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Guardia AE, Wagner A, Busalmen JP, Di Capua C, Cortéz N, Beligni MV. The draft genome of Andean Rhodopseudomonas sp. strain AZUL predicts genome plasticity and adaptation to chemical homeostasis. BMC Microbiol 2022; 22:297. [PMID: 36494611 PMCID: PMC9733117 DOI: 10.1186/s12866-022-02685-w] [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: 07/07/2021] [Accepted: 10/29/2022] [Indexed: 12/13/2022] Open
Abstract
The genus Rhodopseudomonas comprises purple non-sulfur bacteria with extremely versatile metabolisms. Characterization of several strains revealed that each is a distinct ecotype highly adapted to its specific micro-habitat. Here we present the sequencing, genomic comparison and functional annotation of AZUL, a Rhodopseudomonas strain isolated from a high altitude Andean lagoon dominated by extreme conditions and fluctuating levels of chemicals. Average nucleotide identity (ANI) analysis of 39 strains of this genus showed that the genome of AZUL is 96.2% identical to that of strain AAP120, which suggests that they belong to the same species. ANI values also show clear separation at the species level with the rest of the strains, being more closely related to R. palustris. Pangenomic analyses revealed that the genus Rhodopseudomonas has an open pangenome and that its core genome represents roughly 5 to 12% of the total gene repertoire of the genus. Functional annotation showed that AZUL has genes that participate in conferring genome plasticity and that, in addition to sharing the basal metabolic complexity of the genus, it is also specialized in metal and multidrug resistance and in responding to nutrient limitation. Our results also indicate that AZUL might have evolved to use some of the mechanisms involved in resistance as redox reactions for bioenergetic purposes. Most of those features are shared with strain AAP120, and mainly involve the presence of additional orthologs responsible for the mentioned processes. Altogether, our results suggest that AZUL, one of the few bacteria from its habitat with a sequenced genome, is highly adapted to the extreme and changing conditions that constitute its niche.
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Affiliation(s)
- Aisha E. Guardia
- grid.473319.b0000 0004 0461 9871Ingeniería de Interfases y Bioprocesos, Instituto de Tecnología de Materiales (INTEMA-CONICET-UNMdP), Mar del Plata, Argentina
| | - Agustín Wagner
- grid.10814.3c0000 0001 2097 3211Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Juan P. Busalmen
- grid.473319.b0000 0004 0461 9871Ingeniería de Interfases y Bioprocesos, Instituto de Tecnología de Materiales (INTEMA-CONICET-UNMdP), Mar del Plata, Argentina
| | - Cecilia Di Capua
- grid.501777.30000 0004 0638 1836Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Universidad Nacional de Rosario, Rosario, Argentina
| | - Néstor Cortéz
- grid.501777.30000 0004 0638 1836Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Universidad Nacional de Rosario, Rosario, Argentina
| | - María V. Beligni
- grid.412221.60000 0000 9969 0902Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
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Wu X, Chen Y, Li C, Zhang X, Tan X, Lv L, Liu Y, Zhang D. GroEL protein from the potential biocontrol agent Rhodopseudomonas palustris enhances resistance to rice blast disease. PEST MANAGEMENT SCIENCE 2021; 77:5445-5453. [PMID: 34331498 DOI: 10.1002/ps.6584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/24/2021] [Accepted: 07/31/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND GroEL, which is a chaperone, plays a key role in maintaining protein homeostasis and, among other functions, serves to prevent protein misfolding and aggregation. In addition, the GroEL protein also has a significant effect on enhancing plant resistance and inhibiting plant diseases. However, the function of the GroEL protein in the inhibition of rice blast remains unknown. RESULTS Field experiment results show that photosynthetic bacteria PSB-06 have a good control effect on Magnaporthe oryzae. PSB-06 also can promote rice growth and enhance stress resistance. A GroEL protein which was separated and purified from photosynthetic bacteria had a significant antagonistic effect on appressorial formation and pathogenicity of Magnaporthe oryzae, meanwhile transcriptional analysis demonstrated that the GroEL protein could improve the expression of defense gene of rice. CONCLUSION Our results show that the photosynthetic bacteria Rhodopseudomonas palustris significantly controls rice blast disease. Its action involves an extracellular GroEL protein, which inhibits appressoria formation, antagonizes the pathogenicity of Magnaporthe oryzae and promotes a host defense response. The research results provide evidence of the potential of this photosynthetic bacterium as a biocontrol agent at least for rice blast control. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Xiyang Wu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Yue Chen
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Chenggang Li
