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Complete panicle exsertion (CPE) is an economically important quantitative trait that contributes to grain yield in rice. We deployed an integrated approach for understanding the molecular mechanism of CPE using a stable ethyl methanesulfonate mutant line, CPE-109 of the Samba Mahsuri (SM) variety of rice (Oryza sativa), which exhibits CPE. Two consistent genomic regions were identified for CPE through quantitative trait locus (QTL) mapping [ qCPE-4 (28.24–31.22 Mb) and qCPE-12 (2.30–3.18 Mb)] and QTL-sequencing [chr 4 (31.21–33.69 Mb) and chr 12 (0.12–3.15 Mb)]. Two non-synonymous single nucleotide polymorphisms, namely KASP 12–12 (T→C; chr12:1269983) in Os12g0126300 , encoding an AP2/ERF transcription factor, and KASP 12–16 (G→A; chr12:1515198) in Os12g0131400 , encoding an F-box domain-containing protein, explained 81.05% and 59.61% of the phenotypic variance, respectively, and exhibited strong co-segregation with CPE in F2 mapping populations, advanced generation lines, and CPE-exhibiting SM mutants through KASP assays. Down-regulation of these genes in CPE-109 compared with SM (wild type) was observed in transcriptome sequencing of flag leaves, which was validated through qRT-PCR. We propose that the abrogation of Os12g0126300 and Os12g0131400 in CPE-109 combinatorially influences down-regulation of ethylene biosynthetic genes, Os01g0192900 (ACC synthase) and Os05g0497300 (ethylene-responsive factor-2), and up-regulation of a gibberellic acid synthetic gene, Os06g0569900 (ent-kaurene synthase) and the two cytokinin biosynthetic genes Os07g0486700 (cytokinin- O -glucosyltransferase 2) and Os10g0479500 (similar to carboxy-lyase), which results in complete panicle exsertion. [ABSTRACT FROM AUTHOR]

Historically, Xanthomonas species are primarily known for their pathogenicity against plants, but recently, there have been more findings of non-pathogenic xanthomonads. In the present study, we report isolates from healthy rice seeds that belong to a new species, Xanthomonas protegens , a protector of the rice plants against a serious pathogenic counterpart, i.e. X. oryzae pv. oryzae upon leaf clip co-inoculation. The new member species is non-pathogenic to rice and lacks a type III secretion system. The pangenome investigation revealed a large number of unique genes, including a novel lipopolysaccharide biosynthetic gene cluster, that might be important in its adaptation. The phylo-taxonogenomic analysis revealed that X. protegens is a taxonomic outlier species of X. sontii , a core, vertically transmitted rice seed endophyte with numerous probiotic properties. Interestingly, X. sontii is also reported as a keystone species of healthy rice seed microbiome. The findings and resources will help in the development of unique gene markers and evolutionary studies of X. sontii as a successful symbiont and X. oryzae as a serious pathogen. Here, we propose X. protegens sp. nov. as a novel species of the genus Xanthomonas with PPL118 = MTCC 13396 = CFBP 9164 = ICMP 25181 as the type strain. PPL117, PPL124, PPL125, and PPL126 are other strains of the species. [ABSTRACT FROM AUTHOR]

Summary: Many bacterial phytopathogens employ effectors secreted through the type‐III secretion system to suppress plant innate immune responses. The Xanthomonas type‐III secreted non‐TAL effector protein Xanthomonas outer protein Q (XopQ) exhibits homology to nucleoside hydrolases. Previous work indicated that mutations which affect the biochemical activity of XopQ fail to affect its ability to suppress rice innate immune responses, suggesting that the effector might be acting through some other pathway or mechanism. In this study, we show that XopQ interacts in yeast and in planta with two rice 14‐3‐3 proteins, Gf14f and Gf14g. A serine to alanine mutation (S65A) of a 14‐3‐3 interaction motif in XopQ abolishes the ability of XopQ to interact with the two 14‐3‐3 proteins and to suppress innate immunity. Surprisingly, the S65A mutant gains the ability to interact with a third 14‐3‐3 protein that is a negative regulator of innate immunity. The XopQS65A mutant is an inducer of rice immune responses and this property is dominant over the wild‐type function of XopQ. Taken together, these results suggest that XopQ targets the rice 14‐3‐3 mediated immune response pathway and that its differential phosphorylation might enable interaction with alternative 14‐3‐3 proteins. [ABSTRACT FROM AUTHOR]

