Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

Background

MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events.

Results

We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study.

Conclusions

We provide here a set of new small RNAs that contribute to the broader knowledge of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we present here the probable functional regulation associated with the sRNAome and, particularly, in N₂-fixing symbiotic nodules.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1639-5) contains supplementary material, which is available to authorized users.     

Isolation of Legume Glycosyltransferases and Active Site Mapping of the <Emphasis Type="Italic">Phaseolus lunatus</Emphasis> Zeatin O-glucosyltransferase ZOG1

O-Glycosides of the cytokinin zeatin are found in many plant tissues. They provide protection against degradative enzymes and may serve as cytokinin reserves. Two zeatin glycosyltransferase (GT) genes, an O-glucosyltransferase (ZOG1) from Phaseolus lunatus and an O-xylosyltransferase (ZOX1) from P. vulgaris, were previously isolated. Five novel bean and soybean GT genes with high sequence identity to ZOG1 were isolated, sequenced, and expressed, along with two such genes from rice and one from tomato. None of the recombinant proteins showed GT activity with zeatin. By comparing the ZOG1 sequence to the 3D model of Medicago truncatula UGT71G1, four regions possibly important to zeatin binding were identified, and mutation studies identified one amino acid within each region (R59, D87, L127, and F149) whose mutation strongly impaired enzyme activity. The new bean and soybean GTs differ from ZOG1 in one (PlGT2 and GmGT2) to three (GmGT1) of these residues. Mutation of one such GT (PlGT2) to render it identical to ZOG1 at the four implicated residues conferred low enzyme activity, providing further support for the importance of these amino acids in recognizing zeatin as substrate. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Proline-rich cell wall proteins accumulate in growing regions and phloem tissue in response to water deficit in common bean seedlings

Plant cell walls undergo dynamic changes in response to different environmental stress conditions. In response to water deficit, two related proline-rich glycoproteins, called p33 and p36, accumulate in the soluble fraction of the cell walls in Phaseolus vulgaris (Covarrubias et al. in Plant Physiol 107:1119–1128, 1995). In this work, we show that p33 and p36 are able to form a 240 kDa oligomer, which is found in the cell wall soluble fraction. We present evidence indicating that the highest accumulation of these proteins in response to water deficit occurs in the growing regions of common bean seedlings, particularly in the phloem tissues. These proteins were detected in P. vulgaris cell suspension cultures, where the p33/p36 ratio was higher under hyperosmotic conditions than in bean seedlings subjected to the same treatment. The results support a role for these proteins during the plant cell response to changes in its water status, and suggest that cell wall modifications are induced in active growing cells of common bean in response to water limitation. Marina Battaglia and Rosa M. Solórzano contributed equally to this work.     

Effects of <Emphasis Type="Italic">Paecilomyces fumosoroseus</Emphasis> and <Emphasis Type="Italic">Encarsia formosa</Emphasis> on the control of the greenhouse whitefly: preliminary assessment of a compatability study

The effect of separate and combined activity of Paecilomyces fumosoroseus Wize (Brown and Smith) Trinidadian strain T11 and the parasitoid, Encarsia formosa Gahan, was assessed on populations of the greenhouse whitefly, Trialeurodes vaporariorum (Westwood), infesting Phaseolus vulgaris L. (French bean) and Pelargonium x domesticum (regal geranium) plants in replicate experiments. When infested bean and geranium plants were exposed to E. formosa for 2 days, and 4 days later sprayed with P. fumosoroseus blastospores, whitefly percent mortality was 99.5% and 75.5%, 94.6% and 59.4% for experiments 1 and 2, respectively. Treatment of infested bean plants with either E. formosa or P. fumosoroseus resulted in 87.8% and 78.7%, 73.1% and 97.0% whitefly mortality for experiments 1 and 2, respectively, while similar treatment of infested geranium plants resulted in 9.2% and 52.8%, 34.3% and 64.5% whitefly mortality for experiments 1 and 2, respectively. Our results support the use of E. formosa and P. fumosoroseus in combination in Experiment 1 for the treatment of whitefly infested P. vulgaris plants since a significant difference in mortality is observed than when either E. formosa or P. fumosoroseus is applied alone. However, in experiment 2, the combination treatment on P. vulgaris was no more effective than spraying P. fumosoroseus alone. On P. x domesticum plants, only P. fumosoroseus alone is needed for efficient control of the whitefly compared to the combination treatment. The relative timing of parasitoid oviposition and fungal infection are critical in determining the outcome of the interaction and are plant host dependent.     

Plant growth-promoting rhizobacteria for improving nodulation and nitrogen fixation in the common bean (Phaseolus vulgaris L.)

