• Loading metrics

Tripping on Acid: Trans-Kingdom Perspectives on Biological Acids in Immunity and Pathogenesis

  • Michael F. Criscitiello ,

    Affiliations Comparative Immunogenetics Laboratory, Texas A&M University, College Station, Texas, United States of America, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America

  • Martin B. Dickman,

    Affiliations Department of Plant Pathology and Microbiology, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, United States of America, Norman Borlaug Center, Texas A&M University, College Station, Texas, United States of America

  • James E. Samuel,

    Affiliation Department of Microbial and Molecular Pathogenesis, College of Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America

  • Paul de Figueiredo

    Affiliations Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America, Department of Plant Pathology and Microbiology, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, United States of America, Norman Borlaug Center, Texas A&M University, College Station, Texas, United States of America, Department of Microbial and Molecular Pathogenesis, College of Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America

Tripping on Acid: Trans-Kingdom Perspectives on Biological Acids in Immunity and Pathogenesis

  • Michael F. Criscitiello, 
  • Martin B. Dickman, 
  • James E. Samuel, 
  • Paul de Figueiredo


Acid is fundamental to the immune mechanisms of eukaryotes. Therefore pathogens have evolved a myriad of strategies to evade, suppress, or exploit biological acids to gain access to host resources. Here, we describe several intracellular and extracellular pathogens to illustrate our current understanding of how acid plays central roles in animal and plant immunity, and also how it can be produced and exploited by microbes for pathogenic success.

The Importance of Acid

The pH of an aqueous solution constitutes one of its most fundamental properties. Cells and organisms are largely aqueous entities and have evolved sophisticated strategies for sensing, exploiting, and modifying the pH of their surrounding environments for assorted biological processes, including nutrient acquisition, intercellular communication, virulence, and defense against invading pathogens. At the same time, abnormal intracellular or extracellular pH values are found in several human and plant diseases, including cancer [1] and tumorigenesis in plants. The pH of the cytosol of most eukaryotic cells is slightly alkaline, at 7.2–7.4 [2]. However, cells generate and exploit biological acids for essential functions, including the denaturation of proteins destined for degradation and the activation of acid hydrolases that mediate this process [3], and as potent activators of intracellular signaling events [4][7]. Here, we focus on how biological acids are generated, exploited, and manipulated by hosts and pathogens during infection and disease progression. Our analysis features a comparative approach. We consider the function and measurement of acid in several host-pathogen systems. We provide examples of how acid is used in innate and adaptive immunity, inside and outside of cells, by pathogens of medical, agricultural, and economic importance, from bacterial and fungal Kingdoms, parasitizing both plants and animals (Figure 1). We conclude by comparing broad themes that bridge or separate the mechanisms by which evolutionarily divergent pathogens and hosts evade, subvert, or exploit biological acids.

Figure 1. Acid is found in pathogenesis and defense in diverse symbiotic relationships.

Cellular schematic shows the use of acid in innate and adaptive immunity of plant and animal cells (top). Subversion strategies of five model pathogens discussed in detail are shown in lower insets. Acid is denoted by red or H+. PAMP, pathogen-associated molecular patterns; PRR, pattern recognition receptors; R, (plant) resistance genes; MHC, major histocompatibility complex; SA, salicylic acid; JA, jasmonic acid; OA, oxalic acid.

Intracellular Acids and Their Measurement

The endocytic and phagocytic pathways of eukaryotic cells contain acidic intracellular compartments that carry out diverse functions, including nutrient acquisition [8], [9], immunological information processing [10], protein and membrane degradation [3], apoptosis [11], cellular repair and autophagy [12], and host defense [13]. Specialized functions for these pathways have often been described. In plants, for example, endocytic physiology influences gravitropism, guard cell movement, and plant hormone transport (for review, see [14]). Low pH is a critical requirement in several of these processes.

The pH of early endosomes, late endosomes, and lysosomes/vacuoles are approximately 6, 5.5, and below 5, respectively, although their pH varies with cell type, cultivation conditions, and biological context [15]. These acidic compartments communicate with one another through the vectoral exchange of membrane and protein along evolutionarily conserved trafficking pathways [10], [16]. In the endocytic pathway, extracellular proteins that are destined for internalization and degradation are captured by cell surface receptors or fluid phase engulfment. The internalized materials are sequentially trafficked from early to late endocytic compartments for delivery to acidic terminal compartments, which are designated lysosomes or terminal vesicles/vacuoles in animal and plant systems, respectively. During this process, the acidity of endocytic organelles increases. Newly synthesized proteins can also be directly delivered to endocytic compartments from the trans-Golgi network, or transported to the plasma membrane and then subsequently endocytosed. The mannose-6-phosphate receptor pathway mediates the former trafficking event [17]. Finally, contents can be delivered to acidic organelles via the autophagy pathway. In this process, membranes engulf cytoplasmic contents and/or subcellular organelles for eventual maturation and delivery to lysosomes/vacuoles, where these materials are degraded [18]. The autophagy pathway has been shown to be critical for diverse biological processes in plants, animals, and fungi, including survival during periods of nutrient limitation, (embryonic) development, apoptosis, abiotic stress, and host defense [19].

Considerable research, using yeast, insect, worm, plant, and mammalian model systems, has been performed to elucidate the mechanisms by which acidic pH is achieved within the organelles of eukaryotic cells. The acidification of organelles in the endocytic pathway has been shown to be mediated by the activity of vacuolar-type ATPase (V-ATPase) enzymes [20]. These proteins exploit ATP to drive protons into the lumen of endocytic membranes [21], [22]. In parallel with this movement of protons is the pumping of cations out of the organelle, to dissipate the development of a restrictive electrochemical gradient across the vesicular membrane [23]. Mechanisms mediating the biogenesis of acidic compartments have also been extensively investigated. In fact, the biogenesis of lysosomes and vacuoles constitutes an important subfield of cell biology [24], and several excellent reviews on this subject have recently been published [14], [25][27].

The task of measuring the pH of intracellular organelles presents several challenges. First, the subcellular organelles of eukaryotic cells are small (from 0.1 µm in fungi to 50 µm in plants) and provide no direct access to the outside environment once formed [28], [29]. Therefore, biochemical analysis of the lumen of these compartments requires their fractionation and isolation. Moreover, intracellular organelles are highly dynamic entities that change composition as they mature or travel along defined membrane trafficking pathways. This fact poses challenges to the analysis of heterogenous, often nonsynchronous populations of subcellular compartments. Hence, light microscopy approaches are favored for tracking organellar pH in living cells, and a variety of tools have been developed for this purpose.

Early estimates of the pH of intracellular organelles of plants, animals, and microbes were based upon the use of acidotropic dyes [30][33]. These molecules traverse biological membranes and accumulate in acidic intracellular organelles, thereby providing an indirect, low cost, and qualitative estimate of organellar pH. More recently, a variety of sophisticated technologies have been used to estimate intracellular pH values, including the pH of endocytic and other intracellular organelles. These technologies include pH-responsive microelectrodes [34], NMR [35], and absorbance spectroscopy [36]. However, fluorescence microscopy provides the most compelling technology for analyzing (with high sensitivity and resolution) the spatial and temporal dynamics of pH changes inside living cells. For example, probes that emit fluorescence in a manner that is dictated by their state of protonation can be used to estimate organellar pH [37]. These reagents, which include Oregon Green and engineered green fluorescent protein variants [38], also support ratiometric measurements, which can then be converted to absolute pH levels by comparison to calibration curves [39][41]. These ratiometric methods are also insensitive to changes in fluorescence introduced by parameters other than pH, including focal plane or photobleaching. Therefore, approaches that exploit ratiometric indicators provide a more precise, specific, and robust measure of organellar pH than their acidotropic fluorophore counterparts, like LysoTracker [42]. Finally, fluorescent ratiometric analyses of intracellular pH can be extended to investigate interactions between intracellular pathogens and host cells by labeling live pathogens with pH-sensitive dyes (carboxyfluorescein, fluorescein, or Oregon Green) so that viability is not compromised, infecting host cells with the labeled pathogens, and then performing coincident analysis of pathogen intracellular trafficking and vacuolar pH [43].

Acids in Immune Systems

Biological acids play central roles in both innate and adaptive immune systems that dictate host-pathogen interactions. All living things possess innate immune mechanisms, while vertebrates benefit from the classically defined, lymphocyte-mediated adaptive immunity as well.

