No abstract

Summary Whole‐genome annotation error that omits essential protein‐coding genes hinders further research. We developed Target Gene Family Finder ( tgfam‐finder ), an alternative tool for the structural annotation of protein‐coding genes containing target domain(s) of interest in plant genomes. tgfam‐finder took considerably reduced annotation run‐time and improved accuracy compared to conventional annotation tools. Large‐scale re‐annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far‐red‐impaired response 1, nucleotide‐binding and leucine‐rich‐repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. tgfam‐finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.

MSP1 is a Magnaporthe oryzae secreted protein that elicits defense responses in rice. However, the molecular mechanism of MSP1 action is largely elusive. Moreover, it is yet to be established whether MSP1 functions as a pathogen-associated molecular pattern (PAMP) or an effector. Here, we employed a TMT-based quantitative proteomic analysis of cytosolic as well as plasma membrane proteins to decipher the MSP1 induced signaling in rice. This approach led to the identification of 6691 proteins, of which 3049 were identified in the plasma membrane (PM), while 3642 were identified in the cytosolic fraction. A parallel phosphoproteome analysis led to the identification of 1906 phosphopeptides, while the integration of proteome and phosphoproteome data showed activation of proteins related to the proteolysis, jasmonic acid biosynthesis, redox metabolism, and MAP kinase signaling pathways in response to MSP1 treatment. Further, MSP1 induced phosphorylation of some of the key proteins including respiratory burst oxidase homologue-D (RBOHD), mitogen-activated protein kinase kinase kinase-1 (MEKK1), mitogen-activated protein kinase-3/6 (MPK3/6), calcium-dependent protein kinase (CDPK) and calmodulin (CaM) suggest activation of PAMP-triggered immunity (PTI) in response to MSP1 treatment. In essence, our results further support the functioning of MSP1 as a PAMP and provide an overview of the MSP1 induced signaling in rice leaves.

Phytohormones are central to plant growth and development. Despite the advancement in our knowledge of hormone signaling, downstream targets, and their interactions upon hormones action remain largely fragmented, especially at the protein and metabolite levels. With an aim to get new insight into the effects of two hormones, ethylene (ET) and abscisic acid (ABA), this study utilizes an integrated proteomics and metabolomics approach to investigate their individual and combined (ABA+ET) signaling in soybean leaves. Targeting low-abundance proteins, our previously established protamine sulfate precipitation method was applied, followed by label-free quantification of identified proteins. A total of 4129 unique protein groups including 1083 differentially modulated in one (individual) or other (combined) treatments were discerned. Functional annotation of the identified proteins showed an increased abundance of proteins related to the flavonoid and isoflavonoid biosynthesis and MAPK signaling pathway in response to ET treatment. HPLC analysis showed an accumulation of isoflavones (genistin, daidzein, and genistein) upon ET treatment, in agreement with the proteomics results. A metabolome analysis assigned 79 metabolites and further confirmed the accumulation of flavonoids and isoflavonoids in response to ET. A potential cross-talk between ET and MAPK signaling, leading to the accumulation of flavonoids and isoflavonoids in soybean leaves is suggested.

Rice blast disease, caused by Magnaporthe oryzae, is one of the major constraints to rice production, which feeds half of the world’s population. Proteomic technologies have been used as effective tools in plant−pathogen interactions to study the biological pathways involved in pathogen infection, plant response, and disease progression. Advancements in mass spectrometry (MS) and apoplastic and plasma membrane protein isolation methods facilitated the identification and quantification of subcellular proteomes during plant-pathogen interaction. Proteomic studies conducted during rice−M. oryzae interaction have led to the identification of several proteins eminently involved in pathogen perception, signal transduction, and the adjustment of metabolism to prevent plant disease. Some of these proteins include receptor-like kinases (RLKs), mitogen-activated protein kinases (MAPKs), and proteins related to reactive oxygen species (ROS) signaling and scavenging, hormone signaling, photosynthesis, secondary metabolism, protein degradation, and other defense responses. Moreover, post−translational modifications (PTMs), such as phosphoproteomics and ubiquitin proteomics, during rice−M. oryzae interaction are also summarized in this review. In essence, proteomic studies carried out to date delineated the molecular mechanisms underlying rice-M. oryzae interactions and provided candidate proteins for the breeding of rice blast resistant cultivars.