Biology subjects

Singh, A.

Publications and source records attributed to Singh, A..

At least 415 records · Page 23Linked to original sources

bioRxiv2022

Inhibition of early-acting autophagy genes in C. elegans neurons improves protein homeostasis, promotes exopher production, and extends lifespan via the ATG-16.2 WD40 domain

While autophagy is key to maintain cellular homeostasis, tissue-specific roles of individual autophagy genes are less understood. To study neuronal autophagy in vivo, we inhibited autophagy genes specifically in C. elegans neurons, and unexpectedly found that knockdown of early-acting autophagy genes, i.e., involved in formation of the autophagosome, except for atg-16.2, decreased PolyQ aggregates and increased lifespan, albeit independently of the degradation of autophagosomal cargo. Neuronal aggregates can be secreted from neurons via vesicles called exophers, and we found that neuronal inhibition of early-acting autophagy genes atg-7 and lgg-1/Atg8, but not atg-16.2 increased exopher formation. Moreover, atg-16.2 mutants were unable to form exophers, and atg-16.2 was required for the effects of early autophagy gene reduction on neuronal PolyQ aggregation, exopher formation, and lifespan. Notably, neuronal expression of full-length ATG-16.2 but not ATG-16.2 without a functional WD40 domain, important for non-canonical functions of ATG16L1 in mammalian cells, restored these phenotypes. Collectively, we discovered a specific role for C. elegans ATG-16.2 and its WD40 domain in exopher biogenesis, neuronal proteostasis, and lifespan determination, highlighting a possible role for non-canonical autophagy functions in both exopher formation and in aging.

cell biology↗

bioRxiv2022

Capturing long-tailed individual tree diversity using an airborne multi-temporal hierarchical model

Measuring forest biodiversity using terrestrial surveys is expensive and can only capture common species abundance in large heterogeneous landscapes. In contrast, combining airborne imagery with computer vision can generate individual tree data at the scales of hundreds of thousands of trees. To train computer vision models, ground-based species labels are combined with airborne reflectance data. Due to the difficulty of finding rare species in a large landscape, the majority of classification models only include the most abundant species, leading to biased predictions at broad scales. Extending classification models to include rare species requires targeted data collection and algorithmic improvements to overcome large data imbalances between dominant and rare taxa. In addition, large landscapes often require multiple acquisition events, leading to significant within-species variation in reflectance spectra. Using a multi-temporal hierarchical model, we demonstrate the ability to include species predicted at less than 1% frequency in landscape without losing performance on the dominant species. The final model has over 75% accuracy for 14 species with improved rare species classification compared to a baseline deep learning model. After filtering out dead trees, we generate landscape species maps of individual crowns for over 670,000 individual trees at the Ordway Swisher Biological Station within the National Ecological Observatory Network. We estimate the relative abundance of the species within the landscape and provide three measures of uncertainty to generate a range of counts for each species. These maps provide the first estimates of canopy tree diversity within NEON sites to include rare species and provide a blueprint for capturing tree diversity using airborne computer vision at broad scales.

ecology↗

bioRxiv2022

Stress Combinations and their Interactions inPlants Database (SCIPDb): A one-stop resource for understanding combined stress responses in plants

We have developed Stress Combinations and their Interactions in Plants Database (SCIPDb; http://www.nipgr.ac.in/scipdb.php), a compendium and interactive platform offering information on both morpho-physio-biochemical (phenome) and molecular (transcriptome) responses of plants to different combinations of stresses. To delineate the effects of various stress combinations/categories on yield in major agricultural crops, global phenome data from 939 studies was analyzed and results showed that yield was affected to the greatest extent under the abiotic-abiotic stress category, followed by the biotic-biotic and abiotic-biotic stress categories. In the abiotic-abiotic stress category, drought-heat, heat-salinity, and ozone-UV are the major stress combinations causing high yield loss in barley, wheat, soybean, and quinoa crops. In the abiotic-biotic stress category, the salinity-weed stress combination causes highest yield loss in rice crop. In the biotic-biotic stress category, the nematode-fungus combination was most detrimental, causing considerable yield losses in potato, groundnut, and sugar beet crops. Transcriptome datasets from 36 studies hosted in SCIPDb identified novel genes. Thus far, these genes have not been known to play a role in combined stress. Integretome analysis under combined drought-heat stress pinpointed carbohydrate, amino acid, and energy metabolism pathways as the crucial metabolic, proteomic, and transcriptional components in plant tolerance to combined stress. These examples illustrate the application of SCIPDb in identifying novel genes and pathways involved in combined stress tolerance. Further, we showed the application of this database in identifying novel candidate genes and pathways for combined drought and pathogen stress tolerance in Arabidopsis and chickpea. To our knowledge, SCIPDb is the only publicly available platform that provides extensive information and paves the way for advancing mechanistic understanding of plant responses to combined stresses.