Acid in Innate Immunity

In animal innate immunity, acid functions extracellularly and intracellularly. Low pH plays an important role extracellularly in controlling the microbial flora at mucosal sites, particularly in tetrapod vertebrates. The gastric acid of the stomach limits the range of prokaryotes that can continue down the alimentary canal to join intestinal populations [44]. The vaginal microbiome maintains an acidic environment that limits protozoan, fungal, and bacterial infections [45]. Intracellularly, biological acids and acid hydrolase enzymes mediate the killing of non–acid-adapted organisms that are phagocytosed into progressively acidifying vesicles epitomized by the lysosome. This process still provides predatory feeding and phagotrophic nutrition for some protists [46]. Pattern recognition receptors (PRR) such as the Toll-like receptors (TLR) bind perceived threats by recognition of pathogen-associated molecular patterns (PAMPs). In addition to signaling the innate immune system, PRR recognition of PAMPs in triploblastic animals can doom PAMP-bearing microbes to phagosomal degradation in acidic vesicles [47]. Moreover, several PRR such as TLR-3, TLR-7, and TLR-9 have evolved to sense nucleic acid PAMP from acidic endosomes, rather than the cell surface, taking advantage of the acidic degradation of virus and virus-infected cells by the low-pH vesicle to sense pathogen-indicative double-stranded RNA, single-stranded RNA, or DNA with unmethylated CpG dinucleotides [48]. Thus, acid is used both to selectively control microbial populations on animal surfaces by filtering them based upon acid tolerance, and to identify and eradicate those that are engulfed by patrolling leukocytes.

Plants rely on the innate immune system for defense by sensing pathogen-derived molecules for nonself recognition [49]. Plant immune receptors are known as PRR that recognize PAMPs, such as bacterial flagellin and fungal chitin as well as plant-derived signals that arise from damage caused by pathogen challenge, known as damage-associated molecular patterns (DAMPs). PAMP and DAMP recognition is ancient and shared by plants and animals. PRR binding activates broadly but moderately effective PAMP-triggered immunity (PTI). Plant pathogens have evolved mechanisms to breach this line of defense by acquisition of effector molecules that are secreted into the plant cell and perturb host immune responses by either avoiding detection or suppressing PTI signal transduction. In the continuing arms race, plants have developed a second tier of defense in which resistance gene products (R proteins) [49] mediate recognition of specific pathogen effectors and trigger effector-triggered immunity (ETI), which generally culminates in host programmed cell death. R gene products contain leucine-rich repeats (LRR) and nucleotide binding sites and belong to the CATERPILLAR/NOD/NLR family of proteins that mediate cytosolic PAMP surveillance in animals as well [50], thus exhibiting trans-kingdom conservation.

Organic acids are crucial messengers of effector-triggered immunity activated by R gene products of plants. These include the hormone salicylic acid that mediates endogenous defense signals and transmits systemic responses that orchestrate systemic acquired resistance [51]. This response is thought to be one of an antagonistic triumvirate of acid-regulated stress responses in plants, including jasmonic acid for wound healing and insect protection and abscisic acid for environmental stresses [52]. Ethylene signaling has somewhat redundant overlap with these latter two. Acids are also used in the pathogenic counterattack, as several necrotrophic (requiring dead tissue/cells for growth and reproduction) plant pathogens produce oxalic acid to control host cell death programs, as discussed in more detail below.

Acid in Adaptive Immunity

The adaptive immune system shared by jawed vertebrates is mediated by lymphocytes and has hallmark characteristics of specificity and memory. The adaptive system enables the preemptive engineering of our lymphocyte repertoires through immunization, one of the most powerful tools for global public health in the face of infectious disease. Like the plant ETI, the adaptive system is a second line of defense behind the innate system. While slower in initial response in comparison to the innate, the adaptive system is plastic in its mitotic expansion and contraction capability, surgical in the fine molecular specificity of its targeting, and diverse in its effector mechanisms tailored to classes and locales of pathogen.

The vertebrate adaptive immune system works in conjunction with the more ancient innate system. The adaptive system may have originally evolved to manage the vast populations of commensal (better termed mutualistic) bacteria at mucosal surfaces where low pH was already in use [53]. When the relationship between host animal and symbiont turns parasitic, immune mechanisms are used to eliminate or contain the microbe and limit pathology, akin to the “hypersensitive response” of plants.

Most adaptive immune responses require activation of specific helper T lymphocytes, and the low-pH phagolysosomal system is important for this activation. Unlike B cells that recognize free antigen, T cells recognize peptide antigen in the context of major histocompatibility complex (MHC) molecules. Two different classes of MHC molecules present peptide to two different classes of T cells [54]. Helper T cells are restricted to being activated only by MHC class II molecules on antigen-presenting cells (APC) that present peptide antigen. Dendritic cells are the best APC, but macrophages and B cells are also very competent in T cell activation. This APC hurdle is a major checkpoint to initiating an adaptive immune response (Figure 2). For example, macrophages harboring wily intracellular stowaways typically need “help” via cytokine and co-stimulatory signals from an activated helper T cell to in turn become activated and execute effector functions. Helper T cells can only be activated by presentation of peptide antigens specific for their somatically recombined T cell receptor gene products in the context of self-MHC class II molecules. This MHC class II–presented antigen must arise from an APC that has itself been activated by ligation of its innate PRR (such as TLR). The generation of the antigenic peptides presented by APCs is acid dependent.

Figure 2. Acid's role in initiating adaptive immunity.

An antigen-presenting cell activated by innate PRR will present peptide antigen generated in acidic vesicles to a helper T cell via MHC class II. Activated by this presentation of specific antigen, the helper T cell can then mediate many different immune effector functions, depending on the subtype of helper CD4+ T cell, context, and signals from the APC. Five such major immune effector pathways are suggested here.

The low pH of compartments of the phagolysosomal pathway is co-opted by the adaptive as well as the innate immune system for defensive purposes. We suggest that the cellular physiology of this pathway has evolved from functioning in recycling of cellular debris and tissue remodeling in early eukaryotes [46], to functioning primarily for nutritional purposes in heterotrophic protozoa, on to the killing of pathogens in innate immunity [55], and finally to elegant regulation of adaptive immunity via antigen processing [56] (Figure 3). Jawed vertebrates use a sophisticated antigen processing pathway to load MHC class II with peptide antigen from the acidified phagolysosome. Newly synthesized class II α and β chains assemble in the pH-neutral endoplasmic reticulum [57] together with a glycoprotein called the invariant chain [58], [59]. An important role of the invariant chain is to keep MHC class II from being loaded prematurely with peptide from the endoplasmic reticulum or Golgi, retaining that place for products of the acidified phagolysosomal system.

Figure 3. Phylogeny of acidic phagolysosome use in immunity.

Simplified phylogeny of life, marking major hypothesized steps supported by current comparative biology in the co-opting of the acidic phagolysosome system in innate and adaptive immunity (blue). Sister taxon names are illustrative and not necessarily of same phylogenetic rank, and genetic distances are not to scale. All life has innate immunity, but only vertebrates have adaptive immunity (red). Origins of key proteins that regulate the system are shown in green.

In the trans-Golgi, the MHC class II/invariant chain complex is diverted from the secretory pathway to the endocytic pathway (Figure 4). In the low pH of the MHC class II compartment, cathepsin proteases are activated to further cleave the invariant chain, leaving only CLIP (the class II–associated invariant chain peptide) in the peptide binding cleft [60]. HLA-DM can then bind class II and catalyze the release of CLIP, facilitating its exchange for phagolysosomal antigenic peptides before MHC transport to the cell surface. Pathogen blockade (e.g., by the human immunodeficiency virus) of the progressive cleavage of the invariant chain results in the accumulation of invariant chain intermediates, constipation of the antigen presentation pathway, and immunoevasive reduced surface expression of MHC class II [61].

Figure 4. Acid-active cathepsins cleave phagolysosomal antigens in the MHC class II pathway.

Phagocytosed antigens are degraded to peptides (grey) by acids and acid-active cathepsin proteases as the endosomal pH decreases due to fusion with lysosomes (1). During their trafficking from the ER to the cell surface, MHC class II molecules (light green) pass through these acidified vesicles (2). Invariant chain (red) chaperones MHC class II from the ER to an acidified endosome, all the while protecting the peptide binding groove of MHC class II from premature loading (3). Invariant chain is cleaved by cathepsins but leaves the CLIP portion (red triangle) in the MHC peptide binding site (4). In a specialized late endosome, the MHC homolog HLA-DM finally binds to the MHC class II/CLIP complex and releases CLIP (5), allowing other peptides to bind before the MHC class II travels to the cell surface (6). There it can present antigen to T cells (7).

Cathepsins, related to papain, are the crucial acid-activated proteases that cleave the invariant chain and also degrade lysosomal contents to peptides appropriate for antigen to be loaded in MHC class II [62]. The cathepsins primarily involved in antigen processing are L and S. Although invariant chain and cathepsins of adaptive immunity likely evolved with the jawed cartilaginous fishes (gnathostomes, see Figure 3) [63], comparative phagosome proteomics show acid-active cathepsins to be an original and fundamental component of the ancestral eukaryotic phagolysosomal system [64].

Thus, the acidic phagolysosomal system prepares peptide antigens for the initiation of most cellular adaptive immune responses, mediated by the MHC class II system of presentation to helper T cells.