Asub-groupofLuxRfamilyofproteinsthatplaysimportantrolesinquorumsensing,aprocessofcell-cellcommunication,iswidespreadinproteobacteria.TheseproteinshaveatypicalmodularstructureconsistingofN-terautoinducerbindingandC-terhelix-turn-helix(HTH)DNAbindingdomains.TheautoinducerbindingdomainrecognizessignalingmoleculeswhicharemostoftenN-acylhomoserinelactones(AHLs)butcouldalsobeothernovelandyetunidentifiedmolecules.Inthisstudywecarriedoutaseriesofspecificdomainswappingandpromoteractivationexperimentsasafirststeptoengineersyntheticsignalingmodules,takingadvantageofthemodularityandtheversatile/diversesignalspecificitiesofLuxRproteins.InourexperimentstheN-terdomainsfromdifferentLuxRhomologswereeitherinterchangedorplacedintandemfollowedbyaC-terdomain.Therationaldesignofthehybridproteinswassupportedbyastructure-basedhomologymodelingstudiesofthreemembersoftheLuxRfamily(i.e.,LasR,RhlR,andOryRbeingchosenfortheiruniqueligandbindingspecificities)andofselectedchimeras.OurresultsrevealthattheseLuxRhomologswereabletoactivatepromoterelementsthatwerenottheirusualtargets;wealsoshowthathybridLuxRproteinsretainedtheabilitytorecognizethesignalspecificfortheirN-terautoinducerbindingdomain.However,theactivityofhybridLuxRproteinscontainingtwoAHLbindingdomainsintandemappearstodependontheorganizationandnatureoftheintroduceddomains.ThisstudyrepresentsadvancesintheunderstandingofthemodularityofLuxRproteinsandprovidesadditionalpossibilitiestousehybridproteinsinbothbasicandappliedsyntheticbiologybasedresearch. [ABSTRACT FROM AUTHOR]

Xanthomonas species are major pathogens of plants and have been studied extensively. There is increasing recognition of the importance of non-pathogenic species within the same genus. With this came the need to understand the genomic and functional diversity of non-pathogenic Xanthomonas (NPX) at the species and strain level. This study reports isolation and investigation into the genomic diversity and variation in NPX isolates, chiefly Xanthomonas indica, a newly discovered NPX species from rice. The study establishes the relationship of X. indica strains within clade I of Xanthomonads with another NPX species, X. sontii, also associated with rice seeds. Identification of highly diverse strains, open-pan genome, and systematic hyper-variation at the lipopolysaccharide biosynthetic locus when compared to pathogenic Xanthomonas indicates the acquisition of new functions for adaptation. Furthermore, comparative genomics studies established the absence of major virulence genes such as type III secretion system and effectors, which are present in the pathogens, and the presence of a known bacterial-killing type IV secretion system (X-T4SS). The diverse non-pathogenic strains of X. indica and X. sontii were found to protect rice from bacterial leaf blight pathogen, X. oryzae pv. oryzae (Xoo). The absence of phenotype of an X-T4SS mutant suggests redundancy in the genetic basis of the mechanisms involved in the bioprotection function, which may include multiple genetic loci, such as putative bacteriocinencoding gene clusters and involvement of other factors such as nutrient and niche competition apart from induction of innate immunity through shared microbial-associated molecular patterns. The rice-NPX community and its pathogenic counterpart can be a promising model for understanding plant-microbe-microbiome interaction studies. [ABSTRACT FROM AUTHOR]