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Rizzo P, Severini E, Bucci A, Bocchia F, Palladino G, Riboni N, Sanangelantoni AM, Francese R, Giorgi M, Iacumin P, Bianchi F, Mucchino C, Prosser G, Mazzone D, Avagliano D, Coraggio F, Caputi A, Celico F. How do turbidite systems behave from the hydrogeological point of view? New insights and open questions coming from an interdisciplinary work in southern Italy. PLoS One 2022; 17:e0268252. [PMID: 35522687 PMCID: PMC9075667 DOI: 10.1371/journal.pone.0268252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/26/2022] [Indexed: 11/19/2022] Open
Abstract
Turbidite successions can behave either as aquitards or aquifers depending on their lithological and hydraulic features. In particular, post-depositional processes can increase rock permeability due to fracture development in the competent layers. Thus, at a local scale, turbidite systems warrant further detailed investigations, aimed at reconstructing reliable hydrogeological models. The objective of this work was to investigate from the hydrogeological perspective a turbiditic aquifer located in southern Italy, where several perennial and seasonal springs were detected. Considering the complex hydrodynamics of these systems at the catchment scale, to reach an optimal characterization, a multidisciplinary approach was adopted. The conceptual framework employed microbial communities as groundwater tracers, together with the physicochemical features and isotopic signature of springs and streams from water samples. Meanwhile, geophysical investigations coupled with the geological survey provided the contextualization of the hydrogeological data into the detailed geological reconstruction of the study area. This modus operandi allowed us to typify several differences among the samples, allowing identification of sources and paths of surface water and groundwater, along with diffuse groundwater outflow along streams. As a final result, a hydrogeological conceptual model was reconstructed, underlining how at a very local scale the lithologic, hydraulic, and geomorphological heterogeneity of the studied relief can lead to an improved hydrogeological conceptual model compared to that of other turbidite systems. These results open new questions about the hydrogeological behavior of turbiditic aquifers, which could be pivotal in future research. In fact, these systems could support relevant ecosystems and anthropic activities, especially where climate change will force the research of new (and probably less hydrogeologically efficient) water sources.
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Affiliation(s)
- Pietro Rizzo
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
| | - Edoardo Severini
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
- * E-mail:
| | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Pesche, Isernia, Italy
| | - Federico Bocchia
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
| | - Giuseppe Palladino
- Department of Sciences, University of Basilicata, Potenza, Potenza, Italy
| | - Nicolò Riboni
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
| | - Anna Maria Sanangelantoni
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
| | - Roberto Francese
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
| | - Massimo Giorgi
- National Institute of Oceanography and Applied Geophysics–OGS, Sgonico, Trieste, Italy
| | - Paola Iacumin
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
| | - Federica Bianchi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
| | - Claudio Mucchino
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
| | - Giacomo Prosser
- Department of Sciences, University of Basilicata, Potenza, Potenza, Italy
| | | | | | | | | | - Fulvio Celico
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Parma, Italy
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2
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Bergamonti L, Potenza M, Haghighi Poshtiri A, Lorenzi A, Sanangelantoni AM, Lazzarini L, Lottici PP, Graiff C. Ag-functionalized nanocrystalline cellulose for paper preservation and strengthening. Carbohydr Polym 2019; 231:115773. [PMID: 31888832 DOI: 10.1016/j.carbpol.2019.115773] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
Waste paper is an environmentally friendly source of cellulosic material. Here we propose a new treatment based on nanocrystalline cellulose (CNC) for paper preservation and consolidation. Suspensions of CNC were prepared by sulfuric acid hydrolysis using waste paper as cellulose source (CNCWP) and compared with CNC from cotton linter (CNCCL). Both CNCs were obtained with good yield, showing high crystallinity index and comparable morphology, as demonstrated by DLS-ELS, XRD, FTIR, Raman and TEM analyses. CNCs were mixed with silver nanoparticles (CNC/Ag) and their biocidal activity was tested against Escherichia coli and Bacillus subtilis, measuring the minimum inhibitory concentration. CNCs were exploited as treatments for biocidal activity and consolidation on Whatman paper. The presence of silver nanoparticles doesn't affect aesthetic appearance of the original paper and prevents the growth of Aspergillus niger fungus. Mechanical tests demonstrated that the coatings by CNC based products improve stretch and toughness of the paper support.
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Affiliation(s)
- Laura Bergamonti
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, Italy
| | - Marianna Potenza
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, Italy
| | | | - Andrea Lorenzi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, Italy
| | - Anna Maria Sanangelantoni
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, Italy
| | - Laura Lazzarini
- Istituto dei Materiali per l'Elettronica ed il Magnetismo, IMEM, Consiglio delle Ricerche, Parco Area delle Scienze 37/A, Parma, Italy
| | - Pier Paolo Lottici
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, Parma, Italy
| | - Claudia Graiff
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, Italy.
