Zhou Et Al 2023 Mechanisms of Virulence Reprogramming in Bacterial Pathogens

Annual Review of Microbiology
Mechanisms of Virulence
Reprogramming in Bacterial
Pathogens
Annu. Rev. Microbiol. 2023.77:561-581. Downloaded from www.annualreviews.org
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Jianuan Zhou, Hongmei Ma, and Lianhui Zhang

Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory
of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South
China Agricultural University, Guangzhou, China; email: [email protected]
Annu. Rev. Microbiol. 2023. 77:561–81 Keywords

First published as a Review in Advance on
two-component system, quorum sensing, interkingdom cell–cell
July 5, 2023
communication, c-di-GMP, virulence programming
The Annual Review of Microbiology is online at
micro.annualreviews.org Abstract
https://doi.org/10.1146/annurev-micro-032521-
Bacteria are single-celled organisms that carry a comparatively small set
025954
of genetic information, typically consisting of a few thousand genes that
Copyright © 2023 by the author(s). This work is
can be selectively activated or repressed in an energy-efficient manner and
licensed under a Creative Commons Attribution 4.0
International License, which permits unrestricted transcribed to encode various biological functions in accordance with en-
use, distribution, and reproduction in any medium, vironmental changes. Research over the last few decades has uncovered
provided the original author and source are credited.
various ingenious molecular mechanisms that allow bacterial pathogens to
See credit lines of images or other third-party
material in this article for license information. sense and respond to different environmental cues or signals to activate or
suppress the expression of specific genes in order to suppress host defenses
and establish infections. In the setting of infection, pathogenic bacteria
have evolved various intelligent mechanisms to reprogram their virulence
to adapt to environmental changes and maintain a dominant advantage over
host and microbial competitors in new niches. This review summarizes
the bacterial virulence programming mechanisms that enable pathogens
to switch from acute to chronic infection, from local to systemic infec-
tion, and from infection to colonization. It also discusses the implications
of these findings for the development of new strategies to combat bacterial
infections.
561
Contents
1. INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 562
2. FUNDAMENTALS OF BACTERIAL VIRULENCE . . . . . . . . . . . . . . . . . . . . . . . . . . 563
2.1. Virulence Determinants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 563
2.2. Acute and Chronic Infections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 565
3. MAJOR MECHANISMS IN PROGRAMMING BACTERIAL VIRULENCE . . 566
3.1. Two-Component System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 566
3.2. Quorum Sensing System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 567
3.3. Interkingdom Communication System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 567
4. REPROGRAMMING OF BACTERIAL VIRULENCE . . . . . . . . . . . . . . . . . . . . . . . . 568
4.1. Switch from Acute to Chronic Infection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 568
4.2. Switch from Local to Systemic Infection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571
4.3. Switch from Infection to Colonization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 573

5. CONCLUSION AND FUTURE PERSPECTIVE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 574
1. INTRODUCTION
As one of the most ancient forms of life on Earth, bacteria are highly diversified and widespread
in various climate zones and niches (84, 137). An individual bacterium is very small, ranging from
0.2 µm to 0.75 mm in width (116). Bacteria have small genomes, from 0.6 to 14.3 Mbp in size
(91), that generally encode ∼600–6,000 proteins. Free-living bacteria typically encode several
thousand proteins, whereas obligate parasitic bacteria with metabolic restriction encode as few
as 500–1,000 proteins (123). Most bacterial pathogens have relatively large genomes. For exam-
ple, the genome of Escherichia coli O157:H7 is 5,594,447 bp in size and contains 5,361 genes, and
that of Pseudomonas aeruginosa PAO1 is 6,264,404 bp in size and contains 5,697 genes.
Studies of the minimal gene set for sustaining bacterial life have used various approaches
to identify essential genes of various sizes (87; see http://essentialgene.org). An experimental
genome reduction study eliminated approximately 30% of the E. coli genome (303 genes) with-
out causing a detectable viability defect (74), and a transposon insertional mutagenesis approach
unveiled 1,265 genes essential for E. coli growth and colonization (133). In bacterial genomes, nu-
merous genes are involved in pathogenesis and collectively contribute to virulence. A transposon
mutant library consisting of 5,850 clones of P. aeruginosa PA14 was used to carry out a genome-
wide study of virulence-related genes, which identified approximately 170 unique genes necessary
for infection of Caenorhabditis elegans (46). Using a nearly saturated transposon mutant library, a
study of Xanthomonas oryzae pv. oryzicola identified more than 250 individual mutants with reduced
virulence in rice (150).
Bacterial pathogenesis involves sequential processes by which pathogens establish infection
and cause disease in hosts. These processes include migration to infection sites, adherence to host
cells, invasion of the host, suppression of or escape from host defenses, assimilation of essential
nutrients, and accomplishment of systemic infection. During the course of infection, pathogen and
host recognize and respond to each other, and environmental conditions might tip the balance of
pathogen–host interaction by influencing and altering the physiological states of both parties.
Clearly, the pathogen should be able to respond to the cues or signals from both environment
and host and act accordingly in order to gain the upper hand. In this regard, numerous lines of
evidence indicate that pathogens can modulate differential expression of various sets of virulence
(vir) genes according to their needs. For example, Salmonella spp. rely on one type of type III
562 Zhou • Ma • Zhang

secretion system (T3SS) for bacterial adhesion and invasion (122) and utilize another type of
T3SS to survive and flourish in subsequent systemic infections (109). Similarly, P. aeruginosa can
inversely regulate the genes involved in promoting motility and acute infection as well as those
associated with biofilm formation and chronic infection following changes in environmental cues
(34). Finally, Agrobacterium tumefaciens expresses T-DNA-related vir genes at the early stage of
pathogen–host interaction to establish infection, then switches to colonization mode by switching
off transcriptional expression of these genes (131).
The ability to reprogram their virulence machinery may benefit bacteria in at least two ways.
First, expression of vir genes is an energy-intensive process (106, 128), and the ability to activate or
turn off various sets of vir genes according to their needs allows pathogens the flexibility to execute
different biological activities with sufficient energy and raw materials. Second, bacterial infection
is a sequential process involving numerous genes (46, 80, 150), and the ability to reprogram their
virulence would enable pathogens to complete infection in an organized manner without wasting
energy or disturbing the infectious process. For these reasons, pathogens must have evolved, and
most likely will continue to evolve, virulence reprogramming mechanisms in order to survive and
flourish despite stressful conditions in the process of infection. Therefore, investigations of both
virulence programming and reprogramming mechanisms will be indispensable for elucidating the
interaction mechanisms of the disease triangle (i.e., pathogen, host, and environment).
In this review, we briefly discuss the fundamentals of bacterial virulence and the major virulence
programming mechanisms. We then review bacterial virulence reprogramming mechanisms, with
a special focus on the relevant signals or environmental cues and signaling pathways that trigger
and drive virulence reprogramming.
2. FUNDAMENTALS OF BACTERIAL VIRULENCE

2.1. Virulence Determinants
The genomes of pathogenic bacteria commonly encode a wide array of virulence factors (VFs),
which collectively play an essential role in overwhelming host defense responses and causing
disease. Most VFs produced by bacterial pathogens include cell surface structures that facilitate
movement toward and attachment to host cells, cell wall–degrading enzymes (CWDEs) and toxins
that destroy host cells, effectors for immunosuppression, and factors promoting nutrient uptake
to or metabolic modulation of the host cells (60, 90). VFs can be classified as cell membrane–
associated or extracellular, according to their manner of presentation in interactions with host cells.
2.1.1. Cell membrane–associated virulence factors. The bacterial surface structure is essen-
tial for pathogens to approach and interact with host cells, as it contains many VFs responsible for
locomotion, adhesion, nutrient acquisition, biofilm formation, inflammation, invasion, and eva-
sion from innate and adaptive immunity (5, 9, 42, 60). Bacteria use flagella to move toward food
and away from danger, pili for adherence and gene transfer, and capsular polysaccharide (CPS)
to envelop components to provide protection against attack by the host immune response. These
surface-associated structures are vital for adherence to host cells before the bacteria begin a pro-
grammed process of attack, invasion, and defense against host immunity, or while they wait for
suitable conditions to invade.
Most bacteria use adhesive appendages, like pili or filamented fimbriae, to span at least two
different surface proteins, the tips of which often contain the actual adhesins. Such adhesins bind
to specific host components termed receptors (which are fixed and relatively immobile) or ligands
(which are relatively free or even diffusible) (42). Adhesins may be the most important determinant
of host-specific recognition. Nonappendage adhesins exist in the outer membrane or cell wall, are
widely encoded in the genome of pathogenic bacteria, and often bind to different host ligands
www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 563

to adhere to various surfaces and colonize various niches. Such adhesins also maintain biofilm
architecture by linking the bacteria to the biofilm extracellular matrix (9).
Bacteria produce polysaccharides that promote adhesion. These polysaccharides may be firmly
associated with the cell surface, thereby forming a cell envelope via CPS, or loosely associated with
or even released from the cell surface, like extracellular polysaccharide (EPS). Bacteria exploit
CPS and EPS mainly for protective and aggregative purposes, respectively (9). For gram-negative
bacteria, outer polysaccharide (O-antigen) and the core oligosaccharide and membrane-anchored
lipid A together constitute lipopolysaccharide (LPS), which plays important roles in infection and
survival within the host (16).
Bacteria also employ various types of transporters to take up nutrients from the environment
or host cells to support their growth and metabolism. These include (a) passive transporters
for concentration-dependent permeation of molecules, like Fe3+ siderophore scavengers (5), and
(b) active transporters, including the ATP-binding cassette (ABC) superfamily, secondary trans-
porters such as the major facilitator superfamily, and group translocation systems such as the
phosphotransferase system and the fatty acid transporters. Mutation of nutrient transporters im-
pairs bacterial nutrient uptake, thus influencing bacterial growth and the secretion of toxins and
tolerance to antimicrobial agents (72, 112).
Another important group of membrane-associated virulence determinants consists of various
VF delivery systems. At least seven numbered secretion systems (T1SS–T7SS) have been iden-
tified in bacteria (60), in addition to unnumbered secretion systems like the chaperone–usher
pathway and Por (porphyrin accumulation on cell surface) secretion (20). Although these secretion
systems or delivery structures might not directly damage host tissues or cells, they are essential
for bacterial virulence. Most if not all extracellular VFs depend on these systems for either se-
cretion into the host cells’ environment or injection into host cells. The proteins secreted by
secretion systems are diverse; many of them are able to promote colonization and interfere with
host physiology, a topic we discuss in the next section.
2.1.2. Extracellular virulence factors. Bacterial pathogens commonly produce a range of

