In silico analysis of fungal prion-like proteins for elucidating their role in plant-fungi interactions.

Prion-like proteins (PrLPs) have emerged as beneficial molecules with implications in adaptive responses. These proteins possess a conserved prion-like domain (PrLD) which is an intrinsically disordered region capable of adopting different conformations upon perceiving external stimuli. Owing to changes in protein conformation, functional characteristics of proteins harboring PrLDs get altered thereby, providing a unique mode of protein-based regulation. Since PrLPs are ubiquitous in nature and involved in diverse functions, through this study, we aim to explore the role of such domains in yet another important physiological process viz. plant-microbe interactions to get insights into the mechanisms dictating cross-kingdom interactions. We have evaluated the presence and functions of PrLPs in 18 different plant-associated fungi of agricultural importance to unravel their role in plant-microbe interactions. Of the 241,997 proteins scanned, 3,820 (~ 1.6%) were identified as putative PrLPs with pathogenic fungi showing significantly higher PrLP density than their beneficial counterparts. Further, through GO enrichment analysis, we could predict several PrLPs from pathogenic fungi to be involved in virulence and formation of stress granules. Notably, PrLPs involved in (retro)transposition were observed exclusively in pathogenic fungi. We even analyzed publicly available data for the expression alterations of fungal PrLPs upon their interaction with their respective hosts which revealed perturbation in the levels of some PrLP-encoding genes during interactions with plants. Overall, our work sheds light into the probable role of prion-like candidates in plant-fungi interaction, particularly in context of pathogenesis, paving way for more focused studies for validating their role.

Microbial methylglyoxal metabolism contributes towards growth promotion and stress tolerance in plants.

Plant growth promotion by microbes is a cumulative phenomenon involving multiple traits, many of which are not explored yet. Hence, to unravel microbial mechanisms underlying growth promotion, we have analysed the genomes of two potential growth-promoting microbes, viz., Pseudomonas sp. CK-NBRI-02 (P2) and Bacillus marisflavi CK-NBRI-03 (P3) for the presence of plant-beneficial traits. Besides known traits, we found that microbes differ in their ability to metabolize methylglyoxal (MG), a ubiquitous cytotoxin regarded as general consequence of stress in plants. P2 exhibited greater tolerance to MG and possessed better ability to sustain plant growth under dicarbonyl stress. However, under salinity, only P3 showed a dose-dependent induction in MG detoxification activity in accordance with concomitant increase in MG levels, contributing to enhanced salt tolerance. Furthermore, salt-stressed transcriptomes of both the strains showed differences with respect to MG, ion and osmolyte homeostasis, with P3 being more responsive to stress. Importantly, application of either strain altered MG levels and subsequently MG detoxification machinery in Arabidopsis, probably to strengthen plant defence response and growth. We therefore, suggest a crucial role of microbial MG resistance in plant growth promotion and that it should be considered as a beneficial trait while screening microbes for stress mitigation in plants.

Serotonin and Melatonin Biosynthesis in Plants: Genome-Wide Identification of the Genes and Their Expression Reveal a Conserved Role in Stress and Development.

Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.

What signals the glyoxalase pathway in plants?

Glyoxalase (GLY) system, comprising of GLYI and GLYII enzymes, has emerged as one of the primary methylglyoxal (MG) detoxification pathways with an indispensable role during abiotic and biotic stresses. MG homeostasis is indeed very closely guarded by the cell as its higher levels are cytotoxic for the organism. The dynamic responsiveness of MG-metabolizing GLY pathway to both endogenous cues such as, phytohormones, nutrient status, etc., as well as external environmental fluctuations (abiotic and biotic stresses) indicates that a tight regulation occurs in the cell to maintain physiological levels of MG in the system. Interestingly, GLY pathway is also manipulated by its substrates and reaction products. Hence, an investigation of signalling and regulatory aspects of GLY pathway would be worthwhile. Herein, we have attempted to converge all known factors acting as signals or directly regulating GLYI/II enzymes in plants. Further, we also discuss how crosstalk between these different signal molecules might facilitate the regulation of glyoxalase pathway. We believe that MG detoxification is controlled by intricate mechanisms involving a plethora of signal molecules.

Methylglyoxal-glyoxalase system as a possible selection module for raising marker-safe plants in rice.