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Zanini A, Petrella E, Sanangelantoni AM, Angelo L, Ventosi B, Viani L, Rizzo P, Remelli S, Bartoli M, Bolpagni R, Chelli A, Feo A, Francese R, Iacumin P, Menta C, Racchetti E, Selmo EM, Tanda MG, Ghirardi M, Boggio P, Pappalardo F, De Nardo MT, Segadelli S, Celico F. Groundwater characterization from an ecological and human perspective: an interdisciplinary approach in the Functional Urban Area of Parma, Italy. Rend Fis Acc Lincei 2018. [DOI: 10.1007/s12210-018-0748-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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4
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Sanangelantoni AM, Malatrasi M, Trivelloni E, Visioli G, Agrimonti C. A novel β-propeller phytase from the dioxin-degrading bacterium Sphingomonas wittichii RW-1. Appl Microbiol Biotechnol 2018; 102:8351-8358. [DOI: 10.1007/s00253-018-9248-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/12/2018] [Accepted: 07/15/2018] [Indexed: 12/24/2022]
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Agrimonti C, Sanangelantoni AM, Marmiroli N. Simultaneous enumeration of Campylobacter jejuni and Salmonella enterica genome equivalents by melting curve analysis following duplex real time PCR in the presence of SYBR Green. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.03.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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6
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Mattarozzi M, Visioli G, Sanangelantoni AM, Careri M. ESEM-EDS: In vivo characterization of the Ni hyperaccumulator Noccaea caerulescens. Micron 2015; 75:18-26. [DOI: 10.1016/j.micron.2015.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/30/2015] [Accepted: 04/18/2015] [Indexed: 10/23/2022]
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Visioli G, D'Egidio S, Vamerali T, Mattarozzi M, Sanangelantoni AM. Culturable endophytic bacteria enhance Ni translocation in the hyperaccumulator Noccaea caerulescens. Chemosphere 2014; 117:538-44. [PMID: 25277966 DOI: 10.1016/j.chemosphere.2014.09.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/29/2014] [Accepted: 09/02/2014] [Indexed: 05/20/2023]
Abstract
In this work, both culture-dependent and independent approaches were used to identify and isolate endophytic bacteria from roots of the Ni hyperaccumulator Noccaea caerulescens. A total of 17 isolates were cultured from root samples, selected for tolerance to 6mM Ni and grouped by restriction analysis of 16S rDNA. Bacterial species cultivated from roots belonged to seven genera, Microbacterium, Arthrobacter, Agreia, Bacillus, Sthenotrophomonas, Kocuria and Variovorax. The culture-independent approach confirmed the presence of Microbacterium and Arthrobacter while only other five clones corresponding to different amplified ribosomal DNA restriction patterns were detected. Five selected highly Ni-resistant bacteria showing also plant growth promoting activities, were inoculated into seeds of N. caerulescens, and in vivo microscopic analysis showed rapid root colonisation. Inoculated plants showed increased shoot biomass, root length and root-to-shoot Ni translocation. Root colonisation was also evident, but not effective, in the non-hyperaccumulating Thlaspi perfoliatum. Seed inoculation with selected Ni-resistant endophytic bacteria may represent a powerful tool in phytotechnologies, although transferring it to biomass species still requires further studies and screening.
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Affiliation(s)
- Giovanna Visioli
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy.
| | - Sara D'Egidio
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Teofilo Vamerali
- Department of Agronomy, Food, Natural Resources, Animals and the Environment, University of Padova, Viale dell' Università 16, 35020 Legnaro-Padova, Italy
| | - Monica Mattarozzi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, Parma, Italy
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8
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Di Gregorio S, Barbafieri M, Lampis S, Sanangelantoni AM, Tassi E, Vallini G. Combined application of Triton X-100 and Sinorhizobium sp. Pb002 inoculum for the improvement of lead phytoextraction by Brassica juncea in EDTA amended soil. Chemosphere 2006; 63:293-9. [PMID: 16153689 DOI: 10.1016/j.chemosphere.2005.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Revised: 06/28/2005] [Accepted: 07/10/2005] [Indexed: 05/04/2023]
Abstract
The process of EDTA-assisted lead phytoextraction from the Bovisa (Milan, Italy) brownfield soil was optimized in microcosms vegetated with Brassica juncea. An autochthonous plant growth-promoting rhizobacterium (PGPR), Sinorhizobium sp. Pb002, was isolated from the rhizosphere of B. juncea grown on the Pb-contaminated soil in presence of 2 mM EDTA. The strain was augmented (10(8) CFU g(-1) soil) in vegetated microcosms to stimulate B. juncea biomass production and, hence, its phytoextraction potential. Triton X-100 was also added to microcosms at 5 and 10 times the critical micelle concentration (cmc) to increase the permeability of root barriers to the EDTA-Pb complexes. Triton X-100 amendment determined an increase in Pb concentration within plant tissues. However it contextually exerted a phytotoxic effect. Sinorhizobium sp. Pb002 augmentation was crucial to plant survival in presence of both bioavailable lead and Triton X-100. The combination of the two treatments produced up to 56% increase in the efficiency of lead phytoextraction by B. juncea. The effects of these treatments on the structure of the soil bacterial community were evaluated by 16S rDNA denaturing gradient gel electrophoresis (DGGE).
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Affiliation(s)
- Simona Di Gregorio
- Department of Science and Technology, University of Verona, Strada le Grazie 15, 17134 Verona, Italy.
