biology

Review
Bacterial Subcellular Architecture, Structural Epistasis, and
Antibiotic Resistance
Fernando Baquero 1,2, * , José-Luis Martínez 3 , Alvaro Sánchez 3 , Miguel D. Fernández-de-Bobadilla 1,4 ,
Alvaro San-Millán 3,4 and Jerónimo Rodríguez-Beltrán 1,4

1 Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health
Research (IRYCIS), 28034 Madrid, Spain; [email protected] (M.D.F.-d.-B.);
[email protected] (J.R.-B.)
2 CIBER en Epidemiología y Salud Pública (CIBERESP), 28034 Madrid, Spain
3 Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; [email protected] (J.-L.M.);
[email protected] (A.S.); [email protected] (A.S.-M.)
4 CIBER en Enfermedades Infecciosas (CIBERINFECT), 28034 Madrid, Spain
* Correspondence: [email protected]

Simple Summary: The concept of “structural epistasis” expresses the emergence of new phenotypes
which are not based on changes in the products and functions of genes, but on the changes in the
physical–mechanical interactions between biological structural pieces and components of the bacterial
cell architecture. These interactions are fostered by primary physical changes in the shape and size of
the pieces or in spatial (topological) alterations driven by changes in their quantity or local density of
the cell compartments, and might have consequences on antibiotic resistance phenotypes.

Abstract: Epistasis refers to the way in which genetic interactions between some genetic loci affect
phenotypes and fitness. In this study, we propose the concept of “structural epistasis” to emphasize
the role of the variable physical interactions between molecules located in particular spaces inside the
bacterial cell in the emergence of novel phenotypes. The architecture of the bacterial cell (typically
Gram-negative), which consists of concentrical layers of membranes, particles, and molecules with
differing configurations and densities (from the outer membrane to the nucleoid) determines and
Citation: Baquero, F.; Martínez, J.-L.; is in turn determined by the cell shape and size, depending on the growth phases, exposure to
Sánchez, A.; Fernández-de-Bobadilla,
toxic conditions, stress responses, and the bacterial environment. Antibiotics change the bacterial
M.D.; San-Millán, A.;
cell’s internal molecular topology, producing unexpected interactions among molecules. In contrast,
Rodríguez-Beltrán, J. Bacterial
changes in shape and size may alter antibiotic action. The mechanisms of antibiotic resistance (and
Subcellular Architecture, Structural
Epistasis, and Antibiotic Resistance.
their vectors, as mobile genetic elements) also influence molecular connectivity in the bacterial cell
Biology 2023, 12, 640. https:// and can produce unexpected phenotypes, influencing the action of other antimicrobial agents.
doi.org/10.3390/biology12050640
Keywords: bacterial Gram-negative subcellular architecture; structural epistasis; cellular shape and
Academic Editor: Thomas Caspari
volume; antibiotic mode of action; antibiotic resistance
Received: 16 March 2023
Revised: 8 April 2023
Accepted: 20 April 2023
Published: 23 April 2023 1. Introduction
Etymologically, the term “epistasis” means the “act of stopping” (any “on–off” action)
and can be applied to the case where a mutation influences the effect of other mutations,
in a specific or unspecific and less evolutionarily stable manner [1,2]. Epistasis is also a
Copyright: © 2023 by the authors.
phenomenon in which one or more genes influence the function of others. The related term
Licensee MDPI, Basel, Switzerland.
“epigenetics” refers to studies “above the gene” and the heritable (reproducible) changes
This article is an open access article
in gene function that cannot be explained by DNA sequence mutations [3]. In both cases,
distributed under the terms and
conditions of the Creative Commons
the organism exhibits a function that cannot be fully explained by the sequence of a single
Attribution (CC BY) license (https://
gene. The most classic cases of epistasis rely on the interconnection of regulatory networks.
creativecommons.org/licenses/by/ For instance, a mutation that alters the concentration of a metabolite that regulates the
4.0/). expression of other metabolic routes may deeply alter the bacterial physiology, thereby

Biology 2023, 12, 640. https://doi.org/10.3390/biology12050640 https://www.mdpi.com/journal/biology

