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Molecular Determinants
of a Symbiotic Chronic
Infection
Katherine E. Gibson,1,2 Hajime Kobayashi,2
and Graham C. Walker2
Present address 1 Department of Biology, University of Massachusetts, Boston,
Massachusetts 02125
2
Department of Biology, Massachusetts Institute of Technology, Cambridge,
Massachusetts 02139; email: gwalker@mit.edu
Annu. Rev. Genet. 2008. 42:413–41
Key Words
The Annual Review of Genetics is online at
genet.annualreviews.org
Rhizobium, legume, bacterial invasion, signaling, stress response, cell
cycle
This article’s doi:
10.1146/annurev.genet.42.110807.091427
c 2008 by Annual Reviews.
Copyright
All rights reserved
0066-4197/08/1201-0413$20.00
Abstract
Rhizobial bacteria colonize legume roots for the purpose of biological
nitrogen fixation. A complex series of events, coordinated by host and
bacterial signal molecules, underlie the development of this symbiotic
interaction. Rhizobia elicit de novo formation of a novel root organ
within which they establish a chronic intracellular infection. Legumes
permit rhizobia to invade these root tissues while exerting control over
the infection process. Once rhizobia gain intracellular access to their
host, legumes also strongly influence the process of bacterial differentiation that is required for nitrogen fixation. Even so, symbiotic rhizobia
play an active role in promoting their goal of host invasion and chronic
persistence by producing a variety of signal molecules that elicit changes
in host gene expression. In particular, rhizobia appear to advocate for
their access to the host by producing a variety of signal molecules capable of suppressing a general pathogen defense response.
413
INTRODUCTION
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Although nitrogen is one of the most abundant elements present on Earth, it is also one
of the most limiting for biological growth because it is largely found in the inaccessible form
dinitrogen (N2 ). Biological nitrogen fixation
is the process by which chemically inert N2
present in the atmosphere is enzymatically reduced to the metabolically usable form ammonia (NH3 ) through the action of nitrogenase
(129). The ability to catalyze the conversion of
N2 to NH3 has evolved only among microbes,
including the rhizobia, cyanobacteria, azobacteria, frankia, and archaea (137).
This review focuses on developmental
events that underlie biological nitrogen fixation within the context of an intimate symbiosis between rhizobia, a phylogenetically diverse
group of gram-negative soil bacteria within
the family Rhizobiaceae, and their hosts the
Leguminosae (or Fabaceae) family of flowering
plants. This rhizobium-legume symbiosis is established under nitrogen-limiting soil conditions and is estimated to contribute nearly
half of all current biological nitrogen fixation (68). In addition to its environmental and
agricultural significance (170), this symbiosis
provides a tractable model system for identifying and characterizing certain mechanisms employed by invasive bacteria during chronic host
interactions as they transition from a free-living
environment to their niche within the host.
In fact, many rhizobial genes required for either host invasion or chronic persistence have
orthologs in closely related alphaproteobacterial pathogens, such as Agrobacterium and
Brucella, and often these orthologs have an effect on virulence (11, 140, 156). Moreover,
plants can detect phytopathogens using receptors that are evolutionarily related to those
employed by legumes to detect symbiotic rhizobia (144, 180). Thus, the broad importance
of this symbiosis is ever growing.
Due to the wide breadth of biological processes involved in establishing the legumerhizobium symbiosis, as well as the natural
diversity in symbiotic mechanisms, we are un-
414
Gibson
·
Kobayashi
·
Walker
able to review all the events that underlie
this complex interaction. For instance, not discussed here are the Type III and Type IV secretion systems that play an important role in
diverse rhizobial symbioses (32, 112), nor the
bacterial quorum sensing systems that modulate symbiotic interactions (67, 145). In addition, it is clear that plant hormone balance plays
a critical role in regulating nodule development
(122). Rather, our goal is to provide the reader
with molecular insight into several regulatory
aspects of this symbiosis while providing reference to reviews that discuss these processes in
more detail.
EVOLUTION OF SYMBIOSIS
The rhizobium-legume symbiosis, a relatively
recent evolutionary adaptation, is thought to
have evolved from the ancient arbuscular mycorrhizal symbiosis that is nearly ubiquitous
throughout the plant kingdom and provides
plants with the essential mineral nutrient phosphorus (73). This evolutionary relationship has
been inferred based on findings that several
host genes represent common requirements for
the establishment of both rhizobial and mycorrhizal symbioses. Given that nearly all vascular
plants interact with mycorrhizal symbionts, it
remains unclear why the nitrogen-fixing symbiosis is strictly limited to legume species, with
the exception of Parasponia. Current understandings of legume evolution and the appearance of nodulation indicate that the first symbiosis event involved bacterial invasion of roots
via cracks in the host epidermis where lateral
roots emerge (158). Subsequent to this, developmental mechanisms evolved, likely through
the process of gene duplication, to craft the
highly selective symbiosis described here. In
particular, the emergence of a host-derived infection structure allows host control over the
bacterial infection process (59).
The symbiotic capacity of rhizobia is
thought to have evolved in part through horizontal gene transfer events based on several
observations. Within the symbiotic rhizobial
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lineage, Sinorhizobium is estimated to have
diverged from Bradyrhizobium approximately
500 Mya (168), which is well before the initial appearance of legume species approximately
60 Mya (158). Rhizobia also tend to have large
and multipartite genomes consisting of a chromosome supplemented with one or more independent plasmids (81), which contribute to
an evolutionarily dynamic genome through the
process of horizontal gene transfer. Moreover,
rhizobial genes involved in symbiosis are often located within chromosomal islands or on
plasmids: Sinorhizobium meliloti genes involved
in NF biosynthesis (nod, nol, noe) and nitrogen fixation (nif and fix) are located on pSymA
whereas others required for EPS (exopolysaccharide) biosynthesis (exo) and C4 -dicarboxylic
acid utilization (dct) are located on pSymB (60).
Horizontal transfer of these genomic elements
has been observed among bacteria within the
rhizosphere and has the ability to convert a
nonsymbiont into a symbiont through a single transfer event (6, 160, 161). Other than
symbiosis genes, there is no significant synteny
shared between the plasmids of various rhizobial species or rhizobial chromosomes (19, 188).
Finally, it was recently discovered that certain
betaproteobacteria are also capable of establishing nitrogen-fixing symbioses with legumes
(117), and comparative phylogenetic analyses
support the notion that the plasmid-borne symbiotic genes (nod and nif ) in these Burkholderia
are derived from at least one horizontal gene
transfer event (25).
NODULE DEVELOPMENT
To establish the symbiosis, free-living soil rhizobia elicit de novo formation of a specialized root organ, the nodule, from their host.
The root nodule ultimately houses many thousands of individual rhizobia that catalyze nitrogen fixation. Organogenesis of the nodule
occurs via a developmental program that involves dedifferentiation of quiescent (G0 ) root
cortical cells into an actively dividing meristem
(Figure 1a), which is functionally analogous to
an animal stem cell population (159). These di-
viding meristem cells form the initial nodule
primordium from which a mature nodule develops (Figure 1a). A subset of these meristem
cells enter a modified cell cycle program that results in endoreduplication and produces greatly
enlarged cells. It is this subset of endoploid cells
that are invaded and colonized by rhizobia for
the purpose of nitrogen fixation (Figure 1d ).
To colonize the developing nodule, bacteria present in the soil provoke root hair curling
by the host (Figure 1a,b). The root hair curl
traps intimately associated bacteria, which are
then able to invade the nodule through a hostderived structure called the infection thread
(IT) (Figure 1a,c). The IT is a tube originating
at the tip of the root hair that initially forms
via localized hydrolysis of the cell wall and that
continues its growth via deposition of new cell
wall material (59). In this way, the IT carries
bacteria from the root surface toward the population of newly created endoploid cells where it
undergoes significant ramification. Ultimately,
bacteria within the IT are deposited into the
host cell cytoplasm in a process that resembles
endocytosis; they then enter a differentiation
program that results in their ability to catalyze
nitrogen fixation.