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9
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Tiboni O, Cella R, Pasquale G, Sanangelantoni AM, Cammarano P. Immunological heterogeneity of archaebacterial protein synthesis elongation factors Tu (EF-Tu). FEMS Microbiol Lett 2006. [DOI: 10.1111/j.1574-6968.1988.tb02983.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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10
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Nicolis S, Pennati A, Perani E, Monzani E, Sanangelantoni AM, Casella L. Easy Oxidation and Nitration of Human Myoglobin by Nitrite and Hydrogen Peroxide. Chemistry 2006; 12:749-57. [PMID: 16216040 DOI: 10.1002/chem.200500361] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The modification of human myoglobin (HMb) by reaction with nitrite and hydrogen peroxide has been investigated. This reaction is important because NO(2) (-) and H(2)O(2) are formed in vivo under conditions of oxidative and nitrative stress, where protein derivatization has been often observed. The abundance of HMb in tissues and in the heart makes it a potential source and target of reactive species generated in the body. The oxidant and nitrating species produced by HMb/H(2)O(2)/NO(2) (-) are nitrogen dioxide and peroxynitrite, which can react with exogenous substrates and endogenous protein residues. Tandem mass analysis of HMb modified by stoichiometric amounts of H(2)O(2) and NO(2) (-) indicated the presence of two endogenous derivatizations: oxidation of C110 to sulfinic acid (76 %) and nitration of Y103 to 3-nitrotyrosine (44 %). When higher concentrations of NO(2) (-) and H(2)O(2) were used, nitration of Y146 and of the heme were also observed. The two-dimensional gel-electrophoretic analysis of the modified HMbs showed spots more acidic than that of wild-type HMb, a result in agreement with the formation of sulfinic acid and nitrotyrosine residues. By contrast, the reaction showed no evidence for the formation of protein homodimers, as observed in the reaction of HMb with H(2)O(2) alone. Both HMb and the modified HMb are active in the H(2)O(2)/NO(2) (-)-dependent nitration of exogenous phenols. Their catalytic activity is quite similar and the endogenous modifications of HMb therefore have little effect on the reactivity of the protein intermediates.
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Roncone R, Monzani E, Labò S, Sanangelantoni AM, Casella L. Catalytic activity, stability, unfolding, and degradation pathways of engineered and reconstituted myoglobins. J Biol Inorg Chem 2004; 10:11-24. [PMID: 15565498 DOI: 10.1007/s00775-004-0606-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Accepted: 10/13/2004] [Indexed: 10/26/2022]
Abstract
The structural and functional consequences of engineering a positively charged Lys residue and replacing the natural heme with a heme-L-His derivative in the active site of sperm whale myoglobin (Mb) have been investigated. The main structural change caused by the distal T67K mutation appears to be mobilization of the propionate-7 group. Reconstitution of wild-type and T67K Mb with heme-L-His relaxes the protein fragment around the heme because it involves the loss of the interaction of one of the propionate groups which stabilize heme binding to the protein. This modification increases the accessibility of exogenous ligands or substrates to the active site. The catalytic activity of the reconstituted proteins in peroxidase-type reactions is thus significantly increased, particularly with T67K Mb. The T67K mutation slightly reduces the thermodynamic stability and the chemical stability of Mb during catalysis, but somewhat more marked effects are observed by cofactor reconstitution. Hydrogen peroxide, in fact, induces pseudo-peroxidase activity but also promotes oxidative damage of the protein. The mechanism of protein degradation involves two pathways, which depend on the evolution of radical species generated on protein residues by the Mb active species and on the reactivity of phenoxy radicals produced during turnover. Both protein oligomers and heme-protein cross-links have been detected upon inactivation.
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Affiliation(s)
- Raffaella Roncone
- Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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12
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Roncone R, Monzani E, Murtas M, Battaini G, Pennati A, Sanangelantoni AM, Zuccotti S, Bolognesi M, Casella L. Engineering peroxidase activity in myoglobin: the haem cavity structure and peroxide activation in the T67R/S92D mutant and its derivative reconstituted with protohaemin-l-histidine. Biochem J 2004; 377:717-24. [PMID: 14563209 PMCID: PMC1223899 DOI: 10.1042/bj20030863] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2003] [Revised: 10/14/2003] [Accepted: 10/17/2003] [Indexed: 11/17/2022]
Abstract
Atomic co-ordinates and structure factors for the T67R/S92D metMbCN mutant have been deposited with the Protein Data Bank, under accession codes 1h1x and r1h1xsf, respectively. Protein engineering and cofactor replacement have been employed as tools to introduce/modulate peroxidase activity in sperm whale Mb (myoglobin). Based on the rationale that haem peroxidase active sites are characterized by specific charged residues, the Mb haem crevice has been modified to host a haem-distalpropionate Arg residue and a proximal Asp, yielding the T67R/S92D Mb mutant. To code extra conformational mobility around the haem, and to increase the peroxidase catalytic efficiency, the T67R/S92D Mb mutant has been subsequently reconstituted with protohaem-L-histidine methyl ester, yielding a stable derivative, T67R/S92D Mb-H. The crystal structure of T67R/S92D cyano-metMb (1.4 A resolution; R factor, 0.12) highlights a regular haem-cyanide binding mode, and the role for the mutated residues in affecting the haem propionates as well as the neighbouring water structure. The conformational disorder of the haem propionate-7 is evidenced by the NMR spectrum of the mutant. Ligand-binding studies show that the iron(III) centres of T67R/S92D Mb, and especially of T67R/S92D Mb-H, exhibit higher affinity for azide and imidazole than wild-type Mb. In addition, both protein derivatives react faster than wild-type Mb with hydrogen peroxide, showing higher peroxidase-like activity towards phenolic substrates. The catalytic efficiency of T67R/S92D Mb-H in these reactions is the highest so far reported for Mb derivatives. A model for the protein-substrate interaction is deduced based on the crystal structure and on the NMR spectra of protein-phenol complexes.