extracellular VFs that they secrete into or around host cells through various delivery systems
(described in the previous section). These VFs include toxins, CWDEs, EPSs, effectors, and
siderophores (Table 1). Another important VF is T-DNA secreted by tumorigenic A. tumefa-
ciens (31). According to the mechanisms of action of the dominant VFs, pathogenic bacteria can
be divided into three groups: (a) tumorigenic pathogens such as A. tumefaciens, which deliver a
gene cluster into the host genome in order to biosynthesize the specific nutrients needed to sup-
port their own survival and competitive advantage (56); (b) so-called brute-force pathogens, such
as soft rotting Erwinia, Pectobacterium, and Dickeya, which use CWDEs and/or toxins to dismantle
host cell walls or cell membranes (23, 41); and (c) stealthy pathogens, comprising many species
such as Pseudomonas syringae, Xanthomonas campestris, and P. aeruginosa, which inject effector pro-
teins into host cells to manipulate host defense responses so as to facilitate infection (Table 1). Not
uncommonly, bacterial pathogens use a combination of CWDEs/toxins and effectors to facilitate
invasion and infection.
Different extracellular VFs are secreted via different delivery machineries (Table 1). Bacteria
use T1SS and T2SS to secrete CWDEs to invade and macerate host cell walls or cell membranes
(60). Gram-negative bacterial pathogens typically use T3SS to deliver effectors into host cells to
counteract and suppress host basal defense responses (52). T4SS is known for its ability to translo-
cate both nucleic acids and proteins in order to promote bacterial infection and colonization; an
example is A. tumefaciens T-DNA and its coating proteins (56, 98).
A very large number of proteins are secreted via T5SS. Most of them, including adhesins, toxins,
proteases, and cytolysins (60), contribute to the virulence of animal or human pathogens (36, 62).
Table 1 Extracellular VFs deployed by pathogenic bacteria
Pathogen and Typical disease
infection mode Hosts symptoms Major VFs secreted Secretion pathway Reference(s)
Tumorigenic mode
Agrobacterium Dicotyledonous Crown gall tumors T-DNA T4SS 56
tumefaciens plants
Brute-force mode
Erwinia Potato, tomato, rice, Maceration, soft rot CWDEs and/or toxins T1SS, T2SS 23, 41, 146
Pectobacterium banana, and other
Dickeya plants with fresh
tissue
Stealth mode
Pseudomonas syringae Tomato, legumes, Necrotic lesions Effectors T3SS 21
Arabidopsis
Xanthomonas Brassicas, tomato, Necrotic lesions CWDEs, EPSs, T1SS, T2SS, T3SS 38
campestris pepper effectors
Erwinia amylovora Pear, apple Fire blight Effectors T3SS 12
Ralstonia Solanaceae plants, Green wilting EPS, effectors T2SS, T3SS 22
solanacearum banana
Yersinia enterocolitica Human, rat, flea Gastroenteritis, InvA, enterotoxin, T1SS, T3SS 94
septicemia cytokines, effectors
Salmonella Humans and animals Enteric fever, Effectors, invasin, T3SS 51
gastroenteritis endotoxin
Enterococcus faecalis Humans and animals Meningitis, colon Hemolysin, gelatinase, T1SS, T5SS 44
cancer serine protease,
cytolysin,
hemagglutinin
Pseudomonas Human, mouse Cystic fibrosis Exotoxin A, effectors, T1SS, T2SS, T3SS, 80, 111
aeruginosa elastases, T6SS
siderophores,
pyocyanin, EPS,
Tse 1–3
Serratia marcescens Plants, humans, and Sepsis, meningitis, Proteases, hemolysin, T1SS, T5SS 77
animals osteomyelitis, cytolysin
ocular infections
Burkholderia Onion, human Plant rotting, human EPS, effectors T2SS, T3SS 16
cenocepacia cystic fibrosis
Abbreviations: CWDE, cell wall–degrading enzyme; EPS, extracellular polysaccharide; TnSS, type n secretion system; VF, virulence factor.
T6SS, required for virulence in human, animal, and plant pathogens, consists of a phage tail spike–
like injectosome that translocates effector proteins directly into the cytoplasm of host cells (18).
T7SS has been found in gram-positive bacteria that secrete proteins lacking signal sequences. The
ESX-1 cluster encoding for T7SS is required for Mycobacterium marinum virulence and hemolysis
of host cells and for conjugation in the nonpathogenic Mycobacterium smegmatis (1).
2.2. Acute and Chronic Infections

Bacterial infections can be classified into two types on the basis of severity and length. Acute
infections are severe and of relatively short duration, and chronic infections persist over a long

time and can even be a lifelong burden. Typically, acute infections are associated with planktonic
growth and production of a range of destructive or damaging VFs, such as toxins, effectors, pro-
teases, and cell wall or membrane hydrolytic enzymes, which are invasive and frequently result
in substantially systemic tissue damage or cell death (55, 120). In contrast, chronic infections are
rarely invasive and are noncytotoxic or less cytotoxic, and they usually involve biofilm formation
or chronic colonization to prevent assault by the host immune system or to save energy (50, 55).
Some pathogens seem to be capable of causing only one type of infection; the best-known
examples of pathogens that cause lifelong, chronic, asymptomatic infections are Mycobacterium
tuberculosis, Helicobacter pylori, and Salmonella enterica sv. Typhimurium (58, 96). In contrast, quite
a few bacterial pathogens can cause acute or chronic infections following changes in environ-
mental conditions or outcome of pathogen–host interactions (50, 55). These pathogens include
P. aeruginosa, E. coli, Staphylococcus aureus, Staphylococcus epidermidis, Haemophilus influenzae, and My-
cobacterium leprae (34, 59). For example, the opportunistic pathogen P. aeruginosa is notorious for
causing chronic lung infections in individuals suffering from cystic fibrosis (61, 80). However, it
can also cause pneumonia by breaking down host defenses and disseminating in the bloodstream,
leading to death within hours or days (50).
3. MAJOR MECHANISMS IN PROGRAMMING BACTERIAL VIRULENCE

Bacterial pathogens have evolved and can utilize various tactics to overwhelm host defense re-
sponses in order to invade the host and cause infection (2, 40). Research over the last few decades
has found that pathogens can orchestrate the expression of various vir genes and the activity of
the gene products following changes in environmental cues. The conductors of this orchestra are
the virulence programming mechanisms, which allow bacterial cells to execute and exhibit vari-
ous tactics against their host organisms or competitors. Pathogen virulence programming usually
involves perception of and response to signaling molecules from the host or from the pathogen
itself, along with certain environmental cues and modulation of vir gene expression through com-
plex regulatory networks. The major mechanisms of bacterial virulence programming are the
two-component system (TCS), quorum sensing (QS), and the interkingdom communication sys-
tem, which regulate the expression of the genes encoding VFs either directly or, more commonly,
indirectly through engagement of downstream regulatory networks.
3.1. Two-Component System

One of the main mechanisms of signal transduction in eukaryotes and prokaryotes is protein phos-
phorylation, which is catalyzed by kinases. Kinases can be divided into serine/threonine (Ser/Thr),
tyrosine (Tyr), and histidine (His) kinases according to their substrate specificity. Since most
prokaryotes lack Ser/Thr and Tyr kinases, His kinases play a vital role in many aspects of sig-
nal transduction. This signaling system typically comprises a His kinase and a response regulatory
protein, TCS (11, 54).
TCS plays a major role in sensing and connecting environmental changes as input to changes
in cellular physiological output. His kinases are typically transmembrane proteins harboring at
least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain.
Response regulators consist of a conserved receiver domain and a variable effector domain. The
sensor domain of His kinase can detect either in vitro– or in vivo–specific stimuli and catalyze
ATP-dependent specific His autophosphorylation. Thereafter, the response regulator catalyzes
the transfer of the His phosphoryl group to its own aspartate residue in the conserved receiver
domain, which activates and thereby enables its effector domain to interact with the promoters or
proteins of downstream genes to generate a regulatory response (53).

In 1986, Ninfa & Magasanik (99) discovered the first TCS when studying nitrogen regula-
tors in E. coli. Subsequently, almost all of the bacterial genomes sequenced to date were found to
contain genes encoding TCSs. For example, the E. coli genome encodes 62 different TCSs in-
volved in the regulation of various biological processes, such as chemotaxis, osmotic regulation,
metabolism, and transportation (147). The remarkable diversity of signals determines the diversity
of domain composition in His kinase and response regulators, such as transmembrane domains
for detecting temperature changes (69), PAS (Per/Arnt/Sim) and GAF (cGMP-specific phospho-
diesterase/adenylyl cyclase/FhlA) domains for sensing light and oxygen (71, 95), and so on. TCS
signaling is one of the most important players in bacterial virulence programming, as it connects
environmental cues or cellular signals with cellular responses.
3.2. Quorum Sensing System

While TCS allows bacterial pathogens to sense and respond to changes in the environment, QS
enables them to monitor population changes by sensing the self-produced QS signal, also known
as the autoinducer. With such mechanisms, bacteria synchronize target gene expression through
groupwide detection by signal receptors in order to respond through downstream regulatory
networks (2, 103). Such collective-action tactics are extremely useful for mounting attacks and
overwhelming host defense responses (45, 144). This cell density–dependent autoinduction phe-
nomenon was initially observed in the fish symbiont Vibrio fischeri, which produces and responds
to the acylhomoserine lactone (AHL) signal that regulates the generation of bioluminescence (43).
Subsequently, AHL signals with different structural variations were identified and found to play
a key role in the regulation of virulence-related traits in several pathogenic bacterial species, in-
cluding A. tumefaciens, Erwinia carotovora, and P. aeruginosa; these studies gave rise to the iconic
and popular term “quorum sensing” (49).
The typical AHL QS system contains a luxR homolog encoding an AHL sensor and tran-
scriptional regulator (R protein) and a luxI homolog encoding for AHL biosynthesis (I protein).
Upon reaching a threshold population, the accumulated AHL molecules interact and activate
LuxR, which becomes a functional transcriptional factor that directs and boosts transcriptional
expression of luxI and other downstream target genes. In this simple yet ingenious mechanism of
regulation, bacterial pathogens can synchronize transcriptional expression of a range of vir genes
within their local community. For example, a transcriptome analysis found that the QS systems
in P. aeruginosa and X. campestris control the transcriptional expression of more than 300 genes,
many of which are associated with bacterial virulence (38, 117, 129).
Following the identification of AHL-mediated QS systems, which have been found in a wide
range of bacterial species (138), other types of QS systems were discovered. These include the
similarly widely conserved AI-2 system (103), DSF (diffusible signal factor) QS systems in various
bacterial pathogens (38, 149), 3-PAME (3-hydroxy palmitic acid methyl ester) system in Ralstonia
solanacearum (47), PQS (Pseudomonas quinolone signal) and IQS (integrated quorum sensing) sys-
tems in P. aeruginosa (79), and Vfm and putrescine systems in Dickeya spp. (85, 97, 118). These QS
systems differ in the chemical structures of their signals, receptors, and signaling networks, but all
are commonly involved in cell density–dependent modulation of bacterial virulence–related traits
(136).
3.3. Interkingdom Communication System

