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.

Physical descriptions of the bacterial nucleoid at large scales, and their biological implications / V.G. Benza, B. Bassetti, K.D. Dorfman, V.F. Scolari, K. Bromek, P. Cicuta, M. Cosentino Lagomarsino. - In: REPORTS ON PROGRESS IN PHYSICS. - ISSN 0034-4885. - 75:7(2012), pp. 1-20.

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

B. Bassetti;M. Cosentino Lagomarsino
2012

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.
Escherichia-coli chromosome; separte cell halves; single DNA-molecules; gene-expressio; H-NS; spatial-organization; RNA-polymerase; architectural role; dynamic structure; protein fis
Settore FIS/02 - Fisica Teorica, Modelli e Metodi Matematici
Settore FIS/03 - Fisica della Materia
Settore BIO/11 - Biologia Molecolare
Settore BIO/18 - Genetica
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/658004
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