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Affiliation(s)
- Raffaella Roncone
- Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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13
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Abstract
The spectroscopic, conformational, and reactivity characteristics of the T67R variant of sperm whale myoglobin have been studied to assess the effects of introducing an arginine residue into the distal side of this protein, as occurs in the active site of heme peroxidases. The overall circular dichroism (CD) and NMR spectroscopic properties of various derivatives of the protein are little affected by the mutation. The mutant contains a high-spin ferric ion with a water molecule as the sixth ligand, which exhibits slightly enhanced acidity (pK(a)=8.43+/-0.03) with respect to the corresponding derivative of wild-type myoglobin (pK(a)=8.60+/-0.04). The presence of the distal arginine increases the affinity of the Fe(III) center for azide (K=(6.0+/-0.5)x10(4) M(-1)) and decreases that for imidazole (K=12.0+/-0.2 M(-1)), with respect to the wild-type protein (K=(5.0+/-0.1)x10(4) and 24.7+/-0.7 M(-1), respectively). The peroxidase activity of T67R and wild-type myoglobins has been studied with a group of phenolic substrates related to tyrosine. The mutant exhibits an increased rate of reaction with hydrogen peroxide (k=1550+/-10 versus 760+/-10 M(-1) x s(-1)) and a generally increased peroxidase activity with respect to wild-type myoglobin. Relaxation measurements of proton nuclei of the phenolic substrates in the presence of either the T67R variant or the wild-type protein show that binding of these molecules occurs at distances of 8-10 A from the iron center, that is, close to the heme pocket, except for p-cresol, which can approach the heme more closely and, therefore, probably enter into the distal cavity.
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Affiliation(s)
- Cristina Redaelli
- Dipartimento di Chimica Generale, Università di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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14
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Funari E, Cavalieri M, Ade P, Barone R, Garibaldi L, Pomati F, Rossetti C, Sanangelantoni AM, Sechi N, Tartari G, Ventura S. [Environmental and health problems of cyanobacteria blooms in surface waters in reference to the Italian situation]. Ann Ig 2000; 12:381-400. [PMID: 11148975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- E Funari
- Lab. di Igiene Ambientale, Ist. Super. di Sanità, Roma
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15
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Monzani E, Alzuet G, Casella L, Redaelli C, Bassani C, Sanangelantoni AM, Gullotti M, de Gioia L, Santagostini L, Chillemi F. Properties and reactivity of myoglobin reconstituted with chemically modified protohemin complexes. Biochemistry 2000; 39:9571-82. [PMID: 10924154 DOI: 10.1021/bi000784t] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthetic complexes protohemin-6(7)-L-arginyl-L-alanine (HM-RA) and protohemin-6(7)-L-histidine methyl ester (HM-H) were prepared by condensation of suitably protected Arg-Ala or His residues with protohemin IX. HM-RA and HM-H were used for reconstitution of apomyoglobin from horse heart, yielding the Mb-RA and Mb-H derivatives, respectively, of the protein. The spectral, binding and catalytic properties of Mb-RA and Mb-H are significantly different from those of Mb. As shown by MM and MD calculations, these differences are determined by some local structural changes around the heme which are generated by increased mobility of a key peptide segment (Phe43-Lys47), containing the residue (Lys45) that in native Mb interacts with one of the porphyrin carboxylate groups. In the reconstituted Mbs this carboxylate group is bound to the Arg-Ala or His residue and is no longer available for electrostatic interaction with Lys45. The mobility of the peptide segment near the active site allows the distal histidine to come to a closer contact with the heme, and in fact Mb-RA and Mb-H exist as an equilibrium between a high-spin form and a major low-spin, six-coordinated form containing a bis-imidazole ligated heme. The two forms are clearly distinguishable in the NMR spectra, that also show that each of them consists of a mixture of the two most stable isomers resulting from cofactor reconstitution, as also anticipated by MM and MD calculations. Exogenous ligands such as cyanide, azide, or hydrogen peroxide can displace the bound distal histidine, but their affinity is reduced. On the other hand, mobilization of the peptide chain around the heme in the reconstituted Mbs increases the accessibility of large donor molecules at the heme periphery, with respect to native Mb, where a rigid backbone limits access to the distal pocket. The increased active site accessibility of Mb-RA and Mb-H facilitates the binding and electron transfer of phenolic substrates in peroxidase-type oxidations catalyzed by the reconstituted proteins in the presence of hydrogen peroxide.
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Affiliation(s)
- E Monzani
- Dipartimento di Chimica Generale, Università di Pavia, Italy
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16
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Cammarano P, Creti R, Sanangelantoni AM, Palm P. The archaea monophyly issue: A phylogeny of translational elongation factor G(2) sequences inferred from an optimized selection of alignment positions. J Mol Evol 1999; 49:524-37. [PMID: 10486009 DOI: 10.1007/pl00006574] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A global alignment of EF-G(2) sequences was corrected by reference to protein structure. The selection of characters eligible for construction of phylogenetic trees was optimized by searching for regions arising from the artifactual matching of sequence segments unique to different phylogenetic domains. The spurious matchings were identified by comparing all sections of the global alignment with a comprehensive inventory of significant binary alignments obtained by BLAST probing of the DNA and protein databases with representative EF-G(2) sequences. In three discrete alignment blocks (one in domain II and two in domain IV), the alignment of the bacterial sequences with those of Archaea-Eucarya was not retrieved by database probing with EF-G(2) sequences, and no EF-G homologue of the EF-2 sequence segments was detected by using partial EF-G(2) sequences as probes in BLAST/FASTA searches. The two domain IV regions (one of which comprises the ADP-ribosylatable site of EF-2) are almost certainly due to the artifactual alignment of insertion segments that are unique to Bacteria and to Archaea-Eucarya. Phylogenetic trees have been constructed from the global alignment after deselecting positions encompassing the unretrieved, spuriously aligned regions, as well as positions arising from misalignment of the G' and G" subdomain insertion segments flanking the "fifth" consensus motif of the G domain (AE varsson, 1995). The results show inconsistencies between trees inferred by alternative methods and alternative (DNA and protein) data sets with regard to Archaea being a monophyletic or paraphyletic grouping. Both maximum-likelihood and maximum-parsimony methods do not allow discrimination (by log-likelihood difference and difference in number of inferred substitutions) between the conflicting (monophyletic vs. paraphyletic Archaea) topologies. No specific EF-2 insertions (or terminal accretions) supporting a crenarchaeal-eucaryal clade are detectable in the new EF-G(2) sequence alignment.
