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Peng W, Wang Y, Fu Y, Deng Z, Lin S, Liang R. Characterization of the Tellurite-Resistance Properties and Identification of the Core Function Genes for Tellurite Resistance in Pseudomonas citronellolis SJTE-3. Microorganisms 2022; 10:microorganisms10010095. [PMID: 35056544 PMCID: PMC8779313 DOI: 10.3390/microorganisms10010095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Tellurite is highly toxic to bacteria and commonly used in the clinical screening for pathogens; it is speculated that there is a potential relationship between tellurite resistance and bacterial pathogenicity. Until now, the core function genes of tellurite resistance and their characteristics are still obscure. Pseudomonas citronellolis SJTE-3 was found able to resist high concentrations of tellurite (250 μg/mL) and formed vacuole-like tellurium nanostructures. The terZABCDE gene cluster located in the large plasmid pRBL16 endowed strain SJTE-3 with the tellurite resistance of high levels. Although the terC and terD genes were identified as the core function genes for tellurite reduction and resistance, the inhibition of cell growth was observed when they were used solely. Interestingly, co-expression of the terA gene or terZ gene could relieve the burden caused by the expression of the terCD genes and recover normal cell growth. TerC and TerD proteins commonly shared the conserved sequences and are widely distributed in many pathogenic bacteria, highly associated with the pathogenicity factors.
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Affiliation(s)
- Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanqiu Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yali Fu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (W.P.); (Y.W.); (Y.F.); (Z.D.); (S.L.)
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: ; Tel./Fax: +86-21-34204192
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Nguyen TTH, Kikuchi T, Tokunaga T, Iyoda S, Iguchi A. Diversity of the Tellurite Resistance Gene Operon in Escherichia coli. Front Microbiol 2021; 12:681175. [PMID: 34122392 PMCID: PMC8193136 DOI: 10.3389/fmicb.2021.681175] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/30/2021] [Indexed: 11/15/2022] Open
Abstract
Tellurite is highly toxic to most bacteria owing to its strong oxidative ability. However, some bacteria demonstrate tellurite resistance. In particular, some Escherichia coli strains, including Shiga toxin-producing E. coli O157:H7, are known to be resistant to tellurite. This resistance is involved in ter operon, which is usually located on a prophage-like element of the chromosome. The characteristics of the ter operon have been investigated mainly by genome analysis of pathogenic E. coli; however, the distribution and structural characteristics of the ter operon in other E. coli are almost unknown. To clarify these points, we examined 106 E. coli strains carrying the ter operon from various animals. The draft genomes of 34 representative strains revealed that ter operons were clearly classified into four subtypes, ter-type 1–4, at the nucleotide sequence level. Complete genomic sequences revealed that operons belonging to three ter-types (1, 3, and 4) were located on the prophage-like elements on the chromosome, whereas the ter-type 2 operon was located on the IncHI2 plasmid. The positions of the tRNASer, tRNAMet, and tRNAPhe indicated the insertion sites of elements carrying the ter operons. Using the PCR method developed in this study, 106 strains were classified as type 1 (n = 66), 2 (n = 13), 3 (n = 8), and 4 (n = 17), and two strains carried both types 1 and 2. Furthermore, significant differences in the minimum inhibitory concentration (MIC) of tellurite were observed between strains carrying ter-type 4 and the others (p < 0.05). The ter-type was also closely related to the isolation source, with types 2 and 4 associated with chickens and deer, respectively. This study provided new insights related not only to genetic characteristics of the ter operons, but also to phenotypic and ecological characteristics that may be related to the diversity of the operon.