Acids in Host-Pathogen Interactions

Given the role that acid plays in host defense and antigen presentation in animal pathosystems, it is perhaps not surprising that both plant and animal pathogens have evolved sophisticated systems for adapting to, avoiding, or subverting the threats that acidic environments and acid-mediated defense processes pose. We illustrate this point using two intracellular bacterial pathogens—Coxiella burnetii and Brucella melitensis—which have evolved disparate strategies for adapting to life in acidic environments and avoiding killing by acidic organelles. Two extracellular mucosal pathogens—Helicobacter pylori and Escherichia coli—exemplify tactics used to colonize the extreme pH of the alimentary canal. In addition, we describe the way in which the plant pathogens Agrobacterium tumefaciens and Sclerotinia sclerotium exploit and produce acidic environments, respectively, to promote their pathogenic programs. These host-pathogen systems have been chosen both for their position as major models in which acid defense mechanisms have been elucidated as well as their importance in human, animal, and plant pathology.

Intracellular Acid

Many organisms generate and use acidic environments to thwart infection by pathogens. However, some pathogens have evolved elegant strategies to defeat these acidic defense mechanisms, including the ability to withstand or thrive in highly acidic environments. The intracellular pathogen Coxiella burnetii provides a compelling example of such an adaptation. The Gram-negative bacterium C. burnetii is the causative agent of Q fever. Its natural reservoir in the United States consists mainly of dairy cattle, sheep, and goats [65], and its extreme infectivity (single bacterium [66]) led to its weaponization before the United States' biological warfare program was terminated in 1969 [67].

C. burnetii replicates within phagolysosome-like Coxiella-containing vacuoles (CCVs) and is dependent on the low pH of this compartment to activate a developmental process that turns metabolically quiescent small cell variants (SCV) into their metabolically active, replicating large cell counterparts [68] (Figure 5A). C. burnetii is taken up via complement receptor 3 and αvβ3 integrin-mediated mechanisms into macrophages [69]. Actin-dependent phagocytosis leads to trafficking through an early endosome, progressing to late endosome and the phagolysosome-like terminal CCV [70], [71]. The trafficking appears slightly delayed compared with latex bead uptake [72], and membrane markers for Rab5, Rab7, Rab24, microtubule-associated protein-1 light chain alpha 3 (LC3), lysosomal-associated membrane proteins (LAMP)-1, LAMP-2, and LAMP-3, and flotillin 1 and 2 progressively decorate the CCV [73][75]. Connection to the autophagosome compartment appears essential to support the biogenesis of a compartment that can support productive replication of the pathogen [74], [76]. In addition, CCV membrane development to a spacious vacuole requires access to continual host-derived cholesterol biosynthesis [77], [78] and connection to a canonical secretory pathway [79].

Figure 5. Coxiella and Brucella use distinct mechanisms for intracellular pathogenesis.

A. C. burnetti thrives in the acidic phagolysosome system, requiring low pH for the transition from quiescent small cell variants (SCV) to metabolically active large cell variants (LCV). Several of the transmembrane proteins that mark the Coxiella-containing vacuole (CCV) through this transition are shown. The Dot/Icm type IV secretion system is used by C. burnetti to deliver proteins into the host cytosol [138], and renovate the lysosome into a CCV [139]. Cb, Coxiella burnetti; Atg, autophagosome; Lys, lysosome. B. Working model of Brucella intracellular parasitism. Brucella-containing vacuoles avoid fusion with acidic lysosomes, and instead traffic to a compartment that is decorated with ER markers for replication. The Type IV secretion system (T4SS) of the pathogen is critical for appropriate trafficking, and mutants that harbor mutations in the T4SS traffic to the lysosome where they are killed. Several T4SS secretion substrates have been identified, and it has been postulated that these molecules contribute to supporting the intracellular lifestyle of the pathogen. Replicative Brucella can exit cells by trafficking along a pathway that involves selective interactions with components of the host cell autophagy biogenesis machinery. Approximate vesicular/vacuolar pH is indicated by color, and the Golgi is generally more acidic than the ER [57, 140142].

Several lines of investigation support the hypothesis that maintenance of the acidic pH of the spacious vacuole is essential for C. burnetii replication. First, studies using ratiometric, pH-sensitive probes have demonstrated that C. burnetii replicates in vacuoles that possess an acidic pH [80]. Inhibition of host vacuolar ATPase activities that maintain the acidic pH of late endocytic and lysosomal compartments by treatment with bafilomycin significantly impairs the intracellular replication of the pathogen. Similarly, neutralization of vacuolar pH by treatment with the chaotropic agent chloroquine inhibits intracellular replication [81]. Taken together, these data indicate that the C. burnetii replicative niche has an acidic pH, and raise many questions about the mechanisms by which Coxiella and other acid-adapted intracellular pathogens survive in the highly acidic environment of the CCV terminal compartment [82], [83].

Several strategies have been proposed to contribute to acid tolerance of C. burnetii, and the development of axenic growth conditions and suicide plasmid-based targeted gene deletion methods is allowing identification of virulence mechanisms and genes in this model [84]. First, the intracellular trafficking of the pathogen along the endolysosomal pathway pauses immediately after entry [72]. This pause in phagolysosomal maturation has been hypothesized to play a critical role in acid adaptation by providing the pathogen with sufficient time to prepare (through the expression of acid tolerance factors) for the onslaught of acid that follows. Second, stress-response and vacuole-detoxification genes are dramatically upregulated when the pathogen invades host cells, thereby supporting its adaptation to the harsh vacuolar environment [85]. Finally, C. burnetii encodes an unusually high number of basic proteins. The average pI value for all predicted proteins in the genome of the Nine Mile reference strain is 8.25 [86], [87]; 60% of the proteome is acidic [88]. Moreover, approximately 45% of C. burnetii proteins were found to have a pI value of ≥9, which is higher than the sequenced genomes of other intracellular bacterial pathogens [89]. Orthologous products of the RpoS genes of E. coli (pI 4.6) and C. burnetti (pH 9.6) serve as striking examples of the extreme acid adaptation of a protein while maintaining a conserved function. It is hypothesized that Coxiella's skew toward production of basic proteins provides a proton sink to buffer those protons that enter the cytoplasm [88], [90]. While the low pH of the phagolysosome is a crucial parameter, Coxiella tolerates cathepsin and other acid protease action while thriving in this environment. Coxiella therefore illustrates how pathogens can adapt to acidic compartments.

In an alternative strategy, intracellular bacterial pathogens can address the threat that acidic intracellular compartments pose by minimizing their interactions with them. The intracellular bacterial pathogen Brucella spp. provide excellent models to analyze this strategy for addressing the threat that intracellular acidic vacuoles pose to invading pathogens. Brucella spp. are causative agents of brucellosis, a zoonosis of global importance [91]. In humans, the disease causes severe, debilitating, and protracted symptoms, and affects practically every organ system of the body. Brucellosis often presents in the clinic as an undulant fever [92]. However, chronic infections are frequently associated with osteoarticular disease with neurological complications. The reproductive system is also a common site of infection, and infection during pregnancy may increase the risk of spontaneous abortion. Consumption of unpasteurized milk products from infected animals is the most common route to human infection [92]. However, Brucella is highly infectious and can be readily transmitted in aerosolized form [93]. Brucellosis has eluded systematic attempts at eradication, even in most developed countries, and no human vaccine is available [94]. These features contribute to the classification of Brucella as a potential bioterror agent, and to the interest the biosecurity and world health communities have expressed in this organism.

During their intracellular trafficking within host cells, Brucella-containing vacuoles (BCVs) interact but avoid fusion with the host lysosome [95], [96] (Figure 5B). Instead, replicative BCVs become decorated with markers for ER [97]. Mutant strains harboring defects in the Type IV secretion system do not avoid fusion with acidic lysosomal compartments, and instead are rapidly killed after fusion with this organelle [98]. In mouse models of brucellosis, the organism persists for months in the lymph nodes and spleen [99]. However, colonization by even the most virulent strains becomes undetectable with time [100]. The persistence of this organism in the ER of host APCs may be crucial for chronic infection. Thus, avoiding the harsh environment of the host cell's acidic degradative organelles is critical to the survival and replication of this intracellular bacterial pathogen.

Extracellular Acid in Animals

Several notable microbial pathogens, including those that infect the gastrointestinal or urogenital tracts of humans and animals, exploit or create extracellular acidic environments to promote their pathogenic programs. For example, pathogenic E. coli (strain 0157:H7), Vibrio cholerae, Vibrio vulnifus, Shigella flexneri, and Salmonella typhimurium are found in neutral pH environments (on food products or in water). However, after ingestion by their mammalian hosts, these pathogens encounter the severe acidic environment of the stomach (pH = 2 or lower) or urogenital systems, which normally constitute important barriers to infection by non–acid-adapted organisms. These parasites, however, have evolved sophisticated and divergent strategies to tolerate these harsh acidic environments.