The severity and intensity of microbial pathogenesis are largely the outcome of interactions
among the three players in the court of infection (i.e., pathogen, host, and environment). It is not
surprising that pathogens are also capable of detecting and exploiting host molecules as signals to

modulate the expression of vir genes. These interkingdom communication signaling molecules
include plant cell wall degradation products, such as acetosyringone and derivatives that induce
T-DNA transfer in A. tumefaciens (14); insoluble plant cell wall components that induce T3SS
expression in R. solanacearum (3, 139); host cell membrane components that induce T3SS gene
expression in Yersinia pseudotuberculosis and Yersinia enterocolitica (105); small signaling molecules
from host cells such as spermidine, which activates T3SS gene expression in P. aeruginosa (140,
148); the plant hormone indole-3-acetic acid, which regulates T3SS expression in Dickeya dadantii
(141); and putrescine, which modulates bacterial motility and systemic infection in Dickeya oryzae
(118).
Acetosyringone-mediated pathogen–host cell–cell communication is perhaps one of the best-
understood interkingdom communication systems. At the initial stage of infection, phenolic
compounds including acetosyringone are released from wounded plants and are sensed by the
VirA His kinase (121). Phosphorylated VirA then transfers the phosphate moiety to the response
regulator VirG and, subsequently, activates transcription of the vir genes (104). Unlike the acetosy-
ringone system, which recruits a membrane-located TCS for signal perception and response, the
spermidine-mediated cell–cell communication system between P. aeruginosa and its mammalian
host involves a bacterial high-affinity ABC transporter that takes up the spermidine signal from
host cells and specifically activates the transcriptional expression of T3SS genes via an unknown
mechanism (140, 148).
4. REPROGRAMMING OF BACTERIAL VIRULENCE

In contrast to the relatively well studied virulence programming mechanisms of bacterial
pathogens, much less is known about virulence reprogramming mechanisms. Evidence is now
accumulating that bacterial pathogens have evolved various mechanisms to reprogram their vir-
ulence according to their best interests. In the context of pathogen–host interaction, pathogens
seem to have various reasons or logical motivations to develop and optimize virulence reprogram-
ming mechanisms. First, excessive virulence may immobilize or kill the host, thereby impairing the
transmission of pathogens to new hosts or host tissues and hence compromising their fitness (128).
Second, expression of vir genes during pathogenicity is costly in terms of energy and resources.
Once such costs exceed the burden that pathogens can sustain, their growth will be restrained
or retarded (106, 128). These findings suggest that virulence reprogramming may be an essen-
tial strategy for pathogens to stay competitive with potential rivals, which may include the host,
other microorganisms, or environmental stress conditions. In the following subsections, we use
examples to illustrate the regulatory mechanisms through which bacterial pathogens reprogram
virulence by altering gene expression patterns to maximize their potential.
4.1. Switch from Acute to Chronic Infection

P. aeruginosa is a well-known opportunistic human pathogen capable of causing both acute and
chronic infections. Acute infections of P. aeruginosa are characterized by planktonic hypervirulent
phenotypes, which are required for initial colonization of host cells and evasion of host immune
systems. However, establishment of acute infection is usually followed by a switch to the almost
avirulent chronic phase, presenting a perpetual alginate-associated biofilm state; such infections
are difficult to eradicate with conventional antibiotics (2, 17). Correspondingly, the pathogen de-
ploys two types of VFs or products to suit the needs of its different lifestyles. The factors crucial
for acute infection include T3SS, proteases, phospholipases, motility, and adhesion, mediated by
flagella and pili, while those involved in chronic infection include siderophores and biofilms (8,
89), which have little or no toxicity but are likewise detrimental to human health (2, 61).

P. aeruginosa has evolved several signaling mechanisms to program acute infection, such as the
cAMP-Vfr-mediated environmental sensing system, the spermidine-based host–pathogen cell–
cell communication system, and the Las-IQS-PQS-Rhl hierarchy QS systems (Figure 1a). Among
them, the cAMP-Vfr and spermidine systems help activate the bacterial T3SS, and the QS systems
positively regulate bacterial adhesion and motility and the production of extracellular enzymes,
which have been extensively reviewed elsewhere (2, 80). More recent research has shown that
spermidine produced by P. aeruginosa also acts as a QS signal to regulate T3SS expression (83).
For the purposes of this discussion, we summarize two categories of mechanisms associated
with the establishment of P. aeruginosa chronic infection. One appears to be a slowly acting, pas-
sive mechanism that depends on hypermutations, which normally take years to occur after onset of
infection (61). Hypermutations can be caused by null mutations in DNA mismatch repair genes,
including mutS, mutL, and uvrD. These mutations, in turn, lead to the accumulation of mutations
in the regulatory genes associated with acute infection, such as lasR and retS, and consequently
to decreased production of QS-dependent VFs, such as proteases and motility (35, 64) and T3SS
effectors (63, 78). In addition, null mutation in the negative regulator MucA leads to constitutive
expression of AlgU and alginate production, promoting biofilm development and chronic infec-
tion (88). Collectively, mutations in the positive regulatory genes that control production of acute
VFs and the negative regulatory genes that suppress production of the VFs needed for chronic
infection enable a switch from the acute infection mode to the chronic infection mode (61). The
second mechanism that primes chronic infection involves active sensing and responding to envi-
ronmental cues or signals, which is the focus of this review and is discussed in detail in the rest of
this section.
Initiation of chronic infection is typically characterized by downregulated VF production and
boosted biofilm formation. In P. aeruginosa, the hierarchy QS systems headed by LasRI play a key
role in positively regulating the production of an array of VFs, including elastases, proteases, lectin,
and pyocyanin, which are required in order to establish acute infection (80). In this regard, it is
interesting to note that the AHL QS signal of the LasRI system is produced and accumulates along
with bacterial growth and proliferation, followed by a sharp decline in the signal level when the
bacterial cells approach the stationary growth phase (67, 130). This finding suggests that transient
QS signal production or signal degradation may be crucial for switching from acute infection
mode to chronic infection mode (Figure 1b).
So far, at least three genes encoding AHL acylases for AHL QS signal degradation, also known
as quorum quenching, have been identified in the genome of P. aeruginosa (67, 68, 130). Deletion of
the AHL acylase gene quiP leads to greater accumulation of QS signals and continued high-level
production of VFs at the later stage of bacterial growth (130). quiP expression is tightly controlled
in P. aeruginosa but can be induced by decanoyl-l-homoserine lactone, which is a structural analog
of the Las QS signal N-(3-oxododecanoyl)-l-homoserine lactone (68). However, the natural sig-
nal or environmental cue that activates expression of the AHL acylases under in vivo conditions
remains to be investigated.
Another virulence determinant that plays a key role in acute infection of P. aeruginosa is its
T3SS. In line with its role in early infection, T3SS expression levels in P. aeruginosa peak at the
early growth stage and then decline with bacterial growth (148). A recent study found that while
a low–cell density inoculum of P. aeruginosa causes severe cytotoxicity against human lung tissue
cell line A549, increasing the cell density of bacterial inoculum leads to decreased cytotoxicity
(132). Addition of the supernatants from high–cell density bacterial culture to low–cell density
inoculum protects human cells from bacterial cytotoxic damage, suggesting that P. aeruginosa may
produce and accumulate one or more inhibitory metabolites that counteract its pathogenic infec-
tion. A further analysis identified this inhibitor as phenylacetic acid (PAA), which downregulates

a Acute infection (T3SS, type IV pili, endotoxins, proteases, elastases) b Chronic infection (EPSs, T6SS, biofilms)
1 1 3 4
cAMP-Vfr
T3SS Arginine, ethanol,
Ca2+ Type IV effectors O2 depletion, Peroxide,
depletion pili ToxA DHL Psl, SDS bacteriophage Ca2+
570
QuiP PvdQ HacB
CyaB PilA ToxR SiaA GacS LadS
PelD
YfiN
SadC
RoeA
P
Zhou
ATP CyaA
•
pilA toxA P
WspR
toxR
AHL SiaC SiaC P
degradation
Ma
SiaD GacA
•
cAMP Vfr
PtxR
rsmY rsmZ
ptxR
Inner
Outer
Vfr LasA, LasB,
Zhang
vfr
membrane
membrane
2 pyocyanin RsmY/Z
SPD
exsCEB exsA SPD-T3SS
c-di-GMP RsmA
2
Vfr lasR lasI OdDHL Vfr rhlR rhlI
LasA
BHL vfr EPS production
RhlR
LasB LasR Pyocyanin Biofilm formation
ATP exsCEBA T3SS
ambABCDE pqsR
PQS cAMP
pqsABCDE SPD
Pyocyanin IqsR DHL
OdDHL
IQS PqsR PAA
BHL
IqsR 3 PQS c-di-GMP
Las-IQS-PQS-Rhl IQS sRNA
Figure 1
The major mechanisms associated with virulence modulation in Pseudomonas aeruginosa. (a) The key virulence programming mechanisms involved in acute bacterial
infection, including (●
1 ) the cAMP-Vfr system, which responds to Ca2+ depletion stress; (● 2 ) the SPD interkingdom cell–cell communication system, which responds to
SPD signals from host cells; and (●3 ) the Las-IQS-PQS-Rhl QS network, which responds to QS signals produced by bacterial cells. The cAMP-Vfr and SPD systems act
mainly through positive regulation of T3SS expression (cAMP-Vfr also regulates the genes encoding type IV pili), while the QS signaling network regulates the
production of pyocyanin, proteases, and elastases. (b) The key virulence reprogramming mechanisms controlling the switch from acute to chronic infection, including
(●1 ) the QQ system, (●2 ) the PAA metabolite inhibitory system, (●
3 ) the c-di-GMP second messenger system, and (● 4 ) the LadS-Gac-Rsm signaling system, which act by
simultaneously turning off the genes for acute infection and triggering expression of the genes for chronic infection. QQ AHL acylases degrade bacterial AHL signals to
suppress the QS-dependent production of pyocyanin, proteases, and elastases. PAA inhibits the transcription of rsmA and vfr and then turns off the expression of T3SS
genes. The c-di-GMP and LadS-Gac-Rsm signaling systems are activated by various environmental cues to induce polysaccharide production and biofilm formation.
Abbreviations: AHL, acylhomoserine lactone; DHL, decanoyl-l-homoserine lactone, the structural analog of OdDHL; EPS, extracellular polysaccharide; IQS and PQS,
integrated quorum sensing and Pseudomonas quinolone signal, signals of the IQS and PQS QS systems, respectively; OdDHL and BHL, N-(3-oxododecanoyl)-
l-homoserine lactone and N-butanoyl-l-homoserine lactone, cognate AHL signals of the Las and Rhl QS systems, respectively; QQ, quorum quenching; QS, quorum
sensing; PAA, phenylacetic acid; SDS, sodium dodecyl sulfate; SPD, spermidine; sRNA, small RNA; T3SS, type III secretion system.
the transcriptional expression of T3SS genes and the corresponding regulatory genes, including
rsmA and vfr (132) (Figure 1b). These findings suggest that P. aeruginosa can cleverly couple its
cellular metabolism with virulence reprogramming.
Biofilm formation, which confers a multicellular status to P. aeruginosa, is an ingenious adaptive
mechanism that enables a secluded social environment to withstand various in vivo biotic and
abiotic stresses. The key regulatory systems initiating biofilm formation in P. aeruginosa include the
second messenger c-di-GMP and LadS-GacSA signaling systems (119, 127). In general, high c-di-
GMP concentration in the cell promotes biofilm formation, whereas low c-di-GMP levels favor
bacterial motility and the planktonic lifestyle. At least five diguanylate cyclases (DGCs)—namely
WspR, SadC, RoeA, SiaD, and YfiN, which synthesize c-di-GMP using two GTP molecules—
control the transition from planktonic growth to biofilm formation (127). Among them, WspR
is activated by ethanol and other compounds that cause cell envelope stress, including glycerol
and cell membrane–targeting antibiotics (24, 101). SadC responds to arginine (10), ethanol (82),
oxygen limitation stress (115), tellurite (32), and polysaccharide Psl (70). RoeA is also stimulated
by arginine (10). SiaD activity is promoted by quite a few environmental cues, including ethanol
(108), polysaccharide Psl (70), and the detergent sodium dodecyl sulfate (76). YfiN responds to
peroxide (73) and bacteriophage (39).
Although the molecular mechanisms of signal–receptor interaction remain largely unknown,
the enzyme activity of these DGCs is boosted upon sensing these environmental cues, leading
to higher cellular levels of c-di-GMP. As a consequence, the accumulated second messenger in-
duces polysaccharide biosynthesis and biofilm formation through its receptors and effectors (127)
(Figure 1b). Additionally, P. aeruginosa can modulate biofilm formation and switch from acute to
chronic infection mode via the LadS-GacSA TCS, in which calcium stimulates the GacSA-Rsm
pathway through the Gac-associated His kinase LadS and promotes biofilm formation (15).
4.2. Switch from Local to Systemic Infection

