Rice (Oryza sativa L. ssp. indica) seeds as plant microbiome present both an opportunity and a challenge to colonizing bacterial community living in close association with plants. Nevertheless, the roles and activities of bacterial endophytes remain largely unexplored and insights into plant-microbe interaction are compounded by its complexity. In this study, putative functions or physiological properties associated with bacterial endophytic nature were assessed. Also, endophytic roles in plant growth and germination that may allow them to be selectively chosen by plants were also studied. The cultivable seed endophytes were dominated by Proteobacteria particularly class Gammaproteobacteria. Highly identical type strains were isolated from the seed endosphere regardless of the rice host’s physiological tolerance to salinity. Among the type strains, Flavobacterium sp., Microbacterium sp. and Xanthomonas sp. were isolated from the salt-sensitive and salt-tolerant cultivars. PCA-Biplot ordination also showed that specific type strains isolated from different rice cultivars have distinguishing similar characteristics. Flavobacterium sp. strains are phosphate solubilizers and indole-3-acetic acid producers with high tolerance to salinity and osmotic stress. Pseudomonas strains are characterized as high siderophore producers while Microbacterium sp. and Xanthomonas sp. strains have very high pectinase and cellulase activity. Among the physiological traits of the seed endophytes, bacterial pectinase and cellulase activity are positively correlated as well as salt and osmotic tolerance. Overall characterization shows that majority of the isolates could survive in 4–8% salt concentration as well as in 0.6 M and 1.2 M sucrose solution. The activities of catalase, pectinase and cellulase were also observed in almost all of the isolates indicating the importance of these characteristics for survival and colonization into the seed endosphere. Seed bacterial endophytes also showed promising plant growth promoting activities including hormone modulation, nitrogen fixation, siderophore production and phosphate solubilization. Though many of the isolates possess similar PGP and endophytic physiological traits, this study shows some prominent and distinguishing traits among bacterial groups indicating key determinants for their success as endophytes in the rice seed endosphere. Rice seeds are also inhabited by bacterial endophytes that promote growth during early seedling development.

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Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of Rice.

Salinity is a severe abiotic stress limiting agricultural yield and productivity. Plants have evolved various strategies to cope with salt stress. Chloroplasts are important photosynthesis organelles, which are sensitive to salinity. An understanding of molecular mechanisms in chloroplast tolerance to salinity is of great importance for genetic modification and plant breeding. Previous studies have characterized more than 53 salt-responsive genes encoding important chloroplast-localized proteins, which imply multiple vital pathways in chloroplasts in response to salt stress, such as thylakoid membrane organization, the modulation of photosystem II (PS II) activity, carbon dioxide (CO2) assimilation, photorespiration, reactive oxygen species (ROS) scavenging, osmotic and ion homeostasis, abscisic acid (ABA) biosynthesis and signaling, and gene expression regulation, as well as protein synthesis and turnover. This review presents an overview of salt response in chloroplasts revealed by gene characterization efforts.

/pdf/salinity-response-in-chloroplasts-insights-from-gene-3r6wczpzyl.pdf

Salinity Response in Chloroplasts: Insights from Gene Characterization.

Nucleotides are essential for life. It is easy to validate this statement—one just needs to recall that nucleotides are the building blocks of DNA and RNA, and that many molecules that are central for metabolism, for example ATP, NADH, Co-A, and UDP-Glc, are nucleotides or contain nucleotide

http://www.plantphysiol.org/content/plantphysiol/182/1/63.full.pdf

Nucleotide Metabolism in Plants.

Plants need to cope with complex environments throughout their life cycle. Abiotic stresses, including drought, cold, salt and heat, can cause a reduction in plant growth and loss of crop yield. Plants sensing stress signals and adapting to adverse environments are fundamental biological problems. We review the stress sensors in stress sensing and the responses, and then discuss ionic stress signaling and the responses. During ionic stress, the calcineurin B-like proteins (CBL) and CBL-interacting protein kinases (CBL−CIPK) complex is identified as a primary element of the calcium sensor for perceiving environmental signals. The CBL−CIPK system shows specificity and variety in its response to different stresses. Obtaining a deeper understanding of stress signaling and the responses will mitigate or solve crop yield crises in extreme environments with fast-growing populations.

https://www.mdpi.com/1422-0067/19/11/3298/pdf

Sensing of Abiotic Stress and Ionic Stress Responses in Plants

Interactions between metabolites and proteins play an integral role in all cellular functions. Here we describe an affinity purification (AP) approach in combination with LC/MS-based metabolomics and proteomics that allows, to our knowledge for the first time, analysis of protein-metabolite and protein-protein interactions simultaneously in plant systems. More specifically, we examined protein and small-molecule partners of the three (of five) nucleoside diphosphate kinases present in the Arabidopsis genome (NDPK1-NDPK3). The bona fide role of NDPKs is the exchange of terminal phosphate groups between nucleoside diphosphates (NDPs) and triphosphates (NTPs). However, other functions have been reported, which probably depend on both the proteins and small molecules specifically interacting with the NDPK. Using our approach we identified 23, 17, and 8 novel protein partners of NDPK1, NDPK2, and NDPK3, respectively, with nucleotide-dependent proteins such as actin and adenosine kinase 2 being enriched. Particularly interesting, however, was the co-elution of glutathione S-transferases (GSTs) and reduced glutathione (GSH) with the affinity-purified NDPK1 complexes. Following up on this finding, we could demonstrate that NDPK1 undergoes glutathionylation, opening a new paradigm of NDPK regulation in plants. The described results extend our knowledge of NDPKs, the key enzymes regulating NDP/NTP homeostasis.

