Biology subjects

Singh, A. K.

Publications and source records attributed to Singh, A. K..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Dual localization of JA receptor, CaCOI2, explains JA perception dynamics in chickpea

Jasmonates (JAs) form a group of oxylipin-derived phytohormones involved in multiple biotic and abiotic stress responses and regulate plant development. JAs are perceived by the receptor proteins, COI (coronatine insensitive). These JA receptors encoding F-box protein, form SCFCOI ubiquitin ligase complex (Skp, Cullin, F-box) and activate JA signaling by facilitating degradation of the transcriptional repressor (JAZ; Jasmonate associated ZIM domain containing) proteins through 26S proteasomal pathway. However, JA signaling is poorly understood in chickpea, a vital legume plant. Here, we first identified two putative chickpea JA receptor named CaCOI1, CaCOI2 and demonstrated CaCOI2 as a functional JA receptor. Further subcellular localization studies revealed that CaCOI2 is localized to extra-nuclear region and move to the nucleus on JA perception to activate JA signaling. Using domain swapping (between CaCOI1 and CaCOI2) experiments, we have demonstrated that the LRR region of JA receptors, which interact with bioactive JA i.e., JA-Ile, also plays a critical role in regulating subcellular localization of CaCOI proteins. We report that an acidic amino acid in F-box region of COI proteins (AtCOI1T29) stabilizes COI-InsP8 (1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6) tetrakisphosphate) interaction. This interaction is found to be critical for COI-JAZ interaction and therefore, their functionality. Our study thus identified a functional JA receptor in chickpea and revealed novel aspects of JA signaling and perception, which might also have implications in other plants.

plant biology↗

bioRxiv2023

Loss of cis-PTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma

Obesity-linked fatty liver is a significant risk factor for hepatocellular carcinoma (HCC)1,2; however, the molecular mechanisms underlying the transition from non-alcoholic fatty liver disease (NAFLD) to HCC remains unclear. The present study explores the role of the endoplasmic reticulum (ER)-associated protein NgBR, an essential component of the cis-prenyltransferases (cis-PTase) enzyme3, in chronic liver disease. Here we show that genetic depletion of NgBR in hepatocytes of mice (N-LKO) intensifies triacylglycerol (TAG) accumulation, inflammatory responses, ER/oxidative stress, and liver fibrosis, ultimately resulting in HCC development with 100% penetrance after four months on a high-fat diet. Comprehensive genomic and single cell transcriptomic atlas from affected livers provides a detailed molecular analysis of the transition from liver pathophysiology to HCC development. Importantly, pharmacological inhibition of diacylglycerol acyltransferase-2 (DGAT2), a key enzyme in hepatic TAG synthesis, abrogates diet-induced liver damage and HCC burden in N-LKO mice. Overall, our findings establish NgBR/cis-PTase as a critical suppressor of NAFLD-HCC conversion and suggests that DGAT2 inhibition may serve as a promising therapeutic approach to delay HCC formation in patients with advanced non-alcoholic steatohepatitis (NASH).

cancer biology↗

bioRxiv2023

Archaeal origin translation proofreader imparts multialdehyde stress tolerance to land plants

Aldehydes, being an integral part of carbon metabolism, energy generation and signalling pathways, are ingrained in plant physiology. Land plants have developed intricate metabolic pathways which involve production of reactive aldehydes and its detoxification to survive harsh terrestrial environments. Here, we show that physiologically produced aldehydes i.e., formaldehyde and methylglyoxal in addition to acetaldehyde, generate adducts with aminoacyl-tRNAs, a substrate for protein synthesis. Plants are unique in possessing two distinct chiral proofreading systems, D-aminoacyl-tRNA deacylase1 (DTD1) and DTD2, of bacterial and archaeal origins, respectively. Extensive biochemical analysis revealed that only archaeal DTD2 can remove the stable D-aminoacyl adducts on tRNA thereby shielding archaea and plants from these system-generated aldehydes. Using Arabidopsis as a model system, we have shown that the loss of DTD2 gene renders plants susceptible to these toxic aldehydes as they generate stable alkyl modification on D-aminoacyl-tRNAs, which are recycled only by DTD2. Bioinformatic analysis identifies the expansion of aldehyde metabolising repertoire in land plant ancestors which strongly correlates with the recruitment of archaeal DTD2. Finally, we demonstrate that the overexpression of DTD2 offers better protection against aldehydes than in wild-type Arabidopsis highlighting its role as a multi-aldehyde detoxifier that can be explored as a transgenic crop development strategy.

