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Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating...
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Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 22842

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Dr. Vic Norris

E-Mail Website
Guest Editor
Theoretical Biology Unit, EA 4312, University of Rouen, 76821 Mont-Saint-Aignan, France
Interests: integrative approaches to the bacterial cell cycle, origins of life; biotechnology; systems biology
Prof. Dr. Arieh Zaritsky

E-Mail Website1 Website2
Guest Editor
Ben-Gurion University of the Negev, Life/Natural Sciences, Be’er-Sheva, Israel
Interests: Bacterial Cell-Cycle Physiology; Biological Control of Insect Pests

Special Issue Information

Dear Colleagues,

Understanding the bacterial cell cycle is fundamental to understanding the physiology of the cell and, hence, to all the fields that depend on microbial physiology, such as clinical microbiology, industrial biotechnology, the origins of life, xenobiology, environmental microbiology, and synthetic biology.

Charles E. Helmstetter is widely acknowledged as the person who provided the experimental and theoretical bases for our understanding of the bacterial cell cycle. Indeed, the ensemble of his ingenious investigations, designed and performed by himself from the 1960s to the end of the century, is considered to have defined the field, which is exceptional in science.

A group of specialists in this field collaborated to create The Charles E Helmstetter Prize for Groundbreaking Research in Bacterial Cell Cycle Physiology. The Prize will be awarded every two years. The aim of the present Special Issue is to celebrate the The Charles E Helmstetter Prize in 2022. The first three recipients have been selected and will be awarded the Prize in the opening session of the EMBO Workshop “Bacterial cell biophysics: DNA replication, growth, division, size and shape” https://meetings.embo.org/event/22-bacteria-biophysics, to be held in Israel, 11–15 December 2022.

The first session of this workshop (entitled "Bacterial Physiology Comes of Age at 60") will be devoted to the Prize, to the achievements of Dr. Helmstetter and the three laureates, and to the implications stemming from their pioneering investigations. A number of scientists in the field, selected for their relationships to Helmstetter and his work, have been invited to contribute chapters; other colleagues are also welcome to submit relevant chapters.

Prof. Dr. Vic Norris
Prof. Dr. Arieh Zaritsky
Guest Editors

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Keywords

  • synchrony for bacterial cell cycle
  • DNA replication and I-BCD periods
  • cell dimensions, orisome, replisome and divisome
  • overlapping rounds of replication
  • nucleoid structure and membrane domains
  • cell variability and individuality
  • thymine limitation, unbalanced growth, and thymine-less death

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Published Papers (12 papers)

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Editorial

Jump to: Research, Review, Other

5 pages, 734 KiB  
Editorial
Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022
by Vic Norris and Arieh Zaritsky
Life 2023, 13(12), 2260; https://doi.org/10.3390/life13122260 - 27 Nov 2023
Cited by 2 | Viewed by 900
Abstract
This Special Issue celebrates the creation of the Charles E [...] Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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4 pages, 556 KiB  
Editorial
The Birth of the Copenhagen School: Personal Recollections at the EMBO Workshop on Bacterial Growth Physiology, 2022
by Moselio Schaechter
Life 2023, 13(12), 2235; https://doi.org/10.3390/life13122235 - 21 Nov 2023
Cited by 1 | Viewed by 890
Abstract
The future of bacterial growth physiology is shining more brightly than ever [...] Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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Research

Jump to: Editorial, Review, Other

17 pages, 2430 KiB  
Article
The Replicative DnaE Polymerase of Bacillus subtilis Recruits the Glycolytic Pyruvate Kinase (PykA) When Bound to Primed DNA Templates
by Alexandria Holland, Matthaios Pitoulias, Panos Soultanas and Laurent Janniere
Life 2023, 13(4), 965; https://doi.org/10.3390/life13040965 - 7 Apr 2023
Cited by 3 | Viewed by 3113
Abstract
The glycolytic enzyme PykA has been reported to drive the metabolic control of replication through a mechanism involving PykA moonlighting functions on the essential DnaE polymerase, the DnaC helicase and regulatory determinants of PykA catalytic activity in Bacillus subtilis. The mutants of [...] Read more.
The glycolytic enzyme PykA has been reported to drive the metabolic control of replication through a mechanism involving PykA moonlighting functions on the essential DnaE polymerase, the DnaC helicase and regulatory determinants of PykA catalytic activity in Bacillus subtilis. The mutants of this control suffer from critical replication and cell cycle defects, showing that the metabolic control of replication plays important functions in the overall rate of replication. Using biochemical approaches, we demonstrate here that PykA interacts with DnaE for modulating its activity when the replication enzyme is bound to a primed DNA template. This interaction is mediated by the CAT domain of PykA and possibly allosterically regulated by its PEPut domain, which also operates as a potent regulator of PykA catalytic activity. Furthermore, using fluorescence microscopy we show that the CAT and PEPut domains are important for the spatial localization of origins and replication forks, independently of their function in PykA catalytic activity. Collectively, our data suggest that the metabolic control of replication depends on the recruitment of PykA by DnaE at sites of DNA synthesis. This recruitment is likely highly dynamic, as DnaE is frequently recruited to and released from replication machineries to extend the several thousand RNA primers generated from replication initiation to termination. This implies that PykA and DnaE continuously associate and dissociate at replication machineries for ensuring a highly dynamic coordination of the replication rate with metabolism. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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Review