Generally, nodules fall into two morphological classes based on their pattern of meristem
growth: indeterminate, with a meristem derived
from inner cortical cells, and determinate, with
a meristem derived from outer cortical cells. Indeterminate and determinate nodules also differ
in the relative persistence of meristem proliferation. In determinant legumes, including most
Old World tropical species and Lotus japonicus,
the basal meristem undergoes a limited spurt
of cell division such that further nodule growth
depends on an expansion in cell size rather than
in cell number. Both plant and bacterial development proceeds synchronously within this
particular type of nodule; an exception is senescence, which occurs within older nodules on
an individual cellular basis (133). Thus, a determinate nodule contains a relatively homogenous population of developing plant and bacterial cells at any given time point, which allows
precise analysis of temporal gene expression
www.annualreviews.org • Molecular Determinants of a Symbiotic Chronic Infection
Rhizobia: gramnegative
alphaproteobacteria
that engage in
symbiosis with
legumes and fix
nitrogen
Horizontal gene
transfer:
incorporation of
genetic material from
an unrelated organism
(also called lateral gene
transfer)
Chromosomal island:
section within a
genome having
evidence of horizontal
origins
NF: nodulation (Nod)
factor
EPS:
exopolysaccharide
Rhizosphere: local
soil environment
surrounding plant
roots
Synteny: preservation
of gene order on
chromosomes of
related species
Meristem:
undifferentiated plant
cells undergoing cell
growth and division
Endoreduplication:
repeated genomic
replication without
cytokinesis
Endoploid: cells that
have undergone
endoreduplication
IT: infection thread
Indeterminate
nodule: nodule with a
persistent meristem
and a heterogenous
plant and bacterial
developing cell
population
415
and function within both symbiotic partners
(Figure 1e, f ). In contrast, legumes that form
indeterminate nodules, including most temperate species such as Medicago truncatula, create a
persistent meristem. In these nodules, the plant
allows prolonged bacterial invasion of postmitotic (G0 ) endoploid cells that are continuously
generated by the meristem. As a result, each
developmental stage required to establish the
symbiosis is present within a single mature indeterminate nodule and in a spatially organized
manner (Figure 1a). The distinct regions found
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Determinate nodule:
nodule with a
temporary meristem
and a relatively
homogenous plant and
bacterial developing
cell population
a
BACTERIAL INVASION
Rhizobium
b
O - COCH 3
CH2
HO
HO
O C
O -SO3H
C H2-OH
O
O
O
HO
NH
H3C O C
N
CH2
O
HO
O
OH
NH
H3COC
n
H
Nod factors
Flavonoids
in a mature indeterminate nodule, proximal to
distal from the root, are the meristem (Zone I),
the invasion zone (Zone II), the interzone (Zone
II/III), the nitrogen-fixing zone (Zone III), and
the senescent zone (Zone IV) (172). In addition
to distinct morphological features, these zones
can be distinguished by patterns of host gene expression. While much research has focused on
plant and bacterial physiology in Zones I–III,
comparatively less is known regarding the genetic regulation and physiology of senescence
in Zone IV although this process is also of critical agricultural consequence (133).
I
There is often strict specificity in the establishment of a nitrogen-fixing symbiosis between
II
OH
OH
←−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
O
OH
O
HO
OH
Figure 1
O
Root hair
Root hair
curl
III
Root hair
invasion
IT
Nod factors
EPS
ROS
IV
Nodule
primordium
Cell division
c
d
e
IT
f
n
v
Bacteroid
PBM
416
Gibson
·
Kobayashi
·
Walker
Schematic model of nodule development. (a-b) Host
flavonoids exuded into the soil trigger bacterial Nod
Factor production. Nod factor is perceived by host
receptors and elicits various host responses, such as
root hair curling and root hair invasion. Root hair
invasion also requires bacteria EPS and host ROS
production. Nod factors induce mitotic cell division
in the root cortex (represented in blue), leading to
formation of the nodule meristem. An indeterminate
nodule originates from the root inner cortex and has
a persistent meristem (Zone I). The nodule also
contains an invasion zone (Zone II) and a nitrogenfixing zone (Zone III). In older nodules, a senescent
zone (Zone IV) develops in which both plant and
bacterial cells degenerate. (c) Bacteria enter the
nodule through root hairs in a structure called the
infection thread (IT) that elongates toward the
nodule meristem; nucleus (n), vacuole (v). (d ) At the
tip of the growing IT, bacteria are endocytosed into
the cytoplasm of postmitotic endoploid cells. Each
bacterium is surrounded by a host-derived
peribacteroid membrane (PBM) and proceeds to
differentiate into the specialized symbiotic form
called a bacteroid. Bacteroids establish a chronic
infection of the host cytoplasm and enzymatically
reduce dinitrogen to provide a source of biologically
usable nitrogen to the host (Zone III). (e) In contrast
to an indeterminate nodule, a determinate nodule
lacks a persistent meristem and all developmental
stages proceed synchronously. ( f ) Infected cells of
determinate nodules typically lack vacuoles (v).
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host legume species and their symbionts. For
instance, the bacterium S. meliloti is compatible
with species of Medicago (alfalfa), Melilotus
(sweetclover), and Trigonella (fenugreek),
whereas Rhizobium etli is compatible only with
species of Phaseolus (bean). In contrast to these
restricted host range rhizobia, some bacteria
have a broad host range, like Rhizobium sp.
NGR234, which is capable of nodulating 232
legumes from 112 distantly related genera
(132). Based on rhizobial phylogenetic relationships, it was suggested that the restricted
host range symbiosis evolved from an ancestral
broad host range symbiosis (132), and perhaps
the specificity engendered by narrow host
range interactions creates a finely tuned and
more effective symbiosis.
The Host Flavonoid Signal
Compatible rhizobia are uniquely capable of
gaining entry and invading the host nodule
based on a series of reciprocal signaling events
(Figure 1b). The principal signals originating
from the host and perceived by rhizobia in the
soil are derived from the flavonoid family of
secondary plant metabolites (Figure 2a). The
roots of leguminous plants exude a diverse cocktail of flavonoids and isoflavonoids into the soil
(128). Compatible bacteria in the rhizosphere
can elicit quantitative increases and qualitative
changes in flavonoid exudation. Exactly which
flavonoid in the rhizosphere a compatible bacterium perceives can be difficult to determine
since plants secrete a complex mixture. In fact, it
is quite likely that the spectrum of flavonoids exuded by a legume, rather than a single flavonoid
compound, provides a determinant for host
specificity. At least some rhizobia are chemotactic toward compatible flavonoids, suggesting
that certain aspects of host specificity are established before the bacterium and its host physically interact (20).
Host Flavonoids Are Perceived
by Bacterial NodDs
Plant-derived flavonoids elicit a significant
transcriptional response from compatible bac-
teria within the rhizosphere, most of which
is NodD-dependent and results in Nodulation
Factor (NF) signal production (Figure 2b) (23).
While expression of genes required for NF synthesis is induced by host flavonoids, expression
of these same genes can be repressed in the presence of ammonia.
NodD belongs to the LysR family of DNAbinding transcription factors, which have an Nterminal ligand-binding domain that regulates
the activity of the associated C-terminal DNAbinding domain. The NodD ligand-binding
domain is thought to function as a flavonoid
receptor and, in the presence of a compatible host, NodD induces the expression of
genes involved in NF biosynthesis. For example, the daidzein and genistein isoflavonoids of
Glycine max (soybean) induce NF gene expression in Bradyrhizobium japonicum (Figure 2a).
However, daidzein prevents NF production in
the noncompatible bacterium S. meliloti, which
responds positively to the flavone luteolin
(Figure 2a), and does so in a NodD-dependent
manner (127). Generally, the NodDs of broad
host range rhizobia respond to a wider range
of flavonoid species than those present in restricted host range bacteria (128). For instance,
NodD1 from the broad host range symbiont
Rhizobium sp. NGR234 responds positively to
a structurally diverse range of compounds, including phenolics (vanillin and isovanillin) that
are inhibitors for other rhizobia (97). The transfer of Rhizobium sp. NGR234 nodD1 to a restricted host range rhizobium, like S. meliloti,
extends the spectrum of plants the transconjugant recognizes as a symbiotic partner (16).
NodD regulates transcription by binding cisacting regulatory sequences called nod-boxes
and these elements are generally found upstream of the promoters of the nod, nol, and noe
genes involved in NF production (8, 82). However, interesting nuances to NodD-dependent
regulation are beginning to emerge, including
the identification of genes unrelated to NF
biosynthesis within the NodD regulon (87, 109,
165), and a temporal progression to flavonoidinduced gene expression that implies NodD coordinates a complex regulatory hierarchy (87).
www.annualreviews.org • Molecular Determinants of a Symbiotic Chronic Infection
417
a Flavenoids
b Nod factor
OH
NodH
NodL
OH
O
HO
Luteolin
O - COCH3
OH
CH2
O
HO
HO
O
HO
H
O
CH2
O
O
HO
NH
H3C O C
N
O C
HO
O - SO3H
C H 2 -OH
O
n
O
OH
NH
H3COC
Daidzein
NodABC
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O
OH
NodEF
O
HO
Genestin
Figure 2
Representative
signaling molecules
critical for symbiosis.
(a) Host flavonoids:
luteolin, daidzein, and
genestin. (b) The Nod
factor produced by
S. meliloti and
biosynthetic enzymes
(Nod proteins)
involved in its
synthesis. (c) The
S. meliloti
exopolysaccharide
succinoglycan. ExoH
is responsible for
succinyl modification;
succinoglycan
molecular weight is
controlled by ExoPTQ
and two extracellular
glycosylases, ExsH and
ExoK. (d ) Schematic
representation of
S. meliloti
lipopolysaccharide
(LPS). LpsB is a
glycosyltransferase
with broad substrate
specificity involved in
synthesis of the LPS
core. AcpXL, LpsXL,
and BacA are required
for the Very-LongChain Fatty Acid
(C28) modification of
lipid A.
