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Communication in Plants and Microbes
Differences and similarities
Innate immunity in
plants and animals
Cara H. Haney
(Harvard Medical
School and
Massachusetts
General Hospital, USA),
Jonathan Urbach
(Massachusetts General
Hospital, USA) and
Frederick M.
Ausubel (Harvard
Medical School and
Massachusetts General
Hospital, USA)
Plants and animals must avoid becoming a free meal to microbes, which vastly outnumber eukaryotic
life in both quantity and diversity. Adaptive immunity in the strict sense, whereby the host creates an
immunological memory after exposure to a pathogen, is limited to vertebrates. Both plants and animals
(including insects and mammals) have an innate immune system, which helps protect hosts from the
majority of microbes they encounter during their lifetime. Plant and animal innate immune systems
recognize an overlapping set of conserved microbe-associated molecular patterns (MAMPs). This
observation suggests that the innate immune system in plants and animals may have been derived from a
common ancestor. However, the majority of data indicate that innate immunity has arisen independently
in plants and animals and that functional overlap is the result of convergent evolution: confronted with
the same problem, and given the same molecular tools, plants and animals have independently derived
similar solutions. This review discusses the functional and mechanistic details of the innate immune
system in plants and animals including receptor-mediated immunity, endolysosomal immunity, and the
interplay of the innate immune system and host-associated microbial communities.
The evolutionary impetus for an
innate immune system
Microbes thrive in nearly every environment
on the planet, and given nutrient limitations
in soil and water, eukaryotes provide an
ideal habitat for microbes. Plants are able
to synthesize their own carbon, which can
be limiting for microbial growth in soil1.
Animals forage and collect carbon and other
nutrients. A microbe that is lucky enough to
live in association with plant roots or inside an
animal gut has first access to a potential free
meal. Plants and animals also depend on these
microbes; they help with nutrient acquisition,
and in fact act as another line of defence against
pathogenic microbes (discussed below).
Despite potential selection pressures for
microbes to take more and more nutrients from
their hosts, the majority of host-associated
microbes are non-pathogenic. This is in part
Key words: NF-κB-family
transcription factor,
pathogen, resistanceprotein, rhizosphere, type
III effector.
because eukaryotes have sophisticated surveillance systems that monitor
the presence of microbes in their environments and within themselves.
Once a potential pathogen has been perceived, the innate immune
system activates a number of defence responses including production of
antimicrobial compounds and localized host cell death.
Extracellular perception: transmembrane immune
receptors and signalling
Plants and animals must contend with similar microbial diversity and
consequentially have the ability to recognize conserved MAMPs. These
include bacterial flagellin, peptidoglycan and lipopolysaccharide (LPS),
and fungal chitin (Table 1). In plants and animals, some MAMPs are
recognized by pattern-recognition receptors (PRRs) that contain an
extracellular leucine-rich repeat (LRR) domain (Figure 1). After MAMP
recognition, receptors in plants and animals signal through mitogenactivated protein kinase (MAPK) cascades, which in turn activate
transcription of defence-related genes.
In animals and insects, a subset of MAMPs are recognized directly
or indirectly by PRRs called Toll receptors in insects and Toll-like
receptors (TLRs) in vertebrates. Initially identified in Drosophila
Abbreviations: APAF-1, apoptotic protease-activating factor 1; CERK1, chitin elicitor receptor kinase 1; FLS2, Flagellin-Sensing2;
LYSM1, lysin motif domain 1; LPS, ARC, NBS domain in APAF-1; NBS, nucleotide-binding site; PRR, pattern-recognition receptor;
R-protein, resistance-protein; TIR, Toll/interleukin receptor; TLR, Toll-like receptor.
