Biology subjects

Joshi, A.

Publications and source records attributed to Joshi, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

The evolution of competitive effectiveness and tolerance in populations of Drosophila melanogaster adapted to chronic larval crowding at varying combinations of egg number and food volume

The theory of density-dependent selection posits that genotypic fitness can vary depending on the population density. Several long-term selection experiments on outbred populations of Drosophila adapted to chronically high larval densities have shown that the most common evolutionary response of such rearing is an increase in larval competitive ability. Some authors have proposed that a better understanding of the evolution of competitive ability can be achieved by its partitioning into effectiveness and tolerance components. Effectiveness is the amount of competitive inhibition imposed by a competitor on another, whereas tolerance is the degree to which a competitor can withstand inhibition. In this study, we have explored the evolution of effectiveness and tolerance components of competitive ability using three sets of outbred populations of D. melanogaster adapted to chronic larval crowding at different respective combinations of egg number, food volume and container dimensions. Effectiveness and tolerance were found to be dependent on the particular selection regime, the starting food amount and the trait used as the outcome of competition. Eclosion, dry biomass and dry weight per fly distributions over time indicated that competitive ability can also express itself in a time-dependent manner. The results suggest that larval competition and the evolution of competitive ability in Drosophila are extremely nuanced.

evolutionary biology↗

bioRxiv2023

The role of greater competitive ability in countering age disadvantages in larval competition in Drosophila melanogaster

BackgroundPopulations of Drosophila melanogaster adapted to high larval densities evolve increased larval competitive ability compared to low density controls. However, traits contributing to greater competitive ability can differ across such populations, depending on the exact details of high-density conditions imposed. In the current study, we consider three sets of D. melanogaster populations adapted to three different kinds of high-density scenarios. These population sets have evolved different degrees of increases in egg size and decreases in egg hatching time as correlates of increased larval competitive ability. QuestionWe asked two related questions: O_LIDo populations adapted to larval crowding counter an imposed initial age disadvantage in larval competition, better than their controls? C_LIO_LIDo differences in egg size and egg hatching time among crowding-adapted populations matter in competitive performance when suffering age disadvantage? C_LI Study systemWe used three sets of outbred laboratory Drosophila melanogaster populations selected for larval crowding with different egg number, food volume and vial type combinations (named MCU, CCU and LCU). We also used one set of low-density ancestral control populations (named MB). MethodsWe implemented high density cultures with half the eggs from one of the study (focal) populations, and the other half from a common marked competitor population (Orange Eye: OE). We provided head start durations of 0, 3, 5, or 7 hours to the eggs of the common competitor. This imposed the respective age disadvantage to the larvae of the focal population. Pre-adult development time of survivors was the indicator of competitive performance used. ResultsAll crowding-adapted populations countered an initial age disadvantage better than the control populations. We did not see any differences among crowding adapted populations regarding their performance in countering the age disadvantage. The common competitors showed the best competitive performance against the populations with the greatest egg size and shortest hatching time. ConclusionsAdaptation to crowding leads to significantly better chances against age disadvantages in larval competition. Temporal head starts need not be of overwhelming advantage in larval competition against superior competitors in Drosophila. Among crowding adapted populations, evolving greater egg size and shorter hatching time does not seem to better offset the effects of age disadvantage to larvae. Differences in larval effectiveness and tolerance of the populations are likely to explain these results.

evolutionary biology↗

bioRxiv2023

Development of Specific barcodes for identification of Aloe species based on chloroplast DNA barcoding

DNA barcoding is currently an effective and extensively used tool for species identification. The chloroplast matK (maturase K) and rbcL (Ribulose-bisphosphate large subunit) are one of the most variable coding genes of angiosperms and have been recommended as a universal barcode for land plants. Aloe is a large genus of around 500 species, and most species are widely used for traditional medicinal purposes worldwide, viz., Aloe vera, Aloe ferox, Aloe arborescens, and Aloe maculate. This study evaluated the two chloroplast DNA barcodes (matK and rbcL) to develop a theoretical base for species identification and germplasm conservation of Aloe species. The Maximum Parsimony analysis was conducted to study the evolutionary relatedness of Aloe sequences using matK and rbcL sequences retrieved from the NCBI database. The results revealed that 49 Aloe accessions were segregated into four major clades based on the matK sequence. Likewise, the 29 Aloe accessions were distributed into two major clades based on the rbcL sequence. SNP (Single Nucleotide Polymorphism) site analysis was conducted to obtain the specific barcode of Aloe species and generate the corresponding DNA QR code that electronic devices could immediately recognize. This study provides innovative research methods for efficient species identification of the genus Aloe and indicates the possibility of correctly identifying, discriminating, and documenting the Aloe species.