Methylglyoxal (MG) is ubiquitously produced in all living organisms as a byproduct of glycolysis, higher levels of which are cytotoxic, leading to oxidative stress and apoptosis in the living systems. Though its generation is spontaneous but its detoxification involves glyoxalase pathway genes. Based on this understanding, the present study describes the possible role of MG as a novel non-antibiotic-based selection agent in rice. Further, by metabolizing MG, the glyoxalase pathway genes viz. glyoxalase I (GLYI) and glyoxalase II (GLYII), may serve as selection markers. Therefore, herein, transgenic rice harboring GLYI-GLYII genes (as selection markers) were developed and the effect of MG as a selection agent was assessed. The 3 mM MG concentration was observed as optimum for the selection of transformed calli, allowing efficient callus induction and proliferation along with high regeneration frequency (55 ± 2%) of the transgenic calli. Since the transformed calli exhibited constitutively higher activity of GLYI and GLYII enzymes compared to the wild type calli, the rise in MG levels was restricted even upon exogenous addition of MG during the selection process, resulting in efficient selection of the transformed calli. Therefore, MG-based selection method is a useful and efficient system for selection of transformed plants without significantly compromising the transformation efficiency. Further, this MG-based selection system is bio-safe and can pave way towards better public acceptance of transgenic plants.

From methylglyoxal to pyruvate: a genome-wide study for the identification of glyoxalases and D-lactate dehydrogenases in Sorghum bicolor.

BACKGROUND: The glyoxalase pathway is evolutionarily conserved and involved in the glutathione-dependent detoxification of methylglyoxal (MG), a cytotoxic by-product of glycolysis. It acts via two metallo-enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), to convert MG into D-lactate, which is further metabolized to pyruvate by D-lactate dehydrogenases (D-LDH). Since D-lactate formation occurs solely by the action of glyoxalase enzymes, its metabolism may be considered as the ultimate step of MG detoxification. By maintaining steady state levels of MG and other reactive dicarbonyl compounds, the glyoxalase pathway serves as an important line of defence against glycation and oxidative stress in living organisms. Therefore, considering the general role of glyoxalases in stress adaptation and the ability of Sorghum bicolor to withstand prolonged drought, the sorghum glyoxalase pathway warrants an in-depth investigation with regard to the presence, regulation and distribution of glyoxalase and D-LDH genes. RESULT: Through this study, we have identified 15 GLYI and 6 GLYII genes in sorghum. In addition, 4 D-LDH genes were also identified, forming the first ever report on genome-wide identification of any plant D-LDH family. Our in silico analysis indicates homology of putatively active SbGLYI, SbGLYII and SbDLDH proteins to several functionally characterised glyoxalases and D-LDHs from Arabidopsis and rice. Further, these three gene families exhibit development and tissue-specific variations in their expression patterns. Importantly, we could predict the distribution of putatively active SbGLYI, SbGLYII and SbDLDH proteins in at least four different sub-cellular compartments namely, cytoplasm, chloroplast, nucleus and mitochondria. Most of the members of the sorghum glyoxalase and D-LDH gene families are indeed found to be highly stress responsive. CONCLUSION: This study emphasizes the role of glyoxalases as well as that of D-LDH in the complete detoxification of MG in sorghum. In particular, we propose that D-LDH which metabolizes the specific end product of glyoxalases pathway is essential for complete MG detoxification. By proposing a cellular model for detoxification of MG via glyoxalase pathway in sorghum, we suggest that different sub-cellular organelles are actively involved in MG metabolism in plants.

Reassessing plant glyoxalases: large family and expanding functions.

Methylglyoxal (MG), a reactive carbonyl compound, is generated during metabolism in living systems. However, under stress, its levels increase rapidly leading to cellular toxicity. Although the generation of MG is spontaneous in a cell, its detoxification is essentially catalyzed by the glyoxalase enzymes. In plants, modulation of MG content via glyoxalases influences diverse physiological functions ranging from regulating growth and development to conferring stress tolerance. Interestingly, there has been a preferred expansion in the number of isoforms of these enzymes in plants, giving them high plasticity in their actions for accomplishing diverse roles. Future studies need to focus on unraveling the interplay of these multiple isoforms of glyoxalases possibly contributing towards the unique adaptability of plants to diverse environments.