plant biology↗

bioRxiv2022

T-cell receptor specific protein language model for prediction and interpretation of epitope binding (ProtLM.TCR)

The cellular adaptive immune response relies on epitope recognition by T-cell receptors (TCRs). We used a language model for TCRs (ProtLM.TCR) to predict TCR-epitope binding. This model was pre-trained on a large set of TCR sequences (~62.106) before being fine-tuned to predict TCR-epitope bindings across multiple human leukocyte antigen (HLA) of class-I types. We then tested ProtLM.TCR on a balanced set of binders and non-binders for each epitope, avoiding model shortcuts like HLA categories. We compared pan-HLA versus HLA-specific models, and our results show that while computational prediction of novel TCR-epitope binding probability is feasible, more epitopes and diverse training datasets are required to achieve a better generalized performances in de novo epitope binding prediction tasks. We also show that ProtLM.TCR embeddings outperform BLOSUM scores and hand-crafted embeddings. Finally, we have used the LIME framework to examine the interpretability of these predictions.

bioinformatics↗

bioRxiv2022

Trabecular bone remodeling in the ageing mouse: a micro-multiphysics agent-based in silico model using cell-type-specific mechanomic profiles

Bone remodeling is regulated by the interaction between different cells and tissues across many spatial and temporal scales. Notably, in silico models are regarded as powerful tools to further understand the signaling pathways that regulate this intricate spatial cellular interplay. To this end, we have established a 3D multiscale micro-multiphysics agent-based (micro-MPA) in silico model of trabecular bone remodeling using longitudinal in vivo data from the sixth caudal vertebra (CV6) of PolgA(D257A/D257A) mice, a mouse model of premature aging. Our model includes a variety of cells as single agents and receptor-ligand kinetics, mechanomics, diffusion and decay of cytokines which regulate the cells behavior. We highlighted its capabilities by simulating trabecular bone remodeling in the CV6 of 5 mice over 4 weeks and we evaluated the static and dynamic morphometry of the trabecular bone microarchitecture. Based on the progression of the average trabecular bone volume fraction (BV/TV), we identified a configuration of the model parameters to simulate homeostatic trabecular bone remodeling, here named basal. Crucially, we also produced anabolic, anti-anabolic, catabolic and anti-catabolic responses with an increase or decrease by one standard deviation in the levels of osteoprotegerin (OPG), receptor activator of nuclear factor kB ligand (RANKL), and sclerostin (Scl) produced by the osteocytes. Our results showed that changes in the levels of OPG and RANKL were positively and negatively correlated with the BV/TV values after 4 weeks in comparison to basal levels, respectively. Conversely, changes in Scl levels produced small fluctuations in BV/TV in comparison to the basal state. From these results, Scl was deemed to be the main driver of equilibrium while RANKL and OPG were shown to be involved in changes in bone volume fraction with potential relevance for age-related bone features. Ultimately, this micro-MPA model provides valuable insights into how cells respond to their local mechanical environment and can help to identify critical pathways affected by degenerative conditions and ageing.

bioengineering↗

bioRxiv2022

Rate of neuronal turnover in the healthy adult murine myenteric ganglia varies with ganglia size