molecular biology↗

bioRxiv2023

In silico characterization and phylogenetic analysis of Elaeocarpus ganitrus based on ITS2 barcode sequence

Plant molecular systematics relies on using DNA barcodes for studying the evolutionary relationship between species Sequences of the nuclear internal transcribed spacer (ITS) regions have been used widely in molecular phylogenetic studies because of their high variability compared to plastid sequences. Elaeocarpus is a diverse genus within the family Elaeocarpaceae and is widely distributed worldwide among tropical and subtropical climatic zones. Elaeocarpus ganitrus has important medicinal and religious values in India. However, Elaeocarpus ganitrus evolutionary relationship with other Elaeocarpus species is not much explored, especially at the molecular and phylogenetic levels. The present research successfully amplified the nuclear gene ITS2, sequenced and submitted it to NCBI Genbank after using Basic Local Alignment Search Tool (BLAST). Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP) resulted in different numbers of molecular operational taxonomic units (MOTUs). The lowest score of ASAP (4.5) segregated the sequences into 31 MOTUs with the Threshold dist. value of 0.003524. This study establishes an evolutionary relationship between Elaeocarpus ganitrus and other species belonging to the same genus through the neighbor-joining method. The 38 Elaeocarpus samples were clustered into seven major groups based on ITS2 sequence: Group I is represented by Elaeocarpus ganitrus along with Elaeocarpus sylvestris, Elaeocarpus glabripetalus, Elaeocarpus duclouxii, Elaeocarpus decipiens, and Elaeocarpus zollingeri. Group II is characterized by Elaeocarpus austroyunnanensis and Elaeocarpus glaber. Group III comprises Elaeocarpus sphaericus, Elaeocarpus angustifolius, Elaeocarpus grandis, Elaeocarpus ptilanthus, and Elaeocarpus sphaerocarpus. Three accessions of Elaeocarpus hookerianus are placed in group IV. Elaeocarpus largiflorens and Elaeocarpus thelmae represent group V. Groupr VI contains three species: Elaeocarpus sylvestris, Elaeocarpus dubius, and Elaeocarpus johnsonii. Group VII comprises five species which include Elaeocarpus glabripetalus, Elaeocarpus rugosus, Elaeocarpus tuberculatus, Elaeocarpus hainanensis, and Elaeocarpus angustifolius. The study concludes with the possibility of correctly using the ITS2 gene to identify, discriminate, and documentation of Elaeocarpus ganitrus and other species of the same genus.

molecular biology↗

bioRxiv2023

Single-Molecule FRET Illuminates Structural Subpopulations and Dissects Crucial Molecular Events During Phase Separation of a Prion-Like Low Complexity Domain

Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to be associated with a wide range of cellular functions and dysfunctions. We dissect critical molecular events associated with phase separation of an intrinsically disordered prion-like low-complexity domain of Fused in Sarcoma by performing single-molecule studies that permit us to access the wealth of molecular information that is skewed in conventional ensemble experiments. Our single-molecule FRET experiments reveal the coexistence of two conformationally distinct subpopulations in the monomeric form. Single-droplet single-molecule FRET studies coupled with fluorescence correlation spectroscopy, picosecond time-resolved fluorescence anisotropy, and vibrational Raman spectroscopy indicate that structural unwinding switches intramolecular interactions into intermolecular contacts allowing the formation of a dynamic network within condensates. A disease-related mutation introduces enhanced structural plasticity engendering greater interchain interactions that can accelerate pathological aggregation. Our findings provide key mechanistic underpinnings of sequence-encoded dynamically-controlled structural unzipping resulting in biological phase separation.

