You need JavaScript to view this

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

Abstract

Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation. (review article)
Authors:
Benza, Vincenzo G; [1]  Bassetti, Bruno; [2]  Dorfman, Kevin D; [3]  Scolari, Vittore F; Lagomarsino, Marco Cosentino; [4]  Bromek, Krystyna; Cicuta, Pietro [5] 
  1. Dipartimento di Fisica e Matematica, Universita dell'Insubria, Como (Italy)
  2. Universita degli Studi di Milano, Dip. Fisica, Via Celoria 16, 20133 Milano (Italy)
  3. Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 (United States)
  4. CNRS, UMR 7238 'Microorganism Genomics', Genomic Physics Group (France)
  5. Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE (United Kingdom)
Publication Date:
Jul 15, 2012
Product Type:
Journal Article
Resource Relation:
Journal Name: Reports on Progress in Physics; Journal Volume: 75; Journal Issue: 7; Other Information: Country of input: International Atomic Energy Agency (IAEA)
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; 60 APPLIED LIFE SCIENCES; BIOPHYSICS; CHROMOSOMES; COMPLEMENT; MATTER; MICROSCOPY; POLYMERS; SPECTRA; STATISTICS; TIME RESOLUTION; TRANSCRIPTION
OSTI ID:
22041716
Country of Origin:
United Kingdom
Language:
English
Other Identifying Numbers:
Journal ID: ISSN 0034-4885; CODEN: RPPHAG; TRN: GB12P9413001169
Availability:
Available from http://dx.doi.org/10.1088/0034-4885/75/7/076602
Submitting Site:
INIS
Size:
[20 page(s)]
Announcement Date:
Feb 08, 2013

Citation Formats

Benza, Vincenzo G, Bassetti, Bruno, Dorfman, Kevin D, Scolari, Vittore F, Lagomarsino, Marco Cosentino, Bromek, Krystyna, and Cicuta, Pietro. Physical descriptions of the bacterial nucleoid at large scales, and their biological implications. United Kingdom: N. p., 2012. Web. doi:10.1088/0034-4885/75/7/076602.
Benza, Vincenzo G, Bassetti, Bruno, Dorfman, Kevin D, Scolari, Vittore F, Lagomarsino, Marco Cosentino, Bromek, Krystyna, & Cicuta, Pietro. Physical descriptions of the bacterial nucleoid at large scales, and their biological implications. United Kingdom. doi:10.1088/0034-4885/75/7/076602.
Benza, Vincenzo G, Bassetti, Bruno, Dorfman, Kevin D, Scolari, Vittore F, Lagomarsino, Marco Cosentino, Bromek, Krystyna, and Cicuta, Pietro. 2012. "Physical descriptions of the bacterial nucleoid at large scales, and their biological implications." United Kingdom. doi:10.1088/0034-4885/75/7/076602. https://www.osti.gov/servlets/purl/10.1088/0034-4885/75/7/076602.
@misc{etde_22041716,
title = {Physical descriptions of the bacterial nucleoid at large scales, and their biological implications}
author = {Benza, Vincenzo G, Bassetti, Bruno, Dorfman, Kevin D, Scolari, Vittore F, Lagomarsino, Marco Cosentino, Bromek, Krystyna, and Cicuta, Pietro}
abstractNote = {Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation. (review article)}
doi = {10.1088/0034-4885/75/7/076602}
journal = {Reports on Progress in Physics}
issue = {7}
volume = {75}
journal type = {AC}
place = {United Kingdom}
year = {2012}
month = {Jul}
}