A nuclear-localized rice glyoxalase I enzyme, OsGLYI-8, functions in the detoxification of methylglyoxal in the nucleus.

The cellular levels of methylglyoxal (MG), a toxic byproduct of glycolysis, rise under various abiotic stresses in plants. Detoxification of MG is primarily through the glyoxalase pathway. The first enzyme of the pathway, glyoxalase I (GLYI), is a cytosolic metalloenzyme requiring either Ni2+ or Zn2+ for its activity. Plants possess multiple GLYI genes, of which only some have been partially characterized; hence, the precise molecular mechanism, subcellular localization and physiological relevance of these diverse isoforms remain enigmatic. Here, we report the biochemical properties and physiological role of a putative chloroplast-localized GLYI enzyme, OsGLYI-8, from rice, which is strikingly different from all hitherto studied GLYI enzymes in terms of its intracellular localization, metal dependency and kinetics. In contrast to its predicted localization, OsGLYI-8 was found to localize in the nucleus along with its substrate, MG. Further, OsGLYI-8 does not show a strict requirement for metal ions for its activity, is functional as a dimer and exhibits unusual biphasic steady-state kinetics with a low-affinity and a high-affinity substrate-binding component. Loss of AtGLYI-2, the closest Arabidopsis ortholog of OsGLYI-8, results in severe germination defects in the presence of MG and growth retardation under salinity stress conditions. These defects were rescued upon complementation with AtGLYI-2 or OsGLYI-8. Our findings thus provide evidence for the presence of a GLYI enzyme and MG detoxification in the nucleus.

Proteomics of contrasting rice genotypes: Identification of potential targets for raising crops for saline environment.

High salinity is one of the major problems in crop productivity, affecting seed germination as well as yield. In order to enhance tolerance of crops towards salinity, it is essential to understand the underlying physiological and molecular mechanisms. In this endeavor, study of contrasting genotypes of the same species differing in their response towards salinity stress can be very useful. In the present study, we have investigated temporal differences in morphological, physiological and proteome profiles of two contrasting genotypes of rice to understand the basis of salt tolerance. When compared to IR64 rice, Pokkali, the salt-tolerant wild genotype, has enhanced capacity to cope with stress, better growth rate and possesses efficient antioxidant system, as well as better photosynthetic machinery. Our proteome studies revealed a higher and an early abundance of proteins involved in stress tolerance and photosynthesis in Pokkali in comparison with IR64, which, in contrast, showed greater changes in metabolic machinery even during early duration of stress. Our findings suggest important differences in physicochemical and proteome profiles of the two genotypes, which may be the basis of observed stress tolerance in the salt-tolerant Pokkali.

OsCBSCBSPB4 is a Two Cystathionine-ß-Synthase Domain-containing Protein from Rice that Functions in Abiotic Stress Tolerance.

Cystathionine ß-synthase (CBS) domains have been identified in a wide range of proteins of unrelated functions such as, metabolic enzymes, kinases and channels, and usually occur as tandem re-peats, often in combination with other domains. In plants, CBS Domain-Containing Proteins (CDCPs) form a multi-gene family and only a few are so far been reported to have a role in development via regu-lation of thioredoxin system as well as in abiotic and biotic stress response. However, the function of majority of CDCPs still remains to be elucidated in plants. Here, we report the cloning, characterization and functional validation of a CBS domain containing protein, OsCBSCBSPB4 from rice, which pos-sesses two CBS domains and one PB1 domain. We show that OsCBSCBSPB4 encodes a nucleo-cytoplasmic protein whose expression is induced in response to various abiotic stress conditions in salt-sensitive IR64 and salt-tolerant Pokkali rice cultivars. Further, heterologous expression of OsCBSCB-SPB4 in E. coli and tobacco confers marked tolerance against various abiotic stresses. Transgenic tobac-co seedlings over-expressing OsCBSCBSPB4 were found to exhibit better growth in terms of delayed leaf senescence, profuse root growth and increased biomass in contrast to the wild-type seedlings when subjected to salinity, dehydration, oxidative and extreme temperature treatments. Yeast-two hybrid stud-ies revealed that OsCBSCBSPB4 interacts with various proteins. Of these, some are known to be in-volved in abiotic stress tolerance. Our results suggest that OsCBSCBSPB4 is involved in abiotic stress response and is a potential candidate for raising multiple abiotic stress tolerant plants.