418
OH
O
OH
c Succinoglycan
d LPS
O-antigen
O
(
4
Glc
1
β
4
Glc
1
β
6
6
4
Glc
1
β
3
Gal
1
β
)
HO
n
β
1
P
OH
O
O
O
H
ExoPTQ
ExsH, ExoK
β
1
Glc
Lipid A
H
NH H
HO
HO
O
O
6
LpsB
O
H
Acetyl
Glc
Core
OH
HO
H
HO
O
H O
H
O
NH O
O
O
O
β
1
6
Succinyl
4
Pyruvyl
ExoH
3
β
1
Glc 6
CH3
CH3
CH3
CH3
AcpXL
LpsXL
BacA
HO
CH3
Gibson
·
Kobayashi
·
Walker
P
OH
HO
3
Glc
H
OH
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The Bacterial NF Response
Host Responses to NF
Bacterial NF functions as a key that opens the
door to its host (128), meaning there is a high
degree of stringency for NF chemical structure
that determines whether the host allows bacterial invasion to proceed. NF also functions as a
mitogen and modifies the plant hormone balance to elicit the primordium formation that
ultimately gives rise to mature nodule tissue
(Figure 1a) (37, 56, 122). It was recently shown
that NF also plays a role in S. meliloti biofilm development and in a host-independent manner
(58); thus, NF appears to perform a significant
role in both free-living and symbiotic lifestyles.
NF is a complex signaling molecule secreted
from the cell as a cocktail of β-(1,4)-linked
N-acetyl-d-glucosamine (GlcNAc) trimers,
tetramers, or pentamers (Figure 2b) (37). The
chitin backbone is modified on the nonreducing
terminal residue at the C2 position by a fatty
acid; however, the size and saturation-state of
this lipid chain varies in a species-specific manner. NF can be further decorated with a variety of chemical substituents, including acetyl,
arabinosyl, carbamoyl, fucosyl, methyl, and sulfuryl additions. In fact, a given rhizobial species
will produce a mixture of NF compounds, anywhere from 2 to 60 distinct molecules, and this
is especially true of broad host range bacteria
(128).
The diversity of NF structures produced by
rhizobia derives from the combined presence
of species-specific genes and allelic variation of
the common nodulation genes (128). Common
nod genes (including nodA, B, and C ), which
are found in nearly all rhizobial species and are
capable of cross-species complementation, are
responsible for synthesis of the NF chitin backbone. In contrast, host-specific nod genes confer specificity for nodulation of a particular host
and are involved in various modifications of the
chitin backbone. The ability to synthesize and
secrete NF can be transferred to Escherichia coli
by introduction of the NF biosynthetic gene
cluster, and this confers upon E. coli the ability
to elicit several of the early NF host responses
described below (178).
A number of physiological responses to NF are
observed when either bacteria or purified NF
are applied to roots (37), and these responses
have been used to position host genes within a
signaling pathway (122). Purified NF is effective at eliciting most host responses at nanomolar concentrations. Initial root epidermal
responses include an alkalinization of the cytosol, and a depolarization of the plasma membrane within minutes of root inoculation. These
two responses appear to depend on a brief
NF-induced Ca2+ -influx that precedes them by
seconds, and they are closely followed by a
prolonged Ca2+ -spiking response that lasts between 20 to 60 min. Purified NF is also sufficient to induce root hair deformation and root
hair curling within a few hours of application.
Root hair deformation likely relies on Ca2+ induced changes to the organization of the actin
cytoskeleton, which produce a reorientation of
cell growth. In fact, NF can accumulate within
the host plasma membrane (66), and appears to
provide a direct positional cue to the host such
that the tip of the root hair grows toward the
site of greatest NF concentration (51).
NF elicits significant changes in the expression of host genes, including those induced early in nodule development that are referred to as early nodulin, or ENOD, genes (37,
122). More globally, transcriptome profiles reveal that plant genes predicted to be involved
in responses to abiotic and biotic stresses, as
well as cell reorganization and proliferation,
are rapidly induced by rhizobia and largely in
a NF-dependent manner (49, 105, 116). At
the earliest postinoculation time point of 1 h,
M. truncatula genes that encode functions related to abiotic stress and disease resistance are
upregulated while those involved in translation
and cytoskeletal organization are downregulated (105). Abiotic stress and disease resistance
genes become significantly downregulated by
6 h postinoculation and this trend continues until at least 3 days postinoculation (105). As discussed below, some of this regulation may be
enhanced by bacterial EPSs, cyclic β glucans
www.annualreviews.org • Molecular Determinants of a Symbiotic Chronic Infection
Mitogen: a substance
that elicits cell division
Transcriptome:
complete set mRNAs
expressed in a cell or
cell population
419
and LPSs. Concurrent with a dramatic reorientation of root cell growth, genes involved in
cytoskeletal functions and cell-wall biogenesis
are induced from 1–12 h postinoculation (105).
Between 12–48 h, genes involved in translation,
cell growth and division, and chromosomal organization are upregulated in a manner consistent with the initiation of meristem proliferation within the root cortex (105, 116). As one
might predict, increased expression of cell division genes is transient within a determinate
nodule and decreases concurrent with the onset of nitrogen fixation (29, 90).
The importance of NF structure for biological activity has been demonstrated through
biochemical analyses of NFs produced by hostspecific nod gene mutants and the corresponding phenotypic characterization of plant responses. For instance, the first symbiotically
active NF structure described was that produced by S. meliloti, which is a chitin tetramer
with an N-linked C16 unsaturated fatty acid
and both O-sulfuryl and O-acetyl modifications
(Figure 2b) (149). An S. meliloti mutant deficient for the host-specific nodH gene lacks the
O-sulfuryl substitution at the reducing terminus of its NF and correspondingly loses the
capacity to nodulate its natural M. truncatula
host, yet it acquires the novel ability to nodulate
Vicia hirsute (139). The purified nonsulfated NF
produced by a nodH mutant elicits Ca2+ -spiking
from its natural host only when present at concentrations much greater than is required for
wild-type NF (123, 139, 178), suggesting the
sulfate modification contributes to host range
specificity by modulating the affinity between
NF and its host receptor.
While the S. meliloti nodH gene is required
to elicit initial physiological responses from
M. truncatula, the host-specific nodEF (NF acylation) and nodL (NF acetylation) genes are subsequently involved in host invasion. Individual
null mutants have a delayed nodulation phenotype associated with inefficient bacterial invasion, whereas the nodFL double mutant has
a more severe defect in infection thread formation (5, 103). Despite the block in bacterial invasion, a nodFL double mutant (and
LPS:
lipopolysaccharide
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LysM: lysin motif
420
Gibson
·
Kobayashi
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Walker
its purified NFs) triggers certain morphological responses from root hairs in a manner
indistinguishable from the wild type. These
include the early Ca2+ -spiking and root hair
curling responses, as well as induction of certain ENODs and nodule primordium formation
(5, 24, 178). Thus, in M. truncatula there are
distinct structural requirements for early NFdependent root hair responses (i.e., NF sulfation) vs later NF-dependent infection events
(i.e., NF sulfation, and acetylation or acylation).
The relative ease with which plant symbiosis mutants can now be characterized molecularly has significantly expanded our understanding of the host signal transduction
pathway that allows bacterial invasion based
on NF perception (78, 122). Putative NFreceptors, including MtNFP and MtLYK3,
belong to the lysin motif (LysM) receptor-like
kinase family, which have an extracellular domain homologous to the bacterial LysM proteins that bind β-(1,4)-linked GlcNAc derived
from peptidoglycan. Host responses to specific
NF structures depend on the LysM domain
specifically, and a one amino acid difference
within this motif can alter the range of rhizobia
recognized for symbiosis (134).
Additional NF signaling genes have been
identified that function downstream of the
LysM receptor-like kinases (78, 122). For example, several dmi (does not make infections)
mutants have been characterized in M. truncatula, and the affected genes have orthologs
in L. japonicus. Highlighting the importance
of the NF-dependent Ca2+ -spiking response,
MtDMI3 encodes a putative Ca2+ -calmodulindependent protein kinase (CCaMK) (115).
MtDMI1 encodes a nuclear-localized cation
channel that may help modulate Ca2+ -spiking,
and MtDMI2 encodes a putative receptor-like
kinase (76, 119). While all of the dmi mutants
display root hair deformation and rapid Ca2+ influx in response to NF, dmi1 and dmi2 mutants
are unable to elicit the subsequent Ca2+ -spiking
response (50, 72, 75, 159, 177, 179). In contrast,
the dmi3 mutant is indistinguishable from wild
type with regard to each of these physiological NF responses (177). Thus, M. truncatula
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DMI1 and DMI2 appear to function downstream of MtNFP and MtLYK3, but upstream
of the Ca2+ -calmodulin-dependent protein kinase encoded by DMI3. Recent reports showing that DMI3 can be genetically modified to
elicit spontaneous nodule formation suggest it
may be possible to intelligently engineer nonlegume species that are capable of establishing
symbiotic nitrogen fixation (65, 166).