A significant human pathogen that provides an understanding of an alternative strategy by which an extracellular acidic niche can be occupied is Helicobacter pylori, the agent whose colonization is associated with chronic gastrointestinal diseases ranging from dyspepsia to gastric and duodenal ulcers to gastric carcinoma [101], [102]. This organism chronically infects the stomach, surviving the very low pH of the lumen, burrowing into the mucus with flagella to attach to and occasionally invade epithelial cells. Survival in this environment is dependent on expression of copious amounts of urease, converting urea into buffering ammonia plus carbon dioxide [102]. In this strategy, H. pylori maintains a periplasmic pH at ∼6.1, while the extracellular environment can be as low as 2.0. The reaction products of urease apoenzyme (ureA and ureB) are driven specifically to the periplasmic compartment by a protein (UreI) encoded in a gene cluster with urease. UreI is a pH-gated inner membrane urea channel allowing for efficient transit to the cytoplasm of substrate (urea) and periplasmic release of reactant NH3, which is rapidly converted to NH4 by membrane-bound α-carbonic anhydrase. The transcriptional expression control, post-transcriptional recruitment, and enzymatic activity of H. pylori urease is optimized to function in a microenvironment of pH 3.5–∼6.0 [103].

H. pylori is specialized for the extreme pH of the stomach, but enteric species survive passage through the stomach for colonization of the lower gut. Many E. coli efficiently colonize the intestine, and provide a complementary window for understanding how pathogens address the challenge of acidic environments. The acid stress response systems of Gram-negative enteric pathogens are both enzyme and chaperone based, and include resistance pathways that exploit glutamate-, arginine-, and lysine-decarboxylase enzymes [104]. E. coli contains five acid resistance pathways (AR1–5), which work in concert to resist the highly acidic environment that the pathogen encounters in the gut [105]. In the AR2 system of E. coli, for example, the pyridoxal 5′ phosphate (PLP)-dependent GadA and GadB decarboxylases convert glutamate to gamma-amino butyric acid (GABA) and carbon dioxide (CO2) in a reaction that consumes a cytoplasmic proton [106]. The inner membrane antiporter GadC then transports GABA out of the cell in exchange for additional glutamate [106]. Thus, the pathogen mitigates acid stress by promoting the net export of protons outside of the cell at the expense of intracellular glutamate. Analogous systems that exploit arginine and lysine also contribute to maintaining the pH homeostasis of the cytoplasm.

Thus gut pathogens use a variety of active biochemical systems to maintain periplasmic and cytoplasmic pH at tolerable levels amidst the low luminal pH of the gastrointestinal tract.

Extracellular Acid in Plants

Analysis of interactions between plant pathogens and their host plants provides additional insights into the role of acid in host-pathogen interactions that cannot be fully appreciated by the exclusive analysis of animal systems. The bacterial pathogens Agrobacterium tumefaciens and Erwinia amylovora, the causative agents of crown gall disease in diverse dicotyledenous plants and fire blight in apples, pears, and Rosaceous crops, respectively, induce disparate and nonoverlapping disease symptoms in plants. Nevertheless, these pathogens respond to environmental acids by modulating their virulence programs, and thus provide ideal illustrations of an important mechanism by which pathogens of both plants and animals respond to acidic extracellular environments in the context of the host-pathogen interaction.

In the Agrobacterium system, environmental acids drive the induction of the pathogen's virulence program. Specifically, the acidic environment created by wounded plant tissues, as well as plant-derived phenolic compounds present there, activate the expression of bacterial virulence genes (vir regulon) on the tumor-inducing (Ti) plasmid [107]. This activity, in turn, drives the assembly and transfer of the Agrobacterium-derived T-DNA from the bacterial pathogen to host cells. The T-DNA integrates into the host plant genome, triggering factors that mediate the generation of a tumor (gall) in plants. Interestingly, the acidic conditions that initiate the T-DNA virulence program of Agrobacterium elicit two additional and distinct responses in the pathogen—a conserved response associated with the adaptation of the pathogen to environmental acidification, and the intricate response that regulates the establishment of a stable, long-term plant-pathogen interaction [108]. Genes induced by the former response, such as the motility gene flaA and the heat-shock protein ibpA, are highly conserved and play corresponding roles in acid adaptation in other microbial systems, including in the bacterial pathogens of animals (e.g., E. coli, Salmonella spp.) [108]. An important component of the latter response is regulated by the activities of acidic plant hormone signaling molecules, including salicylic acid (SA), indole-3-acetic acid (IAA), and gamma-amino butyric acid (GABA) [109] (more on plant hormones in the following section). These plant acids generally signal through biochemically distinct and independent bacterial pathways to function additively to shut off the Agrobacterium virulence program and activate the quorum-quenching machinery, which promotes the establishment of a stable host-pathogen interaction. However, signal input from one pathway (an environmental stress response signaled through abscisic acid during a drought, for example) can inhibit the activation of another (such as a jasmonic acid signal for wound repair stimulated by herbivory). The activation of quorum-sensing machinery as part of the process of establishing a stable host-pathogen interaction represents a conserved theme in the virulence programs of many bacterial pathogens [110].

Extracellular acidic environments can also influence the virulence of fungal pathogens of plants, including Ustilago maydis [111], Fusarium oxysporum [112], and Sclerotinia sclerotiorum [113], the causative agents of tumorigenic corn smut, Fusarium wilt, and white mold diseases of all broadleaf plants, respectively.

Plant Hormones

Analogous to animal hormones, plant hormones play key roles in the control of development, growth, reproduction, and, of relevance for this discussion, the regulation of immune responses to microbial pathogens. Of the principal plant hormones, five are acids, including: salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), indole acetic acid (IAA), and gibberellic acid (GA) [114]. SA and JA and their derivatives are structurally and functionally akin to aspirin and prostaglandins, respectively. SA and JA are recognized as major defense hormones with the classical view that SA is effective against biotrophic pathogens and JA against necrotrophs, although there are exceptions [52]. Moreover, crosstalk occurs between these hormones that is often antagonistic; elevated biotroph resistance (SA) results in elevated necrotroph susceptibility and vice versa.

Systemic acquired resistance (SAR) is induced in the plant by SA following pathogen challenge. When established, SAR affords long-lasting and broad-spectrum resistance including uninfected tissue. SA levels increase following initial pathogen attack and are strongly correlated with establishment of SAR [115]. This observation is strengthened by the fact that plant treatment with exogenous SA or biologically active chemical analogs leads to SAR. Moreover, blocking SA synthesis inhibits SAR [116]. Considerable effort has been undertaken to identify the regulatory pathways mediating SAR. Of note, mutants of the npr1 locus were found to prevent SA signaling [117]. In the uninduced state, cytosolic NPR1 is present as an oligomer via intermolecular disulfide bridges. Following SA-mediated SAR induction, alterations in cellular redox result in a reduced state leading to disassociation of the complex and release of monomeric species. Monomeric NPR1 translocates to the nucleus, interacts with the leucine zipper transcription factor TGA1 that binds to promoters of SA-responsive genes, and activates defense gene expression [118].

The jasmonate family comprises lipid-derived metabolites synthesized via the oxylipin pathway [119]. Upon synthesis, JA can be metabolized to methyl jasmonate or conjugated to amino acids [120]. Most JA responses are mediated by the F-box protein coronatine insentive 1 (COI1). Coi1 mutants are more resistant to bacterial pathogens and show elevated SA levels [121]. In accordance with SA-JA antagonism, coi1 plants are more susceptible to several, but not all, necrotrophic fungi. Exogenous application of JA induces broad changes in transcription patterns—in particular, of genes regulated by MYC2, a basic helix loop helix transcription factor [122]. Genetic studies revealed a family of 12 jasmonate ZIM-domain–containing (JAZ) proteins that repress JA signaling. JAZ proteins can homo- and heterodimerize in vitro, suggesting a possible mechanism for fine-tuning signaling responses [123]. Binding of conjugated JA or coronatine to SCFCOI1 promotes ubiquitination of JAZs leading to proteasome degradation, relieving repression of MYC2, and facilitating activation of JA-responsive genes [124]. Alternative splicing of the c-terminal JAS domain of JAZ proteins results in reduced ubiquitination and thus reduced degradation.

Although JA is central to modulating defense against necrotrophic pathogens, it is increasingly important in other aspects of plant-pathogen interactions including SAR [125]. Once the JA pathway is activated (e.g., after wounding), a similar JA response can be triggered in distal undamaged parts of the plant. The antagonism between SA and JA signaling pathways in plants show a dramatic resemblance to the effect of the anti-inflammatory drug aspirin, which is an acetylated form of SA, on prostaglandins. Prostaglandins are structurally related to JA, and these hormones function at sites of infection or injury. SA/JA crosstalk shows similarities with the inhibitory effect of aspirin to prostaglandins in mammalian cells; however, the molecular bases of these interactions are not identical [126].

The phytopathogenic fungus Sclerotinia sclerotiorum provides an informative model to illustrate acid-dependent pathogenic development. This fungus produces copious amounts of the dicarboxylic acid oxalic acid (OA) as part of its virulence arsenal, but also uses OA to reprogram host signaling and modulate programmed cell death to coordinate effective pathogenesis [113].

