Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.

Comparison of plant mitochondrial (mt), chloroplast (cp) and nuclear (n) DNA sequences shows that the silent substitution rate in mtDNA is less than one-third that in cpDNA, which in turn evolves only half as fast as plant nDNA. The slower rate in mtDNA than in cpDNA is probably due to a lower mutation rate. Silent substitution rates in plant and mammalian mtDNAs differ by one or two orders of magnitude, whereas the rates in nDNAs may be similar. In cpDNA, the rate of substitution both at synonymous sites and in noncoding sequences in the inverted repeat is greatly reduced in comparison to single-copy sequences. The rate of cpDNA evolution appears to have slowed in some dicot lineages following the monocot/dicot split, and the slowdown is more conspicuous at nonsynonymous sites than at synonymous sites.     

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.The phyllosphere—the aerial surfaces of plants—is an important and ubiquitous habitat for bacteria (1). It is estimated that on a global scale, the phyllosphere spans more than 10⁸ km² and is home to up to 10²⁶ bacterial cells (2). Bacteria are also important to their plant hosts. Leaf-associated bacteria represent a widespread and ancient symbiosis (3, 4) that can influence host growth and function in many ways, including the production of growth-promoting nutrients and hormones (5, 6) and protection of hosts against pathogen infection (7, 8). Phyllosphere bacteria have the potential to influence plant biogeography and ecosystem function through their influence on plant performance under different environmental conditions (9–11), but the drivers of variation in leaf-associated bacterial biodiversity among host plants are not well understood.The ability to quantify microbial community structure in depth with environmental sequencing technologies has led to an increasing focus not only on the ecology of individual microbial taxa but on the entire genomic content of communities of microbes in different habitats, or “microbiomes” (12). Numerous studies of host-associated microbiomes have shown that microbial biodiversity is a trait (13) that forms part of the extended phenotype of the host organism (4, 14, 15) with important effects on the health and fitness (16–18) and evolution (19–21) of the host. Because of the importance of the microbiome for host fitness and function, there is a growing desire to model and manage host–microbiome interactions (22, 23), and understanding the drivers of host-associated microbial community assembly has thus become a cornerstone of microbiome research (24).In animals, the assembly of host-associated microbiomes is known to be driven by ecologically important host attributes, such as diet, that covary with host evolutionary history (20, 25, 26). A similar understanding of the drivers of plant microbiome assembly is lacking. Most of our knowledge of plant–bacterial associations on leaves has been based on studies of individual bacterial strains and individual host species. Different plant species possess characteristic bacterial phyllosphere communities (27, 28), and there are several examples of variation in bacterial biodiversity on leaves among plant genotypes (29–31) as well as among species and higher taxonomic ranks (32). Although these patterns are presumably due to phylogenetic variation in ecologically important plant functional traits (33) among host populations and species, the influence of host functional traits on variation in phyllosphere community structure across host species has not been directly quantified. As a result, we have very little understanding of the potential of plant–microbe interaction networks to influence the distribution and functional biogeography of their hosts at large scales in the face of global change (34).A first step toward integrating phyllosphere microbial communities into the study of plant biogeography will require establishing correlations between microbial community structure on leaves and the functional traits of plant hosts. To address this goal, we used high-throughput sequencing to characterize the structure of the bacterial phyllosphere microbiome on the leaves of multiple host tree species in a diverse neotropical forest in Panama. We combined phyllosphere microbiome data with a rich dataset on the attributes of plant hosts, including functional traits and evolutionary relationships, to (i) quantify the magnitude of leaf-associated bacterial biodiversity in a diverse natural forest community, (ii) identify the host plant attributes that influence microbiome community assembly on leaves, and (iii) understand relationships between bacterial biodiversity and suites of host plant traits and functions and discuss their implications for our understanding of plant functional biogeography.     

Control of bacterial iron homeostasis by manganese

Perception and response to nutritional iron availability by bacteria are essential to control cellular iron homeostasis. The Irr protein from Bradyrhizobium japonicum senses iron through the status of heme biosynthesis to globally regulate iron-dependent gene expression. Heme binds directly to Irr to trigger its degradation. Here, we show that severe manganese limitation created by growth of a Mn²⁺ transport mutant in manganese-limited media resulted in a cellular iron deficiency. In wild-type cells, Irr levels were attenuated under manganese limitation, resulting in reduced promoter occupancy of target genes and altered iron-dependent gene expression. Irr levels were high regardless of manganese availability in a heme-deficient mutant, indicating that manganese normally affects heme-dependent degradation of Irr. Manganese altered the secondary structure of Irr in vitro and inhibited binding of heme to the protein. We propose that manganese limitation destabilizes Irr under low-iron conditions by lowering the threshold of heme that can trigger Irr degradation. The findings implicate a mechanism for the control of iron homeostasis by manganese in a bacterium.     

Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes

Metal cation homeostasis is essential for plant nutrition and resistance to toxic heavy metals. Many plant metal transporters remain to be identified at the molecular level. In the present study, we have isolated AtNramp cDNAs from Arabidopsis and show that these genes complement the phenotype of a metal uptake deficient yeast strain, smf1. AtNramps show homology to the Nramp gene family in bacteria, yeast, plants, and animals. Expression of AtNramp cDNAs increases Cd(2+) sensitivity and Cd(2+) accumulation in yeast. Furthermore, AtNramp3 and AtNramp4 complement an iron uptake mutant in yeast. This suggests possible roles in iron transport in plants and reveals heterogeneity in the functional properties of Nramp transporters. In Arabidopsis, AtNramps are expressed in both roots and aerial parts under metal replete conditions. Interestingly, AtNramp3 and AtNramp4 are induced by iron starvation. Disruption of the AtNramp3 gene leads to slightly enhanced cadmium resistance of root growth. Furthermore, overexpression of AtNramp3 results in cadmium hypersensitivity of Arabidopsis root growth and increased accumulation of Fe, on Cd(2+) treatment. Our results show that Nramp genes in plants encode metal transporters and that AtNramps transport both the metal nutrient Fe and the toxic metal cadmium.     

Indirect activation of a plant nucleotide binding site-leucine-rich repeat protein by a bacterial protease

Nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins mediate pathogen recognition in both mammals and plants. The molecular mechanisms by which pathogen molecules activate NBS-LRR proteins are poorly understood. Here we show that RPS5, a NBS-LRR protein from Arabidopsis, is activated by AvrPphB, a bacterial protease, via an indirect mechanism. When transiently expressed in Nicotiana benthamiana leaves, full-length RPS5 protein triggered programmed cell death, but only when coexpressed with AvrPphB and a second Arabidopsis protein, PBS1, which is a specific substrate of AvrPphB. Using coimmunoprecipitation analysis, we found that PBS1 is in a complex with the N-terminal coiled coil (CC) domain of RPS5 before exposure to AvrPphB. Deletion of the RPS5 LRR domain caused RPS5 to constitutively activate programmed cell death, even in the absence of AvrPphB and PBS1, and this activation depended on both the CC and NBS domains. The LRR and CC domains both coimmunoprecipitate with the NBS domain but not with each other. Thus, the LRR domain appears to function in part to inhibit RPS5 signaling, and cleavage of PBS1 by AvrPphB appears to release RPS5 from this inhibition. An amino acid substitution in the NBS site of RPS5 that is known to inhibit ATP binding in other NBS-LRR proteins blocked activation of RPS5, whereas a substitution thought to inhibit ATP hydrolysis constitutively activated RPS5. Combined, these data suggest that ATP versus ADP binding functions as a molecular switch that is flipped by cleavage of PBS1.     

Chronic stimulation of Nod2 mediates tolerance to bacterial products

The Toll-like receptor (TLR) and nucleotide-binding oligomerization domain (Nod) families of proteins are critical for bacterial recognition, and, acutely, this frequently leads to proinflammatory responses. Polymorphisms in Nod2 (CARD 15) are associated with an increased likelihood of developing Crohn's disease. However, it is not yet clear how Nod2 dysfunctions lead to defects in human intestinal immune homeostasis. Studies to date have focused on functions after acute, rather than chronic, Nod2 stimulation. However, the intestine is an environment of chronic bacterial product exposure with tolerance to luminal flora. We therefore hypothesized that long-term Nod2 stimulation contributes to down-regulation of inflammatory responses from innate immune receptors. We found that pretreatment with muramyl dipeptide (MDP), a ligand for Nod2, significantly decreased production of the proinflammatory cytokines TNF-alpha, IL-8, and IL-1beta upon Nod2, TLR4, and TLR2 restimulation in primary human monocyte-derived macrophages from a large cohort of individuals. Importantly, TNF-alpha-induced production of proinflammatory cytokines remained intact in these same cells. MDP-stimulated macrophages from Crohn's disease-relevant Leu1007insC Nod2 homozygote individuals were deficient in their ability to cross-tolerize to subsequent treatment with TLR2 and TLR4 ligands. We show that acute Nod2 stimulation induced IRAK-1 activation, and that chronic MDP treatment down-regulated IRAK-1 activation upon Nod2 or TLR4 restimulation. In a subset of individuals, chronic Nod2 stimulation induced expression of the IRAK-1 inhibitory protein IRAK-M. Significantly, intestinal macrophages exhibit tolerance to MDP per production of inflammatory cytokines. These results illustrate a role for chronic stimulation of Nod2 in mediating tolerance to bacterial products.     