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22 pages, 700 KiB  
Review
Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle
by Masamichi Kohiyama, John Herrick and Vic Norris
Life 2023, 13(9), 1890; https://doi.org/10.3390/life13091890 - 10 Sep 2023
Cited by 4 | Viewed by 1850
Abstract
The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, [...] Read more.
The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, alias large assemblies of molecules and macromolecules that perform a function. In these dynamics, hyperstructures can (1) emit and receive signals or (2) fuse and separate from one another. We ask whether the DnaA-based initiation hyperstructure acts as a logic gate receiving information from the membrane, the chromosome, and metabolism to trigger replication; we try to phrase some of these questions in terms of DNA supercoiling, strand opening, glycolytic enzymes, SeqA, ribonucleotide reductase, the macromolecular synthesis operon, post-translational modifications, and metabolic pools. Finally, we ask whether, underpinning the regulation of the cell cycle, there is a physico-chemical clock inherited from the first protocells, and whether this clock emits a single signal that triggers both chromosome replication and cell division. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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47 pages, 17635 KiB  
Review
Molecular Cytology of ‘Little Animals’: Personal Recollections of Escherichia coli (and Bacillus subtilis)
by Nanne Nanninga
Life 2023, 13(8), 1782; https://doi.org/10.3390/life13081782 - 21 Aug 2023
Cited by 2 | Viewed by 1518
Abstract
This article relates personal recollections and starts with the origin of electron microscopy in the sixties of the previous century at the University of Amsterdam. Novel fixation and embedding techniques marked the discovery of the internal bacterial structures not visible by light microscopy. [...] Read more.
This article relates personal recollections and starts with the origin of electron microscopy in the sixties of the previous century at the University of Amsterdam. Novel fixation and embedding techniques marked the discovery of the internal bacterial structures not visible by light microscopy. A special status became reserved for the freeze-fracture technique. By freeze-fracturing chemically fixed cells, it proved possible to examine the morphological effects of fixation. From there on, the focus switched from bacterial structure as such to their cell cycle. This invoked bacterial physiology and steady-state growth combined with electron microscopy. Electron-microscopic autoradiography with pulses of [3H] Dap revealed that segregation of replicating DNA cannot proceed according to a model of zonal growth (with envelope-attached DNA). This stimulated us to further investigate the sacculus, the peptidoglycan macromolecule. In particular, we focused on the involvement of penicillin-binding proteins such as PBP2 and PBP3, and their role in division. Adding aztreonam (an inhibitor of PBP3) blocked ongoing divisions but not the initiation of new ones. A PBP3-independent peptidoglycan synthesis (PIPS) appeared to precede a PBP3-dependent step. The possible chemical nature of PIPS is discussed. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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13 pages, 3134 KiB  
Review
Recollections of a Helmstetter Disciple
by Alan C. Leonard
Life 2023, 13(5), 1114; https://doi.org/10.3390/life13051114 - 30 Apr 2023
Cited by 1 | Viewed by 1443
Abstract
Nearly fifty years ago, it became possible to construct E. coli minichromosomes using recombinant DNA technology. These very small replicons, comprising the unique replication origin of the chromosome oriC coupled to a drug resistance marker, provided new opportunities to study the regulation of [...] Read more.