Salmonella is a food- and waterborne pathogen that causes diseases ranging from gastroenteritis to
systemic enteric fever in humans and animals. It can be ingested via contaminated food or water
and transported through the gastrointestinal tract (114). Once inside the human body, Salmonella
enterica can invade different host cell types, including epithelial cells of the ileum and microfold
(M) cells during local infection, followed by immune cells and fibroblasts during systemic dis-
semination (86). The virulence of Salmonella relies mainly on two sets of T3SSs that translocate
bacterial effectors into the host cytosol. The genes encoding two T3SSs (T3SS-1 and T3SS-2)
are located in Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2), respectively (145). SPI-1
is required for initial intestinal invasion into both epithelial and M cells (33, 51), whereas SPI-2
is essential for survival in immune cells and establishment of systemic infection (100). To achieve
invasion and survival at the different stages of infection, Salmonella has evolved distinct mech-
anisms to sense and respond to different physical and chemical signals from host and microbes
along the gut tract to modulate the expression of SPI-1 and SPI-2, respectively (37, 57). Among
the TCSs, BarA/SirA and PhoPQ are at the top of the corresponding signaling and regulatory
networks (Figure 2).
During local invasion of the epithelial cells at the intestinal lumen, several environmental cues
or signals are known to play critical roles in activating the expression of SPI-1 genes, including
T3SS-1. Short-chain fatty acids such as acetate and formate, which are the by-products of dietary
lipid metabolites or remnants of the resident microbiota, activate SPI-1 expression via the TCS
BarA/SirA. The HK BarA is activated by acetate and formate and phosphorylates the response
regulator SirA, which can also be directly phosphorylated by acetyl-P. Phosphorylated SirA then

a Local infection b Systemic infection
Acetate Formate Ileum epithelial cells <2 mM Mg2+ CAMPs Macrophages
Outer
membrane
BarA
Inner
membrane UgtL
P PhoQ
H+
Acetate-P (pH 5–6) P P
P SirA ugtL
CsrB/C P PhoP P SsrB SPI-2

High Fe2+
CsrA Fur CRP

PinT SPI-1 effectors
hilD mRNA hilD
LCFAs
hns RtsA
HilC HilD HilD Propionyl-CoA Propionate

RstA HilA H-NS HilC HilA
SPI-1 SPI-1
Figure 2
The major signal systems modulating local invasion and systemic infection by Salmonella enterica. (a) To
initiate intestinal invasion into epithelial cells, the BarA/SirA TCS senses and responds to host signals
acetate and formate and activates the expression of SPI-1 through the SPI-1 master regulator HilA. High
cellular levels of Fe2+ can also activate HilA by directly inducing the expression of HilD. (b) During systemic
infection, the PhoPQ TCS is the primary mechanism shaping the transition from SPI-1 to SPI-2 expression
in response to CAMPs, Mg2+ depletion, and acidic pH conditions. In addition, LCFAs and propionate help
shut down SPI-1 expression through downregulation of HilD. Abbreviations: CAMP, cationic antimicrobial
peptide; CRP, cyclic AMP receptor protein; LCFA, long-chain fatty acid; SPI, Salmonella pathogenicity
island; TCS, two-component system.
alleviates the CrsA repression on the hilD translation by inducing CsrBC small RNAs (sRNAs)
(48). HilD controls its own expression and that of the regulators HilC and RstA. These two reg-
ulators also control their own expression and that of hilA, which encodes the master regulator
of SPI-1 (102). Subsequently, HilA activates SPI-1 expression in a timely manner to promote
local bacterial invasion. In addition, at the lumen of the small intestine, where dilatory iron is
mainly absorbed, there is abundant free Fe2+ to interact with the ferric uptake regulator Fur.
The resultant Fur-Fe2+ complex directly binds to the promoter of the activator gene hilD to in-
duce its expression, and HilD activates the expression of HilA and then SPI-1 (124). Furthermore,
Fur-Fe2+ can bind to the Fur box in the promoter of hns and repress the expression of this negative
regulator, leading to increased expression of hilA and SPI-1 (113) (Figure 2a).
During systemic infection and gut colonization, Salmonella encounters cationic antimicrobial
peptides (CAMPs) produced by the host cells in the process of immune response (92), and it expe-
riences conditions of low Mg2+ and acidic pH inside macrophage phagosomes (110). To suppress
immune responses and survive in host cells, Salmonella has evolved mechanisms to perceive and
respond to these environmental changes, primarily via the TCS PhoPQ, and uses them as signals
to shut off SPI-1 and activate T3SS-2 and other SPI-2 genes (Figure 2b). Phosphorylation of HK
PhoQ is induced by CAMPs, divalent cations (primarily Mg2+ below 2 mM), and mildly acidic pH
(pH 5–6) (6, 19, 27). CAMPs and divalent cations competitively bind to the periplasmic domain
of PhoQ (37), whereas H+ binds to its cytoplasmic domain (27). Autophosphorylation of PhoQ in
response to mildly acidic pH also requires binding of the regulators UgtL and SsrB (28, 29). The

activated PhoQ then phosphorylates the response regulator PhoP, which negatively regulates hilA
through multiple distinct mechanisms: direct transcriptional repression of the hilA promoter, in-
direct transcriptional repression of both the hilD and rtsA promoters, and activation of the sRNA
PinT (102). PinT is one of the PhoPQ-regulated sRNAs that contributes to this regulation by
repressing the expression of hilA and other SPI-1 genes (75, 134). PinT also indirectly represses
expression of FliZ, a posttranslational regulator of HilD, and directly represses translation of ssrB,
which encodes the primary regulator of the SPI-2 T3SS (75). Furthermore, long-chain fatty acids
and propionate found in the large intestine or colon are capable of repressing SPI-1 expression and
Salmonella invasion (30, 37). Long-chain fatty acids act by directly binding to the SPI-1 regulators
HilD, HilC, and RtsA, inhibiting their attachment to the target promoters (30).
4.3. Switch from Infection to Colonization

Unlike many other bacterial pathogens that significantly damage or even kill host organisms,
A. tumefaciens exemplifies bacterial phytopathogens that can also exploit their host for niche con-
struction (81, 93). This capability implies that the pathogen must have evolved sophisticated and
balanced regulatory mechanisms that allow it to modulate timely expression of the genes encoding
various functions essential for infection, niche construction, survival, and propagation. A. tume-
faciens contains at least five gene clusters or operons associated with virulence and pathogenicity,
including (a) the vir cluster, which contains most of the vir genes that are activated at the early
stage of infection; (b) the T-DNA region, which is transferred from bacterial cells into host cells
and integrated into the host genome (7, 56, 98); (c) the repABC operon, which maintains the repli-
cation and separation of the Ti plasmid carrying the vir gene cluster and T-DNA region; (d) the
tra operon, which regulates and facilitates Ti plasmid conjugal transfer; and (e) the trb operon,
which encodes a delivery system for transmitting the Ti plasmid from pathogenic isolates to non-
pathogenic isolates (125, 135). A recent study found that A. tumefaciens relies on a range of fitness
genes, constituting 3–8% of its genome, for its competitive survival and propagation in plants
(126). These fitness genes encode carbon and nitrogen metabolism; synthesis and repair of DNA,
RNA, and proteins; and envelope-associated functions.
The virulence programming mechanisms that govern A. tumefaciens infection have been well
characterized by numerous excellent review articles (56, 98, 125). In brief, pathogenesis begins
upon sensing plant signals, including acetosyringone and sugars as well as low pH conditions,
that are released from wounded tissues of susceptible plants by the bacterial periplasmic regulator
ChvE and the TCSs ChvGI and VirAG, which collectively activate vir gene expression. The Vir
proteins help generate the T complex and facilitate its trafficking into host cells. The T-DNA
region contains the genes encoding biosynthesis of plant growth hormones and opines, which
stimulate malignant plant tissue growth and enable accumulation of opines as specific nutrients for
A. tumefaciens, thereby creating a new ecological niche for the pathogen. As a result, the integration
of T-DNA into the plant genome and its expression indicate that infection has successfully been
established.
A. tumefaciens infection is sensitive to high temperatures. One study cleverly exploited this fea-
ture to demonstrate that A. tumefaciens infection requires only around 32 ± 2 h to transform
normal cells into neoplastic cells (13). Consistent with this observation, a more recent study
showed that transcript levels of vir genes steadily increased following inoculation until 18 h
postinfection, then decreased sharply and became undetectable (131). This finding indicates that
A. tumefaciens can reprogram its vir gene expression in a timely manner upon achieving infection
in order to switch from a pathogenic lifestyle to colonization or a free-living lifestyle.
A. tumefaciens has at least two compelling reasons to reprogram its virulence after establish-
ment of infection. The first is to avoid or terminate elicitation of unnecessary biostresses or

defense responses from host. Expression of the vir genes, especially virB2 and elf18, activates the
early defense-related genes, namely MPK3, MPK6, WRKY22, WRKY29, FRK1, and PR1, during
Agrobacterium infection (66). Activation of these genes creates a hostile environment characterized
by oxidative burst and toxic metabolites (7, 125). The second reason is to reduce consumption of
limited energy, which could be important for A. tumefaciens because it needs to compete with the
host and support the expression of numerous fitness genes (7, 126). Consistent with this notion,
studies have shown that virulence induction significantly reduces the fitness of A. tumefaciens by
drastically decreasing the population growth rate (107).
Virulence reprogramming in A. tumefaciens is made possible by use of the plant defense signal
salicylic acid (SA), which is a potent inhibitor of vir gene expression and virulence (4, 143). In
plants, most SA conjugates with glucose to form SA β-glucoside (SAG) (26). Wang et al. (131)
recently found that A. tumefaciens can produce a SAG hydrolase, SghA, to hydrolyze SAG in order
to release SA. In the free-living or nonpathogenic stage, SghA is not synthesized because of tight
control by the negative regulator protein SghR, which binds directly to the promoter of sghA and
suppresses its expression (131, 142). In contrast, during infection this binding effect is reversed by
the accumulated plant disaccharide sucrose, which is stimulated by wounding and microbial in-
fection (25). SA significantly inhibits vir gene expression, whereas SAG affects vir gene expression
only in the presence of functional SghA. This finding suggests that SghA has an essential role in
the modulation of vir gene expression by releasing SA from SAG (131).
Significantly, in contrast to vir genes, which are expressed from the early stage of infection
until approximately 18 h postinfection, the transcripts of sghA become detectable only at the late
stage, starting at 18 h postinfection (131). Therefore, differential expression of vir and sghA genes
allows A. tumefaciens to complete infection and switch to a colonization lifestyle (for an illustration
of the mechanisms that drive the A. tumefaciens switch from infection to colonization, see figure 7
of Reference 131).
5. CONCLUSION AND FUTURE PERSPECTIVE

