• Istituto di Biologia e Patologia Molecolari


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gioacchino.micheli@fondazione.uniroma1.it
GIOACCHINO MICHELI
Researcher (ret.)



Summary description
My major research interest concerns the fuctional relevance of 3D architectural features of the genome, an area which could be dubbed in short as functional morphogenomics.
Among more recent studies an exemplification, banking on a long-standing research expertise on eukaryotic systems (please go to the of publications for a deeper insight), is the quest for global and local determinants structuring the bacterial chromosome. At the whole-genome level our studies have highlighted the ancillary involvement of histone-like proteins in the structural constraints which account for the topological integrity of the loop domains in the bacterial nucleoid. As for local determinants, we have found that the activation of the virF gene, the primary regulator of invasivity in human enteropathogens like Shigella and E.coli EIEC, triggered by the transit of the bacteria from the outer environment to the intestinal, warmer, milieu of the host, depends on changes the DNA intrinsic curvature the promoter undergoes with changing temperature. In essence, DNA bending can act as a thermosensor modulating gene expression. Successively we were able to show that the in vitro activity of a bacterial promoter is maximized only within a narrow DNA curvature range.
This research has led to further developments, mostly focused on the structure and function of efflux pumps in bacterial pathogens, in line with my general interest for the functiontal relevance of supramolecular architectures of biological interest, 
As a side activity, I have supervised a dedicated molecular microscopy resource available at my home institute, making specific know‑how available for TEM and AFM investigations on nucleic acids and chromatin.
A more detailed account of my activity is available at my homepage (www.gmicheli.net). After retirement (November 2020) I have stopped most laboratory work on the topics mentioned above, however my strong interest in them has remained alive, mainly in the form of data review and elaboration, and including also the theoretical development of specific approaches and the implementation of software tools.

Keywords (structures, processes, techniques)
3D genome architecture, supramolecular genome structure, chromatin-loops / morphogenomics / cell nucleus and chromosome structure / nuclear matrix, nucleoskeleton, nuclear lamina, chromosome scaffold / bacterial nucleoid structure / DNA, chromatin and nucleoproteins structure and organisation / DNA topology, topoisomerases / DNA intrinsic curvature, bending / supramolecular assemblies of the cell / epigenetics regulation, DNA replication, transcription, gene expression / electron microscopy, TEM, atomic force microscopy, AFM, SFM.

Pasqua M, Zennaro A, Trirocco R, Fanelli G, Micheli G, Grossi M, Colonna B, Prosseda G (2021). Modulation of OMV Production by the Lysis Module of the DLP12 Defective Prophage of Escherichia coli K12. Microorganisms 9(2), 369

Pasqua M, Grossi M, Zennaro A, Fanelli G, Micheli G, Barras F, Colonna B, Prosseda G (2019). The varied role of efflux pumps of the MFS family in the interplay of bacteria with animal and plant cells. Microorganisms 7:285-305
 
Di Felice F, Micheli G, Camilloni G (2019). Restriction enzymes and their use in molecular biology: An overview. J Biosci 44:38-45

Leuzzi A, Grossi M, Di Martino ML, Pasqua M, Micheli G, Colonna B, Prosseda G (2017). Role of the SRRz/Rz1 lambdoid lysis cassette in the pathoadaptive evolution of Shigella. Int. J. Med. Microbiol. 307:268-275

Bolondi A, Caldarelli F, Di Felice F, Durano D, Germani G, Michetti M, Tramutolo A, Micheli G, Camilloni G (2017). What is a Gene? A Two Sided View. Evol. Biol. 44:1-4


Durano D, Lukacs A, Di Felice F, Micheli G, Camilloni G (2017). A novel role for Nhp6 proteins in histone gene regulation in Saccharomyces cerevisiae. Int J Biochem Cell Biol. 83:76-83

Di Martino ML, Falconi M, Micheli G, Colonna B, Prosseda G (2016). The Multifaceted Activity of the VirF Regulatory Protein in the Shigella Lifestyle. Front. Mol. Biosci. 3:61

Leuzzi A, Di Martino ML , Campilongo R, Falconi M, Barbagallo M, Marcocci L, Pietrangeli P, Casalino M, Grossi M, Micheli G, Colonna B, Prosseda G. (2015). Multifactor Regulation of the MdtJI Polyamine Transporter in Shigella. PLoS ONE 10:e0136744

