Meta-analysis of transcriptomics studies identifies novel attributes and set of genes involved in iron homeostasis in rice.

Iron (Fe) is an important micronutrient for humans as well as for plant growth and development. Rice employs multiple mechanisms to counteract the negative effects of Fe deficiency and Fe toxicity. Previously, many transcriptomics studies have identified hundreds of genes affected by Fe deficiency and/or Fe toxicity. These studies are highly valuable to identify novel genes involved in Fe homeostasis. However, in the absence of their systematic integration, they remain underutilized. A systematic meta-analysis of transcriptomics data from such ten previous studies was performed here to identify various common attributes. From this meta-analysis, it is revealed that under Fe deficiency conditions, root transcriptome is more sensitive and exhibits greater similarity across multiple studies than the shoot transcriptome. Furthermore, under Fe toxicity conditions, upregulated genes are more reliable and consistent than downregulated genes in susceptible cultivars. The integration of data from Fe deficiency and Fe toxicity conditions helped to identify key marker genes for Fe stress. As a proof-of-concept of the analysis, among the genes consistently regulated in opposite directions under Fe deficiency and toxicity conditions, two genes were selected: a proton-dependent oligopeptide transporter (POT) family protein and Vacuolar Iron Transporter (VIT)-Like (VTL) gene, and validated their expression and sub-cellular localization. Since VIT genes are known to play an important role in Fe homeostasis in plants, the entire OsVTL gene family in rice was characterized. This meta-analysis has identified many novel candidate genes that exhibit consistent expression patterns across multiple tissues, conditions, and studies. This makes them potential targets for future research aimed at developing Fe-biofortified rice varieties, as well as varieties tolerant to sub-optimal Fe levels in soil.

Rice lipases: a conundrum in rice bran stabilization: a review on their impact and biotechnological interventions.

Rice is a primary food and is one of the most important constituents of diets all around the world. Rice bran is a valuable component of rice, containing many oil-soluble vitamins, minerals, and oil. It is known for its ability to improve the economic value of rice. Further, it contains substantial quantities of minerals like potassium, calcium, magnesium, iron and antioxidants like tocopherols, tocotrienols, and γ-oryzanol, indicating that rice bran can be utilized effectively against several life-threatening disorders. It is difficult to fully utilize the necessary nutrients due to the presence of lipases in rice bran. These lipases break down lipids, specifically Triacylglycerol, into free fatty acids and glycerol. This review discusses physicochemical properties, mechanism of action, distribution, and activity of lipases in various components of rice seeds. The phylogenetic and gene expression analysis helped to understand the differential expression pattern of lipase genes at different growth phases of rice plant. Further, this review discusses various genetic and biotechnological approaches to decrease lipase activity in rice and other plants, which could potentially prevent the degradation of bran oil. The goal is to establish whether lipases are a major contributor to this issue and to develop rice varieties with improved bran stability. This information sets the stage for upcoming molecular research in this area. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01343-3.

Reference gene identification for gene expression analysis in rice under different metal stress.

Real-time quantitative polymerase chain reaction (RT-qPCR) is the most common approach to quantify changes in gene expression. Appropriate internal reference genes are essential for normalization of data of RT-qPCR. In the present study, we identified suitable reference genes for analysis of gene expression in rice seedlings subjected to different heavy metal stresses such as deficiencies of iron and zinc and toxicities of cobalt, cadmium and nickel. First, from publically available RNA-Seq data we identified 10 candidate genes having stable expression. We also included commonly used house-keeping gene OsUBQ5 (Ubiquitin 5) in our analysis. Expression stability of all the 11 genes was determined by two independent tools, NormFinder and geNorm. Our results show that selected candidate reference genes have higher stability in their expression compared to that of OsUBQ5. Genes with locus ID LOC_Os03g16690, encoding an oxysterol-binding protein (OsOBP) and LOC_Os01g56580, encoding Casein Kinase_1a.3 (OsCK1a.3) were identified to be the most stably expressed reference genes under most of the conditions tested. Finally, the study reveals that it is better to use a specific reference gene for a specific heavy metal stress condition rather than using a common reference gene for multiple heavy metal stress conditions. The reference genes identified here would be very useful for gene expression studies under heavy metal stresses in rice.

Mucosal coaptation technique for early urinary continence after robot-assisted radical prostatectomy: a comparative exploratory study.