Although NF signaling is a nearly universal
means of establishing the rhizobium nitrogenfixing symbiosis with compatible legumes, exceptions are emerging. The recent sequencing of photosynthetic Bradyrhizobium sp. BTAi1
and ORS278, which form nitrogen-fixing nodules on the roots and stems of aquatic host,
Aeschynomene sensitiva, revealed that the common nodABC genes are absent in these species
(63). Moreover, a NF-deficient mutant of the
closely related Bradyrhizobium sp. ORS285
forms nitrogen-fixing root and stem nodules
on A. sensitiva with the same efficiency as
its wild-type parental strain. Thus, the host
A. sensitiva initiates nodule development in
a NF-independent manner and instead may
respond to the secretion of bacterial purine
derivatives with cytokinin-like activity, highlighting the importance that host hormone balance plays in nodule formation (63).
REACTIVE OXYGEN
AND NITROGEN SPECIES
As with many host-microbe interactions (39,
118, 187), the rhizobium-legume symbiosis can
be associated with a host-generated release
of reactive oxygen species (ROS: O·−
2 , H2 O2 ,
and HO· ) and reactive nitrogen species (RNS:
NO· ). As discussed below, application of purified S. meliloti LPS can suppress ROS production in response to fungal elicitors in M. truncatula tissue culture cells (1, 148); however, the
role this response plays in symbiosis is unclear.
The application of purified S. meliloti NF to
M. truncatula roots also inhibits ROS production in response to fungal elicitors (151), and
correspondingly limits the expression of putative ROS-generating NADPH oxidase genes
(104). The NF-mediated inhibition of ROS efflux occurs within 1h of treatment and is dependent on the putative NF receptor encoded
by MtNFP but not the downstream DMI1 gene
(104, 151). NF-mediated suppression of ROS
production plays a causative role in the root hair
deformation and curling responses to rhizobia
(104).
However, subsequent stages of symbiosis between M. truncatula and S. meliloti result in the
long-term production of ROS and RNS in distinct areas of the nodule. While RNS are primarily associated with plant cells that have been
infected with bacteria (12), ROS are associated
with the plant cell wall of both infection threads
and infected host cells (142, 147). This ROS
efflux requires NF, arguing that ROS may play
a positive role in bacterial invasion (136). The
M. truncatula response to NF includes induction of the rip1 gene encoding a putative
peroxidase that could be involved in hydrogen peroxide-dependent cross-linking of cell
wall proteins (31). Both the induction of rip1
expression and the production of ROS require that M. truncatula has a functional DMI1
gene (136), genetically separating the early
DMI1-independent decrease in ROS from this
later response. The DMI1 requirement for rip1
induction is bypassed when root tissues are exposed to exogenous H2 O2 (136).
Generally, free-living rhizobia are more susceptible to ROS-mediated killing than are other
common soil bacteria like Bacilli and Pseudomonads (120), suggesting that symbiotic levels of
ROS are probably unable to differentially prevent soil pathogens from taking advantage of
ITs to invade nodules. One role for ROS production may be to promote proper IT development and growth by either cross-linking
cell wall glycoproteins or degrading cell wall–
associated polysaccharides to aid IT elongation.
Only a small percentage of newly formed ITs actually penetrate the inner cortical cell layer, and
the unsuccessful, or aborted, ITs display certain
characteristics of the hypersensitive plant defense response (171), which typically includes
ROS production. Thus, this ROS efflux could
play a role in limiting bacterial invasion.
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ROS: reactive oxygen
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RNS: reactive
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Recent observations are consistent with the
idea that ROS may also function as a positive
signal perceived by bacteria during invasion.
This is based on the finding that an S. meliloti
strain overexpressing the KatB catalase has a
nodule invasion defect that is primarily associated with aberrant IT growth (76). KatB is
responsible for detoxifying H2 O2 and thereby
limits the concentration of exogenously applied
ROS within the bacterial cell (4). Bacterial overexpression of KatB likely acts as a strong catalyst for detoxifying ROS and may lower the
local concentration of free oxygen radicals able
to modify the IT compartment. KatB overexpression presumably also leads to significantly
decreased concentrations of ROS within the
IT-localized bacterial cell. The symbiosis defect associated with KatB overexpression could
therefore reflect the fact that ROS functions
as a cytoplasmic signal that the bacterium uses
to regulate functions essential to invasion. It is
unlikely this ROS signal would be perceived
through the OxyR redox-sensitive regulatory
protein since an S. meliloti oxyR mutant has
no obvious symbiosis defect with M. truncatula
(41, 107). However, the putative redox-sensitive
CbrA two-component histidine kinase is required for bacterial invasion of Medicago hosts
and regulates a number of genes specifically
required for bacterial invasion (61, 62), making CbrA a promising candidate for a bacterial
redox-sensor involved in bacterial invasion.
Although ROS appears to promote rhizobial invasion, these bacteria must also be able to
combat this stress in order to achieve symbiosis.
A screen for ROS-sensitive S. meliloti mutants
that simultaneously display aberrant symbiosis
phenotypes revealed a variety of functions related to bacterial metabolism and exopolysaccharide production (41). With regard to genes
specifically required to detoxify ROS, S. meliloti
has three that encode catalase enzymes (katA,
katB, and katC) and one encoding superoxide dismutase activity (sodB) (77, 146). Several
uncharacterized genes include an extracellular peroxidase (Smc01944), a bacteriocupreinfamily superoxide dismutase (sodC), and an
alkylhydroperoxidase (ahpC), each of which
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may combat ROS exposure; however, null phenotypes for these genes have not been reported
(7, 60). Null mutants for either katA, katB,
katC, or sodA are fully capable of establishing
the symbiosis (40, 77, 152), although the katAC
and katBC double mutants have decreased symbiotic proficiency (77, 152). In particular, the
katBC mutant has a severe symbiosis defect that
results in formation of aberrantly small nodules
that are incapable of nitrogen fixation (77). Although the katB and katC genes are strongly
expressed in bacteria located within growing
ITs, where ROS is concentrated, the phenotype
of the double mutant is subsequently revealed
during bacterial uptake into the host cell cytoplasm: intracellular bacteria lack the surrounding peribacteroid membrane and undergo
rapid senescence for reasons that are unclear
(77).
MODULATION OF THE HOST
DEFENSE RESPONSE
The initiation of ITs is a major checkpoint for
the host in terms of deciding whether to allow
bacterial invasion to proceed. In the past few
years, several plant mutants affected in IT formation and growth have been isolated, and their
further characterization will likely shed light on
some of the mechanisms that the host uses to
create and control the growth of this structure
(30, 91, 106, 163, 176, 189).
Rhizobial invasion of the host nodule via the
IT is strongly influenced by a complex variety of bacterial polysaccharides in addition to
NF, including secreted EPSs and K-antigens,
secreted and periplasmic cyclic β glucans, and
the outer membrane-localized LPSs (14, 57,
78, 155, 157). Similar to NF, several of these
molecules exert their effects on symbiosis in
a structurally dependent manner, arguing that
they may function as signals between invading
bacteria and their host. In fact, recent evidence
suggests that the exopolysaccharide succinoglycan may help further define species-specificity
in addition to NF (153). A shared and outstanding question regarding these bacterial polysaccharides is their potential role in modulating
a plant defense response to bacterial invasion.
However, definitive proof for such possibilities
awaits the identification and characterization of
specific host receptors.
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Exopolysaccharide
The biosynthesis of rhizobial EPS and its regulation have been most extensively studied with
regard to the S. meliloti macromolecule referred
to as succinoglycan, or EPS I, (Figure 2c) (15,
78, 155). S. meliloti succinoglycan is secreted
as a polymer of repeating octasaccharide subunits (one galactose and seven glucose residues)
modified with succinyl, acetyl, and pyruvyl
substituents (Figure 2c). Polymerization of
the succinoglycan monomer results in secretion of either low molecular weight (LMW)
forms (monomers, dimers, and trimers) or high
molecular weight (HMW) forms (polymers of
several hundred subunits).
Succinoglycan plays a critical role in the
S. meliloti symbiosis with Medicago hosts.
Succinoglycan-deficient mutants elicit nodule
organogenesis by virtue of NF signaling (86),
but these aberrantly small nodules are devoid
of bacteria and therefore incapable of nitrogen
fixation (99). These rhizobial mutants are compromised for host invasion to the extent that
IT formation proceeds from only 10% of bacterially colonized root hairs and the ITs that do
form terminate prematurely before they reach
the nodule primordium (27). While EPSs play
a passive role in protecting the bacterium from
host-derived stresses within the IT (36), they
are also thought to perform a signaling function
from rhizobia to their host (78, 79). Part of the
evidence for this is based on the observation that
LMW forms of succinoglycan are more effective at promoting symbiosis than HMW forms
(10, 169, 182). Moreover, an exoH mutant is unable to succinylate the succinoglycan monomer
and therefore produces predominantly HMW
succinoglycan (98); since this mutant is also
severely compromised for symbiosis a merely
protective role is not sufficient to explain all
of the requirements for succinoglycan in host
invasion.
Increasingly, the evidence available suggests
that bacterial EPSs play a role in modulating
the host defense response to bacterial invasion.