biophysics↗

bioRxiv2023

The highly conserved stem-loop II motif is dispensable for SARS-CoV-2

The stem-loop II motif (s2m) is a RNA structural element that is found in the 3 untranslated region (UTR) of many RNA viruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over twenty-five years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growth in vitro, or growth and viral fitness in Syrian hamsters in vivo. We also compared the secondary structure of the 3 UTR of wild type and s2m deletion viruses using SHAPE-MaP and DMS-MaPseq. These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2. IMPORTANCERNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contain functional structures to support virus replication, translation and evasion of the host antiviral immune response. The 3 untranslated region of early isolates of SARS-CoV-2 contained a stem-loop II motif (s2m), which is a RNA structural element that is found in many RNA viruses. This motif was discovered over twenty-five years ago, but its functional significance is unknown. We created SARS-CoV-2 with deletions or mutations of the s2m and determined the effect of these changes on viral growth in tissue culture and in rodent models of infection. Deletion or mutation of the s2m element had no effect on growth in vitro, or growth and viral fitness in Syrian hamsters in vivo. We also observed no impact of the deletion on other known RNA structures in the same region of the genome. These experiments demonstrate that the s2m is dispensable for SARS-CoV-2.

microbiology↗

bioRxiv2023

Adaptive Digital Tissue Deconvolution

MotivationThe inference of cellular compositions from bulk and spatial transcriptomics data increasingly complements data analyses. Multiple computational approaches were suggested and recently, machine learning techniques were developed to systematically improve estimates. Such approaches allow to infer additional, less abundant cell types. However, they rely on training data which do not capture the full biological diversity encountered in transcriptomics analyses; data can contain cellular contributions not seen in the training data and as such, analyses can be biased or blurred. Thus, computational approaches have to deal with unknown, hidden contributions. Moreover, most methods are based on cellular archetypes which serve as a reference; e.g., a generic T-cell profile is used to infer the proportion of T-cells. It is well known that cells adapt their molecular phenotype to the environment and that pre-specified cell archetypes can distort the inference of cellular compositions. ResultsWe propose Adaptive Digital Tissue Deconvolution (ADTD) to estimate cellular proportions of pre-selected cell types together with possibly unknown and hidden background contributions. Moreover, ADTD adapts prototypic reference profiles to the molecular environment of the cells, which further resolves cell-type specific gene regulation from bulk transcriptomics data. We verify this in simulation studies and demonstrate that ADTD improves existing approaches in estimating cellular compositions. In an application to bulk transcriptomics data from breast cancer patients, we demonstrate that ADTD provides insights into cell-type specific molecular differences between breast cancer subtypes. Availability and implementationA python implementation of ADTD and a tutorial are available at Gitlab and zenodo (doi:10.5281/zenodo.7548362). Contactmichael.altenbuchinger@bioinf.med.uni-goettingen.de and sushma.grellscheid@uib.no Supplementary informationSupplementary material is available at Bioinformatics online.

bioinformatics↗

bioRxiv2022

ATP modulates self-perpetuating conformational conversion generating structurally distinct yeast prion amyloids that limit autocatalytic amplification

Prion-like self-perpetuating conformational conversion of proteins into amyloid aggregates is associated with both transmissible neurodegenerative diseases and non-Mendelian inheritance. Here, we demonstrate that ATP modulates the formation and dissolution of amyloids from a yeast prion domain (NM domain of Saccharomyces cerevisiae Sup35) and restricts autocatalytic amplification by controlling the amount of fragmentable and seeding-competent aggregates. ATP, at (high) physiological concentrations in the presence of Mg2+, kinetically accelerates NM aggregation. Interestingly, ATP also promotes phase-separation-mediated aggregation of a human protein harboring a yeast prion-like domain. We also show that ATP dose independently disaggregates preformed NM fibrils. Furthermore, high concentrations of ATP delimited the number of seeds by generating compact, ATP-bound NM fibrils that exhibited nominal fragmentation by either free ATP or Hsp104 disaggregase. Additionally, (low) pathological ATP concentrations restricted autocatalytic amplification by forming structurally distinct seeding-inefficient amyloids. Our results provide mechanistic underpinnings of concentration-dependent chemical chaperoning by ATP against prion-like transmissions.

biochemistry↗

bioRxiv2022

Nucleoid-Associated Proteins Undergo Liquid-Liquid Phase Separation with DNA into Multiphasic Condensates Resembling Bacterial Nucleoids