Nearly fifty years ago, it became possible to construct E. coli minichromosomes using recombinant DNA technology. These very small replicons, comprising the unique replication origin of the chromosome oriC coupled to a drug resistance marker, provided new opportunities to study the regulation of bacterial chromosome replication, were key to obtaining the nucleotide sequence information encoded into oriC and were essential for the development of a ground-breaking in vitro replication system. However, true authenticity of the minichromosome model system required that they replicate during the cell cycle with chromosome-like timing specificity. I was fortunate enough to have the opportunity to construct E. coli minichromosomes in the laboratory of Charles Helmstetter and, for the first time, measure minichromosome cell cycle regulation. In this review, I discuss the evolution of this project along with some additional studies from that time related to the DNA topology and segregation properties of minichromosomes. Despite the significant passage of time, it is clear that large gaps in our understanding of oriC regulation still remain. I discuss some specific topics that continue to be worthy of further study. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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12 pages, 12537 KiB  
Review
Fifty-Five Years of Research on B, C and D in Escherichia coli
by Charles E. Helmstetter
Life 2023, 13(4), 977; https://doi.org/10.3390/life13040977 - 10 Apr 2023
Cited by 2 | Viewed by 1736
Abstract
The basic properties of the Escherichia coli duplication process can be defined by two time periods: C, the time for a round of chromosome replication, and D, the time between the end of a round of replication and cell division. Given [...] Read more.
The basic properties of the Escherichia coli duplication process can be defined by two time periods: C, the time for a round of chromosome replication, and D, the time between the end of a round of replication and cell division. Given the durations of these periods, the pattern of chromosome replication during the cell cycle can be determined for cells growing with any doubling time. In the 55 years since these parameters were identified, there have been numerous investigations into their durations and into the elements that determine their initiations. In this review, I discuss the history of our involvement in these studies from the very beginning, some of what has been learned over the years by measuring the durations of C and D, and what might be learned with additional investigations. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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10 pages, 1645 KiB  
Review
The Bacterial Nucleoid: From Electron Microscopy to Polymer Physics—A Personal Recollection
by Conrad L. Woldringh
Life 2023, 13(4), 895; https://doi.org/10.3390/life13040895 - 28 Mar 2023
Cited by 5 | Viewed by 2796
Abstract
In the 1960s, electron microscopy did not provide a clear answer regarding the compact or dispersed organization of the bacterial nucleoid. This was due to the necessary preparation steps of fixation and dehydration (for embedding) and freezing (for freeze-fracturing). Nevertheless, it was possible [...] Read more.
In the 1960s, electron microscopy did not provide a clear answer regarding the compact or dispersed organization of the bacterial nucleoid. This was due to the necessary preparation steps of fixation and dehydration (for embedding) and freezing (for freeze-fracturing). Nevertheless, it was possible to measure the lengths of nucleoids in thin sections of slow-growing Escherichia coli cells, showing their gradual increase along with cell elongation. Later, through application of the so-called agar filtration method for electron microscopy, we were able to perform accurate measurements of cell size and shape. The introduction of confocal and fluorescence light microscopy enabled measurements of size and position of the bacterial nucleoid in living cells, inducing the concepts of “nucleoid occlusion” for localizing cell division and of “transertion” for the final step of nucleoid segregation. The question of why the DNA does not spread throughout the cytoplasm was approached by applying polymer-physical concepts of interactions between DNA and proteins. This gave a mechanistic insight in the depletion of proteins from the nucleoid, in accordance with its low refractive index observed by phase-contrast microscopy. Although in most bacterial species, the widely conserved proteins of the ParABS-system play a role in directing the segregation of newly replicated DNA strands, the basis for the separation and opposing movement of the chromosome arms was proposed to lie in preventing intermingling of nascent daughter strands already in the early replication bubble. E. coli, lacking the ParABS system, may be suitable for investigating this basic mechanism of DNA strand separation and segregation. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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Other