For example, the premature termination of bacterial infection observed with EPS-deficient
mutants is associated with symptoms of a host
defense response and, in particular, the production of antimicrobial phenolics and phytoalexins (119, 126). To test the hypothesis that
succinoglycan promotes symbiosis as a signaling molecule, a global transcriptome analysis
was performed on M. truncatula plants inoculated with succinoglycan-deficient S. meliloti
at a time point just prior to IT formation
(3 days postinoculation) (79). Thus, this experiment identified host genes differentially regulated in response to EPS production, rather
than IT failure per se, and the largest group
of genes upregulated during an EPS-deficient
interaction encode putative plant defense proteins (79). As mentioned above, M. truncatula
defense genes are upregulated 1 h postinoculation with wild type S. meliloti; however, expression of this same class of genes decreases by
6 h postinoculation and remains low for at least
3 days (105). Taken together, these observations
suggest that a primary consequence of EPS production is the suppression of a potentially lethal
host defense response, and in the absence of
EPS, this unproductive response may cause a
block in IT formation (27).
Insight into how S. meliloti regulates production and modification of exopolysaccharides
is therefore important to our understanding
of the physiological requirements for host invasion. An increasingly large number of regulators modulate succinoglycan production ex
planta, including ExoS, ExoR MucR, SyrA, and
the more recently identified CbrA (62, 155).
The first regulators of succinoglycan to be
identified were the ExoS two-component histidine kinase and ExoR. ExoS is an essential gene
in S. meliloti and forms a two-component signal
transduction pathway with the response regulator ChvI, which is also essential and functions as a DNA-binding transcription factor
(26). ExoS phosphorylates ChvI directly and
thereby promotes increased exo/exs expression
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and greater succinoglycan production (26).
ExoR has no homology to any known regulators, however a null mutation alters the
transcription of several exo biosynthetic genes
(138). Early observations suggested a genetic
link between exoR and exoS: extragenic suppressors of an exoR null mutant symbiosis defect were mapped near exoS and these suppressors displayed a concomitant change in exo
gene transcription (125). More recent evidence
indicates that ExoR is a periplasmic protein
that functions upstream of the ExoS/ChvI twocomponent pathway and is hypothesized to directly repress ExoS kinase activity by binding its periplasmic sensing domain (183). An
outstanding question remains as to the nature of the stimulus perceived by ExoS and/or
ExoR.
The two-component histidine kinase CbrA
has also been identified as a regulator of succinoglycan production. Unlike the overproduction of wild-type forms of succinoglycan in exoS
and exoR mutants (46), a cbrA mutant appears
to overproduce predominantly LMW forms of
succinoglycan, and this phenotype is correlated
with increased transcription of several exo genes
involved in LMW succinoglycan biosynthesis,
including exoH, exoK, and exoT (62). Moreover,
the cbrA mutation leads to increased expression of additional genes involved in promoting bacterial IT invasion, including the ndvA
transporter of cyclic β glycans (described below) and the sinI regulator of galactoglucan
(EPS II) production (61). Thus, it was proposed
that CbrA coordinates multiple aspects of bacterial physiology to promote bacterial invasion
of the nodule, and that the physiology of the
cbrA mutant is optimized for this process. Given
that CbrA contains at least one PAS domain
(62), a motif that commonly monitors redox
changes, CbrA may coordinate bacterial physiology in response to the high redox environment of the IT. However, since the cbrA mutant
remains defective for symbiosis despite a physiology optimized for IT invasion (61), it appears
that CbrA plays an additional role during subsequent bacteroid differentiation, as discussed
below.
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Cyclic β Glucan
Rhizobia generally produce β-(1,2)-glucans
that are macrocyclic and unbranched polymers
of glucose, containing anywhere from 17 to
40 residues depending on the rhizobial strain
(157). The synthesis of cyclic β glucan is dependent on a glycosyltransferase encoded by
ndvB (called cgs in Mesorhizobium loti ) and its
secretion is dependent on the ABC-type inner membrane transporter ndvA. Bradyrhizobium species are an exception and produce
branched macrocyclic glucans that contain both
β-(1,3) and β-(1,6) glycosidic bonds catalyzed
by glycosytransferases encoded by ndvB and
ndvC. The chemical characteristics of cyclic
β glucans can be modified by the addition
of phosphocholine, sn-1-phosphoglycerol, succinic and methylmalonic acid substituents. Disruption of ndvB (cgs) in S. meliloti (M. loti )
blocks symbiosis at the stage of bacterial attachment to root hairs and IT invasion and thereby
results in the formation of aberrantly small and
empty nodules (34, 48). In contrast, a B. japonicum ndvB mutant is able to elicit normal nodule
development and invade host tissues, although
the resulting nodules do not fix nitrogen (47).
Like succinoglycan, the cyclic β glucans may
play a role in modulating a host defense response to bacterial invasion. Specifically, M. loti
cyclic β glycans are required to suppress highlevel production of antimicrobial phytoalexins
during symbiotic development with L. japonicus (35). Many host defense response genes
are induced in a mature nodule during a wildtype symbiosis (29, 90), perhaps to provide
the nutrient-rich nodule with a defense against
parasites. These same genes are generally
expressed at decreased levels during the ineffective symbiosis of the cgs mutant, with the striking exception of highly induced PAL expression (35). PAL encodes an enzyme predicted
to participate in the synthesis of antimicrobial phenolic compounds, and consistent with
increased PAL expression during the cgs mutant symbiosis, L. japonicus nodules accumulate
phenolic compounds to a greater extent than
is observed during a wild-type symbiosis (35).
Purified B. japonicum cyclic β glucans are able
to block a host defense response to fungal elicitors in the determinate legume G. max and in
a structurally dependent manner (17), further
suggesting these polysaccharides may be able
to prevent a host defense response during rhizobial invasion.
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BACTERIAL REQUIREMENTS
FOR INTRACELLULAR
COLONIZATION
Lipopolysaccharide
Throughout symbiotic development the S.
meliloti cell surface is in intimate association
with its host but this is particularly true of
the microsymbiont within the symbiosome.
Not surprisingly then, the bacterial cell surface plays an important role in promoting rhizobial intracellular adaptation, including the
lipopolysaccharide (LPS) component of the
gram-negative outer membrane (14, 83, 157).
LPS is a complex macromolecule composed of
a lipid A membrane anchor and an oligosaccharide core, which can be further modified by
the addition of a variable O-antigen polysaccharide (135). Generally, host perception of
LPS from pathogenic bacteria plays a significant role in defense responses to invasion via
the innate immune system (130). It has therefore been of great interest to understand the
specific role that rhizobial LPS plays in symbiotic development. Bacteroid LPS has increased
hydrophobicity compared to that of free-living
bacteria, suggesting there are LPS modifications in planta that may contribute to symbiosis
(38, 84).
Rhizobia produce a lipid A with unique
structural characteristics that distinguish it
from the potent E. coli innate defense elicitor
endotoxin (135), although there is variation in
certain elements among the rhizobia (14, 83).
For instance, most rhizobia produce lipid A
species lacking either one or both of the 1- and
4′ -phosphate groups present on the β-(1,6)glucosamine disaccharide of E. coli; Sinorhizobium lipid A is an exception to this trend as
it is bisphosphorylated (Figure 2d ). In addition, rhizobial lipid A moieties are most often
modified with a secondary N-linked acyloxyacyl residue composed of a C28 or C30 VeryLong-Chain Fatty Acid (VLCFA) that has the
capacity to span the entire lipid bilayer of the
outer membrane (Figure 2d ). This particular modification has generated much interest
as a structural feature that could shield rhizobial LPS from recognition by the host innate
immune system and thereby promote rhizobial
invasion and persistence. In fact, the presence of
VLCFA modified lipid A has been observed in
several related bacteria that establish persistent
host infections, including all rhizobia, agrobacteria, and brucella that have been analyzed.
The acpXL and lpsXL genes encode an acyl
carrier protein and an acyl transferase, respectively, that together catalyze the VLCFA
secondary acylation of lipid A in rhizobia.
Rhizobial acpXL and lpsXL mutants completely lack the VLCFA-modified lipid A during free-living growth but remain effective at
establishing a nitrogen-fixing symbiosis (53,
150, 175), although bacteroid development
is mildly perturbed and leads to decreased
nitrogen-fixation (173). This weak symbiosis
phenotype is likely explained by the recent discovery that acpXL mutants of R. leguminosarum
b.v. viciae form bacteroids that actually contain VLCFA-modified lipid A, indicating that
they express an alternative system for VLCFA
modification in planta (174); thus, the role that
the VLCFA modification plays in symbiosis remains to be determined.
Alteration of the LPS carbohydrate content,
in either the core or the O-antigen, has an aberrant effect in a variety of symbioses (83). For
example, an S. meliloti lpsB mutant has a dramatically altered LPS core and is incapable of establishing a chronic host infection (21). While the
mutant displays normal host IT invasion and is
taken up into the host cell cytoplasm, it undergoes rapid senescence and is degraded within
the symbiosome compartment, suggesting LPS
plays a critical role in rhizobial adaptation and
persistence within the particular environment
of the host cell cytoplasm (21).