A greenhouse experiment was performed to evaluate the effects of plant growth-promoting rhizobacteria (PGPR) on nodulation, biological nitrogen fixation (BNF) and growth of the common bean (Phaseolus vulgaris L. cv. Tenderlake). Single and dual inoculation treatments of bean with Rhizobium and/or PGPR were administered to detect possible changes in the levels of and interactions between the phytohormones IAA and cytokinin. Bean plants cv. Tenderlake were grown in pots containing Fluvic Neosol eutrophic (pH 6.5). Fourteen kilogram aliquots of soil contained in 15-l pots were autoclaved. Bean seeds were surface sterilized and inoculated with Rhizobium tropici (CIAT 899-standard strain) alone and in combination with one of the PGPR strains: Bacillus endophyticus (DSM 13796), B. pumilus (DSM 27), B. subtilis (DSM 704), Paenibacillus lautus (DSM 13411), P. macerans (DSM 24), P. polymyxa (DSM 36), P. polymyxa (Loutit L.) or Bacillus sp.(65E180). The experimental design was randomized block design with three replications. Beans co-inoculated with Rhizobium tropici (CIAT899) and Paenibacillus polymyxa (DSM 36) had higher leghemoglobin concentrations, nitrogenase activity and N₂ fixation efficiency and thereby formed associations of greater symbiotic efficiency. Inoculation with Rhizobium and P. polymyxa strain Loutit (L) stimulated nodulation as well as nitrogen fixation. PGPR also stimulated specific-nodulation (number of nodules per gram of root dry weight) increases that translated into higher levels of accumulated nitrogen. The activities of phytohormones depended on their content and interactions with Rhizobium tropici and Paenibacillus and/or Bacillus (PGPR) strains which affect the cytokinin in content in the common bean.     

Growth and aroma contribution of <Emphasis Type="Italic">Microbacterium foliorum</Emphasis>, <Emphasis Type="Italic">Proteus vulgaris</Emphasis> and <Emphasis Type="Italic">Psychrobacter</Emphasis> sp. during ripening in a cheese model medium

The growth and aroma contribution of Microbacterium foliorum, Proteus vulgaris and Psychrobacter sp., some common but rarely mentioned cheese bacteria, were investigated in a cheese model deacidified by Debaryomyces hansenii during the ripening process. Our results show that these bacteria had distinct growth and cheese flavour production patterns during the ripening process. P. vulgaris had the greatest capacity to produce not only the widest variety but also the highest quantities of volatile compounds with low olfactive thresholds, e.g. volatile sulphur compounds and branched-chain alcohols. Such compounds produced by P. vulgaris increased after 21 days of ripening and reached a maximum at 41 days. The three bacteria studied exhibited various degrees of caseinolytic, aminopeptidase and deaminase activities. Moreover, P. vulgaris had a greater capacity for hydrolysing casein and higher deaminase activity. Our results show that P. vulgaris, a Gram-negative bacterium naturally present on the surface of ripened cheeses, could produce high concentrations of flavour compounds from amino acid degradation during the ripening process. Its flavouring role in cheese cannot be neglected. Moreover, it could be a useful organism for producing natural flavours as dairy ingredients.     

Plant species variation in bottom‐up effects across three trophic levels: a test of traits and mechanisms

1. An increasing number of studies have addressed the mechanisms by which plant inter‐specific variation influence interactions at higher trophic levels, but little is known about the underlying plant traits driving these dynamics. 2. Here we investigated the effects of host plant species on herbivore‐parasitoid interactions and the underlying traits driving such effects. For this, we measured the abundance of seed‐eating bruchids and their parasitoids across seven sympatric populations of the bean species Phaseolus coccineus and Phaseolus vulgaris in Central Mexico. To investigate the mechanisms underlying differences between bean species in bruchid‐parasitoid interactions, we carried out two laboratory experiments to test whether bruchid and parasitoid performance differed between plant species. We also measured seed size and phenolic compounds to investigate if seed traits mediate bruchid‐parasitoid interactions by influencing herbivore susceptibility or resistance to parasitoids. 3. Field surveys revealed that the rate of parasitoid recruitment to bruchids was significantly higher on P. vulgaris than on P. coccineus. Subsequent laboratory bioassays indicated that bruchids developed more slowly and exhibited lower fitness on P. vulgaris seeds than on P. coccineus seeds. Accordingly, we found that bean species differed in seed size, with P. vulgaris having smaller (less nutritious) seeds, which explains why bruchid development was slower on this plant species. 4. These results provide a mechanism for why bruchids exhibited higher parasitism rates on seeds of P. vulgaris in the field which could be due to Slow‐Growth/High‐Mortality effects, a smaller physical refuge provided by the seed, or both factors. The roles of these mechanisms remain inconclusive without further study.     