Biology 2023, 12, 640 2 of 14

modifying the activities of other genes/proteins. Examples of this include the modification
of the physiology of antibiotic-resistant mutants [4,5] or the various evolutionary pathways
toward resistance that bacteria with differing genomic backgrounds can follow, which is an
example of historical contingency [6]. However, these regulatory and functional alterations
can have an important structural role, a feature largely underexplored.
In general, and in the abovementioned epistatic examples, a phenotype is the result
of the interconnected functions of an ensemble of genes (not necessarily linked), as in the
case of an operon encoding for antibiotic resistance, or in biosynthetic pathways. In the
last case, however, the function of each involved gene is autonomous and specific; for
instance, encoding an enzyme needed for a particular biochemical reaction. The operational
molecules involved in epistasis are the products of interacting genes: proteins interact
with other proteins, small molecules or nucleic acids. In Escherichia coli, the concentration
of these macromolecules can exceed 300 g/L, occupying approximately 30% of the cell
volume [7,8].
In population genetics, epistasis refers to how genetic interactions between some
loci affect phenotypes and fitness [9]. The concept of structural epistasis helps explain
the emergence of new phenotypes that are not based on changes in gene function, but
on the physical–mechanical interactions between the biological “structural pieces” or
components of the cell. These interactions result from primary physical changes in the
piece’s shape and size, or in the spatial (topological) alterations driven by changes in their
quantity or local density. This might result in spatial heterogeneities leading to various
cell-to-cell physical interactions, that also have consequences in microbial cell biology.
The term “cell topology” is employed in studies on the structure of tissues, where spatial
heterogeneity might produce differing biological outcomes [10]. Starting about one decade
ago, new technologies have become available to study intracellular topology, as multi-scale
fluorescence cross-correlation spectroscopy [11].
A bacterial cell is composed of complex physical multimolecular objects, which in-
clude: (1) ball-shaped complex structures, such as ribosomes, supercoiled DNA in the
chromosome (forming a nucleoid) or in bacterial plasmids; (2) lamellar structures, such
as the cell wall, membranes or capsules; (3) elongated structures, such as fimbriae and
flagella; (4) complex-shaped functional organelles, ranging from low complexity, such
as porins, to high complexity, such as extrusion pumps, needle-like protein complexes
in the type III secretion system, or trans-envelope flagella machines; and (5) ball-shaped
inclusion bodies, typically water-insoluble protein aggregates or condensates, glycogen
poly-beta-hydroxybutyrate granules, or cyclic polyphosphate inclusions. These complex
structures in the bacterial cytoplasm, and the molecular crowded cytoplasm itself, have
inherent physical properties, such as viscoelasticity [12] or electric charge, which affect their
function [13]. Molecules have both a physical and chemical dimension. For instance, the in-
teraction and function of proteins depends on their tertiary structure, the three-dimensional
arrangement (folding) of its polypeptide chain in space, and on their four-dimensional
(protein-assembly in multimeric proteins) and fifth-dimensional (quinary structure, see
below) structures, ensuring the interactions between macromolecules that organize the
interior of the cell.
Similarly and most importantly, DNA topology influences replication and gene ex-
pression. The bacterial chromosome is a highly structured molecule organized into various
domains (including macrodomains and replichores) showing varying degrees of gene
expression, supercoiling, protein occupancy, and the binding of xenogeneic silencing pro-
teins (e.g., H–NS, histone-like nucleoid-structuring proteins) [14–16]. All these physical
objects are arranged in a physiological intracellular “ecological topology”, understood as
the pattern of interconnections of a molecular network, and based on physical (structural)
properties that vary over time (according to growth phases) and should be tightly regu-
lated [17]. For instance, the cell should manage the encounters between replication and
transcription machineries, given that conflicts between them can lead to genome instability
and reduced fitness [18].
 transcription machineries, given that conflicts between them can lead to genome instab
ity and reduced fitness [18].
Biology 2023, 12, 640 3 of 14
In turn, healthy topology contributes to molecular (e.g., rRNA, proteins, nutrient
mobility and interaction, at times mediated by particular compounds, such as histone-lik
nucleoid-structuring H–NS proteins, which interact with both proteins and DNA [16]. Th
In turn, healthy topology contributes to molecular (e.g., rRNA, proteins, nutrients)
bacterial
mobilitycell
andtherefore
interaction,exhibits a well-controlled
at times mediated spatial
by particular organization,
compounds, with particular d
such as histone-like
grees of flexibility (adaptive
nucleoid-structuring organization)
H–NS proteins, that arewith
which interact beginning to be explored
both proteins and DNA [19,20].
[16]. The
The bacterial cell therefore exhibits a well-controlled spatial organization,
are precedents for such a type of exploration in the morphogenetic studies of the pa with particular
degreesIn
century. of1952,
flexibility
Alan(adaptive organization)
Turing (the godfatherthat are beginning
of modern to be explored
computing) proposed[19,20].
that biolo
There are precedents for such a type of exploration in the morphogenetic studies of the
ical morphogenesis could be explained by an stochastic activator–inhibitory system, th
past century. In 1952, Alan Turing (the godfather of modern computing) proposed that
gives rise to
biological particular organizational
morphogenesis could be explainedpatterns, with modern
by an stochastic modeling studies
activator–inhibitory system, showin
thethat
plausibility of this approach [21]. In the following section, a succinct description
gives rise to particular organizational patterns, with modern modeling studies showing of th
architectural components
the plausibility of the
of this approach bacterial
[21]. cell is presented
In the following (Figuredescription
section, a succinct 1). of the
architectural components of the bacterial cell is presented (Figure 1).