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The precise function of LPS in promoting
symbiosis remains unclear (14). Defects in LPS
can sensitize bacteria to membrane-disrupting
agents and antimicrobial peptides so that it
may provide a protective barrier against environmental stress and host defense responses.
However, there are indications that S. meliloti
LPS may also play an active role by suppressing the release of ROS (1, 148). Specifically, M.
truncatula tissue culture cells respond to yeast
elicitors with an oxidative burst and the increased expression of defense genes involved in
plant secondary metabolism, like PAL, and cell
wall metabolism (1, 164). When tissue culture
cells are exposed to elicitor in the presence of
S. meliloti lipid A, this LPS component is capable of suppressing the oxidative burst and dampening the plant transcriptional response (148,
164), indicating an interaction between rhizobial LPS and its host could suppress any potential immune response to intracellular bacteria.
This could be particularly important for bacteria within the symbiosome as they no longer
express genes for the biosynthesis of succinoglycan (9), which appears to dampen a potential plant defense response to bacteria within
the IT (78, 79). Lipid A moieties isolated from
the related intracellular mammalian pathogen
Brucella abortus, which also undergo VLCFA
modification, are only weak elicitors of an innate immune response in mouse macrophages
(93, 94). Perhaps these related alphaproteobacteria share some of the strategies that rhizobia
use to evade detection by the innate immune
system during chronic infection.
BacA
The bacA gene encodes an inner membrane
protein that plays an essential role in the early
stages of S. meliloti bacteroid development (64).
With a bacA mutant, the early steps in symbiosis, such as formation and development of infection threads, proceed as efficiently as with
wild type but the mutant lyses shortly after being endocytosed into the cytoplasm of plant
cells. BacA function is also essential for the
chronic infection of B. abortus (100), a mam426
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malian pathogen that can survive and replicate
in host macrophages, highlighting the broad
importance of BacA function to chronic bacterial persistence during intracellular infection
(140).
Generally, the loss of bacA function has been
associated with an increased resistance to certain antimicrobial peptides (74, 96, 113). In
E. coli, deletion of the bacA isofunctional homolog, sbmA, produces increased resistance to
microcins B17 and J25, bleomycin, and Bac7,
which is an antimicrobial peptide of mammalian
origin (96, 113). Similarly, the bacA mutants of
S. meliloti and B. abortus show increased resistance to bleomycin relative to the wild type (74,
100). Thus, BacA may play a role in the transport of modified peptides across the inner membrane (64). In fact, it was proposed that BacA
functions as an importer for host-derived peptide(s) that promote bacteroid differentiation
(114). Specifically, it was suggested that bacterial uptake of Nodule-specific Cysteine-Rich
(NCR) peptides produced by indeterminate
legumes could trigger the terminal differentiation of bacteroids (3, 114), analogous to the
role defensins play in suppressing the proliferation of bacterial pathogens (190).
In S. meliloti and B. abortus, BacA also affects
the VLCFA modification of the lipid A component of LPS (52, 54). BacA has homology to
the transmembrane domain of eukaryotic ATPbinding cassette (ABC) transporters of the
ABCD family (52). ABCD transporters function in the peroxisome and this includes the human adrenoleukodystrophy protein (hALDP)
that is thought to transport activated VLCFAs across the peroxisomal membrane (181).
Approximately 50% of lipid A moieties isolated from S. meliloti bacA mutants (as well as
B. abortus) lack VLCFAs (52). Thus, it was suggested that BacA may export VLCFAs from
the cytoplasm and across the inner membrane,
and perhaps the lack of VLCFA-modified lipid
A causes the defects in chronic infection observed with bacA mutants (52). As mentioned
above, rhizobial acpXL and lpxXL mutants completely lack VLCFA-modified lipid A during
free-living growth and are able to establish
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a successful symbiosis despite bacteroid morphological abnormalities (53, 150, 173, 175).
However, at least R. leguminosarum acpXL bacteroids contain VLCFA-modified lipid A in
planta (174), indicating an alternative system
for VLCFA modification exists that may require
BacA function.
It remains to be determined whether BacA is
directly responsible for either one or both of the
proposed transport reactions. S. meliloti strains
carrying 12 site-directed mutations in bacA have
phenotypes intermediate to the wild-type and
bacA null mutant (101), consistent with a role
for BacA in multiple, nonoverlapping functions.
Moreover, it was reported that functional SbmA
is required for full efficiency of the tetracycline
exporter TetA in E. coli (42), suggesting that
BacA function could similarly affect the activity of other membrane proteins. Future studies
that reconstitute BacA into liposomes, followed
by detailed transport assays, will be needed to
elucidate its precise function.
DEVELOPMENTAL REGULATION
OF THE CELL CYCLE
Symbiotic regulation of the plant cell cycle and
the role of endoreduplication in nodule development has been studied extensively (56, 122).
In contrast, an understanding of how the bacterial cell cycle may be regulated during symbiosis
is just beginning to emerge. Bacteroids within
determinate hosts have the ability to dedifferentiate into free-living bacteria once they are
released from a senescent nodule (114). In contrast, at least some rhizobia that form a symbiosis with indeterminate legumes undergo a
terminal differentiation program that precludes
viability outside the host cell cytoplasm (114).
Whether a given rhizobial species undergoes
terminal differentiation appears to be a decision
controlled by the legume host (114).
During free-living growth, and presumably
within the IT, S. meliloti grows as a rod-shaped
bacterium with no greater than a 2N complement of its genome (Figure 3a,b) (114), which
implies that these bacteria initiate DNA replication only once per cell cycle. In contrast, one
remarkable aspect of terminal bacteroid differentiation is a branched cell morphology that
is accompanied by several rounds of genomic
endoreduplication (Figure 3c) (114). The correlation between bacteroid endoreduplication
and the inability to dedifferentiate and resume
growth outside the host suggests the act of
endoreduplication may be a defining event in
terminal bacteroid differentiation. The indeterminate symbiosis therefore represents a novel
bacterial cell cycle event, i.e., endoreduplication, which may play an important role in either intracellular persistence or efficient nitrogen fixation. Taken together, these observations
imply that the S. meliloti cell cycle has at least
three branch points subject to in planta regulation (Figure 3d ), and it will be of great interest
to understand how the cell decides which path
to choose under different host conditions.
While regulatory aspects of the S. meliloti
cell cycle have been little studied, that of the
related Caulobacter crescentus alphaproteobacterium has been dissected in great detail and
thereby serves as a powerful model on which
to base future studies in S. meliloti. Briefly, in
C. crescentus the CtrA response regulator collaborates with the DnaA replication initiator
and GcrA transcription factor to globally control cell cycle progression (154). Throughout
the cell cycle, CtrA concentrations are strictly
regulated, and this plays a critical role in mediating cell cycle progression. Additionally, an
elaborate two-component signal transduction
pathway containing the essential response regulator DivK regulates the concentration of active
CtrA-P (18). Through this multi-layered regulation of active CtrA-P concentrations, C. crescentus limits the initiation of DNA replication to
once per cell cycle (Figure 4a), in contrast with
E. coli and other fast-growing bacteria. The coordination between DNA replication and cell
division that allows only one replication initiation event per cell cycle is also observed in
S. meliloti (114).
C. crescentus undergoes an asymmetric cell
division during each cell cycle for the purpose
of nutrient adaptation (Figure 4b), and the
DivJ and PleC two-component histidine kinase
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←−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
G1
a
Figure 3
Free-living
S
G2
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b
Infection thread
c
Bacteroid
differentiation
S x 3˜4
d
G2
G1
2
Model for in planta
modulation of cell cycle
1
S
3
G0
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Schematic representation of the rhizobium cell cycle
at different stages of symbiosis. (a) The S. meliloti
cell cycle is modeled after that of the
alphaproteobacterium Caulobacter crescentus. A cell
division cycle is comprised of three distinct phases:
G1 , S, and G2 . In C. crescentus, DNA replication is
initiated only once per cell cycle, in S phase;
however, chromosome segregation begins during S
phase and continues in G2 phase. Cell division
begins in G2 phase and is completed before the next
DNA replication initiation event. During free-living
growth, S. meliloti is thought to initiate DNA
replication only once per cell cycle and divides
asymmetrically to produce daughter cells of
different size. In analogy to C. crescentus, the small
daughter cell likely proceeds into G1 phase while
the larger daughter cell directly re-enters S phase.