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Affiliation(s)
- P Cammarano
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biotecnologie cellulari ed Ematologia, Sezione di Genetica molecolare, Universita' di Roma I "La Sapienza," Policlinico Umberto I, Viale Regina Elena 324, 00161 Roma, Italy
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Sanangelantoni AM, Cammarano P, Tiboni O. Manipulation of the tuf gene provides clues to the localization of sequence element(s) involved in the thermal stability of Thermotoga maritima elongation factor Tu. Microbiology (Reading) 1996; 142 ( Pt 9):2525-32. [PMID: 8828220 DOI: 10.1099/00221287-142-9-2525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Truncated versions of the tuf gene for elongation factor Tu (EF-Tu; 400 aa) from the hyperthermophilic bacterium Thermotoga maritima have been produced by progressive 3'-->5' trimming. The truncated genes have been expressed in Escherichia coli and the thermal stability of the gene products has been assayed by monitoring their GDP-binding capacity after preheating the cell-free extracts at various temperatures (65-95 degrees C). One of the truncated proteins, corresponding to the nucleotide-binding domain (G domain; aa 1-200) appears to be only slightly less stable than the full-length EF-Tu. Replacement of the first 90 N-terminal residues of both the full-length Thermotoga EF-Tu and the isolated G domain with the corresponding sequence of the mesophilic bacterium E. coli, drastically destabilizes both the complete and the truncated protein, indicating that sequence element(s) that are crucial for the attainment of a thermally stable conformation of the Thermotoga EF-Tu lie well within the initial portion of the G domain between residues 1 and 90. The relevant residues defy identification, however, as no amino acid preferences, or exclusive sequence element(s), appear to distinguish the N-terminal region of the thermophilic proteins from those of mesophilic counterparts. It is suggested that the thermal stability of Thermotoga EF-Tu is critically dependent upon unique tertiary structural interactions involving certain N-terminal residues of the molecule.
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Affiliation(s)
- A M Sanangelantoni
- Dipartimento di Genetica e Microbiologia A. Buzzati Traverso, Università di Pavia, Italy.
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Bocchetta M, Ceccarelli E, Creti R, Sanangelantoni AM, Tiboni O, Cammarano P. Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences. J Mol Evol 1995; 41:803-12. [PMID: 8587125 DOI: 10.1007/bf00173160] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The gene fus (for EF-G) of the hyperthermophilic bacterium Aquifex pyrophilus was cloned and sequenced. Unlike the other bacteria, which display the streptomycin-operon arrangement of EF genes (5'-rps12-rps7-fus-tuf-3'), the Aquifex fus gene (700 codons) is not preceded by the two small ribosomal subunit genes although it is still followed by a tuf gene (for EF-Tu). The opposite strand upstream from the EF-G coding locus revealed an open reading frame (ORF) encoding a polypeptide having 52.5% identity with an E. coli protein (the pdxJ gene product) involved in pyridoxine condensation. The Aquifex EF-G was aligned with available homologs representative of Deinococci, high G+C Gram positives, Proteobacteria, cyanobacteria, and several Archaea. Outgroup-rooted phylogenies were constructed from both the amino acid and the DNA sequences using first and second codon positions in the alignments except sites containing synonymous changes. Both datasets and alternative tree-making methods gave a consistent topology, with Aquifex and Thermotoga maritima (a hyperthermophile) as the first and the second deepest offshoots, respectively. However, the robustness of the inferred phylogenies is not impressive. The branching of Aquifex more deeply than Thermotoga and the branching of Thermotoga more deeply than the other taxa examined are given at bootstrap values between 65 and 70% in the fus-based phylogenies, while the EF-G(2)-based phylogenies do not provide a statistically significant level of support (< or = 50% bootstrap confirmation) for the emergence of Thermotoga between Aquifex and the successive offshoot (Thermus genus). At present, therefore, the placement of Aquifex at the root of the bacterial tree, albeit reproducible, can be asserted only with reservation, while the emergence of Thermotoga between the Aquificales and the Deinococci remains (statistically) indeterminate.
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Affiliation(s)
- M Bocchetta
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biopatologia Umana, Universita di Roma I La Sapienza, Policlinico Umberto I, Italy
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Ceccarelli E, Bocchetta M, Creti R, Sanangelantoni AM, Tiboni O, Cammarano P. Chromosomal organization and nucleotide sequence of the genes for elongation factors EF-1 alpha and EF-2 and ribosomal proteins S7 and S10 of the hyperthermophilic archaeum Desulfurococcus mobilis. Mol Gen Genet 1995; 246:687-96. [PMID: 7898436 DOI: 10.1007/bf00290714] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The Desulfurococcus mobilis genes fus (encoding EF-2) and tuf (for EF-1 alpha) were cloned and sequenced together with genes for ribosomal proteins S10 (rps10) and S7 (rps7). Unlike Methanococcus, which displays the bacterial-like fus and tuf gene context 5'-rps12-rps7-fus-tuf-3', and similar to Sulfolobus and Pyrococcus, the Desulfurococcus fus gene (734 codons) has a distinct chromosomal location. Moreover, tuf (441 codons) is the promoter-proximal unit of a three-gene cluster comprising the genes rps10 (98 codons) and tRNA(Ser); the arrangement of the cluster is 5'-tuf-91 bp spacer -rps10-138 bp spacer -tRNA(Ser)-3' and the tuf gene is preceded by a canonical archaeal promoter. The D. mobilis gene rps7 (198 codons) is located further upstream from tuf (535 bp 'silent' intergenic spacing) and no rps12 homolog occurs in its immediate vicinity. Also, judging from putative promoter and transcription termination sequences, rps7 appears to be separately transcribed. Analysis of the predicted fus and tuf gene products revealed the three consensus motifs characteristic of GTP-binding proteins, and the fus-encoded EF-2 protein also displayed the consensus sequence required for ADP-ribosylation by Diphtheria toxin. Both EF sequences were definitely crenarchaeal by comparison with available homologs from other Archaea. Outgroup-rooted phylogenies derived from the sequences of ribosomal proteins S10 and S7 yielded the Sulfolobus-Desulfurococcus association at a high bootstrap confidence level.