Liquid-liquid phase separation offers unique spatiotemporal control over myriad complex intracellular biochemical processes through compartmentalization of biomolecules into highly dynamic, liquid-like condensates known as membrane-less organelles. The bacterial nucleoid is thought to be one such phase-separated condensate; however, its formation, regulation, and biophysical characteristics are poorly understood. Our super-resolution imaging data suggests that nucleoids are dynamic assemblages of sub-micron-sized liquid-like droplets. We demonstrate that non-sequence-specific Nucleoid-Associated Proteins (NAPs) such as HU-A, HU-B and Dps, accrete nucleic acids and spontaneously condense with them into liquid-like, multicomponent, multiphasic, heterotypic phase-separated droplets. Upon mixing of HU-B, DNA and Dps, HU-B-enriched droplets are seen to contain demixed Dps-enriched droplets. Our findings indicate scope for the possible existence of multiphasic liquid-like compartments within nucleoids, providing insights into bacterial growth phase-dependent variations in the levels of different NAPs.

biophysics↗

bioRxiv2022

Medulloblastoma Group 3 and 4 Tumors Comprise a Clinically and Biologically Significant Expression Continuum Reflecting Human Cerebellar Development

Medulloblastoma is currently sub-classified into distinct DNA methylation subgroups/subtypes with particular clinico-molecular features. Using RNA-seq in large well annotated cohorts of medulloblastoma we show that transcriptionally Group3 and Group4 medulloblastomas exist not as discrete types but as intermediates on a bipolar continuum between archetypal Group3 and Group4 entities. Continuum position is prognostic, reflects propensity for specific DNA copy-number changes, key switches in isoform/enhancer usage and RNA-editing. Examining scRNA-seq profiles we show intra-tumoral transcriptional heterogeneity along the continuum is limited in a subtype-dependent manner. By integrating with a human scRNA-seq reference atlas we show this continuum is mirrored by an equivalent continuum of transcriptional cell types in early fetal cerebellar development. We identify unique developmental niches for all four major subgroups and link each to a common developmental antecedent. Our findings show a transcriptional continuum arising from oncogenic disruption of highly specific fetal cerebellar cell types, linked to almost every aspect of Group3/Group4 molecular biology and clinico-pathology.

cancer biology↗

bioRxiv2022

Density-dependent selection at low food levels leads to the evolution of population stability in Drosophila melanogaster even without a clear r-K trade-off

Density-dependent selection, especially together with r-K trade-offs, has been one of the most plausible suggested mechanisms for the evolution of population stability. However, experimental support for this explanation has been both meagre and mixed. One study with Drosophila melanogaster yielded no evidence for populations adapted to chronic larval crowding having also evolved greater population stability. Another study, on D. ananassae, suggested that populations adapted to larval crowding evolved both greater constancy and persistence stability, and the data also suggested an r-K trade-off in those populations, though the evidence for the latter was not conclusive. Moreover, theoretical work suggested that density-dependent selection could result in the evolution of greater population stability, even in the absence of an r-K trade-off. Here, we show that populations of D. melanogaster, selected for adaptation to larval crowding at very low food amounts per vial, evolve enhanced constancy and persistence stability. The enhanced population stability in the crowding-adapted populations seems to have evolved through the increased equlibrium size (K) and reduced sensitivity of realized population growth rates to density ().There was no clear evidence for reduced intrinsic population growth rate (r) in the more stable crowding-adapted populations. Our study adds to the growing evidence in support of the hypothesis that population stability can evolve in response to density-dependent selection through the evolution of certain life-history traits that are associated with higher K and less negative . We discuss our results in the light of previous work, and suggest that a model-free framework might be of great heuristic value in understanding the evolution of population stability through changes in the density-sensitivity of life-history traits, whether or not these changes result from density-dependent selection.

evolutionary biology↗

bioRxiv2022

Density-dependent selection at high food levels leads to the evolution of persistence but not constancy in Drosophila melanogaster populations

Mechanisms through which population dynamics evolve to be stable have been a subject of considerable interest in population biology. One of the ways through which population stability is likely to evolve is via density-dependent selection with or without an r and K trade-off. In this paper, we test whether the specific combination of egg number and food amount under which density-dependent selection is implemented affects the evolution of population stability attributes in D. melanogaster populations that have evolved under density-dependent selection for 75 generations. Our findings show that these populations have evolved higher persistence stability than controls, although constancy stability did not evolve. Moreover, these populations did not show an r-K trade-off, and evolved persistence largely through a significant decrease in sensitivity of growth rate to population density, especially at densities ranging from medium to the equilibrium population size. Qualitative comparison of these findings with those from another set of crowding-adapted D. melanogaster populations that had evolved both constancy and persistence stability, suggests that the ecology of larval crowding influences the consequent evolution of stability attributes. We discuss previous findings on the evolution of life-history traits to argue that differences in the ecology of density-dependent selection experienced at the larval stage affects population stability differently by altering the sensitivity of population growth rate to population density.