Figure 1. Conceptual illustration of structural epistasis. (Left) Simplified concentrical structure of

a normal Gram-negative bacterium. From the outside to inside, in violet, the bilayer outer membrane
Figure 1. Conceptual illustration of structural epistasis. (Left) Simplified concentrical structure
(OM); in grey, the peptidoglycan; in blue, the bilayer internal membrane (IM); in brown, the ribosome-
a normal Gram-negative bacterium. From the outside to inside, in violet, the bilayer outer mem
dense crown; in red, the nucleoid. Proteins (not represented) are particularly dense among the most
brane (OM); in grey, the peptidoglycan; in blue, the bilayer internal membrane (IM); in brown, t
external layers. Black rectangles illustrate structural connections across layers (for simplicity only four
ribosome-dense crown; in red, the nucleoid. Proteins (not represented) are particularly dense amo
are depicted), successively, OM–IM, IM–ribosomes, ribosomes–nucleoid. Continuous red lines across
thethe
most external layers. Black rectangles illustrate structural connections across layers (for simpl
connections illustrate the integrity of the structure. Physiological changes are not expected to
ityeliminate
only four theare depicted),
concentrical successively,
structure, as duringOM–IM,
division, IM–ribosomes, ribosomes–nucleoid.
new centers are created. Continuo
(Right) A distorted
redcellular
lines structure,
across the connections illustrate the integrity of the structure. Physiological
resulting from exposure to stressful conditions, where the layers are losing their changes a
notnormal
expected to eliminate
connectivity the concentrical
(stars) producing structure,
wider spaces as during
in some areas division,
and narrower new
spaces centersThe
in others. are create
(Right)
result of the architectonical distortion influences the relative molecular interactions (interrupted red where t
A distorted cellular structure, resulting from exposure to stressful conditions,
layers
lines),are losing the
changing their normal
local proteinconnectivity (stars) producing
densities and interactions wider
(see Figure 2). spaces in some areas and na
rower spaces in others. The result of the architectonical distortion influences the relative molecul
interactions (interrupted red lines), changing the local protein densities and interactions (see Figu
2).
Biology 2023, 12, x FOR PEER REVIEW 4 of 14
Biology 2023, 12, 640 4 of 14

Figure 2. Effect of structural distortion in the protein–protein and protein–OM interactions. The
upper2.left
Figure Effectpanel shows a normal
of structural density
distortion in the of protein–protein
the proteins (ovals) andin a structuredinteractions.
protein–OM space; functional
The
connections (double-headed broken arrows) between particular
upper left panel shows a normal density of the proteins (ovals) in a structured space;proteins (light–dark red and light–
functional
dark green)(double-headed
connections occur normally.broken
If the protein
arrows) density
betweeninparticular
very highproteins
(mid left panel), these
(light–dark red interactions
and light–
dark green)
might occur normally.
be prevented. On theIf contrary,
the protein density
if the in very
density high
is too low(mid
(lowerleftleft
panel), these
panel), theinteractions
connections
might
cannotbebe prevented. OnThe
established. theupper
contrary,
rightif panels
the density is too
illustrate thelow
3D (lower
foldingleft panel), (orange
of proteins the connections
crumpled
cannot
lines).beIfestablished.
the protein The upper
density is right panels
increased, illustrate
the proteinsthe 3D folding
might interact of and
proteins (orangechange
eventually crumpled
their
lines).
shapeIfnon-specifically.
the protein density is increased,
Eventually, the proteins
conglomerates of themight
same interact and eventually
protein might changeprotein
occur, producing their
shape non-specifically. Eventually, conglomerates of the same protein might occur, producing pro-
inclusion bodies. The lower right panel exemplifies the distortion of the normal topology of the
tein inclusion bodies. The lower right panel exemplifies the distortion of the normal topology of the
OM (up in the panel) due to the overproduction of membrane components (middle panel) or the
OM (up in the panel) due to the overproduction of membrane components (middle panel) or the
locationofofa aprotein
location proteininclusion
inclusionbody
body(e.g.,
(e.g.,ananhyperproduced
hyperproducedprotein,protein,such
suchasasa abeta-lactamase).
beta-lactamase).InIn
both cases, the distortion of the OM (red arrow) might alter the location/interaction ofofparticular
both cases, the distortion of the OM (red arrow) might alter the location/interaction particular
proteins (including porins, specific receptors, and pumps proteins, not represented
proteins (including porins, specific receptors, and pumps proteins, not represented for simplicity), for simplicity),
which
whichresults
resultsininaltered
alteredphenotypes.
phenotypes.