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xin Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xinqiu Tan
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Liang Lv
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, and Hubei Province Key Laboratory for Crop Diseases, Insect Pests and Weeds Control, Institute of Plant Protection & Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
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Mou Z, Yang Y, Hall AB, Jiang X. The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. BMC Genomics 2021; 22:695. [PMID: 34563136 PMCID: PMC8465708 DOI: 10.1186/s12864-021-08004-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/13/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria. RESULTS To identify the histamine-secreting bacteria from in the human gut microbiome, we conducted a systematic search for putative histamine-secreting bacteria in 36,554 genomes from the Genome Taxonomy Database and Unified Human Gastrointestinal Genome catalog. Using bioinformatic approaches, we identified 117 putative histamine-secreting bacteria species. A new three-component decarboxylation system including two colocalized decarboxylases and one transporter was observed in histamine-secreting bacteria among three different phyla. We found significant enrichment of histamine-secreting bacteria in patients with inflammatory bowel disease but not in patients with colorectal cancer suggesting a possible association between histamine-secreting bacteria and inflammatory bowel disease. CONCLUSIONS The findings of this study expand our knowledge of the taxonomic distribution of putative histamine-secreting bacteria in the human gut.
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Affiliation(s)
- Zhongyu Mou
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Yiyan Yang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - A Brantley Hall
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Xiaofang Jiang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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du Toit JP, Pott RWM. Transparent polyvinyl-alcohol cryogel as immobilisation matrix for continuous biohydrogen production by phototrophic bacteria. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:105. [PMID: 32536970 PMCID: PMC7285740 DOI: 10.1186/s13068-020-01743-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/01/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Phototrophic purple non-sulfur bacteria (PNSB) have gained attention for their ability to produce a valuable clean energy source in the form biohydrogen via photofermentation of a wide variety of organic wastes. For maturation of these phototrophic bioprocesses towards commercial feasibility, development of suitable immobilisation materials is required to allow continuous production from a stable pool of catalytic biomass in which energy is not diverted towards biomass accumulation, and optimal hydrogen production rates are realised. Here, the application of transparent polyvinyl-alcohol (PVA) cryogel beads to immobilisation of Rhodopseudomonas palustris for long-term hydrogen production is described. PVA cryogel properties are characterised and demonstrated to be well suited to the purpose of continuous photofermentation. Finally, analysis of the long-term biocompatibility of the material is illustrated. RESULTS The addition of glycerol co-solvent induces favourable light transmission properties in normally opaque PVA cryogels, especially well-suited to the near-infrared light requirements of PNSB. Material characterisation showed high mechanical resilience, low resistance to diffusion of substrates and high biocompatibility of the material and immobilisation process. The glycerol co-solvent in transparent cryogels offered additional benefit by reinforcing physical interactions to the extent that only a single freeze-thaw cycle was required to form durable cryogels, extending utility beyond only phototrophic bioprocesses. In contrast, conventional PVA cryogels require multiple cycles which compromise viability of entrapped organisms. Hydrogen production studies of immobilised Rhodopseudomonas palustris in batch photobioreactors showed higher specific hydrogen production rates which continued longer than planktonic cultures. Continuous cultivation yielded hydrogen production for at least 67 days from immobilised bacteria, demonstrating the suitability of PVA cryogel immobilisation for long-term phototrophic bioprocesses. Imaged organisms immobilised in cryogels showed a monolithic structure to PVA cryogels, and demonstrated a living, stable, photofermentative population after long-term immobilisation. CONCLUSION Transparent PVA cryogels offer ideal properties as an immobilisation matrix for phototrophic bacteria and present a low-cost photobioreactor technology for the further advancement of biohydrogen from waste as a sustainable energy source, as well as development of alternative photo-bioprocesses exploiting the unique capabilities of purple non-sulfur bacteria.