1 October 2014 © Biochemical Society
Communication in Plants and Microbes
Features
Figure 1. Flagellin recognition and signalling is suggestive of convergent evolution in MAMP perception in plants and animals. Plant
and animal flagellin receptors (FLS2 in plants and TLR5 in animals) recognize distinct epitopes of bacterial flagellin. Transmembrane
PRRs in both plants and animals have extracellular LRR receptor domain, but have different cytoplasmic domains. Signalling in plants
and animals makes use of a MAPK cascade but the specific molecular players including PRR-interacting proteins and transcription
factor families are not conserved. The pathways in both FLS2 and TLR5 signalling are vastly simplified to emphasize specific
similarities and differences.
for their role in development, TLRs in mammals were found to
play a role in immunity by binding molecules such as bacterial LPS,
peptidoglycan and flagellin. TLRs have an extracellular LRR receptor
domain and a cytoplasmic Toll/interleukin receptor (TIR) protein–
protein interaction domain. The TIR domains interact with other
cytoplasmic TIR-domain-containing proteins such as MyD88, which
activates NF-κB-family transcription factors. This results in the
synthesis of cytokines in vertebrates and of antimicrobial peptides in
both vertebrates and insects2.
Table 1. MAMPs that are perceived by both plants and animals and their
cognate PRRs.
MAMP
Origin
Plant
receptor(s)
Animal
receptor(s)
Flagellin
Bacterial
FLS23
TLR57,22
LPS
Bacterial
Unknown
TLR423,24
Peptidoglycan
Bacterial
CERK1, LYSM1
and LYSM325,26
Nod120 and
Nod227
Chitin
Fungal
CERK128
Unknown
In plants, the analogous receptors
also have an extracellular LRR-containing
receptor domain and an intracellular kinase
domain. The best-characterized PRR in
plants is the bacterial flagellin receptor,
FLS23,4, which binds a 22-amino-acid flagellin
peptide5. Upon binding bacterial flagellin,
FLS2 interacts with another receptor-like
kinase, BAK16. Together FLS2 and BAK1
activate a MAPK cascade, which activates
transcription via WRKY family transcription
factors4 (Figure 1).
Flagellin perception in animals is
functionally very similar: flagellin perception
by PRRs activates transcription via a MAPK
cascade; however, the molecular details are
not shared (Figure 1). TLR5 performs the
analogous flagellin-perception function in
humans7, although it binds to a distinct epitope
of bacterial flagellin8. TLR5 interacts with the
cytoplasmic TIR-containing MyD88 to activate
(i) transcription via a MAPK signalling cascade
and (ii) NF-κB-dependent transcription
through a MAPK-independent mechanism.
Both MyD88 and NF-κB homologues are
absent from plants.
October 2014 © Biochemical Society 2
Features
Communication in Plants and Microbes
Figure 2. Presence of NBS and LRR domains in plants, animals and bacteria. LRR
(purple) and WD40 repeat (blue) and NBS (green; NB-ARC and NACHT) domains
are present in bacterial and archaeal genomes. The NBS–LRR combination is
extremely rare or non-existent except in plant disease R-proteins and animal
Nod-like immune receptors. Plant and animal innate immune receptors appear
to have independently co-opted these domains for defence purposes. This is
supported by (i) differing domain structure between the plant and animal
NBS-containing proteins, and (ii) apparent functional divergence in proteins
with the most similar NBS domains in plants and animals. Note: there are
additional NBS-domain-containing proteins found in animals, bacteria and
Archaea whose domain structures are not included here.
The flagellin-recognition case exemplifies the parallels and
distinctions in MAMP perception and PRR-dependent signalling in plants
and animals. PRRs in plants and animals share some similarity in protein
domains and domain architecture and have similarly structured signalling
modules. However, although functionally analogous, the organization of
protein domains, and the exact downstream molecular players (such as
transcription factors), are not conserved between plants and animals.
Taken together, these data suggest evolutionarily independent solutions
to the problem of perceiving and responding to bacterial infection9.
Intracellular perception: cytoplasmic NBS–LRR
receptors
Plants and animals have a second class of intracellular innate immune
receptors. Like the transmembrane receptors, these receptors have
homologous domains in plants and animals: they both have nucleotidebinding site (NBS) domains adjacent to either an N-terminal LRR
domain (in both plants and animals) or a WD40-repeat domain (in
animals only; Figure 2). The C-terminal domains are variable in animals
but typically contain either a TIR or a coiled-coil domain in plants. The
variation of C-terminal domains, and divergent functions and molecular
partners (discussed below) suggest that plants and animals have both
co-opted an ancestral NBS-domain-containing protein independently
to perform similar functions.