Sclerotinia is an economically important necrotrophic fungal pathogen of plants with an extremely broad host range (all broadleaf dicot plants). The primary component for pathogenic success is the production and secretion of oxalic acid by the fungus [127]. Oxalic acid is found in plants, animals, and humans and is the endpoint of several metabolic processes such as the breakdown of glyoxylic acid or ascorbic acid [128], [129]. In mammals, oxalic acid plays an important role in kidney stone formation as a counter ion of calcium-forming oxalate crystals [130].

In fungi, this “simple” organic acid is remarkably multifunctional and contributes to numerous physiological and pathogenic processes [131] (Figure 6). Oxalate-deficient mutants of S. sclerotiorum are nonpathogenic on all host plants tested and are also unable to develop sclerotia—highly melanized, durable overwintering structures. Oxalate secretion might enhance Sclerotinia virulence in several ways. Many fungal enzymes secreted during invasion of plant tissues (e.g., pectinases) have maximal activities at acidic pH and have been shown to be activated by OA. A Sclerotinia MAP kinase has also been identified and characterized [132], and has been shown to be required for sclerotia formation in S. sclerotiorum. Gene expression of this Erk-like MAPK (SMK1) is triggered by acidic pH mediated by OA; if acidification does not occur, pathogenic development is blocked [133], [134].

Figure 6. Stages of Sclerotinia pathogenesis.

Early steps of infection create a reducing environment that dampens host defense responses and inhibits reactive oxygen species (ROS). This allows the fungal pathogen to establish and damage host tissues with cell wall degradative enzymes (CWDE). When eventual apoptotic cascades are induced, recognition occurs but too late for the host plant to prevail. (adapted from [143]).

OA has several other deleterious effects upon the plant. It can degrade or weaken the plant cell wall via acidity and/or chelation of cell wall Ca2+. Oxalic acid crystals are sequestered in vacuoles, and when decompartmentalized during infection, these crystals can plug the vascular system. Oxalic acid in and of itself is directly toxic, functioning as a non–host-specific phytotoxin. While these features are correlated with fungal disease development, they do not account for wild-type pathogenesis [135].

OA can function as an elicitor of apoptotic-like plant programmed cell death, involving the modulation of the host redox environment [136]. The induction of apoptosis and disease requires generation of reactive oxygen species (ROS) in the host, a process triggered by fungal-secreted OA. Curiously, the programmed cell death process mediated by OA is independent of acidification; a direct correlation between DNA laddering, ROS induction, and cell death were all observed at neutral pH. When acidification via OA occurs, cells also die but in a mechanistically different way: necrotically without hallmarks of apoptosis such as plasma membrane blebbing and chromosomal DNA fragmentation. The specificity of this interaction is further supported by the observation that DNA fragmentation is specific to OA, as other acids such as citric acid, succinic acid, and hydrochloric acid do not induce DNA ladders [137]. DNA cleavage also was independent of oxalate formulation because OA, potassium oxalate, and sodium oxalate all caused DNA laddering, thus suggesting that programmed cell death induction is not due to the acidic nature of oxalate but rather to a property of OA itself.

Conversely, during the initial stages of infection, OA also dampens the plant oxidative burst—an early host response generally associated with plant defense. Experiments using a transgenic redox-regulated GFP reporter show that, initially, Sclerotinia (via OA) generates a reducing environment in host cells that suppresses host defense responses including the oxidative burst. Once infection is established, however, this necrotroph induces the generation of plant ROS leading to PCD of host tissue, the result of which is of direct and sole benefit to the pathogen. In contrast, a nonpathogenic, OA-deficient mutant failed to alter host redox status and induced autophagy and restricted growth. These results indicate active recognition of the mutant by the plant and further point to the importance of cell death control in mediating host-pathogen interactions.

Taken together, these data suggest that Sclerotinia establishes reductive conditions that dampen the host oxidative burst and suppress defense responses [135]. This scenario buys precious time, allowing for unimpeded fungal growth and establishment. When the plant eventually senses the presence of nonself, it is too late; the fungus is already inducing the programmed cell death of host cells.

Conclusions and Perspective

Just as pH is a fundamental property of living systems, acid is employed by both host and pathogen in their ever-escalating arms race. On the side of the host, acid is used in a variety of mechanisms, including extracellular innate immunity at mucosal surfaces and extreme pH in the case of the mammalian stomach. Yet some pathogens have evolved mechanisms to defeat the natural defense that the acidic environment provides, exemplified by Helicobacter's urease system that keeps its periplasm close to neutral and E. coli's glutamate decarboxylase pathway that removes cytoplasmic protons as a component of its acid response. Acid is important in plant extracellular immunity as well and is a characteristic of wounding, but Agrobacterium senses this drop in pH and counters with acid-based signaling programs to ramp up and attenuate virulence effectors. Fungi such as Sclerotinia use OA to subvert host defense and co-opt host signaling pathways, triggering cell death via apoptosis of host cells. Thus fungal (OA) induced metabolic reprogramming of the host results in apoptosis, providing nutrients exclusively for the benefit of the necrotrophic organism.

The adaptive immune system of vertebrates pirated the acidic phagolysosomal system for not only pathogen killing but also for antigen presentation to T cells. Vesicular acid and acid-activated proteases such as cathepsins are critical to antigen processing for MHC loading. But some microbes have evolved mechanisms to cope with the low pH of vacuoles, such as Coxiella, while others have managed to reprogram the vesicle trafficking to mitigate interactions with harmful acidic organelles (e.g., lysosomes), as does Brucella. Ratiometric dyes have been crucial in facilitating the analysis of these intracellular organelles and the pathogenesis that occurs there. Table 1 lists additional pathogens that exploit or evade acid beyond the scope of this review.

From the perspective of natural history, we see the mechanisms by which organisms exploit or subvert biological acids as central to their evolutionary success. Thus acid is one of a small, select number of fundamental biological arenas in which organic life has long fought. For example, membranes create a defined space for orderly biochemistry where metabolism and other necessities can occur protected from the chaos beyond the phospholipid bilayer. Naturally, immune systems evolve enzymes such as lysozyme, perforin, and the membrane attack complex of the complement cascade to disrupt the membranes, but pathogenic microbes evolve complex cell walls and capsules to protect and then elaborate secretion systems to breach these barriers. These are but a few of the many mechanisms and counter-mechanisms that operate at the theater of war that is the plasma membrane. Similarly, genomic integrity is also an important battleground; therefore, the simplest of organisms have elegant DNA repair systems, high-fidelity replication enzymes, and restriction endonucleases. Yet viruses still integrate, and even counter by exploiting the rapid evolution afforded by replication errors. In turn, the adaptive immune system employs somatic hypermutation of antibody genes in a Darwinian germinal center reaction to hone high-affinity receptors against ever-shifting pathogen antigens.

Just as the plasma membrane and the genome are core components of life to be protected, exploited, and used in defense and offense, so is the pH of spaces large (stomach) and small (phagolysosome). It should come as no surprise that acids are used to great effect in signaling, killing, protecting, hiding, sampling, and evading by both host and microbe, and we should look to the trenches of protons and hydroxides for continued exploitation by both immune and pathogen systems.