plant biology↗

bioRxiv2023

Oral administration of a specific p300/CBP Lysine acetyltransferase activator induces synaptic plasticity and repairing spinal cord injury

TTK21 is a small molecule activator of p300/CBP acetyltransferase activity, which upon conjugation with glucose-derived carbon nanosphere (CSP) can efficiently cross the blood-brain barrier and activate histone acetylation in the brain. Its role in adult neurogenesis and retention of long-term spatial memory upon intraperitoneal (IP) administration is well established. In this study, we have successfully demonstrated that CSP-TTK21 can be effectively administered via oral gavage. Using a combination of molecular biology, microscopy, and electrophysiological techniques, we systematically investigated the comparative efficacy of oral administration of CSP and CSP-TTK21 in wild-type mice, evaluating their functional effects in comparison to intraperitoneal (IP) administration. Our findings indicate that CSP-TTK21, when administered orally, induces long-term potentiation in the hippocampus without significantly altering basal synaptic transmission, a response comparable to that achieved through IP injection. Remarkably, in a spinal cord injury model, oral administration of CSP-TTK21 exhibits equivalent efficacy to IP administration. Furthermore, our research demonstrates that oral delivery of CSP-TTK21 leads to improvements in motor functions, histone acetylation dynamics, and increased expression of regeneration associated genes (RAGs) in a spinal injury rat model, mirroring the effectiveness of IP administration. Collectively, these results underscore the potential utility of CSP as an oral drug delivery system, particularly for targeting the neural system.

neuroscience↗

bioRxiv2023

Base Excision Repair Pathway Regulates Transcription-Replication Conflicts in Pancreatic Ductal Adenocarcinoma

Oncogenic mutations (such as in KRAS) can dysregulate transcription and replication leading to transcription conflicts (TRCs). Unresolved TRCs can cause lethal DNA damage. Here, we sought to investigate the oncogene dependency of TRCs and TRC regulatory pathways in pancreatic ductal adenocarcinoma (PDAC). Human PDAC demonstrated 30-120-fold higher levels of TRC genomic signatures compared to breast, colon and lung cancer (p<0.001). TRCs were significantly enriched in human PDAC cells (Panc-1, BxPC3, MiaPaca2) compared to immortalized human pancreatic ductal epithelial (HPNE). Ectopic oncogenic KRAS(G12D) in HPNE cells enhanced TRCs, and TRC-related DNA:RNA hybrids (R-loops). Inhibition of KRAS or downstream effectors abrogated TRCs in Panc1 and MiaPaca2 cells. An siRNA screen identified several factors in the base-excision repair pathway as regulators of TRCs. In pharmacologic validation, inhibitors of APE1 endonuclease in BER pathway (Methoxyamine and CRT) enhanced TRCs. Mechanistic studies revealed that BER pathway inhibition severely altered RNA polymerase II dynamics at nascent DNA; causing RNAPII trapping and contributing to enhanced TRCs. The ensuing DNA damage activated Chk2-ATR pathway but not Chk1-ATM pathway. Co-treatment with ATR inhibitor (VX970) and BER inhibitor (methoxyamine) at clinically relevant doses, synergistically enhanced DNA damage and reduced cell proliferation in PDAC cells. The study uncovers a novel role of BER pathway defects and oxidative DNA damage in promoting TRCs. Our studies provide mechanistic insights into the regulation of TRCs in PDAC which has implications for genome instability and therapy in PDAC.

cancer biology↗

bioRxiv2023

Insights into the genomic features, lifestyle and therapeutic potential of B1 sub-cluster mycobacteriophages