NBS-containing proteins in plants and animals have diverse
functions and divergent NBS domains. There are 14 mammalian NBScontaining proteins including APAF-1 (apoptotic protease-activating
factor 1) and Nod proteins. Nod1 and Nod2, which contain LRR
domains, recognize peptidoglycan degradation products and like
3 October 2014 © Biochemical Society
TLRs, activate NF-κB-like transcription factors. APAF-1 (which has
a WD40-repeat domain and has homologues in all sequenced animal
genomes including CED-4 in Caenorhabditis elegans), interacts with
caspases to trigger programmed cell death and does not function in
innate immunity10. The NBS domains in APAF-1 and Nod proteins
are divergent (called NB-ARC and NACHT domains respectively) and
appear to have originated in bacteria11,12 (Figure 2).
In plants, NBS–LRR proteins, also called resistance-proteins (or
‘R-proteins’), were initially identified because they conferred resistance
to specific pathogens. Many successful Gram-negative plant pathogens
have type III secretion systems that translocate effector proteins directly
into their host cells. In contrast with MAMP recognition by animal
Nod genes, plant R-genes recognize type III effectors or the damage the
effectors cause to the host cell13.
In addition to functional divergence of NBS-containing proteins
in plants and animals, phylogenetic analysis of NBS domains in plants,
animals and bacteria also points to distinct origins for plant and animal
intracellular receptors11,12 (J. Urbach and F.M. Ausubel, unpublished
work) (Figure 2). The individual domains found in NBS-containing
proteins (LRR, NB-ARC, NACHT, etc.) are found in bacterial and
archaeal genomes, indicating that they have ancient origins11 (Figure
2). Phylogenetic analysis reveals that the NBS domain in plant R-genes
is more similar to the NB-ARC domain in animal APAF-1 (involved
in apoptosis) than it is to the NACHT domain in the functionally
similar animal Nod genes (J. Urbach and F.M. Ausubel, unpublished
work). Collectively, functional and molecular data support convergent
evolution for NBS-containing proteins in plants and animals.
Intracellular innate immunity and endolysosomal
trafficking
Animal macrophages function in the endocytosis and destruction
of potential pathogens. When immunity is successful, invading
microbes are routed to the host lysosome, where the extreme pH and
lytic enzymes provide a powerful means of bacterial extermination. A
successful pathogen must escape this sure destruction and often does
so by convincing the host that it is cargo to be routed elsewhere in the
cell. In addition to using type III effectors to block the PRRs, pathogens
such as Salmonella and Shigella are able to use their type III effectors to
modulate host endolysosomal trafficking14. In animals, endolysosomal
immunity also aids in immunity to toxins and viruses; this is not a wellstudied area in plants and is not discussed here.
In plants, there are no known intracellular bacterial pathogens, and
direct endocytosis of microbes is not considered to be a routine part
of the innate immune system. However, there is some indication that
endolysosomal immunity is functional in plants. Symbiotic nitrogenfixing bacteria, collectively referred to as ‘rhizobia’, live intracellularly
in leguminous plants (including beans, peas and alfalfa). Most rhizobia
are alpha-proteobacteria, and interestingly, the closest relatives of
many rhizobia are intracellular animal pathogens and symbionts,
including the mammalian pathogen Brucella and insect symbiont
Wolbachia. Successful infection among plant- and animal-associated
α-proteobacteria depends on a common set of bacterial genes and traits
including a modified LPS, a type III secretion system, homologous two-
Communication in Plants and Microbes
Features
Figure 3. Functional conservation of innate immune pathways in plants and animals. On a functional and conceptual level, innate
immune pathways are conserved in plants and animals. Innate immune pathways include (1) extracellular MAMP recognition by
PRRs, which activates transcription of defence-related genes; (2) intracellular MAMP and effector recognition by NBS–LRRs, which
activate transcription of defence-related genes; (3) trafficking of microbes to the lytic compartment (in plants this is only known to
be relevant to nitrogen-fixing bacteria); and (4) pathogen protection by association with a stable microbial community. In the case
of (1) and (2), molecular data indicate that functional similarities have arisen through convergent evolution9,11.
component systems and an RpoN family extracytoplasmic σ-factor15:
shared virulence determinants between plant- and animal-associated
α-proteobacteria may indicate common host cell targets.
Rhizobia that are able to infect but lack certain virulence determinants
(type III secretion, RpoN, etc.) are unable to persist within their host cell.