Characteristic Variations and Similarities in Biochemical, Molecular, and Functional Properties of Glyoxalases across Prokaryotes and Eukaryotes.

The glyoxalase system is the ubiquitous pathway for the detoxification of methylglyoxal (MG) in the biological systems. It comprises two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), which act sequentially to convert MG into d-lactate, thereby helping living systems get rid of this otherwise cytotoxic byproduct of metabolism. In addition, a glutathione-independent GLYIII enzyme activity also exists in the biological systems that can directly convert MG to d-lactate. Humans and Escherichia coli possess a single copy of GLYI (encoding either the Ni- or Zn-dependent form) and GLYII genes, which through MG detoxification provide protection against various pathological and disease conditions. By contrast, the plant genome possesses multiple GLYI and GLYII genes with a role in abiotic stress tolerance. Plants possess both Ni2+- and Zn2+-dependent forms of GLYI, and studies on plant glyoxalases reveal the various unique features of these enzymes distinguishing them from prokaryotic and other eukaryotic glyoxalases. Through this review, we provide an overview of the plant glyoxalase family along with a comparative analysis of glyoxalases across various species, highlighting similarities as well as differences in the biochemical, molecular, and physiological properties of these enzymes. We believe that the evolution of multiple glyoxalases isoforms in plants is an important component of their robust defense strategies.

A unique Ni2+ -dependent and methylglyoxal-inducible rice glyoxalase I possesses a single active site and functions in abiotic stress response.

The glyoxalase system constitutes the major pathway for the detoxification of metabolically produced cytotoxin methylglyoxal (MG) into a non-toxic metabolite D-lactate. Glyoxalase I (GLY I) is an evolutionarily conserved metalloenzyme requiring divalent metal ions for its activity: Zn(2+) in the case of eukaryotes or Ni(2+) for enzymes of prokaryotic origin. Plant GLY I proteins are part of a multimember family; however, not much is known about their physiological function, structure and metal dependency. In this study, we report a unique GLY I (OsGLYI-11.2) from Oryza sativa (rice) that requires Ni(2+) for its activity. Its biochemical, structural and functional characterization revealed it to be a monomeric enzyme, possessing a single Ni(2+) coordination site despite containing two GLY I domains. The requirement of Ni(2+) as a cofactor by an enzyme involved in cellular detoxification suggests an essential role for this otherwise toxic heavy metal in the stress response. Intriguingly, the expression of OsGLYI-11.2 was found to be highly substrate inducible, suggesting an important mode of regulation for its cellular levels. Heterologous expression of OsGLYI-11.2 in Escherichia coli and model plant Nicotiana tabacum (tobacco) resulted in improved adaptation to various abiotic stresses caused by increased scavenging of MG, lower Na(+) /K(+) ratio and maintenance of reduced glutathione levels. Together, our results suggest interesting links between MG cellular levels, its detoxification by GLY I, and Ni(2+) - the heavy metal cofactor of OsGLYI-11.2, in relation to stress response and adaptation in plants.

Molecular cloning and characterization of salt overly sensitive gene promoter from Brassica juncea (BjSOS2).

Salt Overly Sensitive (SOS) pathway comprising SOS1, SOS2 and SOS3 genes has been recognized as the key mechanism controlling ion homeostasis under salinity stress. SOS2 component of this pathway encodes a serine/threonine protein kinase that together with SOS3 activates downstream Na(+)/H(+) antiporter SOS1, reestablishing cellular ion homeostasis under salinity stress. In the present study, we have found that the transcript levels of BjSOS2 are induced in response to various abiotic stresses. We have isolated a 713 bp promoter region of SOS2 gene from Brassica juncea to study the regulation of BjSOS2 under various abiotic stress conditions and further, to examine utility of the cloned upstream region in genetic engineering experiments. For this purpose, 713 bp BjSOS2 promoter:ß-glucuronidase (GUS) fusion construct, along with its two subsequent 5' deletion derivatives, D1 (443 bp) and D2 (209 bp), were stably transformed into B. juncea. Functional analysis of transgenic lines revealed significant increase in promoter activity under salinity, desiccation as well as abscisic acid (ABA) treatment which was consistent with increased transcript levels of GUS gene. BjSOS2 promoter possesses strong multi-stress inducible nature, suggesting its involvement in various aspects of stress signaling. Considering the fact that the simultaneous presence of multiple abiotic stress conditions under field conditions is a challenging threat to crop productivity, future studies may utilize the BjSOS2 promoter to drive stress-inducible expression of genes involved in imparting tolerance to multiple stresses.