2.2.The
TheMolecular
MolecularComponents
ComponentsInvolved
InvolvedininStructural
StructuralEpistasis
Epistasis
Bacterialcell
Bacterial cellenvelopes:
envelopes:The Thecomplex
complexmolecular
molecularstructure
structureofofthe
thebacterial
bacterial cell
cell enve-
enve-
lope, consisting of the inner membrane, the peptidoglycan (PG) sacculus,
lope, consisting of the inner membrane, the peptidoglycan (PG) sacculus, and the external and the external
membrane,isisthe
membrane, thereactive
reactiveinterphase
interphaseofofthe
thebacterial
bacterialcell
cellwith
withthe
theenvironment,
environment,and andisis
therefore critical for the bacterial mode of life [22]. The inner membrane (IM, cytoplasmic
therefore critical for the bacterial mode of life [22]. The inner membrane (IM, cytoplasmic
membrane) in bacteria (such as E. coli) has a bilayer structure mostly composed of alpha-
membrane) in bacteria (such as E. coli) has a bilayer structure mostly composed of alpha-
helical proteins and phospholipids. Membrane lipids have a critical architectural value,
helical proteins and phospholipids. Membrane lipids have a critical architectural value,
given that small changes in the lipid acyl chains or head groups alter lipids packaging,
given that small changes in the lipid acyl chains or head groups alter lipids packaging,
assuring the architectural robustness when the cell is confronted by environmental changes,
assuring the architectural robustness when the cell is confronted by environmental
including antibiotic exposure [23,24]. The outer membrane (OM, external to the cell wall)
changes, including antibiotic exposure [23,24]. The outer membrane (OM, external to the
is also formed by a bilayer, but also has an asymmetrical structure, with phospholipids and
cell wall) is also formed by a bilayer, but also has an asymmetrical structure, with phos-
mostly beta-barrel lipoproteins in the inner layer (with more than 100 types in E. coli). Lpp,
pholipids and mostly beta-barrel lipoproteins in the inner layer (with more than 100 types
one of these lipoproteins, is the most abundant protein in E. coli and is covalently attached
in E. coli). Lpp, one of these lipoproteins, is the most abundant protein in E. coli and is
to the peptidoglycan, providing a critical connection between the OM and the cell wall [25].
covalently attached to the peptidoglycan, providing a critical connection between the OM
In the OM layer, there is an external dense lipopolysaccharide (LPS) composed of an LPS
and theascell
core, wellwallas [25]. In thepolysaccharide
extended OM layer, there is an stabilized
chains external dense lipopolysaccharide
by divalent cations (Mg2+(LPS)
, Ca2+ )
composed of an LPS core, as well as extended polysaccharide chains stabilized
forming the highly variable O-antigen. This layer also includes transmembrane proteins by divalent
cations (Mg2+
organized in, Ca
2+) forming the highly variable O-antigen. This layer also includes trans-
trimers to form cylinders (outer membrane proteins, OMPs), which can have
membrane
functional proteins
ectodomains organized in trimers
with enzymatic to form
activity cylinders
(e.g., protease(outer membrane
in OmpT), but are proteins,
essentially
OMPs), which can have functional ectodomains with enzymatic
involved in water and nutrient uptake, and the export of waste products. The activity (e.g., protease in
biogenesis
Biology 2023, 12, 640 5 of 14