Maintenance of normal structure of the enteric nervous system (ENS), which regulates key gastrointestinal functions, requires robust homeostatic mechanisms, since by virtue of its location within the gut wall, the ENS is subject to constant mechanical, chemical, and biological stressors. Using transgenic and thymidine analogue-based experiments, we previously discovered that neuronal turnover - where continual neurogenesis offsets ongoing neuronal loss at steady state - represents one such mechanism. Although other studies confirmed that neuronal death continues into adulthood in the myenteric plexus of the enteric nervous system (ENS), the complicated nature of thymidine analogue presents challenges in substantiating the occurrence of adult neurogenesis. Therefore, its vital to employ alternative, well-recognized techniques to substantiate the existence of adult enteric neurogenesis in the healthy gut. Here, by using established methods of assessing nuclear DNA content and detecting known mitotic marker phosphor-histone H3 (pH3) in Hu+ adult ENS cells, we show that [~]10% of adult murine small intestinal myenteric Hu+ cells, and [~]20% of adult human small intestinal myenteric Hu+ cells show evidence of mitosis and hence are cycling neuroblasts. We observe that proportions of Hu+ cycling neuroblasts in the adult murine ENS neither vary with ganglia size, nor do they differ significantly between two intestinal regions - duodenum and ileum, or between sexes. Confocal microscopy provides further evidence of cytokinesis in Hu+ cells. The presence of a significant population of cycling neuroblasts in adult ENS provide further evidence of steady state neurogenesis in the adult ENS.

neuroscience↗

bioRxiv2022

Targeting host protein G3BP1 for the discovery of novel antiviral inhibitors against the Chikungunya virus

Molecular interactions of Chikungunya virus (CHIKV) nsP3 with the host G3BP1 stress granule (SG) protein is crucial for CHIKV replication. NsP3 binds to the nuclear transport factor 2 (NTF2)-like domain of G3BP1 via its two FGDF motifs, unsettling SGs formation. The present study identified seven small molecules targeting the FGDF binding pocket of G3BP1 using structure-based computer-aided drug discovery. All seven molecules exhibited good binding affinities in the range of [~]3.4 to [~]98M towards NTF2-like G3BP1 domain. Furthermore, identified molecules demonstrate dose-dependent inhibition in CHIKV infected Vero cells (EC50: 0.40 to 7.39{micro}M), and reduced SGs formation in these cells. These results highlight G3BP1 protein as a potential CHIKV therapeutic target and offer potential prospective for developing treatment for CHIKV disease.

microbiology↗

bioRxiv2022

Pyrophosphoproteomics: extensive protein pyrophosphorylation revealed in human cell lines

Reversible protein phosphorylation is a central signaling mechanism in eukaryotic cells. While the identification of canonical phosphorylation sites using mass-spectrometry (MS) based proteomics has become routine, annotation of non-canonical phosphorylation has remained a challenge. Here, we report a tailored pyrophosphoproteomics workflow to detect and reliably assign protein pyrophosphorylation in two human cell lines, providing the first direct evidence of endogenous protein pyrophosphorylation. Detection of protein pyrophosphorylation was reproducible, specific and consistent with previous biochemical evidence relating the installation of the modification to inositol pyrophosphates (PP-InsPs). We manually validated 148 pyrophosphosites across 71 human proteins, the most heavily pyrophosphorylated of which were the nucleolar proteins NOLC1 and TCOF1. A predictive workflow based on the MS data set was established to recognize putative pyrophosphorylation sequences, and UBF1, a nucleolar protein incompatible with the proteomics method, was biochemically shown to undergo pyrophosphorylation. When the biosynthesis of PP-InsPs was perturbed in a model cell line, proteins expressed in this background exhibited lower levels of pyrophosphorylation. Disruption of PP-InsP biosynthesis also significantly reduced rDNA transcription, potentially by lowering pyrophosphorylation on regulatory proteins NOLC1, TCOF1, and UBF1. Overall, protein pyrophosphorylation emerges as an archetype of non-canonical phosphorylation, and should be considered in future phosphoproteomic analyses.

biochemistry↗

bioRxiv2022

Escherichia coli cells are primed for survival before lethal antibiotic stress

Non-genetic factors can cause significant fluctuations in gene expression levels. Regardless of growing in a stable environment, this fluctuation leads to cell-to-cell variability in an isogenic population. This phenotypic heterogeneity allows a tiny subset of bacterial cells in a population, referred to as persister cells, to tolerate long-term lethal antibiotic effects by entering into a non-dividing, metabolically altered state. One fundamental question is whether this heterogeneous persister population is due to a pre-existing genetic mutation or a result of a transiently-primed reversible cell state. To explore this, we tested clonal populations starting from a single cell using a modified Luria-Delbruck fluctuation test. Through we kept the conditions the same, the diversity in persistence level among clones was relatively consistent: varying from [~]60-100 and [~]40-70 fold for ampicillin (Amp) and apramycin (Apr), respectively. Then we divided and diluted each clone to observe whether the same clone had comparable persister levels for more than one generation. Replicates had similar persister levels even when clones were divided, diluted by 1:20, and allowed to grow for [~]5 generations. This result explicitly shows a cellular memory passed on for generations and eventually lost when cells are diluted to 1:100 and regrown (>7 generations). Our result demonstrates 1) the existence of a small population prepared for stress ("primed cells") resulting in higher persister numbers, 2) the primed memory state is reproducible and transient, passed down for generations but eventually lost, and 3) a heterogeneous persister population is a result of a transiently-primed reversible cell state and not due to a pre-existing genetic mutation.