(b) S. meliloti proliferating in the IT originate from a
clonal expansion of founder cells entrapped in the
tip of the root hair curl. Cells appear to lack flagella
and are loosely associated with one another in a
pole-to-pole manner, typically forming two or three
columns with a braided appearance. Active
propagation of bacteria is observed only in a limited
area called the growth zone near the tip of the IT,
while bacteria outside of the growth zone do not
grow or divide. It seems likely that the restricted
growth of bacteria enables synchronization of
bacterial growth with extension of the IT. (c)
Bacteria colonize the cytoplasm of plant cells located
in the invasion zone (see Figure 1d ). Bacteria are
surrounded by a plant-derived membrane and
differentiate into a bacteroid. In S. meliloti, DNA
endoreduplication occurs during bacteroid
differentiation and results in dramatic cell branching
and enlargement to a length of 5–10 µm; in
comparison, free-living counterparts are rod-shaped
cells of 1–2 µm. These terminally differentiated (G0
phase) bacteroids are unable to resume future
growth. Orange lines, host plasma membrane; green
lines, host cell wall. (d ) A model of the S. meliloti cell
cycle in planta has three possible exits from S phase,
two of which (in blue) represent an exit from the
typical free-living cycle (in red ). Bacteria within the
infection thread are thought to progress through the
cell cycle in the same manner as free-living cells, and
in particular transition from S phase into G2 phase
(represented by arrow 1). Bacteria that undergo
bacteroid differentiation undertake the process of
endoreduplication and therefore re-enter G1 phase
after the completion of S phase (represented by
arrow 2); the bacteria may cycle from S to G1
multiple times during endoreduplication. Once
endoreduplication is complete, the bacteroid enters
a terminally differentiated state (G0 ) and is no
longer able to initiate cellular growth or DNA
replication (represented by arrow 3).
a
G1
Cell cycle
S
Replication
initiation
G2
Chromosome
replication
Chromosome
Cell
segregation separation
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b
Caulobacter
Swarmer
Stalked
Predivisional
Daughters
“Small”
“Large”
Predivisional
Daughters
c
Sinorhizobium
DivK
DivK〜P
Figure 4
Schematic representation of cell-cycle progression in C. crescentus and S. meliloti. (a) The cell cycle is
comprised of three distinct phases: G1 , S, and G2 (shown in red ). The timing of cell cycle-related events is
shown in blue. (b) During G1 phase, C. crescentus is a swarmer cell, which is motile and has a polar flagellum
and pili. When entering S phase, the swarmer cell ejects the flagellum, retracts the pili, and differentiates
into a stalked cell. The stalked cell is uniquely competent to initiate DNA replication. After chromosome
segregation in G2 phase, the cell divides asymmetrically to produce two different daughter cells: a swarmer
and a stalked cell. During cell-cycle progression, cellular localization of DivK is controlled by
phosphorylation: nonphosphorylated DivK is uniformly distributed in the cytoplasm and DivK∼P is
localized to the cell poles. (c) Recently it was shown that S. meliloti also divides asymmetrically to form a
“small” cell and a “large” cell. Localization of the DivK homolog indicates that the “small” and “large” cells
are counterparts of the C. crescentus swarmer and stalked cells, respectively. Flagella are omitted from this
scheme because their localization has not been examined during cell cycle progression in S. meliloti.
www.annualreviews.org • Molecular Determinants of a Symbiotic Chronic Infection
429
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sensors mediate this asymmetry. Other alphaproteobacteria also undergo asymmetric
cell division and have orthologs of C. crescentus
cell cycle regulators present in their genomes
(70), including S. meliloti (Figure 4c), B. abortus, and Agrobacterium tumefaciens. CbrA has
strong homology in its C-terminal kinase domain to the DivJ and PleC kinases of DivK (70),
suggesting that its primary function may be to
regulate cell cycle progression in S. meliloti via
regulation of DivK phosphorylation, as was observed for its B. abortus ortholog PdhS (71). In
fact, during free-living growth the cbrA mutant displays a filamentous, branched morphology that coincides with a greater than 2N genomic content, indicating the mutant is unable to coordinate DNA replication with cell
division (K.E. Gibson & G.C. Walker, unpublished). Perhaps CbrA plays a role in modifying the cell cycle program during symbiosis and
loss of this function is primarily responsible for
the in planta defects of the cbrA mutant. If this
is the case, it will be of interest to determine
how CbrA coordinates cell cycle progression
with cell envelope physiology and succinoglycan production. It is possible that at least some
of the cbrA mutant phenotypes are an indirect
consequence of altered cell cycle progression
given that multiple cell surface characteristics
are cell cycle regulated in C. crescentus.
The process of endoreduplication undoubtedly creates an intense demand for dNTPs
within the developing bacteroid. The dNTPs
required for DNA metabolism in all organisms
are synthesized by the enzyme ribonucletide
reductase (RNR) (78). S. meliloti has only one
RNR encoded in its genome, NrdJ, and this
is a vitamin B12 -dependent enzyme (33). As a
Class II RNR that is both oxygen-independent
and oxygen-insensitive (80), this enzyme likely
provides a key adaptation for rhizobial persistence within the microaerobic environment of
the host cell cytoplasm. The B12 biosynthetic
enzyme BluB, which catalyzes formation of the
lower ligand 5,6-dimethylbenzimidazole, was
fortuitously found to be required for symbiosis between S. meliloti and M. sativa based on
its involvement in succinoglycan biosynthesis
430
Gibson
·
Kobayashi
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Walker
(22, 162). A bluB mutant appears able to infect
the host via normal IT growth, suggesting that
any alteration to the succinoglycan does not affect invasion; however, bacteroids are not observed within the host cell cytoplasm and the
nodules that develop are unable to fix nitrogen
(22). Thus, BluB function in B12 biosynthesis is
necessary for symbiosis due to the requirement
for a B12 -dependent enzyme(s), for which NrdJ
is one possible candidate.
During the indeterminate symbiosis between Mesorhizobium huakuii and Astragalus
sinicus, bacterial DNA replication is limited to
those bacteria associated with the meristem in
Infection Zone II and Interzone II/III (89). This
observation suggests that, at least in some rhizobia, DNA replication is permanently blocked
once the bacteroid completes endoreduplication. Bacterial genes involved in DNA repair
are induced within mature nodules (9), suggesting that DNA integrity is maintained within
bacteroids in the absence of DNA replication.
Importantly, these DNA repair genes include
several that encode nonhomologous endjoining (NHEJ) proteins involved in double
strand break repair (88), a process also utilized
by terminally differentiated cells in higher eukaryotes.
Little is currently known regarding rhizobial cell division during symbiosis, although
the altered morphology of bacteroids implies
an underlying regulation of this process. Several S. meliloti genes involved in cell division
have been characterized, for instance ftsZ1 and
ftsZ2 (108, 110, 111), as well as minCDE (28).
Blocking the process of cell division via overexpression of ftsZ1 or minCD causes altered
cell morphology during free-living growth that
is reminiscent of the branched and filamentous bacteroid (28, 95). Treatment of S. meliloti
with DNA-damaging agents, which impinge
on DNA replication and cell division in other
bacteria, also inhibits cell division and results
in branched cell morphology (95). Although
the mechanisms that underlie these changes in
cell morphology and how they relate to bacteroid differentiation are still unknown, ftsZ1
and ftsZ2 expression is decreased in bacteroids
consistent with a block in cell division after differentiation (9, 13).
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NUTRIENT EXCHANGE
Invading bacteria within the IT are ultimately
endocytosed by postmitotic G0 endoploid cells
and remain encapsulated within a modified
plasma membrane called the peribacteroid
membrane (PBM) (Figure 1d, f ). The symbiosome, consisting of the PBM and its microsymbiont, is thereby formed and within this
PBM-bound compartment bacteria establish a
persistent, or chronic, infection of the host. In
this manner, a single host cell will ultimately
house hundreds of bacteria. Only after bacteria have gained access to the host cell cytoplasm do they differentiate into the morphologically distinct bacteroid form that is capable
of nitrogen fixation. The in planta differentiation of rhizobia involves significant metabolic
changes that promote adaptation and nitrogen
fixation (121, 131). For example, rhizobia undertake respiratory chain modifications that allow energy utilization under microaerobic conditions, repress glycolysis genes, and activate
C4 -dicarboxylic acid utilization pathways for
carbon metabolism. Induction of nitrogenase
gene expression is triggered in a FixJ-dependent
manner by the microaerobic conditions of the
host cell cytoplasm (55), which is in turn critical for the activity of this oxygen-sensitive enzyme (45, 92). In addition to genes required for
nitrogenase activity, FixJ is responsible for induction of nearly all the bacterial genes whose
expression increases in mature nodules (9), indicating that the oxygen-sensing two-component
pair FixL and FixJ plays a profound role in regulating bacteroid physiology. In contrast, host
gene expression in nodules colonized by the rhizobial fixJ mutant is largely indistinguishable
from nodules colonized by wild-type rhizobia,
suggesting that nodule morphogenesis and bacterial invasion contribute more to host gene
regulation than does nitrogen fixation (9).