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Affiliation(s)
- Jan-Pierre du Toit
- Department of Process Engineering, Stellenbosch University, Banghoek Road, Stellenbosch, South Africa
| | - Robert W. M. Pott
- Department of Process Engineering, Stellenbosch University, Banghoek Road, Stellenbosch, South Africa
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Thiel V, Tank M, Bryant DA. Diversity of Chlorophototrophic Bacteria Revealed in the Omics Era. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:21-49. [PMID: 29505738 DOI: 10.1146/annurev-arplant-042817-040500] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods. In specific cases, we briefly describe important ecophysiological and metabolic insights that have been gained from the application of genomic methods to these bacteria. In the 20 years since the completion of the Synechocystis sp. PCC 6803 genome in 1996, approximately 1,100 genomes have been sequenced, which represents nearly the complete diversity of known chlorophototrophic bacteria. These data are leading to new insights into many important processes, including photosynthesis, nitrogen and carbon fixation, cellular differentiation and development, symbiosis, and ecosystem functionality.
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Affiliation(s)
- Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; ,
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
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Su P, Tan X, Li C, Zhang D, Cheng J, Zhang S, Zhou X, Yan Q, Peng J, Zhang Z, Liu Y, Lu X. Photosynthetic bacterium Rhodopseudomonas palustris GJ-22 induces systemic resistance against viruses. Microb Biotechnol 2017; 10:612-624. [PMID: 28296178 PMCID: PMC5404195 DOI: 10.1111/1751-7915.12704] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 02/05/2017] [Accepted: 02/20/2017] [Indexed: 01/09/2023] Open
Abstract
Photosynthetic bacteria (PSB) have been extensively used in agriculture to promote plant growth and to improve crop quality. Their potential application in plant disease management, however, is largely overlooked. In this study, the PSB strain Rhodopseudomonas palustris GJ-22 was investigated for its ability to induce resistance against a plant virus while promoting plant growth. In the field, a foliar spray of GJ-22 suspension protected tobacco plants against tobacco mosaic virus (TMV). Under axenic conditions, GJ-22 colonized the plant phyllosphere and induced resistance against TMV. Additionally, GJ-22 produced two phytohormones, indole-3-acetic acid and 5-aminolevulinic acid, which promote growth and germination in tobacco. Furthermore, GJ-22-inoculated plants elevated their immune response under subsequent TMV infection. This research may give rise to a novel biological agent with a dual function in disease management while promoting plant growth.