Bacteria are small, single-celled organisms with limited energy and resources. To survive and
proliferate, bacterial pathogens have to outperform their hosts, which are commonly giant, multi-
cellular living creatures equipped with various defense mechanisms. During long-term interaction
and competition with hosts, pathogens have evolved various ingenious virulence programming and
reprogramming mechanisms enabling orderly deployment of their aims and ammunition. Because
of space constraints, this review has summarized only a few relatively well-studied bacterial viru-
lence reprogramming mechanisms. These ingenious reprogramming mechanisms allow bacterial
pathogens to utilize their energy and resources in a highly efficient and well-organized manner,
thus maximizing their advantages over host organisms by switching from acute to chronic in-
fection, transitioning from local to systemic infection, or shifting from infection to colonization
following changes in new niches.
Signals or cues from the host and the environment play critical roles in triggering and activating
virulence reprogramming mechanisms, which typically involve turning off the expression of genes
used in the previous infection process and simultaneously activating the expression of genes used in
ongoing infection or colonization processes. Therefore, identifying these signals and the relevant
signaling pathways would be crucial for elucidating the virulence reprogramming mechanisms
and for designing and developing therapeutic agents against bacterial infection. For example, the
signals for turning off acute or local infection—such as PAA, which inhibits T3SS expression in
P. aeruginosa, and long-chain fatty acids, which suppress SPI-1 in Salmonella spp. (30, 132)—could
be used as lead compounds in the development of a new generation of antimicrobials. In this

context, it is interesting to note that SA, which is the signal that switches A. tumefaciens from
infection mode to colonization mode (131), and its structural analog can effectively control the
soft rot diseases caused by five Dickeya species by turning down the transcriptional expression of
T3SS (65).
Compared with virulence programming mechanisms, which have been a major focus of micro-
bial research over the last few decades, virulence reprogramming mechanisms are much less well
characterized. We envision that continued effort will help elucidate the signaling and regulatory
mechanisms that control bacterial virulence reprogramming. In particular, given the diversity of
host organisms that pathogens may encounter, it is plausible that pathogens have evolved and will
continue to evolve varied sensing and responding mechanisms to reprogram their virulence so as to
adapt to different in vivo environmental settings. Reminiscent of the genome sequencing technol-
ogy that expedited the identification of vir genes and virulence programming mechanisms, rapid
advances in various omics techniques and tools, which allow the dynamics of gene expression pat-
terns to be visualized, may facilitate our efforts to dissect and explain the virulence reprogramming
mechanisms in various microbial pathogens.
DISCLOSURE STATEMENT
The authors are not aware of any affiliations, memberships, funding, or financial holdings that
might be perceived as affecting the objectivity of this review.
ACKNOWLEDGMENTS
The writing of this review was supported by grants from the Key Research and Development
Program of Guangdong Province (2020200808190001), the National Natural Science Foundation
of China (U22A20480, 31972230), the Guangdong Forestry Science and Technology Innovation
Project (2020KJCX009), and the Science and Technology Planning Project of Shaoguan City
(200805094530618).
LITERATURE CITED
1. Abdallah AM, Gey van Pittius NC, Champion PA, Cox J, Luirink J, et al. 2007. Type VII secretion—
Mycobacteria show the way. Nat. Rev. Microbiol. 5:883–91
2. Ahator SD, Zhang LH. 2019. Small is mighty—chemical communication systems in Pseudomonas
aeruginosa. Annu. Rev. Microbiol. 73:559–78
3. Aldon D, Brito B, Boucher C, Genin S. 2000. A bacterial sensor of plant cell contact controls the
transcriptional induction of Ralstonia solanacearum pathogenicity genes. EMBO J. 19:2304–14
4. Anand A, Uppalapati SR, Ryu CM, Allen SN, Kang L, et al. 2008. Salicylic acid and systemic acquired
resistance play a role in attenuating crown gall disease caused by Agrobacterium tumefaciens. Plant Physiol.
146:703–15
5. Aznar A, Chen NW, Rigault M, Riache N, Joseph D, et al. 2014. Scavenging iron: a novel mechanism
of plant immunity activation by microbial siderophores. Plant Physiol. 164:2167–83
6. Bader MW, Sanowar S, Daley ME, Schneider AR, Cho U, et al. 2005. Recognition of antimicrobial
peptides by a bacterial sensor kinase. Cell 122:461–72
7. Barton IS, Fuqua C, Platt TG. 2018. Ecological and evolutionary dynamics of a model facultative
pathogen: Agrobacterium and crown gall disease of plants. Environ. Microbiol. 20:16–29
8. Ben Haj Khalifa A, Moissenet D, Vu Thien H, Khedher M. 2011. Virulence factors in Pseudomonas
aeruginosa: mechanisms and modes of regulation. Ann. Biol. Clin. 69:393–403
9. Berne C, Ducret A, Hardy GG, Brun YV. 2015. Adhesins involved in attachment to abiotic surfaces by
gram-negative bacteria. Microbiol. Spectr. 3:10

10. Bernier SP, Ha DG, Khan W, Merritt JH, O’Toole GA. 2011. Modulation of Pseudomonas aerugi-
nosa surface-associated group behaviors by individual amino acids through c-di-GMP signaling. Res.
Microbiol. 162:680–88
11. Bhate MP, Molnar KS, Goulian M, DeGrado WF. 2015. Signal transduction in histidine kinases: insights
from new structures. Structure 23:981–94
12. Bogdanove AJ, Bauer DW, Beer SV. 1998. Erwinia amylovora secretes DspE, a pathogenicity factor and
functional AvrE homolog, through the Hrp (type III secretion) pathway. J. Bacteriol. 180:2244–47
13. Braun AC, Mandle RJ. 1948. Studies on the inactivation of the tumor-inducing principle in crown gall.
Growth 12:255–69
14. Brencic A, Winans SC. 2005. Detection of and response to signals involved in host-microbe interactions
by plant-associated bacteria. Microbiol. Mol. Biol. Rev. 69:155–94
15. Broder UN, Jaeger T, Jenal U. 2016. LadS is a calcium-responsive kinase that induces acute-to-chronic
virulence switch in Pseudomonas aeruginosa. Nat. Microbiol. 2:16184
16. Bylund J, Burgess LA, Cescutti P, Ernst RK, Speert DP. 2006. Exopolysaccharides from Burkholderia
cenocepacia inhibit neutrophil chemotaxis and scavenge reactive oxygen species. J. Biol. Chem. 281:2526–
32
17. Calum H, Trøstrup H, Laulund AS, Thomsen K, Christophersen L, et al. 2022. Murine burn lesion
model for studying acute and chronic wound infections. APMIS 130:477–90
18. Cascales E. 2008. The type VI secretion toolkit. EMBO Rep. 9:735–41
19. Castelli ME, García Véscovi E, Soncini FC. 2000. The phosphatase activity is the target for Mg2+
regulation of the sensor protein PhoQ in Salmonella. J. Biol. Chem. 275:22948–54
20. Chagnot C, Zorgani MA, Astruc T, Desvaux M. 2013. Proteinaceous determinants of surface coloniza-
tion in bacteria: bacterial adhesion and biofilm formation from a protein secretion perspective. Front.
Microbiol. 4:303
21. Chan JH, Urbach JM, Law TF, Arnold LW, Hu A, et al. 2005. A high-throughput, near-saturating screen
for type III effector genes from Pseudomonas syringae. PNAS 102:2549–54
22. Chapmen MR, Kao CC. 1998. EpsR modulates production of extracellular polysaccharides in the
bacterial wilt pathogen Ralstonia (Pseudomonas) solanacearum. J. Bacteriol. 180:27–34
23. Chatterjee AK, Starr MP. 1980. Genetics of Erwinia species. Annu. Rev. Microbiol. 34:645–76
24. Chen AI, Dolben EF, Okegbe C, Harty CE, Golub Y, et al. 2014. Candida albicans ethanol stimulates
Pseudomonas aeruginosa WspR–controlled biofilm formation as part of a cyclic relationship involving
phenazines. PLOS Pathog. 10:e1004480
25. Chen LQ. 2014. SWEET sugar transporters for phloem transport and pathogen nutrition. New Phytol.
201:1150–55
26. Chen Z, Klessig DF. 1991. Identification of a soluble salicylic acid–binding protein that may function in
signal transduction in the plant disease-resistance response. PNAS 88:8179–83
27. Choi J, Groisman EA. 2016. Acidic pH sensing in the bacterial cytoplasm is required for Salmonella
virulence. Mol. Microbiol. 101:1024–38
28. Choi J, Groisman EA. 2017. Activation of master virulence regulator PhoP in acidic pH requires the
Salmonella-specific protein UgtL. Sci. Signal. 10:eaan6284
29. Choi J, Groisman EA. 2020. Horizontally acquired regulatory gene regulates ancestral regulatory system
to promote Salmonella virulence. Nucleic Acids Res. 48:10832–47
30. Chowdhury R, Pavinski Bitar PD, Keresztes I, Condo AM Jr., Altier C. 2021. A diffusible signal factor
of the intestine dictates Salmonella invasion through its direct control of the virulence activator HilD.
PLOS Pathog. 17:e1009357
31. Christie PJ, Cascales E. 2005. Structural and dynamic properties of bacterial type IV secretion systems.
Mol. Membr. Biol. 22:51–61
32. Chua SL, Sivakumar K, Rybtke M, Yuan M, Andersen JB, et al. 2015. c-di-GMP regulates Pseudomonas
aeruginosa stress response to tellurite during both planktonic and biofilm modes of growth. Sci. Rep.
20:10052
33. Clark MA, Reed KA, Lodge J, Stephen J, Hirst BH, et al. 1996. Invasion of murine intestinal M cells
by Salmonella typhimurium inv. mutants severely deficient for invasion of cultured cells. Infect. Immun.
64:4363–68