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Affiliation(s)
- Thi Thu Huong Nguyen
- Department of Environment and Resource Sciences, University of Miyazaki, Miyazaki, Japan.,Thai Nguyen University of Agriculture and Forestry, Thai Nguyen, Vietnam
| | - Taisei Kikuchi
- Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tadaaki Tokunaga
- Department of Environment and Resource Sciences, University of Miyazaki, Miyazaki, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Atsushi Iguchi
- Department of Environment and Resource Sciences, University of Miyazaki, Miyazaki, Japan
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Jánošíková L, Pálková L, Šalát D, Klepanec A, Soltys K. Response of Escherichia coli minimal ter operon to UVC and auto-aggregation: pilot study. PeerJ 2021; 9:e11197. [PMID: 34026346 PMCID: PMC8123226 DOI: 10.7717/peerj.11197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
Aim The study of minimal ter operon as a determinant of tellurium resistance (TeR) is important for the purpose of confirming the relationship of these genes to the pathogenicity of microorganisms. The ter operon is widespread among bacterial species and pathogens, implicated also in phage inhibition, oxidative stress and colicin resistance. So far, there is no experimental evidence for the role of the Escherichia coli (E. coli) minimal ter operon in ultraviolet C (UVC) resistance, biofilm formation and auto-aggregation. To identify connection with UVC resistance of the minimal ter operon, matched pairs of Ter-positive and -negative E. coli cells were stressed and differences in survival and whole genome sequence analysis were performed. This study was aimed also to identify differences in phenotype of cells induced by environmental stress. Methods In the current study, a minimal ter operon(terBCDEΔF) originating from the uropathogenic strain E. coli KL53 was used. Clonogenic assay was the method of choice to determine cell reproductive death after treatment with UVC irradiation at certain time intervals. Bacterial suspensions were irradiated with 254 nm UVC-light (germicidal lamp in biological safety cabinet) in vitro. UVC irradiance output was 2.5 mW/cm2 (calculated at the UVC device aperture) and plate-lamp distance of 60 cm. DNA damage analysis was performed using shotgun sequencing on Illumina MiSeq platform. Biofilm formation was measured by a crystal violet retention assay. Auto-aggregation assay was performed according to the Ghane, Babaeekhou & Ketabi (2020). Results A large fraction of Ter-positive E. coli cells survived treatment with 120-s UVC light (300 mJ/cm2) compared to matched Ter-negative cells; ∼5-fold higher resistance of Ter-positive cells to UVC dose (p = 0.0007). Moreover, UVC surviving Ter-positive cells showed smaller mutation rate as Ter-negative cells. The study demonstrated that a 1200-s exposure to UVC (3,000 mJ/cm2) was sufficient for 100% inhibition of growth for all the Ter-positive and -negative E. coli cells. The Ter-positive strain exhibited of 26% higher auto-aggregation activities and was able to inhibit biofilm formation over than Ter- negative strain (**** P < 0.0001). Conclusion Our study shows that Ter-positive cells display lower sensitivity to UVC radiation, corresponding to a presence in minimal ter operon. In addition, our study suggests that also auto-aggregation ability is related to minimal ter operon. The role of the minimal ter operon (terBCDEΔF) in resistance behavior of E. coli under environmental stress is evident.
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Affiliation(s)
- Lenka Jánošíková
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | | | - Dušan Šalát
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | - Andrej Klepanec
- Faculty of Health Sciences, University of St. Cyril and Methodius in Trnava, Trnava, Slovak Republic
| | - Katarina Soltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic.,Comenius University Science Park, Comenius University in Bratislava, Bratislava, Slovak Republic
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Reichert B, Dornbusch AJ, Arguello J, Stanley SE, Lang KM, Lostroh CP, Daugherty MA. Acinetobacter baylyi long-term stationary-phase protein StiP is a protease required for normal cell morphology and resistance to tellurite. Can J Microbiol 2013; 59:726-36. [PMID: 24206355 DOI: 10.1139/cjm-2013-0517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated the Acinetobacter baylyi gene ACIAD1960, known from previous work to be expressed during long-term stationary phase. The protein encoded by this gene had been annotated as a Conserved Hypothetical Protein, surrounded by putative tellurite resistance ("Ter") proteins. Sequence analysis suggested that the protein belongs to the DUF1796 putative papain-like protease family. Here, we show that the purified protein, subsequently named StiP, has cysteine protease activity. Deletion of stiP causes hypersensitivity to tellurite, altered population dynamics during long-term batch culture, and most strikingly, dramatic alteration of normal cell morphology. StiP and associated Ter proteins (the StiP-Ter cluster) are therefore important for regulating cell morphology, likely in response to oxidative damage or depletion of intracellular thiol pools, triggered artificially by tellurite exposure. Our finding has broad significance because while tellurite is an extremely rare compound in nature, oxidative damage, the need to maintain a particular balance of intracellular thiols, and the need to regulate cell morphology are ubiquitous.