Prevalence of multidrug-resistant, coagulase-positive Staphylococcus aureus in nasal carriage, food, wastewater and paper currency in Jalandhar city (north-western), an Indian state of Punjab.

Development of multidrug-resistant pattern in the bacterial community is a major threat to the society. Staphylococcus aureus is perhaps the pathogen of the greatest concern because of its inherent virulence, its ability to cause a diverse array of life-threatening situations and capacity to adapt to different environmental conditions. The aims of this study is to investigate the multidrug-resistant pattern of the coagulase-positive S. aureus isolated from nasal carriage, food, paper currency and wastewater samples. We had also studied the multiple antibiotic resistance index and in vitro production of ß-lactamase. The study had found out 130 coagulase-positive S. aureus strains isolated from total of 595 samples such as anterior nares of preschool children (195), hospital nurses (100), drivers (76), food (86), wastewater (3) and paper currency (135) (Indian rupee). The biotypes pattern were as follows; A > D > B > C> UT. Multiple antibiotic resistance (MAR) value clearly defines the multidrug-resistant pattern of the S. aureus among different sources. Statistical analysis (one-way ANOVA) of results obtained indicated that the difference in the antibiotic resistance observed in the 130 bacterial isolates against the 23 different antibiotics used in this study was statically significant (p < 0.01).

Glyoxalases and stress tolerance in plants.

The glyoxalase pathway is required for detoxification of cytotoxic metabolite MG (methylglyoxal) that would otherwise increase to lethal concentrations under adverse environmental conditions. Since its discovery 100 years ago, several roles have been assigned to glyoxalases, but, in plants, their involvement in stress response and tolerance is the most widely accepted role. The plant glyoxalases have emerged as multigene family and this expansion is considered to be important from the perspective of maintaining a robust defence machinery in these sessile species. Glyoxalases are known to be differentially regulated under stress conditions and their overexpression in plants confers tolerance to multiple abiotic stresses. In the present article, we review the importance of glyoxalases in plants, discussing possible roles with emphasis on involvement of the glyoxalase pathway in plant stress tolerance.

Expression of abiotic stress inducible ETHE1-like protein from rice is higher in roots and is regulated by calcium.

ETHYLMALONIC ENCEPHALOPATHY PROTEIN 1 (ETHE1) encodes sulfur dioxygenase (SDO) activity regulating sulfide levels in living organisms. It is an essential gene and mutations in ETHE1 leads to ethylmalonic encephalopathy (EE) in humans and embryo lethality in Arabidopsis. At present, very little is known regarding the role of ETHE1 beyond the context of EE and almost nothing is known about factors affecting its regulation in plant systems. In this study, we have identified, cloned and characterized OsETHE1, a gene encoding ETHE1-like protein from Oryza sativa. ETHE1 proteins in general are most similar to glyoxalase II (GLYII) and hence OsETHE1 has been earlier annotated as OsGLYII1, a putative GLYII gene. Here we show that OsETHE1 lacks GLYII activity and is instead an ETHE1 homolog being localized in mitochondria like its human and Arabidopsis counterparts. We have isolated and analyzed 1618 bp OsETHE1 promoter (pOsETHE1) to examine the factors affecting OsETHE1 expression. For this, transcriptional promoter pOsETHE1: 5-bromo-5-chloro-3-indolyl-ß-D-glucuronide (GUS) fusion construct was made and stably transformed into rice. GUS expression pattern of transgenic pOsETHE1:GUS plants reveal a high root-specific expression of OsETHE1. The pOsETHE1 activity was stimulated by Ca(II) and required light for induction. Moreover, pOsETHE1 activity was induced under various abiotic stresses such as heat, salinity and oxidative stress, suggesting a potential role of OsETHE1 in stress response.