<Emphasis Type="Italic">RNase</Emphasis>-Based Gametophytic Self-Incompatibility Evolution: Questioning the Hypothesis of Multiple Independent Recruitments of the <Emphasis Type="Italic">S</Emphasis>-Pollen Gene

Multiple independent recruitments of the S-pollen component (always an F-box gene) during RNase-based gametophytic self-incompatibility evolution have recently been suggested. Therefore, different mechanisms could be used to achieve the rejection of incompatible pollen in different plant families. This hypothesis is, however, mainly based on the interpretation of phylogenetic analyses, using a small number of divergent nucleotide sequences. In this work we show, based on a large collection of F-box S-like sequences, that the inferred relationship of F-box S-pollen and F-box S-like sequences is dependent on the sequence alignment software and phylogenetic method used. Thus, at present, it is not possible to address the phylogenetic relationship of F-box S-pollen and S-like sequences from different plant families. In Petunia and Malus/Pyrus the putative S-pollen gene(s) show(s) variability patterns different than expected for an S-pollen gene, raising the question of false identification. Here we show that in Petunia, the unexpected features of the putative S-pollen gene are not incompatible with this gene’s being the S-pollen gene. On the other hand, it is very unlikely that the Pyrus SFBB-gamma gene is involved in specificity determination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Interspecific hybridization between common and tepary beans: increased hybrid embryo growth,fertility, and efficiency of hybridization through recurrent and congruity backcrossing

Cultivated common bean (Phaseolus vulgaris L.) and tepary bean (Phaseolus acutifolius A. Gray) genotypes possessing desirable agronomic traits were hybridized. The F₁ hybrids were backcrossed twice with the common bean (i.e., recurrent backcrossing). Also, alternate backcrosses with common and tepary beans (i.e., congruity backcrossing) were carried out. Embryo culture was necessary for all initial interspecific crosses, and its requirement was proportionally lower when the common bean was used as the recurrent parent and as the last parent of congruity backcrosses. Modification of the embryo culture technique was necessary to produce congruity hybrids. Effects of both tepary and common bean genotypes on the success rate of hybridization were observed. Tepary accession G 40001 and common bean cultivar ICA Pijao facilitated interspecies hybridization. Growth of hybrid embryos before rescue, recovery of mature hybrid plants, and the vigor and fertility of F₁ hybrids all increased with increased recurrent and congruity backcrosses and intermatings between male-sterile F₁ and selected fertile F₂ plants of the third and fifth congruity backcrosses. Introgression of tepary genes was verified by means of seed protein electrophoretic analysis and morphological markers. The results suggest that congruity backcrossing can help to gradually reduce or overcome P. vulgaris x P. acutifolius hybridization barriers such as genotype incompatibility, early embryo abortion, hybrid sterility, and lower frequencies of hybridization.     

Evaluation of the field impact of an adventitious herbivore on an invasive plant,yellow toadflax,in Colorado,USA

Although some introduced plants arrive into their new range without their generalist and specialist herbivores, for others, their herbivores arrive prior to, with, or after the introduction of the plant, reestablishing the link between natural enemies and invaders in the introduced range. Research documenting the effects of adventitiously introduced herbivores on their target plants in the introduced range, and the mechanisms by which those effects occur, can provide insight into potential biological weed control. We studied the effects of an accidentally introduced beetle Brachypterolus pulicarius on the growth and reproduction of its host, the invasive plant Linaria vulgaris (yellow toadflax), growing under field conditions across multiple years and sites in western Colorado, USA. We found that feeding by B. pulicarius on L. vulgaris was variable among 3 years (2002–2004) and across eight local sites. Part of the variation in damage was explained by ramet density; sites with greater ramet density experienced a higher proportion of damage. In an observational study across 2 years, damage was positively correlated with estimates of sexual reproduction, ramet growth, and clonal shoot production. However, opposite trends were observed in an experiment; damage by B. pulicarius decreased estimates of sexual reproduction. Differences between the results of the observational and experimental studies were likely driven by selective feeding by B. pulicarius on larger ramets. Nonetheless, the ability of B. pulicarius to control established L. vulgaris population growth remains uncertain under the environmental conditions we studied. In both the observational and experimental study, B. pulicarius did not affect L. vulgaris survival, and we found no evidence that established L. vulgaris populations were seed limited, suggesting that reductions in seeds may not translate into demographic changes in heavily infested populations. Interactions among insect foraging behavior, individual plant responses to damage, and the demographic consequences of seed input may help to explain the varying degrees to which herbivores affect plants and populations in this and other systems.     