Creation and maintenance of the host microaerobic environment is dependent on structural aspects of the nodule that form an oxygen
diffusion barrier in combination with high expression levels of plant leghemoglobin, which
can be 25% of total soluble protein in a nodule and helps limit the concentration of free
oxygen to 3–22 nM (124, 167, 186). The host
supports high nitrogenase activity by providing
bacteroids with a constant flux of O2 for aerobic respiration and with energy in the form of
C4 -dicarboxylic acids derived from the photosynthate sucrose (102, 141, 143). The metabolic
product of the nitrogenase enzyme reaction is
ammonia, and this appears to be provided to
the host both directly and indirectly through
its incorporation into alanine by the bacterial
enzyme alanine dehydrogenase (2). Generally,
nitrogen secreted from the bacteroid is assimilated by the host through its incorporation into
the amino acids glutamine and glutamate by the
enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT), respectively (185). In
determinate nodules, the large bacterially infected cells are interspersed with small noninfected cells that appear to be specialized for
further nitrogen assimilation, involving conversion of amino acids (glutamine and arginine)
into either ureides or amides that are exported
from the nodule to the rest of the plant.
PBM: peribacteroid
membrane
HOST SANCTIONS ON
SYMBIOTIC RHIZOBIA
From an evolutionary point of view, why do rhizobial bacteria maintain the large number of
genes required for mutualism with their legume
hosts (44)? This question is particularly relevant in light of the recent observation that bacteroids within indeterminate nodules are terminally differentiated and unable to give rise to
progeny (114). However, even a mature indeterminate nodule in the soil can contain anywhere from 105 –1010 clonally related bacteria
that are located within the invasion zone (Zone
II; Figure 1a) and have not yet differentiated.
Thus, a single symbiotic rhizobium is predicted
to have greater fitness if it successfully colonizes
a nodule than its nonsymbiotic cousin residing
in the soil where growth can be severely limited
by nutrient availability.
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431
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While there appears to be a fitness gain for
rhizobia able to invade the nodule, it is also clear
that the host has evolved mechanisms that prevent nonfixing rhizobia from parasitizing the
legume nodule for energy. While the host controls the infection process and nodule morphology, it is the microsymbiont that largely dictates
the efficiency of nitrogen fixation. Mathematical modeling suggests that if legumes treat fixing and nonfixing rhizobial strains within the
nodule similarly, then nonfixing rhizobia would
quickly outcompete nitrogen fixers (184). Perhaps for this reason, the host imposes effective
sanctions on nonfixing rhizobial cheaters within
the nodule (85, 184). So far, host sanctions have
been found to take the form of severe O2 limitation to nonfixing rhizobia within the nodule,
which restricts bacterial growth and viability.
Thus, the legume host is capable of imposing
selective pressure on rhizobia that may affect
the evolution of bacterial populations in favor
of nitrogen fixers (44).
SUMMARY POINTS
1. There tends to be strict species-specificity between legumes and their compatible symbionts, and this specificity is defined in part by NF structure. NF elicits changes in host
physiology and gene expression that lead to nodule development by virtue of a NFperception pathway involving LysM receptor-like kinases. The host specificity engendered by NF structure is dependent on the extracellular LysM domain, which likely binds
NF directly. Initial IT formation and its continued growth also has NF requirements and
in fact displays a greater stringency for chemical modification of the NF backbone than
do earlier physiological responses.
2. NF elicits two temporally and genetically separable effects on host ROS production.
During initial stages of symbiosis, NF is responsible for reducing ROS production and
this promotes early morphological responses in root hairs that initiate the process of
rhizobial invasion. During subsequent nodule development, a host-derived ROS efflux
produced in response to NF plays a positive role in promoting bacterial IT invasion,
possibly by modifying the cell wall of the IT or by providing a redox signal to bacteria
that elicits IT-specific physiological adaptations.
3. A variety of rhizobial cell-surface and secreted polysaccharides appear to function as
signals from the bacterium to its host. In particular, transcriptome analyses of host responses to polysaccharide-deficient bacterial mutants suggest that at least one role for
these macromolecules is to suppress the expression of certain host defense response genes,
such as PAL, that are involved in the production of antimicrobial compounds. Moreover,
purified rhizobial LPS and cyclic β glucan are capable of inhibiting the plant defense
response to fungal elicitor in a tissue culture setting.
4. S. meliloti typically initiates DNA replication only once per cell cycle during free-living
growth and presumably within the host IT. However, bacteria that colonize the host
cell cytoplasm undergo the novel process of endoreduplication as it differentiates into
a bacteroid. Ultimately, this bacteroid becomes terminally differentiated such that no
further DNA replication or cellular growth is observed and its viability becomes strictly
limited to the intracellular environment of the host. These observations imply that the
S. meliloti cell cycle has at least three unique branch points that are subject to in planta
regulation.
432
Gibson
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Kobayashi
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Walker
DISCLOSURE STATEMENT
The authors are not aware of any biases that might be perceived as affecting the objectivity of this
review.
ACKNOWLEDGMENTS
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We apologize to those investigators whose work we could not discuss owing to space limitations.
We thank members of the Walker lab for many thoughtful discussions and for critical reading of
the manuscript. This work was supported by the National Institute of Health grant GM31010 (to
G.C.W.), National Cancer Institute (NCI) grant CA21615-27 (to G.C.W.) and JSPS Postdoctoral
Fellowships for Research Abroad (to H.K.). G.C.W. is an American Cancer Society Research
Professor.
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Contents
Volume 42, 2008
Mid-Century Controversies in Population Genetics
James F. Crow ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 1
Joshua Lederberg: The Stanford Years (1958–1978)
Leonore Herzenberg, Thomas Rindfleisch, and Leonard Herzenberg ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣19
How Saccharomyces Responds to Nutrients
Shadia Zaman, Soyeon Im Lippman, Xin Zhao, and James R. Broach ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣27
Diatoms—From Cell Wall Biogenesis to Nanotechnology
Nils Kroeger and Nicole Poulsen ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣83
Myxococcus—From Single-Cell Polarity to Complex
Multicellular Patterns
Dale Kaiser ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 109
The Future of QTL Mapping to Diagnose Disease in Mice in the Age
of Whole-Genome Association Studies
Kent W. Hunter and Nigel P.S. Crawford ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 131
Host Restriction Factors Blocking Retroviral Replication
Daniel Wolf and Stephen P. Goff ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 143
Genomics and Evolution of Heritable Bacterial Symbionts
Nancy A. Moran, John P. McCutcheon, and Atsushi Nakabachi ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 165
Rhomboid Proteases and Their Biological Functions
Matthew Freeman ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 191
The Organization of the Bacterial Genome
Eduardo P.C. Rocha ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 211
The Origins of Multicellularity and the Early History of the Genetic
Toolkit for Animal Development
Antonis Rokas ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 235
Individuality in Bacteria
Carla J. Davidson and Michael G. Surette ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 253
vii
Transposon Tn5
William S. Reznikoff ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 269
Selection on Codon Bias
Ruth Hershberg and Dmitri A. Petrov ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 287
How Shelterin Protects Mammalian Telomeres
Wilhelm Palm and Titia de Lange ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 301
Annu. Rev. Genet. 2008.42:413-441. Downloaded from arjournals.annualreviews.org
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Design Features of a Mitotic Spindle: Balancing Tension and
Compression at a Single Microtubule Kinetochore Interface in
Budding Yeast
David C. Bouck, Ajit P. Joglekar, and Kerry S. Bloom ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 335
Genetics of Sleep
Rozi Andretic, Paul Franken, and Mehdi Tafti ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 361
Determination of the Cleavage Plane in Early C. elegans Embryos
Matilde Galli and Sander van den Heuvel ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 389
Molecular Determinants of a Symbiotic Chronic Infection
Kattherine E. Gibson, Hajime Kobayashi, and Graham C. Walker ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 413
Evolutionary Genetics of Genome Merger and Doubling in Plants
Jeff J. Doyle, Lex E. Flagel, Andrew H. Paterson, Ryan A. Rapp, Douglas E. Soltis,
Pamela S. Soltis, and Jonathan F. Wendel ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 443
The Dynamics of Photosynthesis
Stephan Eberhard, Giovanni Finazzi, and Francis-André Wollman ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 463
Planar Cell Polarity Signaling: From Fly Development to Human
Disease
Matias Simons and Marek Mlodzik ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 517
Quorum Sensing in Staphylococci
Richard P. Novick and Edward Geisinger ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 541
Weird Animal Genomes and the Evolution of Vertebrate Sex and Sex
Chromosomes
Jennifer A. Marshall Graves ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 565
The Take and Give Between Retrotransposable Elements
and Their Hosts
Arthur Beauregard, M. Joan Curcio, and Marlene Belfort ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 587
Genomic Insights into Marine Microalgae
Micaela S. Parker, Thomas Mock, and E. Virginia Armbrust ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 619
The Bacteriophage DNA Packaging Motor
Venigalla B. Rao and Michael Feiss ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 647
viii
Contents
The Genetic and Cell Biology of Wolbachia-Host Interactions
Laura R. Serbus, Catharina Casper-Lindley, Frédéric Landmann,
and William Sullivan ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 683
Effects of Retroviruses on Host Genome Function
Patric Jern and John M. Coffin ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 709
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X Chromosome Dosage Compensation: How Mammals
Keep the Balance
Bernhard Payer and Jeannie T. Lee ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ ♣ 733
Errata
An online log of corrections to Annual Review of Genetics articles may be found at http://
genet.annualreviews.org/errata.shtml
Contents
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