Immunoinformatics-guided recombinant polypeptide-based enzyme-linked immunosorbent assay for seromonitoring of laboratory animals for minute virus of mice and Kilham rat virus.

Subclinical infection of laboratory animals with one or more of several pathogens affects the results of experiments on animals. Monitoring the health of laboratory animals encompasses routine surveillance for pathogens, including several viruses. This study aimed to explore the development of an alternative assay to the existing ones for detecting infection of mice and rats with the parvoviruses minute virus of mice (MVM) and Kilham rat virus (KRV), respectively. Full-length VP2 and NS1 proteins of these parvoviruses, besides fragments containing multiple predicted epitopes stitched together, were studied for serological detection. The optimal dilution of full-length proteins and antigenic regions containing predicted epitopes for coating, test sera, and conjugate was determined using a checkerboard titration at each step. The assays were evaluated vis-à-vis commercially available ELISA kits. The results showed that an engineered fusion of fragments containing multiple predicted MVM VP2 and NS1 epitopes was better than either of the full-length proteins for detecting antibodies in 90% of the tested sera samples. For KRV ELISA, full-length VP2 was better compared to other individual recombinant protein fragments or combinations thereof for the detection of antibodies in sera. This report is the first description of an ELISA for KRV and an improved assay for MVM. Importantly, our assays could be exploited with small volumes of sera. The results also demonstrate the utility of immunoinformatics-driven polypeptide engineering in the development of diagnostic assays and the potential to develop better tests for monitoring the health status of laboratory animals.

Role of methylglyoxal and redox homeostasis in microbe-mediated stress mitigation in plants.

One of the general consequences of stress in plants is the accumulation of reactive oxygen (ROS) and carbonyl species (like methylglyoxal) to levels that are detrimental for plant growth. These reactive species are inherently produced in all organisms and serve different physiological functions but their excessive accumulation results in cellular toxicity. It is, therefore, essential to restore equilibrium between their synthesis and breakdown to ensure normal cellular functioning. Detoxification mechanisms that scavenge these reactive species are considered important for stress mitigation as they maintain redox balance by restricting the levels of ROS, methylglyoxal and other reactive species in the cellular milieu. Stress tolerance imparted to plants by root-associated microbes involves a multitude of mechanisms, including maintenance of redox homeostasis. By improving the overall antioxidant response in plants, microbes can strengthen defense pathways and hence, the adaptive abilities of plants to sustain growth under stress. Hence, through this review we wish to highlight the contribution of root microbiota in modulating the levels of reactive species and thereby, maintaining redox homeostasis in plants as one of the important mechanisms of stress alleviation. Further, we also examine the microbial mechanisms of resistance to oxidative stress and their role in combating plant stress.

Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants.

Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its "prionome." In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.

Tracing the Evolution of Plant Glyoxalase III Enzymes for Structural and Functional Divergence.

Glyoxalase pathway is the primary route for metabolism of methylglyoxal (MG), a toxic ubiquitous metabolite that affects redox homeostasis. It neutralizes MG using Glyoxalase I and Glyoxalase II (GLYI and GLYII) enzymes in the presence of reduced glutathione. In addition, there also exists a shorter route for the MG detoxification in the form of Glyoxalase III (GLYIII) enzymes, which can convert MG into D-lactate in a single-step without involving glutathione. GLYIII proteins in different systems demonstrate diverse functional capacities and play a vital role in oxidative stress response. To gain insight into their evolutionary patterns, here we studied the evolution of GLYIII enzymes across prokaryotes and eukaryotes, with special emphasis on plants. GLYIII proteins are characterized by the presence of DJ-1_PfpI domains thereby, belonging to the DJ-1_PfpI protein superfamily. Our analysis delineated evolution of double DJ-1_PfpI domains in plant GLYIII. Based on sequence and structural characteristics, plant GLYIII enzymes could be categorized into three different clusters, which followed different evolutionary trajectories. Importantly, GLYIII proteins from monocots and dicots group separately in each cluster and the each of the two domains of these proteins also cluster differentially. Overall, our findings suggested that GLYIII proteins have undergone significant evolutionary changes in plants, which is likely to confer diversity and flexibility in their functions.