BackgroundA large number (about 1200) of mycobacteriophages (phages) have been isolated on Mycobacterium smegmatis mc2155. Their genome analysis shows high sequence diversity; therefore, based on nucleotide sequence similarity and genomic architecture, the related phages have been grouped in clusters and sub-clusters. However, a deeper study of mycobacteriophages has been conducted only for a few clusters. This study explores the traits of phages belonging to the B1 sub-cluster. We have attempted to functionally annotate and experimentally characterize B1 phages to get an insight into their biology and explore their therapeutic potential. MethodsAnalysis of B1 sub-cluster phage genomes to understand their key characteristics & lifestyle and to determine the putative function of hypothetical proteins (HPs), we developed a framework with a specific set of computational tools available online. For the experimental characterization, mycobacteriophages were isolated from environmental samples and were examined for their morphology, lysogeny status, effect on biofilm and activity against drug-resistant M. smegmatis. The B1 sub-cluster phages were identified by PCR using the specific primers. ResultsWe have predicted the function of about 55% of the 77 representative proteins in B1 phages, which were previously deemed hypothetical. We studied ten B1 phages (Phages 1-10) which included their morphological characteristics, lysogeny status and antibiofilm activity. TEM analysis, showing an average head & tail size of 65 nm and 202.12 nm, respectively. The turbid morphology of several plaques suggested these phages to be temperate. To verify, we tested their potential to lysogenize M. smegmatis and later found the spontaneous release from the putative lysogens. Interestingly, a putative RepA-like protein was identified in B1 phage genomes, indicating a possibility of extrachromosomal replication of prophages. Further, the impact of Phages 1-10 on M. smegmatis biofilm was found to be potent; the highest inhibitory and disruptive effect of phages (at a fixed titre of 108 pfu/ml) was 64% and 46%, respectively. Also, all ten phages could kill 4XR1 (the isoniazid-resistant M. smegmatis strain). ConclusionWe believe this combination of experimental analysis and exploration of genomic features of mycobacteriophages belonging to a sub-cluster can provide deeper insights into mycobacteriophage biology and also help in understanding their therapeutic potential.

microbiology↗

bioRxiv2023

Mitochondrial calcium signaling mediated transcriptional regulation of keratin filaments is a critical determinant of melanogenesis

Mitochondria are versatile organelles that regulate several physiological functions. Many mitochondria-controlled processes are driven by mitochondrial Ca2+ signaling. However, role of mitochondrial Ca2+ signaling in melanosome biology remains unknown. Here, we show that pigmentation requires mitochondrial Ca2+ uptake. In vitro gain and loss of function studies demonstrated that Mitochondrial Ca2+ Uniporter (MCU) is crucial for melanogenesis while the MCU rheostats, MCUb and MICU1 negatively control melanogenesis. Zebrafish and mouse models showed that MCU plays a vital role in pigmentation in vivo. Mechanistically, MCU controls activation of transcription factor NFAT2 to induce expression of three keratins (keratin 5, 7 and 8), which we report as positive regulators of melanogenesis. Interestingly, keratin 5 in turn modulates mitochondrial Ca2+ uptake thereby this signaling module acts as a negative feedback loop that fine-tunes both mitochondrial Ca2+ signaling and melanogenesis. Mitoxantrone, an FDA approved drug that inhibits MCU, decreases physiological melanogenesis. Collectively, our data demonstrates a critical role for mitochondrial Ca2+ signaling in vertebrate pigmentation and reveal the therapeutic potential of targeting MCU for clinical management of pigmentary disorders. Given the centrality of mitochondrial Ca2+ signaling and keratin filaments in cellular physiology, this feedback loop may be functional in a variety of other pathophysiological conditions. HighlightsO_LIMCU complex mediated mitochondrial Ca2+ uptake is a novel regulator of vertebrate pigmentation C_LIO_LIKeratin filaments bridge mitochondrial Ca2+ signaling to melanosome biogenesis and maturation C_LIO_LITranscription factor NFAT2 connects mitochondrial Ca2+ dynamics to keratins expression C_LIO_LIMCU-NFAT2-Keratin 5 signaling module generates a negative feedback loop to maintain mitochondrial Ca2+ homeostasis and to ensure optimal melanogenesis C_LIO_LIInhibiting MCU with mitoxantrone, an FDA approved drug, leads to reduction in physiological pigmentation C_LI

cell biology↗

bioRxiv2023

Models to Estimate Genetic Gain of Soybean Seed Yield from Annual Multi-Environment Field Trials

1Genetic improvements of discrete characteristics such as flower color, the genetic improvements are obvious and easy to demonstrate; however, for characteristics that are measured on continuous scales, the genetic contributions are incremental and less obvious. Reliable and accurate methods are required to disentangle the confounding genetic and non-genetic components of quantitative traits. Stochastic simulations of soybean (Glycine max (L.) Merr.) breeding programs were performed to evaluate models to estimate the realized genetic gain (RGG) from 30 years of multi-environment trials (MET). True breeding values were simulated under an infinitesimal model to represent the genetic contributions to soybean seed yield under various MET conditions. Estimators were evaluated using objective criteria of bias and linearity. Results indicated all estimation models were biased. Covariance modeling as well as direct versus indirect estimation resulted in substantial differences in RGG estimation. Although there were no unbiased models, the three best-performing models resulted in an average bias of {+/-}7.41 kg/ha-1/yr-1 ({+/-}0.11 bu/ac-1/yr-1). Rather than relying on a single model to estimate RGG, we recommend the application of multiple models and consider the range of the estimated values. Further, based on our simulations parameters, we do not think it is appropriate to use any single models to compare breeding programs or quantify the efficiency of proposed new breeding strategies. Lastly, for public soybean programs breeding for maturity groups II and III in North America from 1989 to 2019, the range of estimated RGG values was from 18.16 to 39.68 kg/ha-1/yr-1 (0.27 to 0.59 bu/ac-1/yr-1).

