to predict the transcription regulatory network of the JCM 7686 strain, as well as components of the stress response, recombination, repair and methylation machineries. Finally, comparative genomic analyses revealed that P. aminophilus JCM 7686 has a relatively distant relationship to other representatives of the genus Paracoccus. Conclusions P. aminophilus genome exploration provided insights into the overall structure and functions of the genome, with a special focus on the chromids. Based on the obtained results we propose the classification of bacterial chromids into two types: “primary” chromids, which are indispensable for host viability and “secondary” chromids, which are essential, but only under some environmental conditions and which were probably formed quite recently in the course of evolution. Detailed genome investigation and its functional analysis, makes P. aminophilus JCM 7686 a suitable reference strain for the genus Paracoccus. Moreover, this study has increased knowledge on overall genome structure and composition of members within the class Alphaproteobacteria.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Wang X, Wu L, Zhou P, Zhu S, An W, Chen Y, Zhao L. Analysis of synonymous codon usage patterns in the genus Rhizobium. World J Microbiol Biotechnol 2013; 29:2015-24. [PMID: 23653263 DOI: 10.1007/s11274-013-1364-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
Abstract
The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman's rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.
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Affiliation(s)
- Xinxin Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, People's Republic of China,
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21
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Phenotype profiling of Rhizobium leguminosarum bv. trifolii clover nodule isolates reveal their both versatile and specialized metabolic capabilities. Arch Microbiol 2013; 195:255-67. [PMID: 23417392 PMCID: PMC3597991 DOI: 10.1007/s00203-013-0874-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 11/07/2012] [Accepted: 02/01/2013] [Indexed: 11/24/2022]
Abstract
Rhizobium leguminosarum bv. trifolii (Rlt) are soil bacteria inducing nodules on clover, where they fix nitrogen. Genome organization analyses of 22 Rlt clover nodule isolates showed that they contained 3–6 plasmids and majority of them possessed large (>1 Mb), chromid-like replicon with exception of four Rlt strains. The Biolog phenotypic profiling comprising utilization of C, N, P, and S sources and tolerance to osmolytes and pH revealed metabolic versatility of the Rlt strains. Statistical analyses of our results showed a clear bias toward specific metabolic preferences, tolerance to unfavorable osmotic conditions, and increased nodulation activity of the strains having smaller amount of extrachromosomal DNA. The K5.4 and K4.15 lacking a large megaplasmid possessed substantially diverse metabolism and belonged to effective clover inoculants. In conclusion, besides overall metabolic versatility, some metabolic specialization may enable rhizobia to persist in variable environments and to compete successfully with other bacteria.
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Abstract
AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.
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López-Guerrero MG, Ormeño-Orrillo E, Acosta JL, Mendoza-Vargas A, Rogel MA, Ramírez MA, Rosenblueth M, Martínez-Romero J, Martínez-Romero E. Rhizobial extrachromosomal replicon variability, stability and expression in natural niches. Plasmid 2012; 68:149-58. [PMID: 22813963 DOI: 10.1016/j.plasmid.2012.07.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/28/2012] [Accepted: 07/06/2012] [Indexed: 12/25/2022]
Abstract
In bacteria, niche adaptation may be determined by mobile extrachromosomal elements. A remarkable characteristic of Rhizobium and Ensifer (Sinorhizobium) but also of Agrobacterium species is that almost half of the genome is contained in several large extrachromosomal replicons (ERs). They encode a plethora of functions, some of them required for bacterial survival, niche adaptation, plasmid transfer or stability. In spite of this, plasmid loss is common in rhizobia upon subculturing. Rhizobial gene-expression studies in plant rhizospheres with novel results from transcriptomic analysis of Rhizobium phaseoli in maize and Phaseolus vulgaris roots highlight the role of ERs in natural niches and allowed the identification of common extrachromosomal genes expressed in association with plant rootlets and the replicons involved.
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