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Affiliation(s)
- Blake Reichert
- a Department of Chemistry and Biochemistry, Colorado College, 14 East Cache La Poudre Avenue, Colorado Springs, CO 80903, USA
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Anantharaman V, Iyer LM, Aravind L. Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing. MOLECULAR BIOSYSTEMS 2013; 8:3142-65. [PMID: 23044854 DOI: 10.1039/c2mb25239b] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The mode of action of the bacterial ter cluster and TelA genes, implicated in natural resistance to tellurite and other xenobiotic toxic compounds, pore-forming colicins and several bacteriophages, has remained enigmatic for almost two decades. Using comparative genomics, sequence-profile searches and structural analysis we present evidence that the ter gene products and their functional partners constitute previously underappreciated, chemical stress response and anti-viral defense systems of bacteria. Based on contextual information from conserved gene neighborhoods and domain architectures, we show that the ter gene products and TelA lie at the center of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing. Our analysis suggests that the multiple metal-binding and non-binding TerD paralogs and TerC are likely to constitute a membrane-associated complex, which might also include TerB and TerY, and feature several, distinct metal-binding sites. Versions of the TerB domain might also bind small molecule ligands and link the TerD paralog-TerC complex to biosynthetic modules comprising phosphoribosyltransferases (PRTases), ATP grasp amidoligases, TIM-barrel carbon-carbon lyases, and HAD phosphoesterases, which are predicted to synthesize novel nucleoside-like molecules. One of the PRTases is also likely to interact with RNA by means of its Pelota/Ribosomal protein L7AE-like domain. The von Willebrand factor A domain protein, TerY, is predicted to be part of a distinct phosphorylation switch, coupling a protein kinase and a PP2C phosphatase. We show, based on the evidence from numerous conserved gene neighborhoods and domain architectures, that both the TerB and TelA domains have been linked to diverse lipid-interaction domains, such as two novel PH-like and the Coq4 domains, in different bacteria, and are likely to comprise membrane-associated sensory complexes that might additionally contain periplasmic binding-protein-II and OmpA domains. We also show that the TerD and TerB domains and the TerY-associated phosphorylation system are functionally linked to many distinct DNA-processing complexes, which feature proteins with SWI2/SNF2 and RecQ-like helicases, multiple AAA+ ATPases, McrC-N-terminal domain proteins, several restriction endonuclease fold DNases, DNA-binding domains and a type-VII/Esx-like system, which is at the center of a predicted DNA transfer apparatus. These DNA-processing modules and associated genes are predicted to be involved in restriction or suicidal action in response to phages and possibly repairing xenobiotic-induced DNA damage. In some eukaryotes, certain components of the ter system appear to be recruited to function in conjunction with the ubiquitin system and calcium-signaling pathways.
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Affiliation(s)
- Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Abstract
Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.
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Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, Mavromatis K, Pitluck S, Richardson PM, Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM, Wolf YI, Sorokin A, Gerasimova AV, Gelfand MS, Fredrickson JK, Koonin EV, Daly MJ. Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One 2007; 2:e955. [PMID: 17895995 PMCID: PMC1978522 DOI: 10.1371/journal.pone.0000955] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 09/04/2007] [Indexed: 11/19/2022] Open
Abstract
Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail: (KM); (MD)
| | - Marina V. Omelchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elena K. Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - Vera Y. Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - Alexander Vasilenko
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - Min Zhai
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - Alla Lapidus
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alex Copeland
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Edwin Kim
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Miriam Land
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Konstantinos Mavromatis
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Samuel Pitluck
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Paul M. Richardson
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Chris Detter
- US Department of Energy, Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Thomas Brettin
- US Department of Energy, Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Elizabeth Saunders
- US Department of Energy, Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Barry Lai
- Environmental Research Division and Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Bruce Ravel
- Environmental Research Division and Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Kenneth M. Kemner
- Environmental Research Division and Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexander Sorokin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anna V. Gerasimova
- Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Mikhail S. Gelfand
- Institute for Information Transmission Problems of RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - James K. Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael J. Daly
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail: (KM); (MD)
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Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev 2001; 65:44-79. [PMID: 11238985 PMCID: PMC99018 DOI: 10.1128/mmbr.65.1.44-79.2001] [Citation(s) in RCA: 486] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.
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Affiliation(s)
- K S Makarova
- Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799,USA
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Antelmann H, Bernhardt J, Schmid R, Mach H, Völker U, Hecker M. First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis. Electrophoresis 1997; 18:1451-63. [PMID: 9298659 DOI: 10.1002/elps.1150180820] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Data on the identification of proteins of Bacillus subtilis on two-dimensional (2-D) gels as well as their regulation are summarized and the identification of 56 protein spots is included. The pattern of proteins synthesized in Bacillus subtilis during exponential growth, during starvation for glucose or phosphate, or after the imposition of stresses like heat shock, salt- and ethanol stress as well as oxidative stress was analyzed. N-terminal sequencing of protein spots allowed the identification of 93 proteins on 2-D gels, which are required for the synthesis of amino acids and nucleotides, the generation of ATP, for glycolyses, the pentose phosphate cycle, the citric acid cycle as well as for adaptation to a variety of stress conditions. A computer-aided analysis of the 2-D gels was used to monitor the synthesis profile of more than 130 protein spots. Proteins performing housekeeping functions during exponential growth displayed a reduced synthesis rate during stress and starvation, whereas spots induced during stress and starvation were classified as specific stress proteins induced by a single stimulus or a group of related stimuli, or as general stress proteins induced by a variety of entirely different stimuli. The analysis of mutants in global regulators was initiated in order to establish a response regulation map for B. subtilis. These investigations demonstrated that the alternative sigma factor sigma B is involved in the regulation of almost all of the general stress proteins and that the phoPR two-component system is required for the induction of a large part but not all of the proteins induced by phosphate starvation.
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Affiliation(s)
- H Antelmann
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Mikrobiologie und Molekularbiologie, Germany
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