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Fundamental Principles in Bacterial Physiology - History, Recent progress, and the Future with Focus on Cell Size Control: A Review

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Abstract

Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (Sections 1 to 3), we review the first `golden era' of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (Sections 4 to 7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, Section 4 presents the history and current progress of the `adder' principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome `sectors' re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final Section 8, we conclude by discussing the remaining challenges for the future in the field.
Fundamental Principles in Bacterial Physiology -
History, Recent progress, and the Future with
Focus on Cell Size Control: A Review
Suckjoon Jun
Department of Physics, University of California San Diego, 9500 Gilman Dr, La
Jolla, CA 92093, USA
Section of Molecular Biology, Division of Biology, University of California San
Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
E-mail: suckjoon.jun@gmail.com
Fangwei Si
Department of Physics, University of California San Diego, 9500 Gilman Dr, La
Jolla, CA 92093, USA
E-mail: fsi@physics.ucsd.edu
Rami Pugatch
Department of Industrial Engineering and Management, Ben-Gurion University
of the Negev, Beer-Sheva 8410501, Israel
E-mail: rpugatch@bgu.ac.il
Matthew Scott
Department of Applied Mathematics, University of Waterloo, 200 University
Ave West, Waterloo, Ontario N2L 3G1, Canada
E-mail: mscott@uwaterloo.ca
Abstract. Bacterial physiology is a branch of biology that aims to understand
overarching principles of cellular reproduction. Many important issues in bacterial
physiology are inherently quantitative, and major contributors to the field have
often brought together tools and ways of thinking from multiple disciplines.
This article presents a comprehensive overview of major ideas and approaches
developed since the early 20th century for anyone who is interested in the
fundamental problems in bacterial physiology. This article is divided into two
parts. In the first part (Sections 1 to 3), we review the first ‘golden era’ of bacterial
physiology from the 1940s to early 1970s and provide a complete list of major
references from that period. In the second part (Sections 4 to 7), we explain how
the pioneering work from the first golden era has influenced various rediscoveries
of general quantitative principles and significant further development in modern
bacterial physiology. Specifically, Section 4 presents the history and current
progress of the ‘adder’ principle of cell size homeostasis. Section 5 discusses
the implications of coarse-graining the cellular protein composition, and how the
coarse-grained proteome ‘sectors’ re-balance under different growth conditions.
Section 6 focuses on physiological invariants, and explains how they are the key
to understanding the coordination between growth and the cell cycle underlying
cell size control in steady-state growth. Section 7 overviews how the temporal
organization of all the internal processes enables balanced growth. In the final
Section 8, we conclude by discussing the remaining challenges for the future in
the field.
arXiv:1712.00194v1 [q-bio.CB] 1 Dec 2017
Fundamental principles in bacterial physiology 2
Contents
1 Introduction 2
1.1 Prologue.................. 2
1.2 Major questions in bacterial physiology 3
2 The first golden era of bacterial physiol-
ogy (late 1940s - early 1970s) 5
2.1 Part I: Key technology development and
experiments . . . . . . . . . . . . . . . . 7
2.2 Part II: Major models and conceptual
advancements . . . . . . . . . . . . . . . 12
2.3 1970s - 1990s: the age of molecular and
cell biology . . . . . . . . . . . . . . . . 26
2.4 2000s - present: Back to the origin . . . 30
3 Variability and single-cell physiology 31
3.1 Non-equilibrium statistical mechanics
formalism for size control . . . . . . . . 31
3.2 Size control models: sizer and timer . . 33
3.3 The genius of Arthur Koch: how
mathematical insight led to biological
insight, and vice versa . . . . . . . . . . 35
4 Adder as a new phenomenological paradigm
of cell size homeostasis 36
4.1 History of adder . . . . . . . . . . . . . 37
4.2 Mother machine, single-cell growth ex-
periments, data, and choice of control
parameters . . . . . . . . . . . . . . . . 38
4.3 Modeling the adder . . . . . . . . . . . . 38
4.4 Collapse of the probability distributions
and scaling forms . . . . . . . . . . . . . 43
4.5 Other models proposed for the origin
of the adder and the consideration of
chromosome replication . . . . . . . . . 45
4.6 Control of variability (“noise”) and
hierarchy of physiological controls . . . . 45
4.7 Spatial regulation: when absolute size
matters .................. 46
5 Modern bacterial physiology, Part I:
proteome ‘sectors’ 47
5.1 Proteome partitioning constraints on
gene expression . . . . . . . . . . . . . . 47
5.2 Ohmics: Electrical circuit analogies for
proteome constraints . . . . . . . . . . . 49
6 Modern bacterial physiology, Part II: The
fundamental unit of cell size and the
general growth law 52
6.1 General challenges in approaching cell
size control with intensive parameters . 53
6.2 Size tautology and the origin of the
nutrient growth law . . . . . . . . . . . 54
6.3 Decoupling the canonical processes in E.
coli..................... 55
6.4 How do the canonical processes respond
to general physiological perturbations? . 56
6.5 Unit cell: the fundamental unit of cell
size in bacteria . . . . . . . . . . . . . . 57
6.6 Remaining challenges . . . . . . . . . . . 58
6.7 Summary ................. 58
7 Modern bacterial physiology, Part III:
The cell as a factory 59
7.1 History of the self-replicating factory
concept .................. 60
7.2 The transcription-translation machinery—
a realization of the universal constructor 61
7.3 Concurrency in self-replication . . . . . 61
7.4 The cell as a self-replicating queuing
network .................. 64
7.5 A simplified model for biomass growth . 65
7.6 Coordinating DNA replication with
biomass growth . . . . . . . . . . . . . . 67
7.7 Hinshelwood and then Koch’s model of
the cell as a simple autocatalytic cycle . 67
7.8 Non-Markovian model for the Hinshel-
woodcycle ................ 68
7.9 Summary ................. 68
8 Future 68
8.1 Towards “Control laws” . . . . . . . . . 69
8.2 Non-equilibrium thermodynamics of liv-
ingsystems ................ 69
8.3 Issues on the variability and causality of
physiological controls . . . . . . . . . . . 70
8.4 Evolution of physiological controls . . . 70