Global Survey and Expressions of the Phosphate Transporter Gene Families in Brassica napus and Their Roles in Phosphorus Response

Prospects for Using Phosphate-Solubilizing Microorganisms as Natural Fertilizers in Agriculture

Phosphates are known to be essential for plant growth and development, with phosphorus compounds being involved in various physiological and biochemical reactions. Phosphates are known as one of the most important factors limiting crop yields. The problem of phosphorus deficiency in the soil has traditionally been solved by applying phosphate fertilizers. However, chemical phosphate fertilizers are considered ineffective compared to the organic fertilizers manure and compost. Therefore, increasing the bioavailability of phosphates for plants is one of the primary goals of sustainable agriculture. Phosphate-solubilizing soil microorganisms can make soil-insoluble phosphate bioavailable for plants through solubilization and mineralization. These microorganisms are currently in the focus of interest due to their advantages, such as environmental friendliness, low cost, and high biological efficiency. In this regard, the solubilization of phosphates by soil microorganisms holds strong potential in research, and inoculation of soils or crops with phosphate-solubilizing bacteria is a promising strategy to improve plant phosphate uptake. In this review, we analyze all the species of phosphate-solubilizing bacteria described in the literature to date. We discuss key mechanisms of solubilization of mineral phosphates and mineralization of organic phosphate-containing compounds: organic acids secreted by bacteria for the mobilization of insoluble inorganic phosphates, and the enzymes hydrolyzing phosphorus-containing organic compounds. We demonstrate that phosphate-solubilizing microorganisms have enormous potency as biofertilizers since they increase phosphorus bioavailability for the plant, promote sustainable agriculture, improve soil fertility, and raise crop yields. The use of phosphate-solubilizing microbes is regarded as a new frontier in increasing plant productivity.

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

BACKGROUND

Polyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain (MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the MBD gene family is still lacking, so it is necessary to conduct a comprehensive analysis.

RESULTS

In this study, twenty-two, ten and eleven MBD genes were identified in the genome of allotetraploid B. napus and its diploid ancestors, B. rapa and B. oleracea, respectively. Based on the clades of the MBD gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true MBD genes in Brassica existed in only 5 clades. Clade IV and Clade VI were unique in term of MBD genes in dicotyledons. Ka/Ks calculations showed that MBD genes underwent purifying selection in Brassica and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of MBD gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the MBD genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of cis-acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the MBD gene changes, which may be regulated by cis-acting elements and transposable elements. The number imbalance of cis-acting elements and transposable elements in A_n and C_n subgenomes may also lead to biased A_n subgenome expression of the MBD gene in B. napus.

CONCLUSIONS

In this study, by evaluating the number, structure, phylogeny and expression of the MBD gene in B. napus and its diploid ancestors, we increased the understanding of MBD genes in allopolyploids and provided a reference for future analysis of allopolyploidization.

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean

BACKGROUND

SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes.

RESULTS

We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs.

CONCLUSION

This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

A Plant Stress-Responsive Bioreporter Coupled With Transcriptomic Analysis Allows Rapid Screening for Biocontrols of Necrotrophic Fungal Pathogens

Streptomyces are soil-borne Actinobacteria known to produce a wide range of enzymes, phytohormones, and metabolites including antifungal compounds, making these microbes fitting for use as biocontrol agents in agriculture. In this study, a plant reporter gene construct comprising the biotic stress-responsive glutathione S-transferase promoter GSTF7 linked to a luciferase output (GSTF7:luc) was used to screen a collection of Actinobacteria candidates for manipulation of plant biotic stress responses and their potential as biocontrol agents. We identified a Streptomyces isolate (KB001) as a strong candidate and demonstrated successful protection against two necrotrophic fungal pathogens, Sclerotinia sclerotiorum and Rhizoctonia solani, but not against a bacterial pathogen (Pseudomonas syringe). Treatment of Arabidopsis plants with either KB001 microbial culture or its secreted compounds induced a range of stress and defense response-related genes like pathogenesis-related (PR) and hormone signaling pathways. Global transcriptomic analysis showed that both treatments shared highly induced expression of reactive oxygen species and auxin signaling pathways at 6 and 24 h posttreatment, while some other responses were treatment specific. This study demonstrates that GSTF7 is a suitable marker for the rapid and preliminary screening of beneficial bacteria and selection of candidates with potential for application as biocontrols in agriculture, including the Streptomyces KB001 that was characterized here, and could provide protection against necrotrophic fungal pathogens.

Genome-Wide Analysis of the Five Phosphate Transporter Families in Camelina sativa and Their Expressions in Response to Low-P

Phosphate transporters (PHTs) play pivotal roles in phosphate (Pi) acquisition from the soil and distribution throughout a plant. However, there is no comprehensive genomic analysis of the PHT families in Camelina sativa, an emerging oilseed crop. In this study, we identified 73 CsPHT members belonging to the five major PHT families. A whole-genome triplication event was the major driving force for CsPHT expansion, with three homoeologs for each Arabidopsis ortholog. In addition, tandem gene duplications on chromosome 11, 18 and 20 further enlarged the CsPHT1 family beyond the ploidy norm. Phylogenetic analysis showed clustering of the CsPHT1 and CsPHT4 family members into four distinct groups, while CsPHT3s and CsPHT5s were clustered into two distinct groups. Promoter analysis revealed widespread cis-elements for low-P response (P1BS) specifically in CsPHT1s, consistent with their function in Pi acquisition and translocation. In silico RNA-seq analysis revealed more ubiquitous expression of several CsPHT1 genes in various tissues, whereas CsPHT2s and CsPHT4s displayed preferential expression in leaves. While several CsPHT3s were expressed in germinating seeds, most CsPHT5s were expressed in floral and seed organs. Suneson, a popular Camelina variety, displayed better tolerance to low-P than another variety, CS-CROO, which could be attributed to the higher expression of several CsPHT1/3/4/5 family genes in shoots and roots. This study represents the first effort in characterizing CsPHT transporters in Camelina, a promising polyploid oilseed crop that is highly tolerant to abiotic stress and low-nutrient status, and may populate marginal soils for biofuel production.

Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance

Phosphorus transporter (PHT) genes encode H2PO4-/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1-PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.