and integrity of the vital OM requires a constant supply of locally recruited (secreted) OMPs
and lipoproteins. Most secretions occur through the Sec translocon, where unfolded OMP
polypeptides are delivered to the beta-barrel assembly machine (in turn composed of OMPs
and lipoproteins) by periplasmic chaperones, for insertion into the OM. Protein–protein
interactions produce a spatiotemporal patterning of the OM into micro-domains, and are
the basis of beta-barrel protein turnover [26].
In between the outer and inner membranes, there is a more rigid physical structure,
the peptidoglycan sacculus, which is essential for providing the cell shape and volume.
The various shapes during the growth phases are ensured by the modularity of the core
components of the peptidoglycan synthesis [26]. The peptidoglycan molecular network is
formed by sequential chains of the disaccharide N-acetyl glucosamine-N-acetyl muramic
acid, which is cross-linked by small pentapeptide chains [27,28]. The space between the IM
and OM is known as the “periplasmic space” or simply the “periplasm”, and is an aqueous
space extremely rich in proteins and has a higher viscosity than the cytoplasm [29]. An
important aspect of the membranes is the physical–structural relationship among the IM,
PG and OM, constituting a unified network, which obviously influences the periplasm. As
stated earlier, there are membrane adhesion sites joining the IM and OM, such as tripartite
efflux pumps [30], and other cross-envelope structures, such as flagella machinery and type
III secretion systems.
Envelope-associated protein-rich peripheral cytoplasm: The vital multilayered cell
envelope determines the other weakly structured molecular layers within the bacterial
cytoplasm (protein-rich rings, ribosomes crown) (Figure 1). In fact, almost a half of the total
bacterial proteome associates with the bacterial cell envelope [31], constituting a complex
proteomic sacculus. It is to be noticed that at least 25% of the total cell proteome is bound
and interacts with the IM, frequently under the form of structural oligomeric complexes.
Many of these proteins are essential to maintain bacterial life [32].
Envelope-associated ribosomes-rich peripheral cytoplasm: In total, there are ap-
proximately 50,000 ribosomes per cell, although this number greatly depends on the physi-
ological state (i.e., feast or famine) [33]. There is a crown of ribosomes (the so-called protein
factory) bound or in close vicinity (within 50 nm) to the IM, which is compatible with the
“transertion hypothesis” (see next section) [33–35]. In this ribosome-rich compartment, half
of the total osmolality (depending on the number of osmotically active biopolymers per
volume unit) is due to ribosomal particles, producing a substantial excluded volume effect
that influences protein diffusion [36]. By contrast, the density of ribosomes is low in the
cytoplasmic spaces near the bacterial nucleoid [37]. Ribosome density is also affected by
changes in their shape and volume, not only as a result of synthesis and degradation (recy-
cling), but also through the polymerization of 70S ribosomes into inactive 100S ribosomes,
which allows bacteria to hibernate during stress periods [38].
Nucleic acid structures in the bacterial cytoplasm: The bacterial nucleoid is com-
posed of a (most frequently) circular DNA chromosome, floating in the cytosol, but form-
ing in a distinct cell pseudo-compartment that occupies 10–20% of the bacterial cell vol-
ume [39,40]. The chromosome has a complex and functionally efficient topology, with
plectonemic wound loops of DNA, more or less tightly coiled (positively or negatively
supercoiled) and forming approximately 500 supercoiled domains. The multiplicity of the
domains limits general damages and facilitates repair processes or relaxation of a single
domain without consequences of the superhelicity of other DNA regions. Proteins, particu-
larly topoisomerases, ensure the maintenance, relaxation and restoration of this supercoiled
structure, allowing the large RNA polymerase complex to progress along the individual
helical turns of DNA. Histone-like proteins, such as the inversion stimulation protein (Fis),
the integration host factor (IHF), the heat stable nucleoid-structuring protein (H–NS) and
the heat-unstable protein (HU), also contribute to the nucleoid dynamics. During chro-
mosomal segregation, structural maintenance of chromosome (SMC) protein complexes
ensure the nucleoid’s architectural preservation (“the choreography”) [41]. Interestingly,
the nucleoid might interact with the bacterial envelopes, mostly to fulfill the suggested
Biology 2023, 12, 640 6 of 14

coupled transcription and translation (CTT) process of the membrane proteins (transertion),
which means that the ribosomes initiate the translation of mRNAs, of which the transcrip-
tion from DNA has not yet concluded, giving rise to “RNA polymerase-.mRNA-ribosome”
complexes. The involved gene loci (uracil richness appears to characterize membrane-
traversing domains) migrate from the nucleoid complex topology to the vicinity of the
inner membrane, and thus become exposed to the ribosome-rich crown in the peripheral
cytoplasm. During such a process, additional regulatory mechanisms are involved, such as
the levels of the alarmone (p)ppGpp [42].
In the case of plasmid DNA, the replication, partition and transfer processes have
been proposed to be dependent on the interaction of plasmid DNA with a limited number
of membrane structures (domains) [43]; however, the full demonstration of this plausible
hypothesis remains elusive [44]. The localization of plasmid DNA in the cell depends on
plasmid-encoded partition genes, moving from the mid-cell position to the 1/4 and 3/4
positions at the time of cell division [45].
Molecular structures in the bacterial cytoplasm fluid: Unlike eukaryotic cells, bacte-
ria are devoid of a endoplasmic membranaceous reticulum formed by cytoskeletal proteins,
which are mostly involved in cellular functions such as protein synthesis, folding, mod-
ification, compartmentalization and transport. However, the bacterial cytoplasm has
cytoskeletal-like proteins that might be involved in polymerizing activities [46]. Even in the
absence of a real cytoplasmic compartmentalization, as it occurs by overexpressing geneti-
cally engineered proteins, the bacterial cytoplasmic organization is ensured by constructing
protein and nucleic acid scaffolds that form through liquid–liquid phase separation (LLPS),
local dynamic membraneless functional condensates that can enrich specific nucleic acid,
and protein components [47,48]. In addition, there are bacterial cytoskeletal protein fil-
aments involved in various processes, including cell elongation, cell division (such as
the treadmilling protein, tubulin homolog, FtsZ), chromosomal and plasmid segregation,
and cell motility [49]. The structure of the bacterial cytoplasm allows for temporal and
spatial localization of proteins (“check points”) involved in the growth cycle progression,
maintaining a “cell memory” and ensuring the right topological distributions required for
division planes, as it occurs in eukaryotic cells [10]. The preservation of molecular crossroad
interactions among nucleotides and proteins is certainly critical at the time of bacterial
division [50]. In summary, the bacterial cytoplasm is indeed a crowded microenvironment
where numerous potential physical interactions among molecules, macromolecules and
protein condensates occur, facilitating structural epistasis.