5 pages, 465 KiB  
Hypothesis
The Nordström Question
by William D. Donachie
Life 2023, 13(7), 1442; https://doi.org/10.3390/life13071442 - 26 Jun 2023
Cited by 1 | Viewed by 1174
Abstract
It is suggested that the absolute dimensions of cells of Escherichia coli may be set by the separation distance between newly completed sister nucleoids. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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11 pages, 1371 KiB  
Opinion
The Quantification of Bacterial Cell Size: Discrepancies Arise from Varied Quantification Methods
by Qian’andong Cao, Wenqi Huang, Zheng Zhang, Pan Chu, Ting Wei, Hai Zheng and Chenli Liu
Life 2023, 13(6), 1246; https://doi.org/10.3390/life13061246 - 24 May 2023
Cited by 1 | Viewed by 2309
Abstract
The robust regulation of the cell cycle is critical for the survival and proliferation of bacteria. To gain a comprehensive understanding of the mechanisms regulating the bacterial cell cycle, it is essential to accurately quantify cell-cycle-related parameters and to uncover quantitative relationships. In [...] Read more.
The robust regulation of the cell cycle is critical for the survival and proliferation of bacteria. To gain a comprehensive understanding of the mechanisms regulating the bacterial cell cycle, it is essential to accurately quantify cell-cycle-related parameters and to uncover quantitative relationships. In this paper, we demonstrate that the quantification of cell size parameters using microscopic images can be influenced by software and by the parameter settings used. Remarkably, even if the consistent use of a particular software and specific parameter settings is maintained throughout a study, the type of software and the parameter settings can significantly impact the validation of quantitative relationships, such as the constant-initiation-mass hypothesis. Given these inherent characteristics of microscopic image-based quantification methods, it is recommended that conclusions be cross-validated using independent methods, especially when the conclusions are associated with cell size parameters that were obtained under different conditions. To this end, we presented a flexible workflow for simultaneously quantifying multiple bacterial cell-cycle-related parameters using microscope-independent methods. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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6 pages, 187 KiB  
Perspective
Unbalanced Growth, the DNA Replication Cycle and Discovery of Repair Replication
by Philip C. Hanawalt
Life 2023, 13(4), 1052; https://doi.org/10.3390/life13041052 - 20 Apr 2023
Viewed by 2166
Abstract
This article recounts my graduate research at Yale University (1954–1958) on unbalanced growth in Eschericia coli during thymine deprivation or following ultraviolet (UV) irradiation, with early evidence for the repair of UV-induced DNA damage. Follow-up studies in Copenhagen (1958–1960) in the laboratory of [...] Read more.
This article recounts my graduate research at Yale University (1954–1958) on unbalanced growth in Eschericia coli during thymine deprivation or following ultraviolet (UV) irradiation, with early evidence for the repair of UV-induced DNA damage. Follow-up studies in Copenhagen (1958–1960) in the laboratory of Ole Maaløe led to my discovery that the DNA replication cycle can be synchronized by inhibiting protein and RNA syntheses and that an RNA synthesis step is essential for initiation of the cycle, but not for its completion. This work set the stage for my subsequent research at Stanford University, where the repair replication of damaged DNA was documented, to provide compelling evidence for an excision-repair pathway. That universal pathway validates the requirement for the redundant information in the complementary strands of duplex DNA to ensure genomic stability. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
8 pages, 1082 KiB  
Opinion
Extending Validity of the Bacterial Cell Cycle Model through Thymine Limitation: A Personal View
by Arieh Zaritsky
Life 2023, 13(4), 906; https://doi.org/10.3390/life13040906 - 29 Mar 2023
Cited by 1 | Viewed by 1446
Abstract
The contemporary view of bacterial physiology was established in 1958 at the “Copenhagen School”, culminating a decade later in a detailed description of the cell cycle based on four parameters. This model has been subsequently supported by numerous studies, nicknamed BCD (The Bacterial [...] Read more.
The contemporary view of bacterial physiology was established in 1958 at the “Copenhagen School”, culminating a decade later in a detailed description of the cell cycle based on four parameters. This model has been subsequently supported by numerous studies, nicknamed BCD (The Bacterial Cell-Cycle Dogma). It readily explains, quantitatively, the coupling between chromosome replication and cell division, size and DNA content. An important derivative is the number of replication positions n, the ratio between the time C to complete a round of replication and the cell mass doubling time τ; the former is constant at any temperature and the latter is determined by the medium composition. Changes in cell width W are highly correlated to n through the equation for so-called nucleoid complexity NC (=(2n − 1)/(ln2 × n)), the amount of DNA per terC (i.e., chromosome) in genome equivalents. The narrow range of potential n can be dramatically extended using the method of thymine limitation of thymine-requiring mutants, which allows a more rigorous testing of the hypothesis that the nucleoid structure is the primary source of the signal that determines W during cell division. How this putative signal is relayed from the nucleoid to the divisome is still highly enigmatic. The aim of this Opinion article is to suggest the possibility of a new signaling function for nucleoid DNA. Full article
(This article belongs to the Special Issue Novel Principles and Methods in Bacterial Cell Cycle Physiology: Celebrating the Charles E. Helmstetter Prize in 2022)
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