genetics↗

bioRxiv2023

Pulmonary Matrix Derived Hydrogels from Patients with Idiopathic Pulmonary Fibrosis Induce a Proinflammatory State in Lung Fibroblasts In Vitro

Idiopathic pulmonary fibrosis (IPF), one of the most common forms of interstitial lung disease, is a poorly understood, chronic, and often fatal fibroproliferative condition with only two FDA-approved medications. Understanding the pathobiology of the fibroblast in IPF is critical to evaluating and discovering novel therapeutics. Unfortunately, our ability to interrogate this biology in vitro is greatly limited by the well-documented effects of tissue culture plastic on the fibroblast phenotype. Using a decellularized lung matrix derived from IPF patients, we generate three-dimensional (3D) hydrogels as in vitro models of lung physiology and characterize the phenotype of fibroblasts seeded into the hydrogels. When cultured in our hydrogels, IPF fibroblasts display differential contractility compared to their normal counterparts, lose the classical myofibroblast marker -smooth muscle actin, and increase expression of proinflammatory cytokines compared to fibroblasts seeded two-dimensionally (2D) on tissue culture dishes. We validate this proinflammatory state in fibroblast conditioned media studies with monocytes and monocyte-derived macrophages. These findings add to a growing understanding of the lung microenvironment effect on fibroblast phenotypes, shed light on the potential role of fibroblasts as immune signaling hubs during lung fibrosis, and suggest intervention in fibroblast-immune cell crosstalk as a possible novel therapeutic avenue.

molecular biology↗

bioRxiv2023

Comparative transcriptome analysis in contrasting finger millet (Eleusine coracana (L.) Gaertn) genotypes for heat stress

Eleusine coracana (L.) Gaertn is a crucial C4 species renowned for its stress robustness and nutritional significance. Because of its adaptability traits, finger millet (ragi) is a storehouse of critical genomic resources for crop improvement. However, more knowledge about this crops molecular responses to heat stress must be gained. Hence, in the present study, we generated RNA seq data from the leaf tissue of the finger millet to observe the physiological changes and gene expression study in heat-sensitive (KJNS-46) and heat-tolerant (PES-110) genotypes of Ragi in response to high temperatures. On average, each sample generated about 24 million reads. Nearly 684 transcripts were differentially expressed (DEGs) between the heat-stressed samples of both genotypes. Pathway analysis and functional annotation analysis revealed the activation of various genes involved in response to stress, precisely heat, oxidation-reduction process, water deprivation, heat shock protein and transcription factors, calcium, and kinase signaling. The basal regulatory genes, such as bZIP, were involved in response to heat stress, indicating that heat stress activates genes related to basal regulatory processes or housekeeping. A substantial percentage of the DEGs belonged to proteins of unknown functions (PUFs), i.e., uncharacterized. The expression pattern of a few selected DEGs genes was analyzed in both genotypes by quantitative RT-PCR. The present study found some candidate genes and pathways that may confer tolerance to heat stress in ragi. These results will provide valuable information to improve heat tolerance in heat-susceptible agronomically important varieties of ragi and other crop plants.

plant biology↗

bioRxiv2023

An associative transcriptomics study on rice bean (Vigna umbellata) provides new insights into genetic basis and candidate genes governing flowering, maturity and seed weight