3. The Bacterial Cell Molecular Architecture and Shape Is Altered by

Antibiotic Exposure
Aminoglycosides and fluoroquinolones induce cytoplasmic condensation resulting
from cellular membrane damage, with changes in lipid composition and outflow of the cyto-
plasmic content, and the separation of the OM and IM (larger periplasmic space), ultimately
resulting in the release of reactive oxygen species [51,52]. Cytoplasmic condensation favors
macromolecule compactification and eventually structural interactions (Figure 2), resulting
in either positive (favoring functional enzyme clustering) or negative (by the aggregation
of interfering proteins in these functional clusters) epistasis [53–55]. In addition, antibiotics
that inhibit transcription (as rifamycins) or ribosomal protein synthesis (as chlorampheni-
col), alter the spatial organization of the bacterial chromosome and ribosomal particles,
possibly as a result of changes in cytoplasmic crowding density [56,57]. Consequently, there
are changes in intracellular protein and nucleic acid mobility [58], influencing unspecific (re-
sulting from Brownian motion) and specific associations between molecules, such as within
multiprotein complexes. Proteins diffuse to reach their functional target locations (Figure 2).
Protein and nucleic acids motility and diffusion are critical in exponential growth: their
impairment, resulting in diminished intracellular dynamics, could be a reason for the faster
antimicrobial effect in fast-growing cells [59], perhaps synergistically with the increased
amount of such target structures accessible for antibiotic action.
Biology 2023, 12, 640 7 of 14

Due to their specific mechanisms of action, numerous antibiotics affect the architecture
and shape of bacterial cells, modifying their normal physical interactions among molecules.
Typically, the subinhibitory action of various beta-lactams results (for instance in E. coli) in
cell elongation or filamentation, as what happens during ampicillin exposure; or cellular
rounding, blebbing and dimpling, as during carbapenems challenge [60], which is due
to the inhibition of particular penicillin-binding proteins (PBPs) involved in the cell wall
synthesis. PBP3 inhibition (as in aztreonam exposure) produces elongated cells, while PBP2
inhibition (as in mecillinam exposure) results in spherical cells [61]. Changes in shapes can
also be due to the effect of stress responses; for instance, DNA-targeting antibiotics induce
an SOS response involving elongation [62–64]. In certain cases, the mechanism of action
provokes adaptive response, modifying the cell size and shape; for instance, if the number
of active ribosomes is reduced by ribosome-targeting drugs, there is a compensatory over-
synthesis of ribosomes, and the cells invest in growth rather than in replication, which
results in smaller cells [65]. Protein synthesis inhibition could result in a disbalance in
the number of proteins and protein-nucleic acid interactions, thereby deeply affecting
bacterial fitness. This disbalance can cause a disturbance in protein and mRNA content
that propagates through genetic networks, thereby altering interactions between genes. For
instance, microbial cells must coordinate gene expression with cell size and shape [66], and
this coordination is essential for phenotypes that affect local fitness, such as motility [67].
Disturbing this coordination has significant effects on cellular phenotypes.
Any change in the cell shape requires an expansion or constriction of the membrane
layers (and the volume of the periplasm), involving a quantitative change in their molecular
components, or the distance between them, and therefore in their physical interaction. The
concept of structural epistasis is applied here to discuss whether these changes might have
functional consequences beyond those resulting from classical epistasis, including altered
gene expression [68,69]. Protein folding, and hence protein functionality and connectivity,
can be altered by membrane molecular changes in the lipid bilayer composition, particularly
if influencing the systems (translocons, insertases and chaperones) assuring a correct folding
in the membrane [70]. Interestingly, biophysical forces that affect the molecular topology of
bacterial cells are still active during cell death; for instance, nanotubes, resulting from the
cannibalization of the disintegrated cell membrane, are a post-mortem manifestation [71].

4. The Bacterial Cell Architecture and Shape Is Altered by Antibiotic Resistance

Antibiotics frequently promote (or select for) a few phenotypic variants in the popula-
tion (known as “persisters”) that tolerate antibiotic action at the expense of changing the
cellular architecture, resulting in altered cell shapes. In E. coli tolerating ampicillin exposure,
the persisters are frequently smaller and the cells are swollen, altering physical molecu-
lar interactions by changing elasticity or surface-to-volume ratio [72]. In Staphylococcus
aureus, antibiotic persisters are usually recognized as “small colony variants”, frequently
changing the envelope (thicker cell walls) and, correspondingly, a denser granulation in
the peripheral cytoplasm, or have branched or multiple cross walls, which are sometimes
defective [73]. In addition, exposure to bacteriostatic agents, such as macrolides and chlo-
ramphenicol, results in small colony variants [74]. Given that it also occurs in pH-driven
transitions, bacterial dormancy or persistence could possibly be due to a transition of the
cytoplasm from a fluid to a gel-solid-like state [75,76].
Changes in cell shape induced by antibiotic action have real consequences for the
molecular mobility inside the cells (and consequently metabolic activity), which has been
tested by using the intracellular diffusion of green fluorescent protein (GFP) in the presence
of antibiotics [60,77,78]. The hyperexpression of resistance mechanisms might also affect
bacterial architecture. In general, protein hyperexpression leads to the formation of small
colony variants and reduces bacterial growth, as was signaled in recombinant strains
modified to hyperproduce (for instance using strong promoters) proteins for chemical or
pharma industries. To address this problem, the shape of the bacteria should be modified
(through morphology engineering) [79]. High levels of TEM-1 beta-lactamase expression
Biology 2023, 12, 640 8 of 14

results in sequestration of the mature excreted polypeptide in insoluble protein aggregates

