Microbe-Responsive Proteomes During Plant–Microbe Interactions Between Rice Genotypes and the Multifunctional Methylobacterium oryzae CBMB20

Abstract

Background Rice is colonized by plant growth promoting bacteria such as Methylobacterium leading to mutually beneficial plant–microbe interactions. As modulators of the rice developmental process, Methylobacterium influences seed germination, growth, health, and development. However, little is known about the complex molecular responsive mechanisms modulating microbe-driven rice development. The application of proteomics to rice-microbe interactions helps us elucidate dynamic proteomic responses mediating this association. Results In this study, a total of 3908 proteins were detected across all treatments of which the non-inoculated IR29 and FL478 share up to 88% similar proteins. However, intrinsic differences appear in IR29 and FL478 as evident in the differentially abundant proteins (DAPs) and their associated gene ontology terms (GO). Successful colonization of M. oryzae CBMB20 in rice resulted to dynamic shifts in proteomes of both IR29 and FL478. The GO terms of DAPs for biological process in IR29 shifts in abundance from response to stimulus, cellular amino acid metabolic process, regulation of biological process and translation to cofactor metabolic process (6.31%), translation (5.41%) and photosynthesis (5.41%). FL478 showed a different shift from translation-related to response to stimulus (9%) and organic acid metabolic acid (8%). Both rice genotypes also showed a diversification of GO terms due to the inoculation of M. oryzae CBMB20. Specific proteins such as peptidyl-prolyl cis–trans isomerase (A2WJU9), thiamine thiazole synthase (A2YM28), and alanine—tRNA ligase (B8B4H5) upregulated in IR29 and FL478 indicate key mechanisms of M. oryzae CBMB20 mediated plant growth promotion in rice. Conclusions Interaction of Methylobacterium oryzae CBMB20 to rice results in a dynamic, similar, and plant genotype-specific proteomic changes supporting associated growth and development. The multifaceted CBMB20 expands the gene ontology terms and increases the abundance of proteins associated with photosynthesis, diverse metabolic processes, protein synthesis and cell differentiation and fate potentially attributed to the growth and development of the host plant. The specific proteins and their functional relevance help us understand how CBMB20 mediate growth and development in their host under normal conditions and potentially link subsequent responses when the host plants are exposed to biotic and abiotic stresses.

Induction of microbe-mediated responsive proteomes by Methylobacterium oryzae CBMB20 on the salt-tolerant and salt-sensitive rice genotypes towards enhanced salt tolerance

“…The DAP NADPH-protochlorophyllide oxidoreductase (OsI_17934) is involved in the phototransformation of protochlorophyllide to chlorophyllide, an essential process in the transformation of chloroplast from etioplasts (Apel et al, 1980). This enzyme was also observed to be upregulated in non-stressed, M. oryzae CBMB20 inoculated IR29 (Walitang et al, 2023b). Our current result showed very high upregulation of this DAP due to M. oryzae CBMB20 in salt-stressed rice plants.…”

“…The application of M. oryzae CBMB20 changed the proteomes of IR29 and FL478 even under ideal growing environment (Walitang et al, 2023b). One of the most prominent changes observed after inoculating IR29 and FL479 followed by salt stress imposition is the 'restoration' of function of proteins.…”

“…tomato (Indiragandhi et al, 2008), although all these studies have mainly attributed this to ACC deaminase and the regulation of stress ethylene. In a recent study, stress and defense responses have been activated and modulated by the application of M. oryzae CBMB20 under normal conditions in both IR29 and FL478 when M. oryzae CBMB20 endophytically colonized the rice plants (Walitang et al, 2023b). We are proposing that stress and defense responses have been primed due to the application of the M. oryzae CBMB20 inducing systemic resistance leading to a more effective response when the rice cultivars were subsequently exposed to severe salt stress leading to the observed dynamic proteomic responses observed in this study.…”

“…Oftentimes, shifts in the transcriptional level do not exactly correlate to the shifts at the level of proteomes (Li et al, 2018). Also, inherent differences and similarities clearly exist between IR29 and FL478 rice genotypes and their proteomic response when inoculated with M. oryzae CBMB20 under normal growing conditions (Walitang et al, 2023b). Therefore, understanding dynamic proteomic changes and protein identi cation of DAPs associated to salt stress or microbe-mediated stress responses distinguishingly observed in IR29 and FL478 offer supportive outlook at the molecular mechanisms and are helpful for developing stress tolerance through plant-microbe interactions.…”

“…Walitang et al, 2023b) and in Oryza sativa ssp. japonica under severe salt stress(Roy Choudhury et al, 2022).…”