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Affiliation(s)
- E Ceccarelli
- Instituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biopatologia Umana, Università di Roma I, Policlinico Umberto I, Italy
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Sanangelantoni AM, Bocchetta M, Cammarano P, Tiboni O. Phylogenetic depth of S10 and spc operons: cloning and sequencing of a ribosomal protein gene cluster from the extremely thermophilic bacterium Thermotoga maritima. J Bacteriol 1994; 176:7703-10. [PMID: 8002596 PMCID: PMC197229 DOI: 10.1128/jb.176.24.7703-7710.1994] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A segment of Thermotoga maritima DNA spanning 6,613 bp downstream from the gene tuf for elongation factor Tu was sequenced by use of a chromosome walking strategy. The sequenced region comprised a string of 14 tightly linked open reading frames (ORFs) starting 50 bp downstream from tuf. The first 11 ORFs were identified as homologs of ribosomal protein genes rps10, rpl3, rpl4, rpl23, rpl2, rps19, rpl22, rps3, rpl16, rpl29, and rps17 (which in Escherichia coli constitute the S10 operon, in that order); the last three ORFs were homologous to genes rpl14, rpl24, and rpl5 (which in E. coli constitute the three promoter-proximal genes of the spectinomycin operon). The 14-gene string was preceded by putative -35 and -10 promoter sequences situated 5' to gene rps10, within the 50-bp spacing between genes tuf and rps10; the same region exhibited a potential transcription termination signal for the upstream gene cluster (having tuf as the last gene) but displayed also the potential for formation of a hairpin loop hindering the terminator; this suggests that transcription of rps10 and downstream genes may start farther upstream. The similar organization of the sequenced rp genes in the deepest-branching bacterial phyla (T. maritima) and among Archaea has been interpreted as indicating that the S10-spc gene arrangement existed in the (last) common ancestor. The phylogenetic depth of the Thermotoga lineage was probed by use of r proteins as marker molecules: in all except one case (S3), Proteobacteria or the gram-positive bacteria, and not the genus Thermotoga, were the deepest-branching lineage; in only two cases, however, was the inferred branching order substantiated by bootstrap analysis.
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Affiliation(s)
- A M Sanangelantoni
- Dipartimento di Genetica e Microbiologia A. Buzzati Traverso, Università di Pavia, Italy
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Creti R, Ceccarelli E, Bocchetta M, Sanangelantoni AM, Tiboni O, Palm P, Cammarano P. Evolution of translational elongation factor (EF) sequences: reliability of global phylogenies inferred from EF-1 alpha(Tu) and EF-2(G) proteins. Proc Natl Acad Sci U S A 1994; 91:3255-9. [PMID: 8159735 PMCID: PMC43555 DOI: 10.1073/pnas.91.8.3255] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The EF-2 coding genes of the Archaea Pyrococcus woesei and Desulfurococcus mobilis were cloned and sequenced. Global phylogenies were inferred by alternative tree-making methods from available EF-2(G) sequence data and contrasted with phylogenies constructed from the more conserved but shorter EF-1 alpha(Tu) sequences. Both the monophyly (sensu Hennig) of Archaea and their subdivision into the kingdoms Crenarchaeota and Euryarchaeota are consistently inferred by analysis of EF-2(G) sequences, usually at a high bootstrap confidence level. In contrast, EF-1 alpha(Tu) phylogenies tend to be inconsistent with one another and show low bootstrap confidence levels. While evolutionary distance and DNA maximum parsimony analyses of EF-1 alpha(Tu) sequences do show archaeal monophyly, protein parsimony and DNA maximum-likelihood analyses of these data do not. In no case, however, do any of the tree topologies inferred from EF-1 alpha(Tu) sequence analyses receive significant bootstrap support.
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Affiliation(s)
- R Creti
- Istituto Pasteur-Fondazione Cenci-Bolognetti, Dipt. Biopatologia Umana, Università di Roma I, Policlinico Umberto I., Italy
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Sanangelantoni AM, Tiboni O. The chromosomal location of genes for elongation factor Tu and ribosomal protein S10 in the cyanobacterium Spirulina platensis provides clues to the ancestral organization of the str and S10 operons in prokaryotes. J Gen Microbiol 1993; 139:2579-84. [PMID: 8277243 DOI: 10.1099/00221287-139-11-2579] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The structural gene (rps10) encoding ribosomal protein S10 of the cyanobacterium Spirulina platensis has been localized both on chromosomal DNA and the previously characterized recombinant plasmid pSp7 harbouring the 3'-terminal portion of the gene for elongation factor G (fus) and the gene for elongation factor Tu (tuf). Alignment of the predicted S10 sequence of S. platensis with the homologous sequences from cyanelles, bacteria, archaea and eukarya showed that the cyanobacterial S10 shares a high degree of sequence homology (74% amino acid identity) with the cyanellar protein. Unlike the situation in Escherichia coli, the rps10 gene of S. plantensis is unlinked to the S10 operon genes, being adjacent to the str operon genes. Since a similar organization could be observed in cyanelles of Cyanophora paradoxa and in all archaea so far analysed, this probably represents the ancestral state.