(inclusion bodies) located within the periplasmic space. Given that correct protein folding is
altered in these aggregates, the function is lost [80]. The constitutive hyperexpression of the
AmpC-type beta-lactamase might also have a deleterious effect on cellular fitness [81,82].
Studies on Salmonella, the only Enterobacteriaceae that does not possess AmpC, have shown
that the acquisition of exogenous AmpC causes changes in cellular morphology, with
longer cells indicating an effect on septation, and produces small changes in the structure
of the peptidoglycan. These effects fully abolish Salmonella Typhimurium viability, unless
ampC expression is under control of its regulator, AmpR [81]. A similar effect of a severe
fitness cost occurs in Pseudomonas aeruginosa [82]. The metallo-carbapenemase NDM-1 is
related with lipoproteins of the OM and can be packaged into the periplasmic space by
physical interactions with the OM layer, determining “envelope stress” and facilitating
its extrusion inside membrane vesicles [83]. MDR efflux pump hyperexpression should
also physically disturb the anatomical and functional structure of the cell envelope, with
consequent effects of an altered cell physiology. However, this structural disturbance is
still an underexplored area. The fact that particular Stenotrophomonas maltophilia resistant
mutants present a reduced cell size and a lower plate efficiency might shed light the
direction of future studies [84].
Nevertheless, efflux pump overexpression modifies the activity of other unrelated
cell machineries, thereby providing an example of structural epistasis. This is the case
for MexEF-OprN in the Pseudomonas aeruginosa, of which the overexpression increases
oxygen respiration, modifies the intracellular pH and triggers the activation of the nitrate
respiratory pathway [85]. Notably MexEF-OprN overexpression is associated with a
reduction in type III secretion [86], and type III secretion requires significant activity
of the proton motive force [87]. Whether MexEF-OprN overexpression inactivates type
III secretion by modifying the proton motive force, thereby impeding the simultaneous
induction of these two energetically costly cell machineries, and if the reduction in fitness
is also influenced by less efficient basic metabolic pathways (as energy in invested in
overexpression of the secreted protein), are questions that remain unanswered.
The conjugative process of plasmids (which eventually encode antibiotic resistance)
might produce (probably small) alterations in the bacterial architecture of the donor cell,
because of the relaxosome protein complex (docked to the Type IV secretion system)
and the entire conjugative apparatus, forming an envelope structure bridging the IM
and the OM [88]. In the donor and recipient cells, the exit and the entry of the ssDNA
plasmid triggers the local recruitment of Ssb (single-strand binding protein) molecules
and the formation of membrane conjugative foci, which are apparently located at specific
membrane positions, possibly related to the density and stability of the outer membrane
protein OmpA, a beta-barrel porin collaborating in the process [89]. Eventually, mobile
genetic elements (preferentially small plasmids) might contribute to increasing particular
gene dosages, and thus gene dosage toxicity is based on abnormal protein abundance levels.
Dihydrofolate reductase overexpression in E. coli causes a metabolic imbalance, reducing
bacterial fitness [90].

5. Cell Architecture and Cell Size Influences Antibiotic Effects

Any change in the cell shape requires an expansion or constriction of the membrane
layers (and the periplasm volume), which involves a quantitative change in their molecular
components or in the distance between them, and therefore their physical interaction. The
concept of structural epistasis is applied here to discuss whether these changes might
have functional consequences, including the susceptibility to antimicrobial action [66].
Quantitative modeling has shown that bacteria might adapt (reduce their susceptibility) to
antibiotic challenges by reducing the surface-to-volume (S/V) ratio, and consequently, the
antibiotic influx and intracellular concentration. In certain cases, however, increasing this
ratio might provide an increase in antibiotic efflux rate, and thereby reduced susceptibility.
Moreover, the concentration of membrane-associated antibiotics is reduced [65]. In fact,
Biology 2023, 12, 640 9 of 14