  1. 1. Webb BA, Chimenti M, Jacobson MP, Barber DL (2011) Dysregulated pH: a perfect storm for cancer progression. Nat Rev Cancer 11: 671–677.
  2. 2. Roos A, Boron WF (1981) Intracellular pH. Physiol Rev 61: 296–434.
  3. 3. Ciechanover A (2012) Intracellular protein degradation: from a vague idea thru the lysosome and the ubiquitin-proteasome system and onto human diseases and drug targeting. Biochim Biophys Acta 1824: 3–13.
  4. 4. Chen Y, Kung HN, Chen CH, Huang SH, Chen KH, et al. (2011) Acidic extracellular pH induces p120-catenin-mediated disruption of adherens junctions via the Src kinase-PKCdelta pathway. FEBS Lett 585: 705–710.
  5. 5. Tomura H, Wang JQ, Komachi M, Damirin A, Mogi C, et al. (2005) Prostaglandin I(2) production and cAMP accumulation in response to acidic extracellular pH through OGR1 in human aortic smooth muscle cells. J Biol Chem 280: 34458–34464.
  6. 6. Kato Y, Lambert CA, Colige AC, Mineur P, Noel A, et al. (2005) Acidic extracellular pH induces matrix metalloproteinase-9 expression in mouse metastatic melanoma cells through the phospholipase D-mitogen-activated protein kinase signaling. J Biol Chem 280: 10938–10944.
  7. 7. Xu L, Fukumura D, Jain RK (2002) Acidic extracellular pH induces vascular endothelial growth factor (VEGF) in human glioblastoma cells via ERK1/2 MAPK signaling pathway: mechanism of low pH-induced VEGF. J Biol Chem 277: 11368–11374.
  8. 8. Korolchuk VI, Saiki S, Lichtenberg M, Siddiqi FH, Roberts EA, et al. (2011) Lysosomal positioning coordinates cellular nutrient responses. Nat Cell Biol 13: 453–460.
  9. 9. Kuma A, Mizushima N (2010) Physiological role of autophagy as an intracellular recycling system: with an emphasis on nutrient metabolism. Semin Cell Dev Biol 21: 683–690.
  10. 10. Watts C (2012) The endosome-lysosome pathway and information generation in the immune system. Biochim Biophys Acta 1824: 14–21.
  11. 11. Rikiishi H (2012) Novel insights into the interplay between apoptosis and autophagy. Int J Cell Biol 2012: 317645.
  12. 12. Frank M, Wolburg H (1996) Cellular reactions at the lesion site after crushing of the rat optic nerve. Glia 16: 227–240.
  13. 13. Bradfield CJ, Kim BH, MacMicking JD (2012) Crossing the Rubicon: new roads lead to host defense. Cell Host Microbe 11: 221–223.
  14. 14. Otegui MS, Spitzer C (2008) Endosomal functions in plants. Traffic 9: 1589–1598.
  15. 15. Kornfeld S, Mellman I (1989) The biogenesis of lysosomes. Annu Rev Cell Biol 5: 483–525.
  16. 16. Platta HW, Stenmark H (2011) Endocytosis and signaling. Curr Opin Cell Biol 23: 393–403.
  17. 17. Brown WJ, DeWald DB, Emr SD, Plutner H, Balch WE (1995) Role for phosphatidylinositol 3-kinase in the sorting and transport of newly synthesized lysosomal enzymes in mammalian cells. J Cell Biol 130: 781–796.
  18. 18. Orsi A, Polson HE, Tooze SA (2010) Membrane trafficking events that partake in autophagy. Curr Opin Cell Biol 22: 150–156.
  19. 19. Mizushima N (2009) Physiological functions of autophagy. Curr Top Microbiol Immunol 335: 71–84.
  20. 20. Arai K, Shimaya A, Hiratani N, Ohkuma S (1993) Purification and characterization of lysosomal H(+)-ATPase. An anion-sensitive v-type H(+)-ATPase from rat liver lysosomes. J Biol Chem 268: 5649–5660.
  21. 21. Forgac M (2007) Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology. Nat Rev Mol Cell Biol 8: 917–929.
  22. 22. Hirata T, Nakamura N, Omote H, Wada Y, Futai M (2000) Regulation and reversibility of vacuolar H(+)-ATPase. J Biol Chem 275: 386–389.
  23. 23. Tilly BC, Mancini GM, Bijman J, van Gageldonk PG, Beerens CE, et al. (1992) Nucleotide-activated chloride channels in lysosomal membranes. Biochem Biophys Res Commun 187: 254–260.
  24. 24. Fukuda M (1994) Biogenesis of the lysosomal membrane. Subcell Biochem 22: 199–230.
  25. 25. Weidberg H, Shvets E, Elazar Z (2011) Biogenesis and cargo selectivity of autophagosomes. Annu Rev Biochem 80: 125–156.
  26. 26. Korolchuk VI, Rubinsztein DC (2011) Regulation of autophagy by lysosomal positioning. Autophagy 7: 927–928.
  27. 27. Saftig P, Klumperman J (2009) Lysosome biogenesis and lysosomal membrane proteins: trafficking meets function. Nat Rev Mol Cell Biol 10: 623–635.
  28. 28. Marshall WF (2008) Engineering design principles for organelle size control systems. Semin Cell Dev Biol 19: 520–524.
  29. 29. Alberts B, Bray D, JLewis, Raff M, Roberts K, et al. (1994) The molecular biology of the cell. New York: Garland.
  30. 30. Thomas JA, Buchsbaum RN, Zimniak A, Racker E (1979) Intracellular pH measurements in Ehrlich ascites tumor cells utilizing spectroscopic probes generated in situ. Biochemistry 18: 2210–2218.
  31. 31. Braun FJ, Hegemann P (1999) Direct measurement of cytosolic calcium and pH in living Chlamydomonas reinhardtii cells. Eur J Cell Biol 78: 199–208.
  32. 32. Palmgren MG (1991) Acridine orange as a probe for measuring pH gradients across membranes: mechanism and limitations. Anal Biochem 192: 316–321.
  33. 33. Lin HJ, Szmacinski H, Lakowicz JR (1999) Lifetime-based pH sensors: indicators for acidic environments. Anal Biochem 269: 162–167.
  34. 34. Aryasomayajula A, Derix J, Perike S, Gerlach G, Funk RH (2010) DC microelectrode array for investigating the intracellular ion changes. Biosens Bioelectron 26: 1268–1272.
  35. 35. Gallagher FA, Kettunen MI, Brindle KM (2011) Imaging pH with hyperpolarized 13C. NMR Biomed 24: 1006–1015.
  36. 36. Kneen M, Farinas J, Li Y, Verkman AS (1998) Green fluorescent protein as a noninvasive intracellular pH indicator. Biophys J 74: 1591–1599.
  37. 37. Llopis J, McCaffery JM, Miyawaki A, Farquhar MG, Tsien RY (1998) Measurement of cytosolic, mitochondrial, and Golgi pH in single living cells with green fluorescent proteins. Proc Natl Acad Sci U S A 95: 6803–6808.
  38. 38. Nehrke K (2006) Intracellular pH measurements in vivo using green fluorescent protein variants. Methods Mol Biol 351: 223–239.
  39. 39. Haggie PM, Verkman AS (2009) Unimpaired lysosomal acidification in respiratory epithelial cells in cystic fibrosis. J Biol Chem 284: 7681–7686.
  40. 40. Neal MD, Leaphart C, Levy R, Prince J, Billiar TR, et al. (2006) Enterocyte TLR4 mediates phagocytosis and translocation of bacteria across the intestinal barrier. J Immunol 176: 3070–3079.
  41. 41. Han J, Burgess K (2010) Fluorescent indicators for intracellular pH. Chem Rev 110: 2709–2728.
  42. 42. Chazotte B (2011) Labeling lysosomes in live cells with LysoTracker. Cold Spring Harb Protoc 2011: pdb prot5571.
  43. 43. Oh YK, Straubinger RM (1996) Intracellular fate of Mycobacterium avium: use of dual-label spectrofluorometry to investigate the influence of bacterial viability and opsonization on phagosomal pH and phagosome-lysosome interaction. Infect Immun 64: 319–325.
  44. 44. El-Omar EM, Oien K, El-Nujumi A, Gillen D, Wirz A, et al. (1997) Helicobacter pylori infection and chronic gastric acid hyposecretion. Gastroenterology 113: 15–24.
  45. 45. McLean NW, Rosenstein IJ (2000) Characterisation and selection of a Lactobacillus species to re-colonise the vagina of women with recurrent bacterial vaginosis. J Med Microbiol 49: 543–552.
  46. 46. deCathelineau AM, Henson PM (2003) The final step in programmed cell death: phagocytes carry apoptotic cells to the grave. Essays Biochem 39: 105–117.
  47. 47. Mushegian A, Medzhitov R (2001) Evolutionary perspective on innate immune recognition. J Cell Biol 155: 705–710.
  48. 48. Buckley KM, Rast JP (2012) Dynamic evolution of toll-like receptor multigene families in echinoderms. Front Immunol 3: 136.
  49. 49. Jones JD, Dangl JL (2006) The plant immune system. Nature 444: 323–329.
  50. 50. Ting JP, Davis BK (2005) CATERPILLER: a novel gene family important in immunity, cell death, and diseases. Annu Rev Immunol 23: 387–414.
  51. 51. Hammond-Kosack KE, Parker JE (2003) Deciphering plant-pathogen communication: fresh perspectives for molecular resistance breeding. Curr Opin Biotechnol 14: 177–193.