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Affiliation(s)
- A M Sanangelantoni
- Dipartimento di Genetica e Microbiologia A. Buzzati-Traverso, Università di Pavia, Italy
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Tiboni O, Cammarano P, Sanangelantoni AM. Cloning and sequencing of the gene encoding glutamine synthetase I from the archaeum Pyrococcus woesei: anomalous phylogenies inferred from analysis of archaeal and bacterial glutamine synthetase I sequences. J Bacteriol 1993; 175:2961-9. [PMID: 8098326 PMCID: PMC204614 DOI: 10.1128/jb.175.10.2961-2969.1993] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The gene glnA encoding glutamine synthetase I (GSI) from the archaeum Pyrococcus woesei was cloned and sequenced with the Sulfolobus solfataricus glnA gene as the probe. An operon reading frame of 448 amino acids was identified within a DNA segment of 1,528 bp. The encoded protein was 49% identical with the GSI of Methanococcus voltae and exhibited conserved regions characteristic of the GSI family. The P. woesei GSI was aligned with available homologs from other archaea (S. solfataricus, M. voltae) and with representative sequences from cyanobacteria, proteobacteria, and gram-positive bacteria. Phylogenetic trees were constructed from both the amino acid and the nucleotide sequence alignments. In accordance with the sequence similarities, archaeal and bacterial sequences did not segregate on a phylogeny. On the basis of sequence signatures, the GSI trees could be subdivided into two ensembles. One encompassed the GSI of cyanobacteria and proteobacteria, but also that of the high-G + C gram-positive bacterium Streptomyces coelicolor (all of which are regulated by the reversible adenylylation of the enzyme subunits); the other embraced the GSI of the three archaea as well as that of the low-G + C gram-positive bacteria (Clostridium acetobutilycum, Bacillus subtilis) and Thermotoga maritima (none of which are regulated by subunit adenylylation). The GSIs of the Thermotoga and the Bacillus-Clostridium lineages shared a direct common ancestor with that of P. woesei and the methanogens and were unrelated to their homologs from cyanobacteria, proteobacteria, and S. coelicolor. The possibility is presented that the GSI gene arose among the archaea and was then laterally transferred from some early methanogen to a Thermotoga-like organism. However, the relationship of the cyanobacterial-proteobacterial GSIs to the Thermotoga GSI and the GSI of low-G+C gram-positive bacteria remains unexplained.
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Affiliation(s)
- O Tiboni
- Dipartimento Genetica e Microbiologia A. Buzzati-Traverso, Università di Pavia, Italy
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Cammarano P, Palm P, Creti R, Ceccarelli E, Sanangelantoni AM, Tiboni O. Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: phylogenetic coherence and structure of the archaeal domain. J Mol Evol 1992; 34:396-405. [PMID: 1602493 DOI: 10.1007/bf00162996] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the "eocyte tree" (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletic-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.
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Affiliation(s)
- P Cammarano
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biopatologia Umana, Università di Roma, La Sapienza, Roma, Italy
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Sanangelantoni AM, Forlani G, Ambroselli F, Cammarano P, Tiboni O. The glnA gene of the extremely thermophilic eubacterium Thermotoga maritima: cloning, primary structure, and expression in Escherichia coli. ACTA ACUST UNITED AC 1992; 138:383-93. [PMID: 1348781 DOI: 10.1099/00221287-138-2-383] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The structural gene (glnA) encoding the glutamine synthetase (GS) of the extremely thermophilic eubacterium Thermotoga maritima has been cloned on a 6.0 kb HindIII DNA fragment. Sequencing of the region containing the glnA gene (1444 bp) showed an ORF encoding a polypeptide (439 residues) with an estimated mass of 50,088 Da, which shared significant homology with the GSI sequences of other Bacteria (Escherichia coli, Bacillus subtilis) and Archaea (Pyrococcus woesei, Sulfolobus solfataricus). The T. maritima glnA gene was expressed in E. coli, as shown by the ability to complement a glnA lesion in the glutamine-auxotrophic strain ET8051. The recombinant GS has been partially characterized with respect to the temperature dependence of enzyme activity, molecular mass and mode of regulation. The molecular mass of the Thermotoga GS (590,000 Da), estimated by gel filtration, was compatible with a dodecameric composition for the holoenzyme, as expected for a glutamine synthetase of the GSI type. Comparison of the amino acid sequence of T. maritima GS with those from thermophilic and mesophilic micro-organisms failed to detect any obvious features directly related to thermal stability.
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Affiliation(s)
- A M Sanangelantoni
- Dipartimento di Genetica e Microbiologia A. Buzzati-Traverso, Università di Pavia, Italy
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Tiboni O, Cantoni R, Creti R, Cammarano P, Sanangelantoni AM. Phylogenetic depth of Thermotoga maritima inferred from analysis of the fus gene: amino acid sequence of elongation factor G and organization of the Thermotoga str operon. J Mol Evol 1991; 33:142-51. [PMID: 1920450 DOI: 10.1007/bf02193628] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The gene (fus) coding for elongation factor G (EF-G) of the extremely thermophilic eubacterium Thermotoga maritima was identified and sequenced. The EF-G coding sequence (2046 bp) was found to lie in an operon-like structure between the ribosomal protein S7 gene (rpsG) and the elongation factor Tu (EF-Tu) gene (tuf). The rpsG, fus, and tuf genes follow each other immediately in that order, which corresponds to the order of the homologous genes in the str operon of Escherichia coli. The derived amino acid sequence of the EF-G protein (682 residues) was aligned with the homologous sequences of other eubacteria, eukaryotes (hamster), and archaebacteria (Methanococcus vannielii). Unrooted phylogenetic dendrograms, obtained both from the amino acid and the nucleotide sequence alignments, using a variety of methods, lend further support to the notion that the (present) root of the (eu)bacterial tree lies between Thermotoga and the other bacterial lineages.