Campilongo R, Di Martino ML, Marcocci L, Pietrangeli P, Leuzzi A, Grossi M, Casalino M, Nicoletti M, Micheli G, Colonna B, Prosseda G. (2014). Molecular and functional profiling of the polyamine content in enteroinvasive E. coli: looking into the gap between commensal E. coli and harmful Shigella. PLos ONE 9:e106589

Di Martino ML, Campilongo R, Casalino M, Micheli G, Colonna B, Prosseda G. (2013). Polyamines: Emerging players in bacteria-host interactions. Int J Med Microbiol. 303:484-491

Prosseda G, Di Martino ML, Campilongo R, Fioravanti R, Micheli G, Casalino M, Colonna B. (2012). Shedding of genes that interfere with the pathogenic lifestyle: the Shigella model. Res Microbiol. 163:399-406

Prosseda G., Mazzola A., Di Martino M.L., Tielker D., Micheli G., Colonna B. (2010). A temperature-induced narrow DNA curvature range sustains the maximum activity of a bacterial promoter in vitro. Biochemistry 49:2778-2785

Irene C., Maciariello C., Micheli G., Theis J.F., Newlon C.S., Fabiani L. (2007). DNA elements modulating the KARS12 chromosomal replicator in Kluyveromyces lactis. Mol Genet Genomics 277:287-299

Panelli S., Damiani G., Espen L, Micheli G., Sgaramella V. (2006). Towards the analysis of the genomes of single cells: further characterisation of the multiple displacement amplification. Gene 372:1-7

Prosseda G., Falconi M., Giangrossi M., Gualerzi C.O., Micheli G., Colonna B. (2004). The virF promoter in Shigella: more than just a curved DNA stretch.2004. Mol. Microbiol. 51:523-537

Prosseda G., Falconi M., Nicoletti M., Casalino M., Micheli G., Colonna B. (2002). Histone like proteins and the Shigella invasivity regulon. Res. Microbiol. 153:461-468

Brunetti R.,Prosseda G., Beghetto E., Colonna B., Micheli G. (2001). The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains. Biochimie 83:873-82

Falconi M., Colonna B., Prosseda G., Micheli G., Gualerzi C.O. (1998). Thermoregulation of Shigella and Escherichia coli EIEC pathogenicity. A temperature-dependent structural transition od DNA modulates accessibility of virF promoter to transcriptional repressor H-NS. EMBO J. 17:7033-7043

Prosseda G., Fradiani P.A., Di Lorenzo M., Falconi M., Micheli G., Casalino M., Nicoletti M., Colonna B. (1998). A role for H-NS in the regulation of the virF gene of Shigella and enteroinvasive Escherichia coli. Res. Microbiol. 149:15-25

Ghelardini P, Liebart J.C., Di Zenzo G., Micheli G., D'Ari R., Paolozzi L. (1994). A novel illegitimate recombination event: precise excision and reintegration with the Mu gem mutant prophage. Mol. Microbiol. 13:709-718

Steinkühler C, Carrì MT, Micheli G, Knoepfel L, Weser U, Rotilio G. (1994). Copper-dependent metabolism of Cu, Zn-superoxide dismutase in human K562 cells. Lack of specific transcriptional activation and accumulation of a partially inactivated enzyme. Biochemical Journal 302 (Pt 3):687-694

Dente L., Cesareni G., Micheli G., Felici F., Folgori A., Luzzago A., Monaci P., Nicosia A., Delmastro P. (1994). Monoclonal antibodies that recognise filamentous phage: tools for phage display technology. Gene 148:7-13

Carrì MT, Steinküler C, Micheli G, Rotilio G. (1994). Study on the regulation of Cu, Zn SOD in response to stress by copper. In: Frontiers of Reactive Oxygen Species in Biology and Medicine (Asada K, Yoshikawa T. eds), p.291-292, Elsevier Science B.V.

Micheli G., Ciofi Luzzatto A.R., Carrì M.T., de Capoa A., Peliccia F. (1993). Chromosome length and DNA loop size dur ing early embryonic development of Xenopus laevis. Chromosoma 102:478-483

Colonna B., Bernardini M.L., Micheli G., Maimone F., Nicoletti M., Casalino M. (1989). Antibiotic resistance transposons on a virulence plasmid from Salmonella wien. J. Chemother.1, 313-314.