synthetic biology↗

bioRxiv2022

The N-terminal domain of the human mitochondrial helicase Twinkle has DNA binding activity crucial for supporting processive DNA synthesis by Polymerase γ

Twinkle is the ring-shaped replicative helicase within the human mitochondria with high homology to bacteriophage T7 gp4 helicase-primase. Unlike many orthologs of Twinkle, the N-terminal domain (NTD) of human Twinkle has lost its primase activity through evolutionarily acquired mutations. The NTD has demonstrated no observed activity thus far, hence its role has remained unclear. In this study, we have biochemically characterized the isolated NTD and C-terminal domain with linker (CTD) to decipher their contributions to the activities of the full-length (FL) Twinkle. This novel CTD construct hydrolyzes ATP, has weak DNA unwinding activity, and assists Pol{gamma}-catalyzed strand-displacement synthesis on short replication forks. However, CTD fails to promote multi-kilobase length product formation by Pol{gamma} in rolling-circle DNA synthesis. Thus, CTD retains all the motor functions but struggles to implement them for processive translocation. We show that NTD has DNA binding activity, and its presence stabilizes Twinkle oligomerization. The CTD oligomerizes on its own, but loss of NTD results in heterogeneously-sized oligomeric species. The CTD also exhibits weaker and salt-sensitive DNA binding compared to FL Twinkle. Based on these results, we propose that NTD directly contributes to DNA binding and holds the DNA in place behind the central channel of the CTD like a doorstop, preventing helicase slippages and sustaining processive unwinding. Consistent with this model, mtSSB compensate for the NTD loss and partially restore kilobase length DNA synthesis by CTD and Pol{gamma}. The implications of our studies are foundational for understanding the mechanisms of disease-causing Twinkle mutants that lie in the NTD.

biochemistry↗

bioRxiv2022

HIV-1 Vpr induces ciTRAN to prevent transcriptional silencing of the provirus

The functional relevance of circular RNA (circRNA) expression in HIV-1 infection remains unclear. By developing a customized protocol involving direct RNA nanopore sequencing here, we captured circRNAs in their native state from HIV-1 infected T cells and identified ciTRAN, a circRNA modulator of HIV-1 Transcription. We show that HIV-1 infection of monocytic, T cell lines and primary CD4+ T cells induces ciTRAN expression in a Vpr-dependent manner. ciTRAN protein interactome analysis by proximity biotinylation and mass spectrometry identified SRSF-1 as a prominent interactor of the circular RNA. SRSF-1 is known to negatively regulate HIV-1 transcription, which the virus overcomes by a yet unknown mechanism. We demonstrate that HIV-1 Vpr induced ciTRAN sequesters SRSF1 away from the viral transcriptional complex to promote efficient viral transcription. Accordingly, ciTRAN depletion by CRISPR-Cas phenocopied the effects of SRSF1 overexpression and improved SRSF1 association with HIV-1 transcriptional complex. Finally, we show that an SRSF-1-inspired competing peptide can inhibit HIV-1 transcription regardless of ciTRAN induction. The hijacking of a host circRNA thus represents a new facet of primate lentiviruses in overcoming transmission bottlenecks.

microbiology↗

bioRxiv2022

Dynamic growth re-orientation orchestrates flatness in the Arabidopsis leaf

The growth and division of cells in plant leaves is highly dynamic in time and space, even though cells cannot move relative to their neighbors. Thus, organ shape must emerge from carefully coordinated growth, especially in leaves that remain relatively flat as they grow. Here we explored the phenotype of the jagged and wavy (jaw-D) mutant in Arabidopsis thaliana, in which the leaves do not remain flat. It has previously been shown that the jaw-D mutant phenotype is caused by the overexpression of miR319, which represses TCP transcription factors, thus delaying maturation of the leaf. We analyzed cell dynamics in wild type and jaw-D by performing time lapse live imaging of developing leaves. We found that the progression of maturation from the tip of the leaf downward was delayed in jaw-D relative to wild type based on several markers of maturation, in agreement with the role of TCP transcription factors in promoting maturation. We further found that these changes in maturation were accompanied by differences in the coordination of growth across the leaf, particularly across the medial-lateral axis, causing growth conflicts that prevent the leaf from remaining flat. Although leaf flatness is often framed as a problem that requires the local synchronization of growth on the abaxial vs adaxial sides of the leaf, our results based on the jaw-D phenotype suggest that wild-type plants also need to coordinate growth more globally across the leaf blade to maintain flatness.