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Affiliation(s)
- O Tiboni
- Dipartimento di Genetica e Microbiologia A. Buzzati-Traverso, Universita di Pavia, Italy
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Sanangelantoni AM, Barbarini D, Di Pasquale G, Cammarano P, Tiboni O. Cloning and nucleotide sequence of an archaebacterial glutamine synthetase gene: phylogenetic implications. Mol Gen Genet 1990; 221:187-94. [PMID: 1973523 DOI: 10.1007/bf00261719] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The glnA gene of the thermophilic sulphur-dependent archaebacterium Sulfolobus solfataricus was identified by hybridization with the corresponding gene of the cyanobacterium Spirulina platensis and cloned in Escherichia coli. The nucleotide sequence of the 1696 bp DNA fragment containing the structural gene for glutamine synthetase was determined, and the derived amino acid sequence (471 residues) was compared to the sequences of glutamine synthetases from eubacteria and eukaryotes. The homology between the archaebacterial and the eubacterial enzymes is higher (42%-49%) than that found with the eukaryotic counterpart (less than 20%). This was true also when the five most conserved regions, which it is possible to identify in both eubacterial and eukaryotic glutamine synthetases, were analysed.
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Affiliation(s)
- A M Sanangelantoni
- Dipartimento di Genetica e Microbiologia A. Buzzati Traverso, Pavia, Italy
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Sanangelantoni AM, Calogero RC, Butarelli FR, Gualerzi CO, Tiboni O. Organization and nucleotide sequence of the genes for ribosomal protein S2 and elongation factor Ts inSpirulina Platensis. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb03986.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Sanangelantoni AM, Calogero RC, Buttarelli FR, Gualerzi CO, Tiboni O. Organization and nucleotide sequence of the genes for ribosomal protein S2 and elongation factor Ts in Spirulina platensis. FEMS Microbiol Lett 1990; 54:141-5. [PMID: 2108895 DOI: 10.1016/0378-1097(90)90272-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A 6.5 kb region from the genome of the cyanobacterium Spirulina platensis was cloned using as a probe the Escherichia coli gene for ribosomal protein S2. Sequence analysis revealed, in this region, the presence of the gene for ribosomal protein S2 and part of the gene for the elongation factor Ts (EF-Ts). The arrangement rpsB-spacer-tsf resembles that reported for E. coli. The deduced amino acid sequences of the platensis S2 and EF-Ts show significant homology with the E. coli counterparts.
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Affiliation(s)
- A M Sanangelantoni
- Dipartimento di Genetica e Microbiologia A. Buzzati Traverso, Pavia, Italy
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Cammarano P, Tiboni O, Sanangelantoni AM. Phylogenetic conservation of antigenic determinants in archaebacterial elongation factors (Tu proteins). Can J Microbiol 1989; 35:2-10. [PMID: 2470483 DOI: 10.1139/m89-002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
By using affinity chromatography methods, we have purified elongation factor Tu (EF-Tu) proteins from a host of archaebacteria covering all known divisions in the archaebacterial tree except halophiles, and from such distantly related eubacteria as Thermotoga maritima and Escherichia coli. Polyclonal antibodies were raised against the Tu proteins of Sulfolobus solfataricus, Thermoproteus tenax, Thermococcus celer, Pyrococcus wosei, Archaeoglobus fulgidus, Methanococcus thermolitotrophicus, Thermoplasma acidophilum, and Thermotoga and used to probe the immunochemical relatedness of elongation factors both within and across kingdom boundaries. A selection of the results, presented here, indicates that (i) every archaebacterial EF-Tu is closer (immunochemically) to every other archaebacterial EF-Tu than to the functionally analogous proteins of eubacteria and eukaryotes, with only one possible exception concerning the recognition of eukaryotic (EF-1 alpha) factors by Thermococcus EF-Tu antibodies, and (ii) within the archaebacteria there appears to be a correlation between EF-Tu immunochemical similarities and the phylogenetic relatedness of the organisms inferred from other (sequence) criteria. On the whole, immunochemical similarity data argue against the proposal that the archaebacterial taxon should be split and redistributed between two superkingdoms.
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Affiliation(s)
- P Cammarano
- Dipartimento di Biopatologia Umana, Università di Roma I, Italy
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Rossi E, Riccardi G, Sanangelantoni AM, Ciferri O. Construction of a cosmid library of Spirulina platensisas an approach to DNA physical mapping. FEMS Microbiol Lett 1985. [DOI: 10.1111/j.1574-6968.1985.tb01019.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Riccardi G, Sanangelantoni AM, Sarasini A, Ciferri O. Altered methionyl-tRNA synthetase in a Spirulina platensis mutant resistant to ethionine. J Bacteriol 1982; 151:1053-5. [PMID: 7096264 PMCID: PMC220363 DOI: 10.1128/jb.151.2.1053-1055.1982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Compared with the parental strain, a Spirulina platensis mutant that is resistant to ethionine incorporated methionine into protein at a reduced rate, whereas ethionine incorporation was practically nil. The methionyl-tRNA synthetase present in crude extracts from the resistant strain showed a reduced affinity for methionine and ethionine.
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