Colonna B., Bernardini M.L., Micheli G., Maimone F., Nicoletti M., Casalino M. (1988). The Salmonella wien virulence plasmid pZM3 carries Tn1935, a multiresistance transposon containing a composite IS1936-kanamycin resistance element. Plasmid 20:221-231.

Amaldi F, Bertolini B, Carrì MT, Hassan G, Micheli G. (1987) In ricordo di Mario buongiorno-nardelli 1937–1983. Italian Journal of Zoology (formerly: Bollettino di Zoologia) 54:91-93

Carrì M.T., Micheli G., Graziano E., Pace T., Buongiorno-Nardelli M. (1986). The relationship between chromosomal origins of replication and the nuclear matrix during the cell cycle. Exp. Cell Res. 164:426-436.

Brunori M., Condò S., Bellelli A., Giardina B., Micheli G. (1985). Tadpole Xenopus laevis hemoglobin. Correlation between stucture and functional properties. J. Mol. Biol. 181:327-329.

Guardiola J, Grimaldi G, Costantino P, Micheli G, Cervone F (1982). Loss of Nitrofuran Resistance in Fusarium oxysporum is Correlated with Loss of a 46.7 kb Circular DNA Molecule. Microbiology (formerly: Journal of General Microbiology) 128:2235-2242

Buongiorno-Nardelli M., Micheli G., Carrì M.T., Marilley M. (1982). A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. Nature 298:100-102.

Micheli G., Baldari C.T., Carrì M.T., Di Cello G., Buongiorno-Nardelli M. (1982). An electron microscope study of chromosomal DNA replication in different eukaryotic systems. Exp. Cell Res. 137:127-140.

Costantino P., Mauro M.L., Micheli G., Risuleo G., Hooykaas P.J.J., Schilperoort R. (1981). Fingerprinting and sequence homology of plasmids from different virulent strains of Agrobacterium rhizogenes. Plasmid 5:170-182.

Buongiorno-Nardelli M, MicheliG, Amaldi F, Baldari CT, Bozzoni I (1980). Electron microscopic analysis of DNA replication in eukaryotes. Italian Journal of Zoology (formerly: Bollettino di Zoologia) 47:253-261

Mauro M.L., Micheli G. (1979). DNA reassociation kinetics in diploid and phylogenetically tetraploid cyprinidae. J. Exp. Zool. 208:407-415.


Gianni Prosseda, Bianca Colonna and Giorgio Camilloni (Dept. Biology & Biotechnology, Univ. Sapienza, Rome, Italy)

 

Personal homepage (additional information on the research activity as well as on the TEM/AFM molecular microscopy unit, and a constantly updated list of publications): http://www.gmicheli.net

Bilbiometric information pages:
- Google Scholar
- OrchidID
- ScopusAuthorID
- ResearchGate
- ResearcherID

Upon getting my degree in Biology in 1980 at the University of Rome (Italy) with an EM study of DNA replication intermediates in eukaryotes, I spent a research period with my thesis supervisor, Prof. M. Buongiorno‑Nardelli, at the Institute of Histology and Embriology of the University of Rome working on the nuclear compartmentalization of DNA replication.Successively, in Prof. R. Weber’s laboratory at the University of Bern (Switzerland), I was involved in studies on the transcriptional regulation of amphibian globin genes. Since 1984 I have been a staff scientist of the Italian National Research Council working at the IBPM, where I have been a member of the lab's Advisory Board from 2009 to 2012. In 1995 I have worked as visiting scientist in Carlos Bustamante’s laboratory at the University of Oregon in Eugene (USA), studying structural aspects of DNA and metaphase chromosomes by means of atomic force microscopy. Over the years of my scientific career my major research interest has been in issues connected to 3D genome organization and, more in general, to the structure-function relationships in supramolecular architectures of biological interest.  At IBPM I have also supervised the local TEM/AFM molecular microscopy resource.  I have been active as peer reviewer for international scientific journals and, since 2008, I have operated as expert in the evaluation of EC FP7 and H2020 projects. My home page (www.gmicheli.net) hosts further information on my activity.
Following retirement (Nov. 1st 2020) I am no longer involved in wet-bench work but I maintain a strong interest in the above mentoned subjects, mostly in the form of data analysis,review and elaboration, including also the theoretical development of specific approaches and the implementation of software tools.