evolutionary biology↗

bioRxiv2022

Effects of larval and adult crowding on fitness components in Drosophila populations adapted to larval crowding experienced under different combinations of food amount and egg number

Since the realization in the 1970s that simple discrete-time population growth models can show complex unstable dynamics of population size, many explanations were proposed for the evolution of enhanced population stability. The most plausible of these was density-dependent selection, suggested to favour greater stability due to r-K trade-offs. However, the first experiment aimed at testing this prediction revealed that Drosophila melanogaster populations adapted to larval crowding did not evolve greater constancy stability than their ancestral controls. A subsequent study showed that D. ananassae populations adapted to larval crowding had evolved greater constancy and persistence than ancestral controls. These D. ananassae populations had experienced chronic larval crowding in conditions of very low amounts of food, whereas the earlier studied D. melanogaster populations had experienced chronic larval crowding at fairly high food amounts. Further theoretical work also suggested that populations adapting to crowding could evolve greater stability even in the absence of r-K trade-offs. Most recently, studies in our laboratory showed that two sets of crowding adapted D. melanogaster populations, derived from a common ancestral lineage, which differed in the food amounts at which they experienced larval crowding, evolved different patterns of constancy and persistence stability. These two sets of populations also differed in the traits, e.g. larval feeding rate, that evolved as they became more competitive. Here, we examine the response of key fitness components to larval and adult densities in these two sets of populations, to see whether differences in their stability attributes can be explained by variation in how their life-histories respond to crowding at different life stages. Of all traits examined, only pre-adult survivorship responded differently to larval density across the two sets of populations. The populations that adapted to larval crowding at low food amounts showed reduced sensitivity of pre-adult survivorship to larval density, compared to those that adapted to larval crowding at high food amounts. We discuss our results in the context of different ways in which density-dependent selection may facilitate the evolution of greater constancy or persistence, depending on the ecological details of how crowding was experienced.

evolutionary biology↗

bioRxiv2022

ACE2 engagement exposes the fusion peptide to pan-coronavirus neutralizing antibodies

Coronaviruses use diverse Spike (S) glycoproteins to attach to host receptors and fuse with target cells. Using a broad screening approach, we isolated from SARS-CoV-2 immune donors seven monoclonal antibodies (mAbs) that bind to all human alpha and beta coronavirus S proteins. These mAbs recognize the fusion peptide and acquire high affinity and breadth through somatic mutations. Despite targeting a conserved motif, only some mAbs show broad neutralizing activity in vitro against alpha and beta coronaviruses, including Omicron BA.1 variant and bat WIV-1, and reduce viral titers and pathology in vivo. Structural and functional analyses show that the fusion peptide-specific mAbs bind with different modalities to a cryptic epitope which is concealed by prefusion-stabilizing 2P mutations and becomes exposed upon binding of ACE2 or ACE2-mimicking mAbs. This study identifies a new class of pan-coronavirus neutralizing mAbs and reveals a receptor-induced conformational change in the S protein that exposes the fusion peptide region.

immunology↗

bioRxiv2022

Prevalence of Bourbon and Heartland viruses in field collected ticks at an environmental field station in St. Louis County, Missouri, USA

Heartland and Bourbon viruses are pathogenic tick-borne viruses putatively transmitted by Amblyomma americanum, an abundant tick species in Missouri. To assess the prevalence of these viruses in ticks, we collected 2778 ticks from 8 sampling sites at Tyson Research Center, an environmental field station within St. Louis County and close to the City of St. Louis, from May - July in 2019 and 2021. Ticks were pooled according to life stage and sex, grouped by year and sampling site to create 355 pools and screened by RT-qPCR for Bourbon and Heartland viruses. Overall, 14 (3.9%) and 27 (7.6%) of the pools were positive for Bourbon virus and Heartland virus respectively. In 2019, 11 and 23 pools were positive for Bourbon and Heartland viruses respectively. These positives pools were of males, females and nymphs. In 2021, there were 4 virus positive pools out of which 3 were positive for both viruses and were comprised of females and nymphs. Five out of the 8 sampling sites were positive for at least one virus. This included a site that was positive for both viruses in both years. Detection of these viruses in an area close to a relatively large metropolis presents a greater public health threat than previously thought.