  52. 52. Yasuda M, Ishikawa A, Jikumaru Y, Seki M, Umezawa T, et al. (2008) Antagonistic interaction between systemic acquired resistance and the abscisic acid-mediated abiotic stress response in Arabidopsis. Plant Cell 20: 1678–1692.
  53. 53. McFall-Ngai M (2007) Adaptive immunity: care for the community. Nature 445: 153.
  54. 54. Morrison LA, Lukacher AE, Braciale VL, Fan DP, Braciale TJ (1986) Differences in antigen presentation to MHC class I-and class II-restricted influenza virus-specific cytolytic T lymphocyte clones. J Exp Med 163: 903–921.
  55. 55. Ratcliffe NA (1985) Invertebrate immunity–a primer for the non-specialist. Immunol Lett 10: 253–270.
  56. 56. Kagan JC, Iwasaki A (2012) Phagosome as the organelle linking innate and adaptive immunity. Traffic 13: 1053–1061.
  57. 57. Kim JH, Johannes L, Goud B, Antony C, Lingwood CA, et al. (1998) Noninvasive measurement of the pH of the endoplasmic reticulum at rest and during calcium release. Proc Natl Acad Sci U S A 95: 2997–3002.
  58. 58. Lamb CA, Cresswell P (1992) Assembly and transport properties of invariant chain trimers and HLA-DR-invariant chain complexes. J Immunol 148: 3478–3482.
  59. 59. Jones PP, Murphy DB, Hewgill D, McDevitt HO (1979) Detection of a common polypeptide chain in I–A and I–E sub-region immunoprecipitates. Mol Immunol 16: 51–60.
  60. 60. Blum JS, Cresswell P (1988) Role for intracellular proteases in the processing and transport of class II HLA antigens. Proc Natl Acad Sci U S A 85: 3975–3979.
  61. 61. Neefjes JJ, Ploegh HL (1992) Inhibition of endosomal proteolytic activity by leupeptin blocks surface expression of MHC class II molecules and their conversion to SDS resistance alpha beta heterodimers in endosomes. EMBO J 11: 411–416.
  62. 62. Riese RJ, Chapman HA (2000) Cathepsins and compartmentalization in antigen presentation. Curr Opin Immunol 12: 107–113.
  63. 63. Criscitiello MF, Ohta Y, Graham MD, Eubanks JO, Chen PL, et al. (2012) Shark class II invariant chain reveals ancient conserved relationships with cathepsins and MHC class II. Dev Comp Immunol 36: 521–533.
  64. 64. Boulais J, Trost M, Landry CR, Dieckmann R, Levy ED, et al. (2010) Molecular characterization of the evolution of phagosomes. Mol Syst Biol 6: 423.
  65. 65. Shannon JG, Heinzen RA (2009) Adaptive immunity to the obligate intracellular pathogen Coxiella burnetii. Immunol Res 43: 138–148.
  66. 66. Tiggert W, Benenson A, Gochenour W (1961) Airborne Q fever. Bacteriol Rev 25: 285–293.
  67. 67. Croddy E, Perez-Armendariz C, Hart J (2002) Chemical and biological warfare: a comprehensive survey for the concerned citizen. New York: Springer-Verlag.
  68. 68. Coleman SA, Fischer ER, Howe D, Mead DJ, Heinzen RA (2004) Temporal analysis of Coxiella burnetii morphological differentiation. J Bacteriol 186: 7344–7352.
  69. 69. Dellacasagrande J, Ghigo E, Machergui-El S, Hammami, Toman R, et al. (2000) αvβ3 integrin and bacterial lipopolysaccharide are involved in Coxiella burnetii-stimulated production of tumor necrosis factor by human monocytes. Infect Immun 68: 5673–5678.
  70. 70. Meconi S, Capo C, Remacle-Bonnet M, Pommier G, Raoult D, et al. (2001) Activation of protein tyrosine kinases by Coxiella burnetii: role in actin cytoskeleton reorganization and bacterial phagocytosis. Infect Immun 69: 2520–2526.
  71. 71. Meconi S, Jacomo V, Boquet P, Raoult D, Mege J-L, et al. (1998) Coxiella burnetii induces reorganization of the actin cytoskeleton in human monocytes. Infect Immun 66: 5527–5533.
  72. 72. Howe D, Mallavia LP (2000) Coxiella burnetii exhibits morphological change and delays phagolysosomal fusion after internalization by J774A.1 cells. Infect Immun 68: 3815–3821.
  73. 73. Heinzen RA, Scidmore MA, Rockey DD, Hackstadt T (1996) Differential interaction with endocytic and exocytic pathways distinguish parasitophorous vacuoles of Coxiella burnetti and Chlamydia trachomatis. Infect Immun 64: 796–809.
  74. 74. Colombo MI, Gutierrez MG, Romano PS (2006) The two faces of autophagy: Coxiella and Mycobacterium. Autophagy 2: 162–164.
  75. 75. Howe D, Melnicakova J, Barak I, Heinzen RA (2003) Maturation of the Coxiella burnetii parasitophorous vacuole requires bacterial protein synthesis but not replication. Cell Microbiol 5: 469–480.
  76. 76. Romano PS, Gutierrez MG, Beron W, Rabinovitch M, Colombo MI (2007) The autophagic pathway is actively modulated by phase II Coxiella burnetii to efficiently replicate in the host cell. Cell Microbiol 9: 891–909.
  77. 77. Howe D, Heinzen RA (2005) Replication of Coxiella burnetii is inhibited in CHO K-1 cells treated with inhibitors of cholesterol metabolism. Ann N Y Acad Sci 1063: 123–129.
  78. 78. Howe D, Heinzen RA (2006) Coxiella burnetii inhabits a cholesterol-rich vacuole and influences cellular cholesterol metabolism. Cell Microbiol 8: 496–507.
  79. 79. Campoy EM, Zoppino FCM, Colombo MI (2011) The early secretory pathway contributes to the growth of the Coxiella-replicative niche. Infect Immun 79: 402–413.
  80. 80. Andreoli WK, Mortara RA (2003) Acidification modulates the traffic of Trypanosoma cruzi trypomastigotes in Vero cells harbouring Coxiella burnetii vacuoles. Int J Parasitol 33: 185–197.
  81. 81. Raoult D, Drancourt M, Vestris G (1990) Bactericidal effect of doxycycline associated with lysosomotropic agents on Coxiell burnetii in P388D1 cells. Antimicrob Agents Chemother 34: 1512–1514.
  82. 82. Voth DE, Heinzen RA (2007) Lounging in a lysosome: the intracellular lifestyle of Coxiella burnetii. Cell Microbiol 9: 829–840.
  83. 83. Omsland A, Heinzen RA (2011) Life on the outside: the rescue of Coxiella burnetii from its host cell. Annu Rev Microbiol 65: 111–128.
  84. 84. Beare PA, Larson CL, Gilk SD, Heinzen RA (2012) Two systems for targeted gene deletion in Coxiella burnetii. Appl Environ Microbiol 78: 4580–4589.
  85. 85. Mertens K, Lantsheer L, Ennis DG, Samuel JE (2008) Constitutive SOS expression and damage-inducible AddAB-mediated recombinational repair systems for Coxiella burnetii as potential adaptations for survival within macrophages. Mol Microbiol 69: 1411–1426.
  86. 86. Seshadri R, Samuel J (2005) Genome analysis of Coxiella burnetii species: insights into pathogenesis and evolution and implications for biodefense. Ann N Y Acad Sci 1063: 442–450.
  87. 87. Zhang Y, Zhang G, Hendrix LR, Tesh VL, Samuel JE (2012) Coxiella burnetii induces apoptosis during early stage infection via a caspase-independent pathway in human monocytic THP-1 cells. PLoS ONE 7: e30841 doi:10.1371/journal.pone.0030841.
  88. 88. Minnick MF, Raghavan R (2012) Developmental biology of Coxiella burnetii. Adv Exp Med Biol 984: 231–248.
  89. 89. Seshadri R, Heidelberg JF, Paulsen IT, Eisen JA, Read TD, et al. (2003) Complete genome sequence of the Q-fever pathogen, Coxiella burnetii. Proc Natl Acad Sci U S A 100: 5455–5460.
  90. 90. Seshadri R, Samuel JE (2001) Characterization of a stress-induced alternate sigma factor, RpoS, of Coxiella burnetii and its expression during the development cycle. Infect Immun 69: 4874–4883.
  91. 91. Pappas G (2010) The changing Brucella ecology: novel reservoirs, new threats. Int J Antimicrob Agents 36 Suppl 1: S8–11.
  92. 92. Sarinas PS, Chitkara RK (2003) Brucellosis. Semin Respir Infect 18: 168–182.
  93. 93. Gamazo C, Lecaroz MC, Prior S, Vitas AI, Campanero MA, et al. (2006) Chemical and biological factors in the control of Brucella and brucellosis. Curr Drug Deliv 3: 359–365.
  94. 94. Oliveira SC, Giambartolomei GH, Cassataro J (2011) Confronting the barriers to develop novel vaccines against brucellosis. Expert Rev Vaccines 10: 1291–1305.
  95. 95. Pizarro-Cerda J, Moreno E, Sanguedolce V, Mege JL, Gorvel JP (1998) Virulent Brucella abortus prevents lysosome fusion and is distributed within autophagosome-like compartments. Infect Immun 66: 2387–2392.
  96. 96. Starr T, Ng TW, Wehrly TD, Knodler LA, Celli J (2008) Brucella intracellular replication requires trafficking through the late endosomal/lysosomal compartment. Traffic 9: 678–694.