34. Coggan KA, Wolfgang MC. 2012. Global regulatory pathways and cross-talk control Pseudomonas
aeruginosa environmental lifestyle and virulence phenotype. Curr. Issues Mol. Biol. 14:47–70
35. D’Argenio DA, Wu M, Hoffman LR, Kulasekara HD, Déziel E, et al. 2007. Growth phenotypes of
Pseudomonas aeruginosa lasR mutants adapted to the airways of cystic fibrosis patients. Mol. Microbiol.
64:512–33
36. Dautin N, Bernstein HD. 2007. Protein secretion in gram-negative bacteria via the autotransporter
pathway. Annu. Rev. Microbiol. 61:89–12
37. De Nisco NJ, Rivera-Cancel G, Orth K. 2018. The biochemistry of sensing: enteric pathogens regulate
type III secretion in response to environmental and host cues. mBio 9:e02122
38. Deng Y, Wu J, Tao F, Zhang LH. 2011. Listening to a new language: DSF-based quorum sensing in
gram-negative bacteria. Chem. Rev. 111:160–73
39. De Smet J, Wagemans J, Hendrix H, Staes I, Visnapuu A, et al. 2021. Bacteriophage-mediated
interference of the c-di-GMP signalling pathway in Pseudomonas aeruginosa. Microb. Biotechnol. 14:967–78
40. Diard M, Hardt WD. 2017. Evolution of bacterial virulence. FEMS Microbiol. Rev. 41:679–97
41. Duarté X, Anderson CT, Grimson M, Barabote RD, Strauss RE, et al. 2000. Erwinia chrysanthemi
strains cause death of human gastrointestinal cells in culture and express an intimin-like protein. FEMS
Microbiol. Lett. 190:81–86
42. Dunne WM. 2002. Bacterial adhesion: Seen any good biofilms lately? Clin. Microbiol. Rev. 15:155–66
43. Eberhard A, Burlingame AL, Eberhard C, Kenyon GL, Nealson KH, et al. 1981. Structural identification
of autoinducer of Photobacterium fischeri luciferase. Biochemistry 20:2444–49
44. Elsner HA, Sobottka I, Mack D, Claussen M, Laufs R, et al. 2000. Virulence factors of Enterococcus faecalis
and Enterococcus faecium blood culture isolates. Eur. J. Microbiol. Infect. Dis. 19:39–42
45. Federle MJ, Bassler BL. 2003. Interspecies communication in bacteria. J. Clin. Investig. 112:1291–99
46. Feinbaum RL, Urbach JM, Liberati NT, Djonovic S, Adonizio A, et al. 2012. Genome-wide identifi-
cation of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model.
PLOS Pathog. 8:e1002813
47. Flavier AB, Clough SJ, Schell MA, Denny TP. 1997. Identification of 3-hydroxypalmitic acid methyl
ester as a novel autoregulator controlling virulence in Ralstonia solanacearum. Mol. Microbiol. 26:251–59
48. Fortune DR, Suyemoto M, Altier C. 2006. Identification of CsrC and characterization of its role in
epithelial cell invasion in Salmonella enterica serovar Typhimurium. Infect. Immun. 74:331–39
49. Fuqua WC, Winans SC, Greenberg EP. 1994. Quorum sensing in bacteria: the LuxR-LuxI family of
cell density–responsive transcriptional regulators. J. Bacteriol. 176:269–75
50. Furukawa S, Kuchma SL, O’Toole GA. 2006. Keeping their options open: acute versus persistent
infections. J. Bacteriol. 188:1211–17
51. Galán JE, Curtiss R III. 1989. Cloning and molecular characterization of genes whose products allow
Salmonella typhimurium to penetrate tissue culture cells. PNAS 86:6383–87
52. Galán JE, Lara-Tejero M, Marlovits TC, Wagner S. 2014. Bacterial type III secretion systems: specialized
nanomachines for protein delivery into target cells. Annu. Rev. Microbiol. 68:415–38
53. Gao R, Bouillet S, Stock AM. 2019. Structural basis of response regulator function. Annu. Rev. Microbiol.
73:175–97
54. Gao R, Stock AM. 2009. Biological insights from structures of two-component proteins. Annu. Rev.
55. García-Betancur JC, Goñi-Moreno A, Horger T, Schott M, Sharan M, et al. 2017. Cell differentiation
defines acute and chronic infection cell types in Staphylococcus aureus. eLife 6:e28023
56. Gelvin SB. 2017. Integration of Agrobacterium T-DNA into the plant genome. Annu. Rev. Genet. 51:195–
217
57. Groisman EA, Duprey A, Choi J. 2021. How the PhoP/PhoQ system controls virulence and Mg2+
homeostasis: lessons in signal transduction, pathogenesis, physiology, and evolution. Microbiol. Mol. Biol.
Rev. 85:e0017620
58. Gomez JE, McKinney JD. 2004. M. tuberculosis persistence, latency, and drug tolerance. Tuberculosis
84:29–44
59. Grant SS, Hung DT. 2013. Persistent bacterial infections, antibiotic tolerance, and the oxidative stress
response. Virulence 4:273–83

60. Green ER, Mecsas J. 2016. Bacterial secretion systems: an overview. Microbiol. Spectr. 4:215–39
61. Hall KM, Pursell ZF, Morici LA. 2022. The role of the Pseudomonas aeruginosa hypermutator phenotype
on the shift from acute to chronic virulence during respiratory infection. Front. Cell Infect. Microbiol.
12:943346
62. Henderson IR, Navarro-Garcia F, Desvaux M, Fernandez RC, Ala’Aldeen D. 2004. Type V protein
secretion pathway: the autotransporter story. Microbiol. Mol. Biol. Rev. 68:692–44
63. Hoboth C, Hoffmann R, Eichner A, Henke C, Schmoldt S, et al. 2009. Dynamics of adaptive microevolu-
tion of hypermutable Pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic
fibrosis. J. Infect. Dis. 200:118–30
64. Hoffman LR, Kulasekara HD, Emerson J, Houston LS, Burns JL, et al. 2009. Pseudomonas aeruginosa
lasR mutants are associated with cystic fibrosis lung disease progression. J. Cyst. Fibros. 8:66–70
65. Hu A, Hu M, Chen S, Xue Y, Xu T, Zhou J. 2022. Five plant natural products are potential type III
secretion system inhibitors to effectively control the soft rot disease caused by Dickeya. Front. Microbiol.
13:839025
66. Huang FC, Hwang HH. 2020. Arabidopsis RETICULON-LIKE4 (RTNLB4) protein participates in
Agrobacterium infection and VirB2 peptide–induced plant defense response. Int. J. Mol. Sci. 21:1722
67. Huang JJ, Han JI, Zhang LH, Leadbetter JR. 2003. Utilization of acyl-homoserine lactone quorum
signals for growth by a soil pseudomonad and Pseudomonas aeruginosa PAO1. Appl. Environ. Microbiol.
69:5941–49
68. Huang JJ, Petersen A, Whiteley M, Leadbetter JR. 2006. Identification of QuiP, the product of gene
PA1032, as the second acyl-homoserine lactone acylase of Pseudomonas aeruginosa PAO1. Appl. Environ.
69. Inda ME, Almada JC, Vazquez DB, Bortolotti A, Fernández A, et al. 2020. Driving the catalytic activity
of a transmembrane thermosensor kinase. Cell Mol. Life Sci. 77:3905–12
70. Irie Y, Borlee BR, O’Connor JR, Hill PJ, Harwood CS, et al. 2012. Self-produced exopolysaccharide is
a signal that stimulates biofilm formation in Pseudomonas aeruginosa. PNAS 109:20632–36
71. Ishii E, Eguchi Y. 2021. Diversity in sensing and signaling of bacterial sensor histidine kinases.
Biomolecules 11:1524
72. Jiang X, Yu T, Xu Y, Wang H, Korkeala H, et al. 2019. MdrL, a major facilitator superfamily efflux
pump of Listeria monocytogenes involved in tolerance to benzalkonium chloride. Appl. Microbiol. Biotechnol.
103:1339–50
73. Katharios-Lanwermeyer S, Koval SA, Barrack KE, O’Toole GA. 2022. The diguanylate cyclase YfiN of
Pseudomonas aeruginosa regulates biofilm maintenance in response to peroxide. J. Bacteriol. 204:e0039621
74. Kato J, Hashimoto M. 2007. Construction of consecutive deletions of the Escherichia coli chromosome.
Mol. Syst. Biol. 3:132
75. Kim K, Palmer AD, Vanderpool CK, Slauch JM. 2019. The small RNA PinT contributes to PhoP-
mediated regulation of the Salmonella pathogenicity island 1 type III secretion system in Salmonella
enterica serovar Typhimurium. J. Bacteriol. 201:e00312
76. Klebensberger J, Birkenmaier A, Geffers R, Kjelleberg S, Philipp B. 2009. SiaA and SiaD are essential for
inducing autoaggregation as a specific response to detergent stress in Pseudomonas aeruginosa. Environ.
77. Kurz CL, Chauvet S, Andrès E, Aurouze M, Vallet I, et al. 2003. Virulence factors of the human
opportunistic pathogen Serratia marcescens identified by in vivo screening. EMBO J. 22:1451–60
78. La Rosa R, Rossi E, Feist AM, Johansen HK, Molin S. 2021. Compensatory evolution of Pseudomonas
aeruginosa’s slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis. Nat. Commun.
12:3186
79. Lee J, Wu J, Deng Y, Wang J, Wang C, et al. 2013. A cell-cell communication signal integrates quorum
sensing and stress response. Nat. Chem. Biol. 9:339–43
80. Lee J, Zhang LH. 2015. The hierarchy quorum sensing network in Pseudomonas aeruginosa. Protein Cell
6:26–41
81. Leonard S, Hommais F, Nasser W, Reverchon S. 2017. Plant–phytopathogen interactions: bacterial
responses to environmental and plant stimuli. Environ. Microbiol. 19:1689–716