Rice bean is an underrated legume with significant potential to support food and nutritional security worldwide, being a rich source of proteins, minerals, and essential fatty acids. Therefore, we considered three pivotal production traits of rice bean; flowering, maturity and seed weight, to identify associated candidate genes. One-hundred diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank were considered for phenotypic data collection and genotyping by transcriptome sequencing approach. Association analysis involving various GWAS models was conducted to identify significant marker-trait associations. The results revealed association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The annotation of associated transcripts unraveled the functional genes related to the considered traits. Among the significant candidate genes identified, HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A were found associated with flowering. Further, associations of WRKY1 and DEAD-box-RH27 with seed weight, PIF3 and pentatricopeptide-repeat-containing-gene with maturity & seed weight and aldo-keto-reductase with flowering & maturity have been revealed. The present investigation provides insights into the genetic mechanisms governing economically-essential traits like flowering, maturity and seed weight that can be potentially utilized for rice bean improvement. HighlightsThe present investigation is the first associative transcriptomics approach implemented on Vigna umbellata. Based on the marker-trait association analysis, candidate genes for flowering, maturity and seed weight traits are reported.

bioinformatics↗

bioRxiv2022

Proteins with amino acid repeats constitute rapidly evolvable and human-specific essentialome

Protein products of essential genes, indispensable for organismal survival, are highly conserved and bring about fundamental functions. Interestingly, proteins that contain amino acid homorepeats that tend to evolve rapidly are enriched in eukaryotic essentialomes. Why are proteins with hypermutable homorepeats enriched in conserved and functionally vital essential proteins? We solve this function versus evolutionary paradox by demonstrating that human essential proteins with homorepeats bring about cross-talk across biological processes through high interactability and have distinct regulatory functions affecting expansive global regulation. Importantly, essential proteins with homorepeats rapidly diverge with the amino acid substitutions frequently affecting functional sites, likely facilitating rapid adaptability. Strikingly, essential proteins with homorepeats influence human-specific embryonic and brain development, implying that the presence of homorepeats could contribute to the emergence of human-specific processes. Thus, we propose that homorepeat containing essential proteins affecting species-specific traits can be potential intervention targets across pathologies including cancers and neurological disorders.

systems biology↗

bioRxiv2022

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often the HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes (such as E6/E7) is well known, the cis-regulatory effect of integrated HPV DNA on host chromatin structure and gene regulation remains less understood. Here, we investigate the genome-wide patterns of HPV integrations and associated host gene expression changes in the context of chromatin states and topologically associating domains (TADs). We find that HPV integrations are significantly enriched and depleted in active and inactive chromatin regions, respectively. Interestingly, regardless of the chromatin state, the genomic regions flanking HPV integrations showed transcriptional upregulation. Nevertheless, the upregulation (both local and long-range) is mostly confined to the TADs with integration and does not affect the adjacent TADs. Few TADs showed recurrent integrations associated with overexpression of oncogenes within them (such as MYC, PVT1, TP63 and ERBB2), regardless of the proximity. To further understand the long-range effect, we performed HiC and 4C-seq analyses in HeLa and observed chromatin looping interaction between the integrated HPV and MYC/PVT1 regions (situated [~]500 kb apart), leading to allele-specific overexpression of these genes. Again, these chromatin interactions involving integrated HPV are mostly observed within the same TAD. Together, these results suggest the cis-regulatory potential of integrated HPV DNA that drives host gene upregulation at intra-TAD level in cervical cancer. Based on this, we propose HPV integrations can trigger multimodal oncogenic activation to promote cancer progression.

genomics↗

bioRxiv2022

Using Machine Learning Enabled Phenotyping To Characterize Nodulation In Three Early Vegetative Stages In Soybean

The symbiotic relationship between soybean [Glycine max L. (Merr.)] roots and bacteria (Bradyrhizobium japonicum) lead to the development of nodules, important legume root structures where atmospheric nitrogen (N2) is fixed into bio-available ammonia (NH3) for plant growth and development. With the recent development of the Soybean Nodule Acquisition Pipeline (SNAP), nodules can more easily be quantified and evaluated for genetic diversity and growth patterns across unique soybean root system architectures. We explored six diverse soybean genotypes across three field year combinations in three early vegetative stages of development and report the unique relationships between soybean nodules in the taproot and non-taproot growth zones of diverse root system architectures of these genotypes. We found unique growth patterns in the nodules of taproots showing genotypic differences in how nodules grew in count, size, and total nodule area per genotype compared to non-taproot nodules. We propose that nodulation should be defined as a function of both nodule count and individual nodule area resulting in a total nodule area per root or growth regions of the root. We also report on the relationships between the nodules and total nitrogen in the seed at maturity, finding a strong correlation between the taproot nodules and final seed nitrogen at maturity. The applications of these findings could lead to an enhanced understanding of the plant-Bradyrhizobium relationship, and exploring these relationships could lead to leveraging greater nitrogen use efficiency and nodulation carbon to nitrogen production efficiency across the soybean germplasm. Core IdeasO_LIThe growth and development of soybean nodules on the taproot and non-taproots have unique growth and development patterns. C_LIO_LIIn general, taproot nodules increase in area, while non-taproot nodules increase in count and area. C_LIO_LINodulation should be defined by the total nodule area as a function of both nodule count and individual nodule size. C_LIO_LIGenotypes adjust their nodulation through either increasing nodule count or nodule size to increase the total nodule area per root between each growth stage. C_LIO_LIThere is a strong correlation between early growth stage taproot nodules and final seed nitrogen content. C_LI