microbiology↗

bioRxiv2022

Dynamic Synchronization between Hippocampal Spatial Representations and the Stepping Rhythm

Summary paragraphThe hippocampus is a vertebrate brain structure that expresses spatial representations1 and is critical for navigation2,3. Navigation in turn intricately depends on locomotion; however, current accounts suggest a dissociation between hippocampal spatial representations and the details of locomotor processes. Specifically, the hippocampus is thought to primarily represent higher-order cognitive and locomotor variables like position, speed, and direction of movement4-7, while the limb movements that propel the animal are thought to be computed and represented primarily in subcortical circuits, including the spinal cord, brainstem, and cerebellum8-11. Whether hippocampal representations are actually decoupled from the detailed structure of locomotor processes remains unknown. To address this question, we simultaneously monitored hippocampal spatial representations and ongoing limb movements underlying locomotion at fast timescales. We found that the forelimb stepping cycle in freely behaving rats is rhythmic and peaks at ~8 Hz during movement, matching the ~8 Hz organization of information processing in the hippocampus during locomotion12. We also discovered precisely timed coordination between the time at which the forelimbs touch the ground ( plant times of the stepping cycle) and the hippocampal representation of space. Notably, plant times coincide with hippocampal representations closest to the actual position of the animal, while in-between these plant times, the hippocampal representation progresses towards possible future locations. This synchronization was specifically detectable when animals approached upcoming spatial decisions. Taken together, our results reveal profound and dynamic coordination on a timescale of tens of milliseconds between central cognitive representations and peripheral motor processes. This coordination engages and disengages rapidly in association with cognitive demands and is well suited to support rapid information exchange between cognitive and sensory-motor circuits.

neuroscience↗

bioRxiv2022

Single-Droplet Surface-Enhanced Raman Scattering Decodes the Molecular Language of Liquid-Liquid Phase Separation

Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are involved in a myriad of critical cellular functions and debilitating neurodegenerative diseases. Elucidating the role of intrinsic disorder and conformational heterogeneity of intrinsically disordered proteins/regions (IDPs/IDRs) in these phase-separated membrane-less organelles is crucial to understanding the mechanism of formation and regulation of biomolecular condensates. Here we introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that utilizes surface-engineered, plasmonic, metal nanoparticles to unveil the inner workings of mesoscopic liquid droplets of Fused in Sarcoma (FUS) in the absence and presence of RNA. These highly sensitive measurements offer unprecedented sensitivity to capture the crucial interactions, conformational heterogeneity, and structural distributions within the condensed phase in a droplet-by-droplet manner. Such an ultra-sensitive single-droplet vibrational methodology can serve as a potent tool to decipher the key molecular drivers of biological phase transitions of a wide range of biomolecular condensates involved in physiology and disease.

biophysics↗

bioRxiv2022

Ocimum sanctum, OscWRKY1, regulates phenylpropanoid pathway genes and promotes resistance to pathogen infection in Arabidopsis

WRKY transcription factor (TF) family regulates various developmental and physiological functions in plants. PAL genes encode enzymes which are involved in plant defense responses, but the direct regulation of PAL genes and phenylpropanoid pathway through WRKY TFs is not well characterized. In the present study, we have characterized an OscWRKY1 gene from O. sanctum which shows induced expression after methyl jasmonate (MeJA), salicylic acid (SA), and wounding. Recombinant OscWRKY1 protein binds to the W-box cis-element TTGAC[C/T] and activates the reporter gene in yeast. Overexpression of OscWRKY1 enhances Arabidopsis resistance towards Pseudomonas syringae pv. tomato Pst DC3000. Upstream activator sequences of PAL and C4H have identified the conserved W-box cis-element (TTGACC) in both O. sanctum and Arabidopsis. OscWRKY1 was found to interact with W-box cis-element present in the PAL and C4H promoters. Silencing of OscWRKY1 using VIGS resulted in reduced expression of PAL, C4H, COMT, F5H and 4CL transcripts. OscWRKY1 silenced plants exhibit reduced PAL activity, whereas, the overexpression lines of OscWRKY1 in Arabidopsis exhibit increased PAL activity. These results revealed that OscWRKY1 positively regulates the phenylpropanoid pathway genes and enhances the resistance against bacterial pathogen in Arabidopsis.

plant biology↗