82. Lewis KA, Baker AE, Chen AI, Harty CE, Kuchma SL, et al. 2019. Ethanol decreases Pseudomonas
aeruginosa flagellar motility through the regulation of flagellar stators. J. Bacteriol. 201:e00285
83. Lin Q, Wang H, Huang J, Liu Z, Chen Q, et al. 2022. Spermidine is an intercellular signal modulating
T3SS expression in Pseudomonas aeruginosa. Microbiol. Spectr. 10:e0064422
84. Louca S, Mazel F, Doebeli M, Parfrey LW. 2019. A census-based estimate of Earth’s bacterial and
archaeal diversity. PLOS Biol. 17:e3000106
85. Lv M, Hu M, Li P, Jiang Z, Zhang L, et al. 2019. A two-component regulatory system VfmIH modulates
multiple virulence traits in Dickeya zeae. Mol. Microbiol. 111:1493–99
86. Luk CH, Enninga J, Valenzuela C. 2022. Fit to dwell in many places—the growing diversity of
intracellular Salmonella niches. Front. Cell Infect. Microbiol. 12:989451
87. Luo H, Lin Y, Liu T, Lai FL, Zhang CT, et al. 2021. DEG 15, an update of the Database of Essential
Genes that includes built-in analysis tools. Nucleic Acids Res. 49:D677–86
88. Malhotra S, Hayes D Jr., Wozniak DJ. 2019. Mucoid Pseudomonas aeruginosa and regional inflammation
in the cystic fibrosis lung. J. Cyst. Fibros. 18:796–93
89. Malone M, Bjarnsholt T, McBain AJ, James GA, Stoodley P, et al. 2017. The prevalence of biofilms in
chronic wounds: a systematic review and meta-analysis of published data. J. Wound Care 26:20–25
90. Maresso AW. 2019. The practice of the microbe hunter. In Bacterial Virulence—A Conceptual Primer, ed.
AW Maresso, pp. 19–30. Cham, Switz.: Springer
91. Martinez-Gutierrez CA, Aylward FO. 2022. Genome size distributions in bacteria and archaea are
strongly linked to evolutionary history at broad phylogenetic scales. PLOS Genet. 18:e1010220
92. Matamouros S, Miller SI. 2015. S. typhimurium strategies to resist killing by cationic antimicrobial
peptides. Biochim. Biophys. Acta Biomembr. 1848:3021–25
93. Meyer T, Thiour-Mauprivez C, Wisniewski-Dyé F, Kerzaon I, Comte G, et al. 2019. Ecological
conditions and molecular determinants involved in Agrobacterium lifestyle in tumors. Front. Plant Sci.
10:978
94. Mills SD, Boland A, Sory MP, Van Der Smissen P, Kerbourch C, et al. 1997. Yersinia enterocolitica in-
duces apoptosis in macrophages by a process requiring functional type III secretion and translocation
mechanisms and involving YopP, presumably acting as an effector protein. PNAS 94:12638–43
95. Moglich A, Ayers RA, Moffat K. 2009. Design and signaling mechanism of light-regulated histidine
kinases. J. Mol. Biol. 385:1433–44
96. Monack DM, Mueller A, Falkow S. 2004. Persistent bacterial infections: the interface of the pathogen
and the host immune system. Nat. Rev. Microbiol. 2:747–65
97. Nasser W, Dorel C, Wawrzyniak J, Van Gijsegem F, Groleau MC, et al. 2013. Vfm a new quorum
sensing system controls the virulence of Dickeya dadantii. Environ. Microbiol. 15:865–80
98. Nester EW. 2015. Agrobacterium: nature’s genetic engineer. Front. Plant Sci. 5:730
99. Ninfa AJ, Magasanik B. 1986. Covalent modification of the glnG product, NRI, by the glnL product,
NRII, regulates the transcription of the glnALG operon in Escherichia coli. PNAS 83:5909–13
100. Ochman H, Soncini FC, Solomon F, Groisman EA. 1996. Identification of a pathogenicity island
required for Salmonella survival in host cells. PNAS 93:7800–4
101. O’Neal L, Baraquet C, Suo Z, Dreifus JE, Peng Y, et al. 2022. The Wsp system of Pseudomonas aeruginosa
links surface sensing and cell envelope stress. PNAS 119:e2117633119
102. Palmer AD, Kim K, Slauch JM. 2019. PhoP-mediated repression of the SPI1 type 3 secretion system in
Salmonella enterica serovar Typhimurium. J. Bacteriol. 201:e00264
103. Papenfort K, Bassler BL. 2016. Quorum sensing signal-response systems in gram-negative bacteria. Nat.
Rev. Microbiol. 14:576–88
104. Pazour GJ, Das A. 1990. Characterization of the VirG binding site of Agrobacterium tumefaciens. Nucleic
Acids Res. 18:6909–13
105. Pettersson J, Nordfelth R, Dubinina E, Bergman T, Gustafsson M, et al. 1996. Modulation of virulence
factor expression by pathogen target cell contact. Science 273:1231–33
106. Peyraud R, Cottret L, Marmiesse L, Gouzy J, Genin S. 2016. A resource allocation trade-off between vir-
ulence and proliferation drives metabolic versatility in the plant pathogen Ralstonia solanacearum. PLOS
Pathog. 12:e1005939

107. Platt TG, Bever JD, Fuqua C. 2012. A cooperative virulence plasmid imposes a high fitness cost under
conditions that induce pathogenesis. Proc. Biol. Sci. 279:1691–99
108. Poh WH, Lin J, Colley B, Müller N, Goh BC, et al. 2020. The SiaABC threonine phosphorylation
pathway controls biofilm formation in response to carbon availability in Pseudomonas aeruginosa. PLOS
ONE 15:e0241019
109. Ramsden AE, Mota LJ, Munter S, Shorte SL, Holden DW. 2007. The SPI-2 type III secretion system
restricts motility of Salmonella-containing vacuoles. Cell. Microbiol. 9:2517–29
110. Rathman M, Sjaastad MD, Falkow S. 1996. Acidification of phagosomes containing Salmonella
Typhimurium in murine macrophages. Infect. Immun. 64:2765–73
111. Russell AB, Hood RD, Bui NK, LeRoux M, Vollmer W, et al. 2011. Type VI secretion delivers
bacteriolytic effectors to target cells. Nature 475:343–47
112. Saier MH Jr. 2015. The bacterial phosphotransferase system: new frontiers 50 years after its discovery.
J. Mol. Microbiol. Biotechnol. 25:73–78
113. Schechter LM, Jain S, Akbar S, Lee CA. 2003. The small nucleoid-binding proteins H-NS, HU, and Fis
affect hilA expression in Salmonella enterica serovar Typhimurium. Infect. Immun. 71:5432–35
114. Scherer CA, Miller SI. 2001. Molecular pathogenesis of salmonellae. In Principles of Bacterial Pathogenesis,
ed. EA Groisman, pp. 265–33. San Diego, CA: Academic
115. Schmidt A, Hammerbacher AS, Bastian M, Nieken KJ, Klockgether J, 2016. Oxygen-dependent regu-
lation of c-di-GMP synthesis by SadC controls alginate production in Pseudomonas aeruginosa. Environ.
116. Schulz H, Jorgensen B. Big bacteria. 2001. Annu. Rev. Microbiol. 55:105–37
117. Schuster M, Lostroh CP, Ogi T, Greenberg EP. 2003. Identification, timing, and signal specificity of
Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis. J. Bacteriol. 185:2066–79
118. Shi Z, Wang Q, Li Y, Liang Z, Xu L, et al. 2019. Putrescine is an intraspecies and interkingdom cell-cell
communication signal modulating the virulence of Dickeya zeae. Front. Microbiol. 10:1950
119. Singkham-In U, Phuengmaung P, Makjaroen J, Saisorn W, Bhunyakarnjanarat T, 2022. Chlorhexi-
dine promotes psl expression in Pseudomonas aeruginosa that enhances cell aggregation with preserved
pathogenicity demonstrates an adaptation against antiseptic. Int. J. Mol. Sci. 23:8308
120. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR, et al. 2006. Genetic adaptation of
Pseudomonas aeruginosa to the airways of cystic fibrosis patients. PNAS 103:8487–92
121. Stachel SE, Nester EW, Zambryski PC. 1986. A plant-cell factor induces Agrobacterium tumefaciens vir
gene expression. PNAS 83:379–83
122. Steele-Mortimer O, Brumell JH, Knodler LA, Méresse S, Lopes A, et al. 2002. The invasion-associated
type III secretion system of Salmonella enterica serovar Typhimurium is necessary for intracellular
proliferation and vacuole biogenesis in epithelial cells. Cell Microbiol. 4:43–54
123. Tampakaki AP, Hatziloukas E, Panopoulos NJ. 2009. Plant pathogens, bacterial. In Encyclopedia of
Microbiology, ed. M Schaechter, pp. 655–77. Amsterdam: Elsevier. 3rd ed.
124. Teixidó L, Carrasco B, Alonso JC, Barbé J, Campoy S. 2011. Fur activates the expression of Salmonella
enterica pathogenicity island 1 by directly interacting with the hilD operator in vivo and in vitro. PLOS
ONE 6:e19711
125. Tiwari M, Mishra AK, Chakrabarty D. 2022. Agrobacterium-mediated gene transfer: recent advance-
ments and layered immunity in plants. Planta 256:37
126. Torres M, Jiquel A, Jeanne E, Naquin D, Dessaux Y, et al. 2022. Agrobacterium tumefaciens fitness genes
involved in the colonization of plant tumors and roots. New Phytol. 233:905–18
127. Valentini M, Filloux A. 2016. Biofilms and cyclic di-GMP (c-di-GMP) signaling: lessons from
Pseudomonas aeruginosa and other bacteria. J. Biol. Chem. 291:12547–55
128. Vasanthakrishnan RB, de Las Heras A, Scortti M, Deshayes C, Colegrave N, et al. 2015. PrfA regulation
offsets the cost of Listeria virulence outside the host. Environ. Microbiol. 17:4566–79
129. Wagner VE, Bushnell D, Passador L, Brooks AI, Iglewski BH. 2003. Microarray analysis of Pseudomonas
aeruginosa quorum-sensing regulons: effects of growth phase and environment. J. Bacteriol. 185:2080–95
130. Wahjudi M, Papaioannou E, Hendrawati O, van Assen AHG, van Merkerk R, et al. 2011. PA0305 of
Pseudomonas aeruginosa is a quorum quenching acylhomoserine lactone acylase belonging to the Ntn
hydrolase superfamily. Microbiology 157:2042–55