/pdf/affinity-purification-with-metabolomic-and-proteomic-jqga4jerq0.pdf

Affinity purification with metabolomic and proteomic analysis unravels diverse roles of nucleoside diphosphate kinases.

Chloroplast is a crucial organelle for plant photosynthesis and maintaining normal life activities in higher plants. Although some genes related to chloroplast development and pigment synthesis have been identified or cloned in rice, little is known about the relationship between these genes and abiotic stress response. In this study, we identified a novel mutant white stripe leaf 12 (wsl12) affecting pigment synthesis, chloroplast development and abiotic stress response in rice. The mutant phenotype was obvious at seeding and tillering stages and in response to the temperature change. Genetic analysis of reciprocal crosses between wsl12 and wild-type plants showed that wsl12 was a recessive mutant in a single nuclear locus. Map-based cloning revealed that the WSL12 locus encoded OsNDPK2, one of the three nucleoside diphosphate kinases (OsNDPKs). WSL12 expressed in all tested tissues, while it highly expressed in leaves and young tissues. The WSL12 protein localized to the chloroplast. The wsl12 mutant showed higher superoxide anion level and enhanced sensitivity to abscisic acid (ABA) and salinity. The transcription pattern of many genes involved in chlorophyll biosynthesis, ABA synthesis, light signaling pathway, reactive oxygen species-scavenging pathway and the other two OsNDPKs was altered in the wsl12 mutant. These results indicate that the OsNDPK2 encoded by WSL12 plays an important role in chloroplast development and chlorophyll biosynthesis by regulating the expression levels of related genes. In addition, WSL12 also affects the response to abiotic stress, such as ABA and salinity in rice, and is beneficial to molecular breeding of stress tolerance.

/pdf/white-stripe-leaf-12-wsl12-encoding-a-nucleoside-diphosphate-3qal65zvsm.pdf

White stripe leaf 12 (WSL12), encoding a nucleoside diphosphate kinase 2 (OsNDPK2), regulates chloroplast development and abiotic stress response in rice (Oryza sativa L.).

Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed.

The invention discloses rice spikelet development regulation protein.The amino acid sequence of the protein is as shown in (A) Seq ID No: 2; or the protein is formed as shown in (B) formed in the mode that one or more amino acids are added to and/or substituted for in and/or deleted from the amino acid sequence defined by (A), has a function of regulating rice spikelet development and is derived by the (A).The invention further discloses genes for encoding the protein, such as the gene as shown in SEQ ID No:1 and the gene as shown in SEQ ID No:3.; the invention further discloses a recombinant vector and a transformant which contain the genes, a method for regulating gramineous plant spikelet development through gene transformed cells and application of the protein, the genes, the recombinant vector and the transformant to improvement of the yield and quality of gramineous plants.According to the rice spikelet development regulation protein, the encoding genes MSi thereof and application, a map-based cloning technology is utilized to separate the MS1 genes influencing rice spikelet development, the functions of the genes are identified through a genetically modified complementary experiment, and the genes can be utilized to research the molecular mechanism of rice glumes and seed size so that the yield of gramineous plants can be raised, and quality of gramineous plant can be improved.

Rice spikelet development regulation protein, encoding genes MS1 thereof and application

The invention discloses a protein coded by a rice leaf senescence regulation gene OsNaPRT1, wherein the protein is (A) a protein with an amino acid sequence shown by Seq ID No:2, or (B) a protein obtained by adding, substituting and/or deleting one or multiple amino acids of the amino acid sequence defined in (A) and having a function of regulating the rice leaf senescence The invention also discloses a gene (shown by SEQ ID No:1, etc) coding the protein as well as a recombinant vector and a transformant containing the gene, a method for regulating the rice leaf senescence by using the gene and an application of the gene in regulation of plant leaf senescence, plant height and/or grain shape In the invention, the OsNaPRT1 gene is obtained by the map-based cloning technology, the function of the gene is identified by a transgenic complementary experiment, and the rice leaf senescence, plant height and grain shape can be influenced at the same time so as to influence the whole morphological characteristics of the rice plant; and by adopting the gene product for regulation, an ideal plant capable of delaying leaf senescence can be obtained, and the rice yield is increased

Rice leaf senescence regulation gene OsNaPRT1 as well as protein coded thereby and application thereof

The invention discloses a rice weakness premature senility-relevant gene, protein, a molecular marker and application. Map-based cloning technology is utilized to obtain the rice weakness premature senility-relevant gene LOC_Os05g04900 and encoded protein thereof, and on the base, the application of the relevant gene, protein and molecular marker in rice weakness premature senility control or seedbreeding is developed.

Wu Liwen

Papers

White stripe leaf 12 (WSL12), encoding a nucleoside diphosphate kinase 2 (OsNDPK2), regulates chloroplast development and abiotic stress response in rice (Oryza sativa L.).

Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed.

Rice spikelet development regulation protein, encoding genes MS1 thereof and application

Rice leaf senescence regulation gene OsNaPRT1 as well as protein coded thereby and application thereof

Rice weakness premature senility-relevant gene, protein, molecular marker and application