Systemic movement of an RNA plant virus determined by a point substitution in a 5'' leader sequence.

The ability of viruses to move through infected plants is an important determinant of host range and pathogenicity. We have investigated the genetic basis for the inability of the Type strain of barley stripe mosaic hordeivirus to undergo long-range systemic movement in the tobacco Nicotiana benthamiana. We show that, in this model system, a short open reading frame in the 5' leader of the smallest viral genomic RNA prevents long-range vascular movement. As predicted by the ribosome scanning model, the leader open reading frame decreases the efficiency with which the 5'-proximal gene is translated in vitro. Thus, systemic pathogenicity in this system may be determined by the efficiency of translation of a viral gene in vivo and is not determined by the primary sequence of the encoded protein.     

Induction of early-phase tolerance to endotoxin-induced mucosal injury, xanthine oxidase activation, and bacterial translocation by pretreatment with endotoxin.

The goal of this study was to determine whether tolerance would develop to endotoxin-induced mucosal injury, xanthine oxidase activation, and bacterial translocation. To accomplish this goal, four groups of mice were studied: 1) mice receiving ip injections of saline 96 and 24 hr prior to sacrifice, 2) mice receiving ip injections of saline 96 and endotoxin (0.1 mg) 24 hr prior to sacrifice, 3) mice receiving ip injections of endotoxin 96 and 24 hr prior to sacrifice, and 4) mice receiving ip injections of endotoxin 96 hr and saline 24 hr prior to sacrifice. In contrast to the saline control animals or mice sacrificed 96 hr after a single dose of endotoxin, mice sacrificed 24 hr after receiving a single dose of endotoxin had evidence of mucosal injury, elevated levels of ileal xanthine oxidase activity, and an 81% incidence of bacterial translocation. Mice sacrificed 24 hr after a second dose of endotoxin were largely protected against the toxic effects of endotoxin. Thus tolerance to endotoxin-induced bacterial translocation does develop and is associated with tolerance to endotoxin-induced ileal mucosal injury and xanthine oxidase activation.     

Enhanced resistance of bone marrow transplanted mice to bacterial infection induced by recombinant granulocyte-macrophage colony- stimulating factor

The in vivo effect of recombinant murine granulocyte-macrophage colony stimulating factor (rGM-CSF) on the resistance of mice to bacterial infection and on the number and function of neutrophils was studied in lethally irradiated mice transplanted with syngeneic bone marrow cells. Bone marrow transplanted (BMT) mice were injected intraperitoneally with 150 ng rGM-CSF or buffer solution (diluent) twice daily for 18 consecutive days. Total neutrophil recovery from the peripheral blood and the number of neutrophils mobilized into the peritoneal cavity were accelerated in rGM-CSF-treated recipients. Peritoneal neutrophils isolated from mice treated with rGM-CSF exhibited primed superoxide generation (O2-) after in vitro stimulation with suboptimal concentrations of phorbol myristate acetate (PMA), as compared with control mice (treated with diluent). No additional increase in O2- production occurred upon in vitro incubation of these cells with rGM- CSF. The protective activity of rGM-CSF was examined in mice injected with Salmonella typhimurium. There was a 44- and 9-fold increase in the number of S typhimurium at 96 hours postinfection in the spleen and liver, respectively, of control mice, as compared with rGM-CSF-treated mice, after a single injection of the bacteria (3 X 10(7) per mouse). All the untreated control mice died within 14 days postinoculation (1 X 10(7) bacteria per mouse), whereas 35% of the mice treated with rGM-CSF remained alive for more than 30 days postinfection. These findings support the concept that increased granulopoiesis and enhanced functional activity of phagocytic cells is induced by rGM-CSF and is responsible for enhanced resistance of BMT mice to bacterial infection.     