most tested antibiotics decrease the S/V ratio. Such a reduction also decreases nutrient
uptake, slowing the bacterial metabolism and consequently the antibiotic action [91]. As
expected, the morphological cell response to membrane-targeting and membrane-transport-
targeting antibiotics is a reduction in the cell surface area. Other effects of the S/V can be
considered secondary to the bacterial adaptation to drug action; for instance, the inhibition
of translation by ribosome-targeting antibiotics (as chloramphenicol) is compensated by a
higher ribosomal biosynthesis, leading to the predominance of growth versus replication,
with the consequences of an increased cell volume [91].
Membrane changes are not necessarily global. Different bacterial processes are con-
fined to membrane microdomains that are similar to lipid eukaryotic cell lipid rafts, which
accumulate multimeric protein complexes favoring their oligomerization. One of these
proteins, PBP2a, causes beta-lactam resistance in methicillin-resistant Staphylococcus aureus
(MRSA). Notably, the disruption of these membrane microdomains with available drugs
(such as statins, regularly used for treating hypercholesterolemia) interferes with PBP2a
oligomerization, resulting in MRSA infections that are treatable with penicillin [92]. This
example shows that structural alterations in a cellular element (the cell membrane) impedes
the structural changes (oligomerization) required for the activity of a wide-spread antibiotic
resistance gene.
In addition, bacteria readily alter their shape in response to non-antibiotic cues. For
instance, during urinary tract infections, E. coli produces long multi-nucleated filaments
in response to a still unknown urine component [93]. In addition to decreasing the S/V
ratio, filamentation has numerous consequences for the bacterial lifestyle. For instance,
filamented bacteria are less likely to be attacked by phagocytes [94], and thanks to the extra
body-mass, filamented bacteria might have an improved ability to resist shear forces in the
bladder and adhere to the epithelium [95,96]. Beyond the urinary tract, filamentation allows
intracellular bacteria to spread among host cells [97] and might promote the evolution of
antibiotic resistance [98], which provides an excellent example of how physical changes in
cell structure can shape numerous, non-related phenotypes.

6. Spatial Cell Biology, Molecular Interactome, and Antibiotic Actions

The main concept suggested in this review is that antibiotics and antibiotic resistance
modify the intracellular “molecular ecology” [99], particularly the structural (membranes,
cytoskeleton) and functional (proteins, nucleic acids) components that determine the spatial
bacterial cell biology. More than 1300 unique proteins have been identified in E. coli [98].
Most functional molecules should move within the cell to localize their target sites, which
may change according to the cell phase and stress conditions. In the case of proteins,
localization is frequently determined by binding to another previously localized protein that
serves to target a particular functional site [100,101]. Binding to the signaling protein can be
expected to be hampered by molecular crowding and loss of cytoplasmic fluidity, and might
produce abnormalities if the right site is not reached by the guiding protein. Moreover,
the number of potential protein–protein interactions (PPIs) inside the cell is huge: in E.
coli, there are several hundreds of macromolecular complexes, and the total PPIs in these
groups probably exceed 10,000. However, many PPIs are not in complexes or are difficult
to detect because they are transient [102]. However, transient interactions between proteins
determine the “quinary structure” (meta-PPI in multimeric proteins), which provides
important features regarding intracellular organization and compartmentalization [103]. In
fact, an increase in nonspecific interactions (e.g., mediated by protein membrane charge) in
the crowded cellular space should compete with specific interactions and interfere with
cellular functions [103,104]. It could be expected that forced PPIs derived from alterations
in protein density following cellular architectural alterations might result in aggregation,
misfolding, and functional impairment (Figure 2), but this is still an open field for further
research. Bioinformatics techniques based on deep learning are expected to be applied
soon to predict PPIs (also protein domain–domain and protein–RNA interactions), and
Biology 2023, 12, 640 10 of 14

to ascertain their possible consequences in the presence of changes in architectural and

physical cellular damage [104,105].

7. Conclusions
We are far from understanding the effects of the alterations in the balance and phys-
ical (structural) molecular interactions among the various gene products, which should
produce functional abnormalities in the bacterial cell, eventually pushing cells to death.
Bacterial death, and any death, is the result of cellular architectural disorganization [106].
Unfortunately, establishing a catalog of consequences of the modifications in the inter-
actome that result from changes in the cellular shape and architecture, caused by either
antimicrobial exposure or the expression of antibiotic resistance, is not an easy task. We
expect, however, that these changes should necessarily occur. How the architecture of
bacterial cells has evolved, so that differing lineages exposed to different environments and
requiring different adaptive needs have different cellular shapes and subcellular spatial
compartmentalization, and this is a starting field of research [27]. The acquisition of this
knowledge, in combination with the establishment of a physical interactive landscape
of various intracellular interactions under differing conditions of growth and stress, is
certainly needed. Such knowledge could contribute to the better understanding of the
mechanism of action of antimicrobials [107], the mechanisms governing the laws of as-
sociations between drugs, and the fitness costs of the acquisition of antibiotic resistance
determinants.

Author Contributions: Conceptualization, F.B. and J.-L.M.; writing—original draft preparation, F.B.;
writing—review and editing, J.-L.M., J.R.-B., A.S.-M., A.S. and M.D.F.-d.-B. All authors have read and
agreed to the published version of the manuscript.
Funding: This research received no external funding.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: There are no available datasets analyzed or generated during the study.
Conflicts of Interest: The authors declare no conflict of interest.

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