plant biology↗

bioRxiv2022

Quantifying noise modulation from coupling of stochastic expression to cellular growth: An analytical approach

The overexpression of many proteins can often have a detrimental impact on cellular growth. This expression-growth coupling leads to positive feedback - any increase of intracellular protein concentration reduces the growth rate of cell size expansion that in turn enhances the concentration via reduced dilution. We investigate how such feedback amplifies intrinsic stochasticity in gene expression to drive a skewed distribution of the protein concentration. Our results provide an exact solution to this distribution by analytically solving the Chapman-Kolmogorov equation, and we use it to quantify the enhancement of noise/skewness as a function of expression-growth coupling. This analysis has important implications for the expression of stress factors, where high levels provide protection from stress, but come at the cost of reduced cellular proliferation. Finally, we connect these analytical results to the case of an actively degraded gene product, where the degradation machinery is working close to saturation.

systems biology↗

bioRxiv2022

YAP/TAZ inactivation with simvastatin attenuates glucocorticoid-induced human trabecular meshwork cell dysfunction

PurposeImpairment of the trabecular meshwork (TM) is the principal cause of increased outflow resistance in the glaucomatous eye. Yes-associated protein (YAP) and transcriptional coactivator with PDZ binding motif (TAZ) are emerging as potential mediators of TM cell/tissue dysfunction. Furthermore, YAP/TAZ activity was recently found to be controlled by the mevalonate pathway in non-ocular cells. Clinically-used statins block the mevalonate cascade and were shown to improve TM cell pathobiology; yet, the link to YAP/TAZ signaling was not investigated. In this study, we hypothesized that YAP/TAZ inactivation with simvastatin attenuates glucocorticoid-induced human TM (HTM) cell dysfunction. MethodsPrimary HTM cells were seeded atop or encapsulated within bioengineered extracellular matrix (ECM) hydrogels. Dexamethasone was used to induce a pathologic phenotype in HTM cells in the absence or presence of simvastatin. Changes in YAP/TAZ activity, actin cytoskeletal organization, phospho-myosin light chain levels, hydrogel contraction/stiffness, and fibronectin deposition were assessed. ResultsSimvastatin potently blocked pathologic YAP/TAZ nuclear localization/activity, actin stress fiber formation, and myosin light chain phosphorylation in HTM cells. Importantly, simvastatin co-treatment significantly attenuated dexamethasone-induced ECM contraction/stiffening and extracellular fibronectin deposition. Sequential treatment was similarly effective but did not match clinically-used Rho kinase inhibition. ConclusionsYAP/TAZ inactivation with simvastatin attenuates HTM cell pathobiology in a tissue-mimetic ECM microenvironment. Our data may help explain the association of statin use with a reduced risk of developing glaucoma via indirect YAP/TAZ inhibition as a proposed regulatory mechanism.