Heterologous expression of IAP1, a seed protein from bean modified by indole-3-acetic acid,in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> and <Emphasis Type="Italic">Medicago truncatula</Emphasis>

The seed protein IAP1 from bean (PvIAP1; Phaseolus vulgaris L.) that is modified by the phytohormone indole-3-acetic acid (IAA) was heterologously expressed in the two reference plant species Arabidopsis thaliana and Medicago truncatula. For the transformation of Medicago we devised a novel protocol using seedling infiltration. When PvIAP1 was overexpressed under the control of the constitutive 35SCaMV promoter in Arabidopsis, the plants showed signs of earlier bolting and enhanced branching. Expression of a fusion protein of PvIAP1 with both a green fluorescence protein (GFP) as reporter and 6× histidine (His) tag under the control of the native bean IAP1 promoter resulted in the accumulation of the protein in both plant species exclusively in seeds as shown by immunoblotting and by fluorescence microscopy. During seed development, PvIAP1 was first expressed in the vascular bundle of Arabidopsis, whereas in later stages GFP fluorescence was visible essentially in all tissues of the seed. Fluorescence decreased rapidly after imbibition in the seeds for both Arabidopsis and Medicago, although the fluorescence persisted longer in Arabidopsis. GFP fluorescence was distributed evenly between an organelle fraction, the microsomal membrane fraction, and the cytosol. This was also confirmed by immunoblot analysis. Clusters of higher GFP fluorescence were observed by confocal microscopy. Although PvIAP1 protein accumulated in seeds of both Arabidopsis and Medicago, neither species post-translationally modified the protein with an indoleacyl moiety as shown by quantitative GC–MS analysis after alkaline hydrolysis. These results indicate an apparent specificity for IAA attachment in different plant species. Alexander Walz and Claudia Seidel contributed equally to the paper.     

Use of the gusA gene marker in a competition study of the Rhizobium strains nodulating the common bean (Phaseolus vulgaris) in Senegal soils

Indigenous rhizobial population is among the factors which influence increased crop yield through inoculation with elite strains. In this study, we compared in greenhouse conditions the competitiveness of Rhizobium strain ISRA 355 for nodulation of the common bean (Phaseolus vulgaris) cultivated in different unsterile Senegal soils in terms of pH, N and C contents. The strain ISRA 355 produced a stable GUS+ transconjugant which was used for competition with indigenous soil rhizobia in six localities. At Bayakh, the transconjugant ISRA 355gusA was less competitive than the indigenous rhizobial strains, whereas in the other localities, it was more competitive since it occupied more than 90% of the nodules. Thus the Rhizobium strain ISRA 355 should be used for successfully inoculating the common bean in Senegal soils.     

Effects of ethylene and inhibitors of ethylene synthesis and action on nodulation in common bean (Phaseolus vulgaris L.)

The ethylene releasing compound, 2-chloroethylphosphonic acid (ethephon) inhibited nodule development in common bean (Phaseolus vulgaris L.) plants. In contrast, inhibitors of ethylene synthesis or its physiological activity enhanced nodulation. In a co-culture of bean seeds and rhizobia, ethephon inhibited rhizobial growth while inhibitors of ethylene synthesis or action did not influence the growth and proliferation of rhizobia. These data emphasize the role of ethylene as a regulator of nodulation in determinate nodulators and indicate that the ethylene signaling pathway involved in the nodulation process is not limited to the plant host but also involves the bacterial symbiont.     

Alleviation of Salt Stress in Common Bean (Phaseolus vulgaris) by Exogenous Abscisic Acid Supply

In this work the effect of abscisic acid (ABA) and 100 mM NaCl on common bean (Phaseolus vulgaris var. Coco) growth, nitrogenase activity, and nodule metabolism was studied. Experiments were carried out in a controlled environmental chamber and plants, at the vegetative growth stage (16 days old), were treated with ABA (1 μM and 10 μM) and 48 h later were exposed to saline treatment. Results revealed that plant dry weight, nodule dry weight, nitrogen fixation (acetylene reduction activity and ureides content), and most enzymes of ammonium and ureides metabolism were affected by both ABA and NaCl. The addition of 1 μM ABA to the nutrient solution before the exposure to salt stress reduced the negative effect of NaCl. Based on our results, we suggest that ABA application improves the response of Phaseolus vulgaris symbiosis under saline stress conditions, including the nitrogen fixation process and enzymes of ammonium assimilation and purine catabolism.