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Affiliation(s)
- Pin Su
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Xinqiu Tan
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Chenggang Li
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Deyong Zhang
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Ju'e Cheng
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Songbai Zhang
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Xuguo Zhou
- Department of EntomologyUniversity of KentuckyLexingtonKY40546USA
| | - Qingpin Yan
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Jing Peng
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Zhuo Zhang
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Yong Liu
- Hunan Academy of Agricultural SciencesHunan Plant Protection InstituteChangsha410125China
| | - Xiangyang Lu
- College of Bioscience and BiotechnologyHunan Agricultural UniversityChangsha410128China
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Isokpehi RD, Wollenberg Valero KC, Graham BE, Pacurari M, Sims JN, Udensi UK, Ndebele K. Secondary Data Analytics of Aquaporin Expression Levels in Glioblastoma Stem-Like Cells. Cancer Inform 2015; 14:95-103. [PMID: 26279619 PMCID: PMC4524166 DOI: 10.4137/cin.s22058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 01/18/2023] Open
Abstract
Glioblastoma is the most common brain tumor in adults in which recurrence has been attributed to the presence of cancer stem cells in a hypoxic microenvironment. On the basis of tumor formation in vivo and growth type in vitro, two published microarray gene expression profiling studies grouped nine glioblastoma stem-like (GS) cell lines into one of two groups: full (GSf) or restricted (GSr) stem-like phenotypes. Aquaporin-1 (AQP1) and aquaporin-4 (AQP4) are water transport proteins that are highly expressed in primary glial-derived tumors. However, the expression levels of AQP1 and AQP4 have not been previously described in a panel of 92 glioma samples. Therefore, we designed secondary data analytics methods to determine the expression levels of AQP1 and AQP4 in GS cell lines and glioblastoma neurospheres. Our investigation also included a total of 2,566 expression levels from 28 Affymetrix microarray probe sets encoding 13 human aquaporins (AQP0-AQP12); CXCR4 (the receptor for stromal cell derived factor-1 [SDF-1], a potential glioma stem cell therapeutic target]); and PROM1 (gene encoding CD133, the widely used glioma stem cell marker). Interactive visual representation designs for integrating phenotypic features and expression levels revealed that inverse expression levels of AQP1 and AQP4 correlate with distinct phenotypes in a set of cell lines grouped into full and restricted stem-like phenotypes. Discriminant function analysis further revealed that AQP1 and AQP4 expression are better predictors for tumor formation and growth types in glioblastoma stem-like cells than are CXCR4 and PROM1. Future investigations are needed to characterize the molecular mechanisms for inverse expression levels of AQP1 and AQP4 in the glioblastoma stem-like neurospheres.
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Affiliation(s)
- Raphael D Isokpehi
- College of Science, Engineering, and Mathematics, Bethune-Cookman University, Daytona Beach, FL, USA
| | | | - Barbara E Graham
- Laboratory of Cancer Immunology, Target Identification and Validation, Department of Biology, Jackson State University, MS, USA
- NIH RCMI-Center for Environmental Health, College of Science, Engineering, and Technology, Jackson State University, Jackson, MS, USA
| | | | - Jennifer N Sims
- Laboratory of Cancer Immunology, Target Identification and Validation, Department of Biology, Jackson State University, MS, USA
| | - Udensi K Udensi
- NIH RCMI-Center for Environmental Health, College of Science, Engineering, and Technology, Jackson State University, Jackson, MS, USA
| | - Kenneth Ndebele
- Laboratory of Cancer Immunology, Target Identification and Validation, Department of Biology, Jackson State University, MS, USA
- NIH RCMI-Center for Environmental Health, College of Science, Engineering, and Technology, Jackson State University, Jackson, MS, USA
- Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA, USA
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Degli Esposti M, Chouaia B, Comandatore F, Crotti E, Sassera D, Lievens PMJ, Daffonchio D, Bandi C. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 2014; 9:e96566. [PMID: 24804722 PMCID: PMC4013037 DOI: 10.1371/journal.pone.0096566] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/07/2014] [Indexed: 11/26/2022] Open
Abstract
The ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. However, the identity and relatives of proto-mitochondria remain elusive. Here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. We reached this conclusion after reconstructing the possible evolutionary pathways of the bioenergy systems of proto-mitochondria with a genomic survey of extant α-proteobacteria. Results obtained with complementary molecular and genetic analyses of diverse bioenergetic proteins converge in indicating the pathway stemming from methylotrophic bacteria as the most probable route of mitochondrial evolution. Contrary to other α-proteobacteria, methylotrophs show transition forms for the bioenergetic systems analysed. Our approach of focusing on these bioenergetic systems overcomes the phylogenetic impasse that has previously complicated the search for mitochondrial ancestors. Moreover, our results provide a new perspective for experimentally re-evolving mitochondria from extant bacteria and in the future produce synthetic mitochondria.