  97. 97. Celli J, de Chastellier C, Franchini DM, Pizarro-Cerda J, Moreno E, et al. (2003) Brucella evades macrophage killing via VirB-dependent sustained interactions with the endoplasmic reticulum. J Exp Med 198: 545–556.
  98. 98. Marchesini MI, Herrmann CK, Salcedo SP, Gorvel JP, Comerci DJ (2011) In search of Brucella abortus type IV secretion substrates: screening and identification of four proteins translocated into host cells through VirB system. Cell Microbiol 13: 1261–1274.
  99. 99. Ficht TA (2003) Intracellular survival of Brucella: defining the link with persistence. Vet Microbiol 92: 213–223.
  100. 100. Eskra L, Canavessi A, Carey M, Splitter G (2001) Brucella abortus genes identified following constitutive growth and macrophage infection. Infect Immun 69: 7736–7742.
  101. 101. Ruggiero P (2012) Helicobacter pylori infection: what's new. Curr Opin Infect Dis 25: 337–344.
  102. 102. Murakami M, Yoo JK, Teramura S, Yamamoto K, Saita H, et al. (1990) Generation of ammonia and mucosal lesion formation following hydrolysis of urea by urease in the rat stomach. J Clin Gastroenterol 12 Suppl 1: S104–109.
  103. 103. Stingl K, Altendorf K, Bakker EP (2002) Acid survival of Helicobacter pylori: how does urease activity trigger cytoplasmic pH homeostasis? Trends Microbiol 10: 70–74.
  104. 104. Zhao B, Houry WA (2010) Acid stress response in enteropathogenic gammaproteobacteria: an aptitude for survival. Biochem Cell Biol 88: 301–314.
  105. 105. Foster JW (2004) Escherichia coli acid resistance: tales of an amateur acidophile. Nat Rev Microbiol 2: 898–907.
  106. 106. Bearson S, Bearson B, Foster JW (1997) Acid stress responses in enterobacteria. FEMS Microbiol Lett 147: 173–180.
  107. 107. Rogowsky PM, Powell BS, Shirasu K, Lin TS, Morel P, et al. (1990) Molecular characterization of the vir regulon of Agrobacterium tumefaciens: complete nucleotide sequence and gene organization of the 28.63-kbp regulon cloned as a single unit. Plasmid 23: 85–106.
  108. 108. Yuan ZC, Liu P, Saenkham P, Kerr K, Nester EW (2008) Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions. J Bacteriol 190: 494–507.
  109. 109. Yuan ZC, Haudecoeur E, Faure D, Kerr KF, Nester EW (2008) Comparative transcriptome analysis of Agrobacterium tumefaciens in response to plant signal salicylic acid, indole-3-acetic acid and gamma-amino butyric acid reveals signalling cross-talk and Agrobacterium–plant co-evolution. Cell Microbiol 10: 2339–2354.
  110. 110. Antunes LC, Ferreira RB, Buckner MM, Finlay BB (2010) Quorum sensing in bacterial virulence. Microbiology 156: 2271–2282.
  111. 111. Klosterman SJ, Perlin MH, Garcia-Pedrajas M, Covert SF, Gold SE (2007) Genetics of morphogenesis and pathogenic development of Ustilago maydis. Adv Genet 57: 1–47.
  112. 112. Takken F, Rep M (2010) The arms race between tomato and Fusarium oxysporum. Mol Plant Pathol 11: 309–314.
  113. 113. Hegedus DD, Rimmer SR (2005) Sclerotinia sclerotiorum: when “to be or not to be” a pathogen? FEMS Microbiol Lett 251: 177–184.
  114. 114. Vanstraelen M, Benkova E (2012) Hormonal interactions in the regulation of plant development. Annu Rev Cell Dev Biol 28: 463–487.
  115. 115. Carr JP, Lewsey MG, Palukaitis P (2010) Signaling in induced resistance. Adv Virus Res 76: 57–121.
  116. 116. Park SW, Liu PP, Forouhar F, Vlot AC, Tong L, et al. (2009) Use of a synthetic salicylic acid analog to investigate the roles of methyl salicylate and its esterases in plant disease resistance. J Biol Chem 284: 7307–7317.
  117. 117. Moreau M, Tian M, Klessig DF (2012) Salicylic acid binds NPR3 and NPR4 to regulate NPR1-dependent defense responses. Cell Res 22: 1631–1633.
  118. 118. Despres C, Chubak C, Rochon A, Clark R, Bethune T, et al. (2003) The Arabidopsis NPR1 disease resistance protein is a novel cofactor that confers redox regulation of DNA binding activity to the basic domain/leucine zipper transcription factor TGA1. Plant Cell 15: 2181–2191.
  119. 119. Browse J (2005) Jasmonate: an oxylipin signal with many roles in plants. Vitam Horm 72: 431–456.
  120. 120. Piotrowska A, Bajguz A (2011) Conjugates of abscisic acid, brassinosteroids, ethylene, gibberellins, and jasmonates. Phytochemistry 72: 2097–2112.
  121. 121. Browse J (2009) The power of mutants for investigating jasmonate biosynthesis and signaling. Phytochemistry 70: 1539–1546.
  122. 122. Gfeller A, Liechti R, Farmer EE (2010) Arabidopsis jasmonate signaling pathway. Sci Signal 3: cm4.
  123. 123. Pauwels L, Goossens A (2011) The JAZ proteins: a crucial interface in the jasmonate signaling cascade. Plant Cell 23: 3089–3100.
  124. 124. Wasternack C, Kombrink E (2010) Jasmonates: structural requirements for lipid-derived signals active in plant stress responses and development. ACS Chem Biol 5: 63–77.
  125. 125. Shah J (2009) Plants under attack: systemic signals in defence. Curr Opin Plant Biol 12: 459–464.
  126. 126. Pieterse CM, Leon-Reyes A, Van der Ent S, Van Wees SC (2009) Networking by small-molecule hormones in plant immunity. Nat Chem Biol 5: 308–316.
  127. 127. Cessna SG, Sears VE, Dickman MB, Low PS (2000) Oxalic acid, a pathogenicity factor for Sclerotinia sclerotiorum, suppresses the oxidative burst of the host plant. Plant Cell 12: 2191–2200.
  128. 128. Holmes RP (2000) Oxalate synthesis in humans: assumptions, problems, and unresolved issues. Mol Urol 4: 329–332.
  129. 129. Yu L, Jiang J, Zhang C, Jiang L, Ye N, et al. (2010) Glyoxylate rather than ascorbate is an efficient precursor for oxalate biosynthesis in rice. J Exp Bot 61: 1625–1634.
  130. 130. Eichner ER (2010) Throw no stones: how to prevent calcium oxalate renal stones. Curr Sports Med Rep 9: 260–261.
  131. 131. Dutton M, Evans C (1996) Oxalate production by fungi: its role in pathogenicity and ecology in the soil environment. Can J Microbiol 42: 881–895.
  132. 132. Dickman MB, Yarden O (1999) Serine/threonine protein kinases and phosphatases in filamentious fungi. Fungal Genet Biol 26: 99–117.
  133. 133. Rollins JA, Dickman MB (2001) pH signaling in Sclerotinia sclerotiorum: identification of a pacC/RIM1 homolog. Appl Environ Microbiol 67: 75–81.
  134. 134. Chen C, Harel A, Gorovoits R, Yarden O, Dickman MB (2004) MAPK regulation of sclerotial development in Sclerotinia sclerotiorum is linked with pH and cAMP sensing. Mol Plant Microbe Interact 17: 404–413.
  135. 135. Williams B, Kabbage M, Kim H-J, Britt R, Dickman MB (2011) Tipping the balance: Sclerotinia sclerotiorum secreted oxalic acid suppresses host defenses by manipulating the host redox environment. PLoS Pathog 7: e1002107 doi:10.1371/journal.ppat.1002107.
  136. 136. Williams B, Dickman M (2008) Plant programmed cell death: can't live with it; can't live without it. Mol Plant Pathol 9: 531–544.
  137. 137. Kim KS, Min JY, Dickman MB (2008) Oxalic acid is an elicitor of plant programmed cell death during Sclerotinia sclerotiorum disease development. Mol Plant Microbe Interact 21: 605–612.
  138. 138. Chen C, Banga S, Mertens K, Weber MM, Gorbaslieva I, et al. (2010) Large-scale identification and translocation of type IV secretion substrates by Coxiella burnetii. Proc Natl Acad Sci U S A 107: 21755–21760.
  139. 139. Newton HJ, Roy CR (2011) The Coxiella burnetii Dot/Icm system creates a comfortable home through lysosomal renovation. MBio 2: e00226–11.
  140. 140. Kim JH, Lingwood CA, Williams DB, Furuya W, Manolson MF, et al. (1996) Dynamic measurement of the pH of the Golgi complex in living cells using retrograde transport of the verotoxin receptor. J Cell Biol 134: 1387–1399.
  141. 141. Starr T, Child R, Wehrly TD, Hansen B, Hwang S, et al. (2012) Selective subversion of autophagy complexes facilitates completion of the Brucella intracellular cycle. Cell Host Microbe 11: 33–45.
  142. 142. Lacerda TL, Salcedo SP, Gorvel JP (2013) Brucella T4SS: the VIP pass inside host cells. Curr Opin Microbiol 16: 45–51.
  143. 143. Kabbage M, Williams B, Dickman MB (2013) Cell death control: the interplay of apoptosis and autophagy in the pathogenicity of Sclerotinia sclerotiorum. PLoS Pathog 9: e1003287 doi:10.1371/journal.ppat.1003287.