INTRODUCTION: Urinary incontinence is a troublesome complication following radical prostatectomy. Various robot-assisted radical prostatectomy (RARP). We describe our technique (Santosh-PGI) of urethral and urinary bladder mucosa coaptation for early continence following RARP. MATERIAL AND METHODS: We performed a prospective comparative study of patients planned for RARP between July 2018 and December 2019 at our centre. A total of 40 patients were enrolled in the study protocol. Following prostatectomy, patients were alternatively assigned into two groups. In one group, urethral and urinary bladder coaptation sutures were placed in a purse string manner using 3-0 Monocryl sutures and none in the another group. All patients underwent standard end to end vesico-urethral anastomosis as described by Van Velthoven. The urinary catheter was removed on day 10 after surgery. All patients were evaluated on day 1, 30 and 90 after catheter removal. RESULTS: The two groups, each with 20 patients, were comparable in terms of age, clinical staging and D'Amico risk classification. The operative time, blood loss and surgical margin positivity were comparable. Following catheter removal, 75% of patients in Group A (Mucosal coaptation) and 50% in Group B (Standard technique) were continent (p = 0.264). At 30 and 90 days, 90% and 95% in Group A and 60% and 80% in Group B reported continence respectively (p-0.078). Four patients in group B reported bothersome incontinence at 90 days follow-up. CONCLUSIONS: Urethral and urinary bladder mucosal coaptation is a simple innovative technique for early continence following RARP.

Immunoglobulin G4-related disease mimicking gallbladder cancer with associated choledochal cyst: A case report of a malignant masquerade.

Immunoglobulin G4 (IgG4)-related disease is a recently described autoimmune disease that can involve diverse organ systems, causing pancreatitis, cholangitis, retroperitoneal fibrosis, and thyroiditis to name a few. Key histological features include storiform fibrosis, obliterative venulitis, and intense inflammatory infiltrate composed of lymphoplasmacytic cells. The disease has a tendency to present with mass-forming lesions, often difficult to differentiate from malignant processes. We report the case of a 48-year-old male from an area endemic for gallbladder cancer (north India). He presented with a short history of abdominal pain and was found to have asymmetric thickening of the gallbladder wall with a soft-tissue mass invading the adjacent liver. In addition, the bile duct was dilated throughout its extent. A clinical and radiological diagnosis of gallbladder cancer with choledochal cyst was made, and the patient underwent radical cholecystectomy with bile duct excision. Histopathology surprisingly demonstrated IgG4-related disease with no evidence of malignancy. Notably, serum levels of immunoglobulins were found to be normal. Preoperative diagnosis was challenging due to the absence of other manifestations. IgG4-related disease is a possible diagnostic pitfall and should be included as a possible differential diagnosis for gallbladder masses.

Insertional Mutagenesis Approaches and Their Use in Rice for Functional Genomics.

Insertional mutagenesis is an indispensable tool for engendering a mutant population using exogenous DNA as the mutagen. The advancement in the next-generation sequencing platform has allowed for faster screening and analysis of generated mutated populations. Rice is a major staple crop for more than half of the world's population; however, the functions of most of the genes in its genome are yet to be analyzed. Various mutant populations represent extremely valuable resources in order to achieve this goal. Here, we have reviewed different insertional mutagenesis approaches that have been used in rice, and have discussed their principles, strengths, and limitations. Comparisons between transfer DNA (T-DNA), transposons, and entrapment tagging approaches have highlighted their utilization in functional genomics studies in rice. We have also summarised different forward and reverse genetics approaches used for screening of insertional mutant populations. Furthermore, we have compiled information from several efforts made using insertional mutagenesis approaches in rice. The information presented here would serve as a database for rice insertional mutagenesis populations. We have also included various examples which illustrate how these populations have been useful for rice functional genomics studies. The information provided here will be very helpful for future functional genomics studies in rice aimed at its genetic improvement.

Mapping the 'Two-component system' network in rice.

Two-component system (TCS) in plants is a histidine to aspartate phosphorelay based signaling system. Rice genome has multifarious TCS signaling machinery comprising of 11 histidine kinases (OsHKs), 5 histidine phosphotransferases (OsHPTs) and 36 response regulators (OsRRs). However, how these TCS members interact with each other and comprehend diverse signaling cascades remains unmapped. Using a highly stringent yeast two-hybrid (Y2H) platform and extensive in planta bimolecular fluorescence complementation (BiFC) assays, distinct arrays of interaction between various TCS proteins have been identified in the present study. Based on these results, an interactome map of TCS proteins has been assembled. This map clearly shows a cross talk in signaling, mediated by different sensory OsHKs. It also highlights OsHPTs as the interaction hubs, which interact with OsRRs, mostly in a redundant fashion. Remarkably, interactions between type-A and type-B OsRRs have also been revealed for the first time. These observations suggest that feedback regulation by type-A OsRRs may also be mediated by interference in signaling at the level of type-B OsRRs, in addition to OsHPTs, as known previously. The interactome map presented here provides a starting point for in-depth molecular investigations for signal(s) transmitted by various TCS modules into diverse biological processes.

Tissue specific and abiotic stress regulated transcription of histidine kinases in plants is also influenced by diurnal rhythm.