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Affiliation(s)
| | - Bessem Chouaia
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Francesco Comandatore
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
| | - Elena Crotti
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Davide Sassera
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
| | | | - Daniele Daffonchio
- Department of Food, Environmental and Evolutionary Sciences, University of Milan, Milan, Italy
| | - Claudio Bandi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, University of Milan, Milan, Italy
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Di Nocera PP, De Gregorio E, Rocco F. GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes. BMC Genomics 2013; 14:522. [PMID: 23902135 PMCID: PMC3733652 DOI: 10.1186/1471-2164-14-522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/30/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND REPs (Repetitive Extragenic Palindromes) are small (20-40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization. RESULTS We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in multiple species. CONCLUSIONS CGTC REPs apparently lack a dedicated transposase. Future work will clarify whether these elements may be mobilized by RAYTs or other transposases, and assess if de-novo formation of either GTAG or CGTC repeats type still occurs.
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Affiliation(s)
- Pier Paolo Di Nocera
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Via S, Pansini 5 80131, Naples, Italy.
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Williams BS, Isokpehi RD, Mbah AN, Hollman AL, Bernard CO, Simmons SS, Ayensu WK, Garner BL. Functional Annotation Analytics of Bacillus Genomes Reveals Stress Responsive Acetate Utilization and Sulfate Uptake in the Biotechnologically Relevant Bacillus megaterium. Bioinform Biol Insights 2012; 6:275-86. [PMID: 23226010 PMCID: PMC3511254 DOI: 10.4137/bbi.s7977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacillus species form an heterogeneous group of Gram-positive bacteria that include members that are disease-causing, biotechnologically-relevant, and can serve as biological research tools. A common feature of Bacillus species is their ability to survive in harsh environmental conditions by formation of resistant endospores. Genes encoding the universal stress protein (USP) domain confer cellular and organismal survival during unfavorable conditions such as nutrient depletion. As of February 2012, the genome sequences and a variety of functional annotations for at least 123 Bacillus isolates including 45 Bacillus cereus isolates were available in public domain bioinformatics resources. Additionally, the genome sequencing status of 10 of the B. cereus isolates were annotated as finished with each genome encoded 3 USP genes. The conservation of gene neighborhood of the 140 aa universal stress protein in the B. cereus genomes led to the identification of a predicted plasmid-encoded transcriptional unit that includes a USP gene and a sulfate uptake gene in the soil-inhabiting Bacillus megaterium. Gene neighborhood analysis combined with visual analytics of chemical ligand binding sites data provided knowledge-building biological insights on possible cellular functions of B. megaterium universal stress proteins. These functions include sulfate and potassium uptake, acid extrusion, cellular energy-level sensing, survival in high oxygen conditions and acetate utilization. Of particular interest was a two-gene transcriptional unit that consisted of genes for a universal stress protein and a sirtuin Sir2 (deacetylase enzyme for NAD+-dependent acetate utilization). The predicted transcriptional units for stress responsive inorganic sulfate uptake and acetate utilization could explain biological mechanisms for survival of soil-inhabiting Bacillus species in sulfate and acetate limiting conditions. Considering the key role of sirtuins in mammalian physiology additional research on the USP-Sir2 transcriptional unit of B. megaterium could help explain mammalian acetate metabolism in glucose-limiting conditions such as caloric restriction. Finally, the deep-rooted position of B. megaterium in the phylogeny of Bacillus species makes the investigation of the functional coupling acetate utilization and stress response compelling.
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Affiliation(s)
- Baraka S Williams
- Center for Bioinformatics and Computational Biology, Department of Biology, Jackson State University, Jackson, MS, USA. ; Department of Biology, Division of Natural Science, Tougaloo College, 500 West County Line Road, Tougaloo, MS, USA
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