131. Wang C, Ye F, Chang C, Liu X, Wang J, et al. 2019. Agrobacteria reprogram virulence gene expression
by controlled release of host conjugated signals. PNAS 116:22331–40
132. Wang J, Dong Y, Zhou T, Liu X, Deng Y, et al. 2013. Pseudomonas aeruginosa cytotoxicity is attenuated
at high cell density and associated with the accumulation of phenylacetic acid. PLOS ONE 8:e60187
133. Warr AR, Hubbard TP, Munera D, Blondel CJ, Abel zur Wiesch P, et al. 2019. Transposon-insertion
sequencing screens unveil requirements for EHEC growth and intestinal colonization. PLOS Pathog.
15:e1007652
134. Westermann AJ, Forstner KU, Amman F, Barquist L, Chao Y, et al. 2016. Dual RNA-seq unveils
noncoding RNA functions in host-pathogen interactions. Nature 529:496–91
135. Wetzel ME, Olsen GJ, Chakravartty V, Farrand SK. 2015. The repABC plasmids with quorum-regulated
transfer systems in members of the Rhizobiales divide into two structurally and separately evolving groups.
Genome Biol. Evol. 7:3337–57
136. Whiteley M, Diggle SP, Greenberg EP. 2017. Progress in and promise of bacterial quorum sensing
research. Nature 551:313–20
137. Whitman W, Coleman D, Wiebe W. 1998. Prokaryotes: the unseen majority. PNAS 95:6578–83
138. Williams P. 2007. Quorum sensing, communication and cross-kingdom signalling in the bacterial world.
Microbiology 153:3923–38
139. Wu D, Ding W, Zhang Y, Liu X, Yang L. 2015. Oleanolic acid induces the type III secretion system of
Ralstonia solanacearum. Front. Microbiol. 6:1466
140. Wu D, Lim SC, Dong Y, Wu J, Tao F, et al. 2012. Structural basis of substrate binding specificity revealed
by the crystal structures of polyamine receptors SpuD and SpuE from Pseudomonas aeruginosa. J. Mol.
Biol. 416:697–12
141. Yang S, Zhang Q, Guo J, Charkowski AO, Glick BR, et al. 2007. Global effect of indole-3-acetic
acid biosynthesis on multiple virulence factors of Erwinia chrysanthemi 3937. Appl. Environ. Microbiol.
73:1079–88
142. Ye F, Wang C, Fu Q, Yan XF, Bharath SR, et al. 2020. Structural basis of a novel repressor, SghR,
controlling Agrobacterium infection by cross-talking to plants. J. Biol. Chem. 295:12290–94
143. Yuan ZC, Edlind MP, Liu P, Saenkham P, Banta LM, et al. 2007. The plant signal salicylic acid shuts
down expression of the vir regulon and activates quormone-quenching genes in Agrobacterium. PNAS
104:11790–95
144. Zhang LH. 2003. Quorum quenching and proactive host defense. Trends Plant Sci. 8:238–44
145. Zhou D, Galán J. 2001. Salmonella entry into host cells: the work in concert of type III secreted effector
proteins. Microbes Infect. 3:1293–98
146. Zhou J, Zhang H, Wu J, Liu Q, Xi P, et al. 2011. A novel multi-domain polyketide synthase is essential for
zeamine antibiotics production and the virulence of Dickeya zeae. Mol. Plant Microbe Interact. 24:1156–64
147. Zhou L, Lei XH, Bochner BR, Wanner BL. 2003. Phenotype microarray analysis of Escherichia coli K-12
mutants with deletions of all two-component systems. J. Bacteriol 185:4956–72
148. Zhou L, Wang J, Zhang LH. 2007. Modulation of bacterial type III secretion system by a spermidine
transporter dependent signaling pathway. PLOS ONE 12:e1291
149. Zhou L, Zhang LH, Cámara M, He YW. 2017. The DSF family of quorum sensing signals: diversity,
biosynthesis, and turnover. Trends Microbiol. 25:293–303
150. Zou HS, Yuan L, Guo W, Li YR, Che YZ, et al. 2011. Construction of a Tn5-tagged mutant library
of Xanthomonas oryzae pv. oryzicola as an invaluable resource for functional genomics. Curr. Microbiol.
62:908–16

MI77_FrontMatter ARjats.cls August 12, 2023 17:59
Annual Review of
Microbiology
Volume 77, 2023 Contents
Raising a Bacterium to the Rank of a Model System:

The Listeria Paradigm
Pascale Cossart p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 1
Small RNAs, Large Networks: Posttranscriptional Regulons
in Gram-Negative Bacteria
Kai Papenfort and Sahar Melamed p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p23

Transporter Proteins as Ecological Assets and Features of Microbial
Eukaryotic Pangenomes
David S. Milner, Luis Javier Galindo, Nicholas A.T. Irwin,
and Thomas A. Richards p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p45
TonB-Dependent Transport Across the Bacterial Outer Membrane
Augustinas Silale and Bert van den Berg p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p67
Understanding Fungi in Glacial and Hypersaline Environments
Cene Gostinčar and Nina Gunde-Cimerman p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p89
Targeting Aminoacyl tRNA Synthetases for Antimalarial
Drug Development
Stanley C. Xie, Michael D.W. Griffin, Elizabeth A. Winzeler,
Lluis Ribas de Pouplana, and Leann Tilley p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 111
The ChvG-ChvI Regulatory Network: A Conserved Global
Regulatory Circuit Among the Alphaproteobacteria with Pervasive
Impacts on Host Interactions and Diverse Cellular Processes
Jennifer L. Greenwich, Brynn C. Heckel, Melene A. Alakavuklar, and Clay Fuqua p p p p 131
The Microbiology of Biological Soil Crusts
Ferran Garcia-Pichel p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 149
Frameworks for Interpreting the Early Fossil Record of Eukaryotes
Susannah M. Porter and Leigh Anne Riedman p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 173
Habitat Transition in the Evolution of Bacteria and Archaea
Alexander L. Jaffe, Cindy J. Castelle, and Jillian F. Banfield p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 193
The phc Quorum-Sensing System in Ralstonia solanacearum
Species Complex
Kenji Kai p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 213
vi
The Brucella Cell Envelope

Melene A. Alakavuklar, Aretha Fiebig, and Sean Crosson p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 233
Epigenetic Regulation and Chromatin Remodeling in Malaria Parasites
Thomas Hollin, Zeinab Chahine, and Karine G. Le Roch p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 255
Are Bacteria Leaky? Mechanisms of Metabolite Externalization
in Bacterial Cross-Feeding
James B. McKinlay p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 277
Molecular Biology of Cytoplasmic Incompatibility Caused by
Wolbachia Endosymbionts
Mark Hochstrasser p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 299
Versatility and Complexity: Common and Uncommon Facets

of LysR-Type Transcriptional Regulators

Alyssa C. Baugh, Cory Momany, and Ellen L. Neidle p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 317
The Dynamic Fungal Genome: Polyploidy, Aneuploidy and Copy
Number Variation in Response to Stress
Pétra Vande Zande, Xin Zhou, and Anna Selmecki p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 341
Factors Affecting Variation of the Human Gut Phageome
Ciara A. Tobin, Colin Hill, and Andrey N. Shkoporov p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 363
Microbiome Assembly in Fermented Foods
Nicolas L. Louw, Kasturi Lele, Ruby Ye, Collin B. Edwards,
and Benjamin E. Wolfe p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 381
Recent Advances in Understanding the Human Fungal Pathogen
Hypoxia Response in Disease Progression
Charles Puerner, Sandeep Vellanki, Julianne L. Strauch, and Robert A. Cramer p p p p p p p p 403
Toward Microbiome Engineering: Expanding the Repertoire of
Genetically Tractable Members of the Human Gut Microbiome
James W. Marsh, Christian Kirk, and Ruth E. Ley p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 427
Collab or Cancel? Bacterial Influencers of Inflammasome Signaling
Beatrice I. Herrmann, James P. Grayczyk, and Igor E. Brodsky p p p p p p p p p p p p p p p p p p p p p p p p p p 451
Essential Amino Acid Metabolites as Chemical Mediators
of Host-Microbe Interaction in the Gut
Jessica R. McCann and John F. Rawls p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 479
The Origin of Metazoan Multicellularity: A Potential Microbial
Black Swan Event
Iñaki Ruiz-Trillo, Koryu Kin, and Elena Casacuberta p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 499
Electron Transfer Beyond the Outer Membrane: Putting
Electrons to Rest
J.A. Gralnick and D.R. Bond p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 517
Contents vii
Unique Properties of Apicomplexan Mitochondria

Ian M. Lamb, Ijeoma C. Okoye, Michael W. Mather, and Akhil B. Vaidya p p p p p p p p p p p p p p 541
Mechanisms of Virulence Reprogramming in Bacterial Pathogens
Jianuan Zhou, Hongmei Ma, and Lianhui Zhang p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 561
Candida auris Genetics and Emergence
Anuradha Chowdhary, Kusum Jain, and Neeraj Chauhan p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 583
Mobile Genetic Element Flexibility as an Underlying Principle
to Bacterial Evolution
Alexandra J. Weisberg and Jeff H. Chang p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 603
Past, Present, and Future of Extracytoplasmic Function σ Factors:
Distribution and Regulatory Diversity of the Third Pillar

of Bacterial Signal Transduction

Thorsten Mascher p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p 625
License to Clump: Secretory IgA Structure–Function Relationships
Across Scales
Alyson Hockenberry, Emma Slack, and Beth M. Stadtmueller p p p p p p p p p p p p p p p p p p p p p p p p p p p p 645
Structural Insights into Type III Secretion Systems of the Bacterial
Flagellum and Injectisome
Liam J. Worrall, Dorothy D. Majewski, and Natalie C.J. Strynadka p p p p p p p p p p p p p p p p p p p p 669
Errata
An online log of corrections to Annual Review of Microbiology articles may be found at

http://www.annualreviews.org/errata/micro
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Zhou Et Al 2023 Mechanisms of Virulence Reprogramming in Bacterial Pathogens

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Annual Review of Microbiology

Jianuan Zhou, Hongmei Ma, and Lianhui Zhang

Annu. Rev. Microbiol. 2023. 77:561–81 Keywords

4.3. Switch from Infection to Colonization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 573

562 Zhou • Ma • Zhang

2. FUNDAMENTALS OF BACTERIAL VIRULENCE

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 563

2.1.2. Extracellular virulence factors. Bacterial pathogens commonly produce a range of

2.2. Acute and Chronic Infections

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 565

3. MAJOR MECHANISMS IN PROGRAMMING BACTERIAL VIRULENCE

3.1. Two-Component System

566 Zhou • Ma • Zhang

3.2. Quorum Sensing System

3.3. Interkingdom Communication System

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 567

4. REPROGRAMMING OF BACTERIAL VIRULENCE

4.1. Switch from Acute to Chronic Infection

568 Zhou • Ma • Zhang

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 569

4.2. Switch from Local to Systemic Infection

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 571

CsrB/C P PhoP P SsrB SPI-2

CsrA Fur CRP

HilC HilD HilD Propionyl-CoA Propionate

RstA HilA H-NS HilC HilA

572 Zhou • Ma • Zhang

4.3. Switch from Infection to Colonization

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 573

5. CONCLUSION AND FUTURE PERSPECTIVE

574 Zhou • Ma • Zhang

mechanisms in various microbial pathogens.

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 575

576 Zhou • Ma • Zhang

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 577

578 Zhou • Ma • Zhang

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 579

580 Zhou • Ma • Zhang

www.annualreviews.org • Mechanisms of Bacterial Virulence Reprogramming 581

Volume 77, 2023 Contents

Raising a Bacterium to the Rank of a Model System:

Kai Papenfort and Sahar Melamed p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p p23

The Brucella Cell Envelope

Versatility and Complexity: Common and Uncommon Facets

of LysR-Type Transcriptional Regulators

Unique Properties of Apicomplexan Mitochondria

Distribution and Regulatory Diversity of the Third Pillar

of Bacterial Signal Transduction

An online log of corrections to Annual Review of Microbiology articles may be found at

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