The influence of the synergistic anion on iron chelation by ferric binding protein,a bacterial transferrin

Although the presence of an exogenous anion is a requirement for tight Fe(3+) binding by the bacterial (Neisseria) transferrin nFbp, the identity of the exogenous anion is not specific in vitro. nFbp was reconstituted as a stable iron containing protein by using a number of different exogenous anions [arsenate, citrate, nitrilotriacetate, pyrophosphate, and oxalate (symbolized by X)] in addition to phosphate, predominantly present in the recombinant form of the protein. Spectroscopic characterization of the Fe(3+)anion interaction in the reconstituted protein was accomplished by UV-visible and EPR spectroscopies. The affinity of the protein for Fe(3+) is anion dependent, as evidenced by the effective Fe(3+) binding constants (K'(eff)) observed, which range from 1 x 10(17) M(-1) to 4 x 10(18) M(-1) at pH 6.5 and 20 degrees C. The redox potentials for Fe(3+)nFbpXFe(2+)nFbpX reduction are also found to depend on the identity of the synergistic anion required for Fe(3+) sequestration. Facile exchange of exogenous anions (Fe(3+)nFbpX + X' --> Fe(3+)nFbpX' + X) is established and provides a pathway for environmental modulation of the iron chelation and redox characteristics of nFbp. The affinity of the iron loaded protein for exogenous anion binding at pH 6.5 was found to decrease in the order phosphate > arsenate approximately pyrophosphate > nitrilotriacetate > citrate approximately oxalate carbonate. Anion influence on the iron primary coordination sphere through iron binding and redox potential modulation may have in vivo application as a mechanism for periplasmic control of iron delivery to the cytosol.     

Host structural carbohydrate induces vector transmission of a bacterial plant pathogen

Many insect-borne pathogens have complex life histories because they must colonize both hosts and vectors for successful dissemination. In addition, the transition from host to vector environments may require changes in gene expression before the pathogen''s departure from the host. Xylella fastidiosa is a xylem-limited plant-pathogenic bacterium transmitted by leafhopper vectors that causes diseases in a number of economically important plants. We hypothesized that factors of host origin, such as plant structural polysaccharides, are important in regulating X. fastidiosa gene expression and mediating vector transmission of this pathogen. The addition of pectin and glucan to a simple defined medium resulted in dramatic changes in X. fastidiosa''s phenotype and gene-expression profile. Cells grown in the presence of pectin became more adhesive than in other media tested. In addition, the presence of pectin and glucan in media resulted in significant changes in the expression of several genes previously identified as important for X. fastidiosa''s pathogenicity in plants. Furthermore, vector transmission of X. fastidiosa was induced in the presence of both polysaccharides. Our data show that host structural polysaccharides mediate gene regulation in X. fastidiosa, which results in phenotypic changes required for vector transmission. A better understanding of how vector-borne pathogens transition from host to vector, and vice versa, may lead to previously undiscovered disease-control strategies.     

Cloning a plant amino acid transporter by functional complementation of a yeast amino acid transport mutant.

Amino acids are transported across the plasma membrane of plant cells by proton-amino acid symports. We report here the successful cloning of a neutral amino acid carrier by functional complementation. A histidine transport deletion mutant of Saccharomyces cerevisiae was transformed with an Arabidopsis thaliana cDNA library constructed in a yeast expression vector. Forty transformants, out of 10(5), allowed growth on a histidine-limiting medium. The acquired ability to grow on low histidine was shown to be strictly dependent on the protein encoded by the expression plasmid. Histidine and alanine transport activity were 10- to 20-fold greater in the transformants. The transport kinetics, inhibitor sensitivity, and substrate specificity match those of neutral system II, a neutral amino acid carrier we previously described in plasma membrane vesicles isolated from leaf tissue. The cDNA insert is 1.7 kb with an open reading frame that codes for a protein containing 486 amino acids with a calculated molecular mass of 52.9 kDa and three sites of potential N-linked glycosylation. Hydropathy analysis of the deduced amino acid sequence suggests this is an integral membrane protein with 10-12 membrane-spanning alpha-helices. Overall, the sequence of this amino acid carrier is not closely related to any other protein sequences in the GenBank data base. Interestingly, however, there are small regions of sequence that exhibit significant levels of similarity with at least seven other integral membrane proteins.     

Priming, induction and modulation of plant defence responses by bacterial lipopolysaccharides

Bacterial lipopolysaccharides (LPSs) have multiple roles in plant-microbe interactions. LPS contributes to the low permeability of the outer membrane, which acts as a barrier to protect bacteria from plant-derived antimicrobial substances. Conversely, perception of LPS by plant cells can lead to the triggering of defence responses or to the priming of the plant to respond more rapidly and/or to a greater degree to subsequent pathogen challenge. LPS from symbiotic bacteria can have quite different effects on plants to those of pathogens. Some details are emerging of the structures within LPS that are responsible for induction of these different plant responses. The lipid A moiety is not solely responsible for all of the effects of LPS in plants; core oligosaccharide and O-antigen components can elicit specific responses. Here, we review the effects of LPS in induction of defence-related responses in plants, the structures within LPS responsible for eliciting these effects and discuss the possible nature of the (as yet unidentified) LPS receptors in plants.