Similarly, RpoN is required for Burkholderia cenocepacia to avoid fusion
to the animal lysosome16. Plant endosomal compartments containing
nitrogen-fixing bacteria undergo a natural senescence where they fuse to
the plant lytic vacuole (analogous to the animal lysosome); this process
requires a plant Rab7 small GTPase, also required for endolysosomal
trafficking in animals17. At the functional level, this indicates a shared
mechanism of endolysosomal immunity.
Immunity and commensal microbial communities
Plants and animals both associate with rich microbial communities,
on which they depend for defence, nutrient acquisition and normal
development. In animals, there is a growing body of evidence
indicating that the innate immune system is essential for structuring
these communities, and for preventing commensals from turning into
pathogens. This is most clearly apparent in immunocompromised
individuals where normally commensal
microbes can cause disease.
The molecular and biochemical details of
how the innate immune system contributes
to maintaining a balance with commensal
microbes is just beginning to be elucidated
in animals. A number of antimicrobial
compounds are essential for limiting the
numbers of microbes in the human gut or
maintaining the balance of bacterial phyla.
These include C-type lectins involved in
restricting bacterial proliferation near the
epithelial cell layer18, and defensins required
for limiting growth of Bacteroidetes19. The
role of the plant innate immune system
in establishing and maintaining microbial
communities is an area of active research in
our and other laboratories.
In plants, there is a huge body of evidence
indicating that the microbiome itself is
a natural component of the plant innate
October 2014 © Biochemical Society 4
Features
Communication in Plants and Microbes
immune system. Root-associated bacteria, including Bacillus and
Pseudomonas spp., and fungi, including Trichoderma, have long been
known to protect their plant hosts from pathogens through a variety of
mechanisms, including (i) the production of antimicrobial compounds,
(ii) induction of host defences and (iii) out-competing pathogens in
the rhizosphere20,21. There is some evidence in animals that the gut
microbiome may play a protective function against potential pathogens.
After disruption of normal gut microbes (through antibiotic treatment,
for instance), normally commensal microbes such as Clostridium
difficile can become pathogenic, suggesting the microbiome normally
functions to keep C. difficile in a non-pathogenic state. The molecular
mechanisms underlying the specificity of host–microbiome associations
and how they contribute to protection against pathogens are areas of
active research.
Perspectives and conclusions
Innate immunity in plants and animals has functionally analogous
features. These include (i) recognition of MAMPs via PRRs and
activation of defence responses by transmembrane; (ii) intracellular
PRRs; (iii) endolysosomal trafficking to destroy invading microbes; and
(iv) give-and-take with host-associated microbial communities (Figure
3). In cases where the molecular details are well understood (mainly
PRRs), all evidence points to convergent evolution of mechanisms in
innate immunity in plants and animals. It remains to be seen if the same
is true for the role of the endolysosomal pathways in innate immunity
and if common mechanisms are involved in shaping plant- and animalassociated microbial communities.
■
Cara Haney is funded by the Gordon and Betty Moore Foundation through
Grant GBMF [grant number 2550.01] to the Life Sciences Research Foundation.
Jonathan Urbach and Cara Haney are supported in part by National Institutes
of Health [grant number R37GM48707], awarded to Frederick Ausubel.
Cara Haney graduated from Cornell University in 2003
with a BS in plant science and received her PhD in cell
and molecular biology from Stanford University in 2011.
Dr Haney is a Gordon and Betty Moore Foundation
postdoctoral fellow of the Life Sciences Research
Foundation. She is currently a postdoctoral fellow in the
Ausubel Lab at Harvard Medical School/Massachusetts General Hospital studying
beneficial host-associated microbes. email: [email protected]
Jonathan Urbach received his BA from Cornell University
in 1989 and a PhD in chemistry from Harvard University
in 2000. He is currently a bioinformatics specialist in the
Molecular Biology Department at Massachusetts General
Hospital. email: [email protected]
Frederick Ausubel is a Professor of genetics and molecular
biology at Harvard Medical School and Massachusetts
General Hospital. Dr Ausubel was elected to the National
Academy of Sciences in 1994 and received the 2014 Thomas
Hunt Morgan Medal for lifetime achievement in the field
of genetics. His laboratory focuses on innate immunity in
model systems including Arabidopsis and C. elegans. email: ausubel@molbio.
mgh.harvard.edu
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