cell biology↗

bioRxiv2022

Bat pluripotent stem cells reveal unique entanglement between host and viruses

Bats have evolved features unique amongst mammals, including flight, laryngeal echolocation, and certain species have been shown to have a unique immune response that may enable them to tolerate viruses such as SARS-CoVs, MERS-CoVs, Nipah, and Marburg viruses. Robust cellular models have yet to be developed for bats, hindering our ability to further understand their special biology and handling of viral pathogens. To establish bats as new model study species, we generated induced pluripotent stem cells (iPSCs) from a wild greater horseshoe bat (Rhinolophus ferrumequinum) using a modified Yamanaka protocol. Rhinolophids are amongst the longest living bat species and are asymptomatic carriers of coronaviruses, including one of the viruses most closely related to SARS-CoV-2. Bat induced pluripotent stem (BiPS) cells were stable in culture, readily differentiated into all three germ layers, and formed complex embryoid bodies, including organoids. The BiPS cells were found to have a core pluripotency gene expression program similar to that of other species, but it also resembled that of cells attacked by viruses. The BiPS cells produced a rich set of diverse endogenized viral sequences and in particular retroviruses. We further validated our protocol by developing iPS cells from an evolutionary distant bat species Myotis myotis (greater mouse-eared bat) non-lethally sampled in the wild, which exhibited similar attributes to the greater horseshoe bat iPS cells, suggesting that this unique pluripotent state evolved in the ancestral bat lineage. Although previous studies have suggested that bats have developed powerful strategies to tame their inflammatory response, our results argue that they have also evolved mechanisms to accommodate a substantial load of endogenous viral sequences and suggest that the natural history of bats and viruses is more profoundly intertwined than previously thought. Further study of bat iPS cells and their differentiated progeny should advance our understanding of the role bats play as virus hosts, provide a novel method of disease surveillance, and enable the functional studies required to ascertain the molecular basis of bats unique traits.

developmental biology↗

bioRxiv2022

UBA52 attunes VDAC1-mediated mitochondrial dysfunction and dopaminergic neuronal death

Mitochondrial homeostasis regulates energy metabolism, calcium buffering, cell function and apoptosis. The present study has been conducted to investigate the implications of ubiquitin-encoding gene UBA52 in mitochondrial physiology. Transient expression of Myc-UBA52 in neurons significantly inhibited the rotenone-induced increase in reactive oxygen species generation, nitrite level and depleted glutathione level. Mass spectrometric and co-immunoprecipitation data suggested the profound interaction of UBA52 with mitochondrial outer membrane channel protein, VDAC1 in both the wild-type and Myc--synuclein overexpressed neuronal cells and in the Parkinsons disease (PD)-specific substantia nigra and striatal region of the rat brain. In vitro ubiquitylation assay revealed that UBA52 participates in the ubiquitylation of VDAC1 through E3 ligase CHIP. Myc-UBA52 overexpression in neurons further improved the mitochondrial functionality and cell viability by preventing the alteration in mitochondrial membrane potential, mitochondrial complex-I activity, translocation of cytochrome-c and p-Nrf2 along with effect on intracellular calcium uptake, thus collectively inhibiting the opening of mitochondrial permeability transition pore. Additionally, Myc-UBA52 expression in neuronal cells offered protection against apoptotic and autophagic cell death. Altogether, our findings delineate functional association between UBA52 and mitochondrial homeostasis, providing new insights into the deterrence of dopaminergic cell death during acute PD pathogenesis.

neuroscience↗

bioRxiv2022

Transcription factor TFII-I fine tunes innate properties of B lymphocytes

The ubiquitously expressed transcription factor TFII-I is a multifunctional protein with pleiotropic roles in gene regulation. TFII-I associated polymorphisms are implicated in Sjogrens syndrome and Lupus in humans and, germline deletion of the Gtf2i gene in mice leads to embryonic lethality. Here we report a unique role for TFII-I in homeostasis of innate properties of B lymphocytes. Loss of Gtf2i in murine B lineage cells leads to a change in transcriptome and chromatin landscape, which resembles myeloid-like features and coincides with enhanced sensitivity to LPS induced transcription. TFII-I deficient B cells also show increased switching to IgG3, a phenotype associated with inflammation. These results demonstrate a role for TFII-I in maintaining immune homeostasis and provide clues for GTF2I polymorphisms associated with B cell dominated autoimmune diseases in humans.

immunology↗

bioRxiv2022

Deep phylotaxonogenomic revision of the genus Xanthomonas within family Xanthomonadaceae and proposal of novel family Frateuriaceae within order Xanthomonadales

Genus Xanthomonas is primarily comprise phytopathogenic species. In a recent study by carrying out deep phyto-taxonogenomics, we reported that even the genera Xylella, Stenotrophomonas and Pseudoxanthomonas are miss-classified and belong to genus Xanthomonas. Hence to understand the breadth of the genus, we carried out deep phylo-taxonogenomics of the order Xanthomonadales. Such investigation revealed that at least four more genera belong to genus Xanthomonas with prominent being Lysobacter. Further order level deep phylo-taxonogenomics revealed two major families. One being the original family Xanthomonadaceae and other is proposed as Frateuriaceae fam. nov. as synonym of family Rhodanobacteraceae with novel genus Frateuria gen. nov.

microbiology↗