Two-component system (TCS) is one of the key signal sensing machinery which enables species to sense environmental stimuli. It essentially comprises of three major components, sensory histidine kinase proteins (HKs), histidine phosphotransfer proteins (Hpts), and response regulator proteins (RRs). The members of the TCS family have already been identified in Arabidopsis and rice but the knowledge about their functional indulgence during various abiotic stress conditions remains meager. Current study is an attempt to carry out comprehensive analysis of the expression of TCS members in response to various abiotic stress conditions and in various plant tissues in Arabidopsis and rice using MPSS and publicly available microarray data. The analysis suggests that despite having almost similar number of genes, rice expresses higher number of TCS members during various abiotic stress conditions than Arabidopsis. We found that the TCS machinery is regulated by not only various abiotic stresses, but also by the tissue specificity. Analysis of expression of some representative members of TCS gene family showed their regulation by the diurnal cycle in rice seedlings, thus bringing-in another level of their transcriptional control. Thus, we report a highly complex and tight regulatory network of TCS members, as influenced by the tissue, abiotic stress signal, and diurnal rhythm. The insights on the comparative expression analysis presented in this study may provide crucial leads toward dissection of diverse role(s) of the various TCS family members in Arabidopsis and rice.

A suite of new genes defining salinity stress tolerance in seedlings of contrasting rice genotypes.

Salinity is one of the major constraints adversely influencing crop productivity. Saltol QTL is a major QTL associated with Na⁺-K⁺ ratio and seedling stage salinity tolerance in rice. With an aim to understand the contribution of individual genes localized within saltol towards salinity tolerance, we analysed the transcript abundance of a set of these genes in seedlings of contrasting genotypes of rice. We hypothesize that this approach may be helpful in identifying new 'candidate genes' for improving salinity tolerance in crops. For this purpose, seedlings of Oryza sativa cv. IR64 (sensitive) and the landrace Pokkali (tolerant) were subjected to short/long durations of salinity. qRT-PCR analysis clearly exhibited differential regulation of genes encoding signaling related protein (SRPs), where higher transcript abundance for most of them was observed in Pokkali than IR64 under non-stress conditions, thereby indicating towards well preparedness of the former to handle stress, in anticipation. Genes encoding proteins of unknown function (PUFs), though, constitute a considerable portion of plant genome, have so far been neglected in most studies. Time course analysis of these genes showed a continuous increase in their abundance in Pokkali, while in IR64, their abundance increased till 24 h followed by a clear decrease, thereby justifying their nomenclature as 'salinity induced factors' (SIFs). This is the first report showing possible involvement of SIFs localized within salinity related QTL towards salinity stress response. Based on the phenotypes of insertional mutants, it is proposed that these SIFs may have a putative function in vegetative growth (SIFVG), fertility (SIFF), viability (SIFV) or early flowering (SIFEF).

Salt overly sensitive pathway members are influenced by diurnal rhythm in rice.

The diurnal rhythm controls many aspects of plant physiology such as flowering, photosynthesis and growth. Rice is one of the staple foods for world's population. Abiotic stresses such as salinity, drought, heat and cold severely affect rice production. Under salinity stress, maintenance of ion homeostasis is a major challenge, which also defines the tolerance level of a given genotype. Salt overly sensitive (SOS) pathway is well documented to play a key role in maintaining the Na(+) homeostasis in plant cell. However, it is not reported yet whether the transcriptional regulation of genes of this pathway are influenced by diurnal rhythm. In the present work, we have studied the diurnal pattern of transcript abundance of SOS pathway genes in rice at seedling stage.To rule out the effect of temperature fluctuations on the expression patterns of these genes, the seedlings were grown under constant temperature. We found that OsSOS3 and OsSOS2 exhibited a rhythmic and diurnal expression pattern, while OsSOS1did not have any specific pattern of expression. This analysis establishes a cross-link between diurnal rhythm and SOS pathway and suggests that SOS pathway is influenced by diurnal rhythm in rice.

Histidine kinases in plants: cross talk between hormone and stress responses.

Two-component signaling pathways involve sensory histidine kinases (HK), histidine phosphotransfer proteins (HpT) and response regulators (RR). Recent advancements in genome sequencing projects for a number of plant species have established the TCS family to be multigenic one. In plants, HKs operate through the His-Asp phosphorelay and control many physiological and developmental processes throughout the lifecycle of plants. Despite the huge diversity reported for the structural features of the HKs, their functional redundancy has also been reported via mutant approach. Several sensory HKs having a CHASE domain, transmembrane domain(s), transmitter domain and receiver domain have been reported to be involved in cytokinin and ethylene signaling. On the other hand, there are also increasing evidences for some of the sensory HKs to be performing their role as osmosensor, clearly indicating toward a possible cross-talk between hormone and stress responsive cascades. In this review, we bring out the latest knowledge about the structure and functions of histidine kinases in cytokinin and ethylene signaling and their role(s) in development and the regulation of environmental stress responses.