plant biology↗

bioRxiv2022

Structural insights into acetylated histone ligand recognition by the BDP1 bromodomain of Plasmodium falciparum

Plasmodium falciparum requires a two-host system, moving between Anopheles mosquito and humans, to complete its life cycle. To overcome such dynamic growth conditions its histones undergo various post-translational modifications to up-regulate and down-regulate certain genes required for invasion and replication. The P. falciparum genome encodes six bromodomaincontaining proteins, of which Bromodomain Protein 1 (PfBDP1) has been shown to interact with acetylated lysine modifications on histone H3 to regulate the expression of invasion-related genes. Here, we investigated the ability of the PfBDP1 bromodomain to interact with acetyllsyine modifications on additional core and variant histones. A crystal structure of the PfBDP1 bromodomain (PfBDP1-BRD) reveals it contains the conserved bromodomain fold, but our comparative analysis between the PfBDP1-BRD and the 8 human bromodomain families indicates it has a unique binding mechanism. Solution NMR spectroscopy and ITC binding assays carried out with acetylated histone ligands demonstrate that it preferentially recognizes tetra-acetylated histone H4, and we detected weaker interactions with multi-acetylated H2A.Z in addition to the previously reported interactions with acetylated histone H3. Our findings indicate PfBDP1 may play additional roles in the P. falciparum life cycle, and the distinctive features of its bromodomain binding pocket could be leveraged for the development of new therapeutic agents to help overcome the continuously evolving resistance of P. falciparum against currently available drugs.

biophysics↗

bioRxiv2022

The FANCC-FANCE-FANCF complex is evolutionarily conserved and regulates meiotic recombination

At meiosis, programmed meiotic DNA double-strand breaks are repaired via homologous recombination, resulting in crossovers (COs). From a large excess of DNA double-strand breaks that are formed, only a small proportion gets converted into COs because of active mechanisms that restrict CO formation. The Fanconi anemia (FA) complex proteins AtFANCM, MHF1, and MHF2 were previously identified in a genetic screen as anti-CO factors that function during meiosis in Arabidopsis thaliana. Here, pursuing the same screen, we identify FANCC as a new anti-CO gene. FANCC was previously only identified in mammals because of low primary sequence conservation. We show that FANCC, and its physical interaction with FANCE-FANCF, is conserved from vertebrates to plants. Further, we show that FANCC, together with its subcomplex partners FANCE and FANCF, regulates meiotic recombination. Mutations of any of these three genes partially rescues CO-defective mutants, which is particularly marked in female meiosis. Functional loss of FANCC, FANCE, or FANCF results in synthetic meiotic catastrophe with the pro-CO factor MUS81. This work reveals that FANCC is conserved outside mammals and has an anti-CO role during meiosis together with FANCE and FANCF.

genetics↗

bioRxiv2022

The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction

The nucleoplasmin family of histone chaperones is a key player in governing the dynamic architecture of chromatin, thereby regulating various DNA-templated processes. The crystal structure of the N-terminal domain of Arabidopsis thaliana FKBP43 (AtFKBP43), an FK506-binding immunophilin protein, revealed a characteristic nucleoplasmin fold, thus confirming it to be a member of the FKBP nucleoplasmin class. Small-Angle X-ray Scattering (SAXS) analyses confirmed its pentameric nature in solution, and additional studies confirmed the nucleoplasmin fold to be highly stable. The AtFKBP43 nucleoplasmin core domain could not interact with histones and required the acidic arms, C-terminal to the core, for histone association. Furthermore, SAXS generated low-resolution envelope structure, ITC, and AUC results revealed that an AtFKBP43 pentamer with C-terminal extensions interacts with H2A/H2B dimer and H3/H4 tetramer in an equimolar ratio. Put together, AtFKBP43 belongs to a hitherto unreported subclass of FKBP nucleoplasmins that requires the C-terminal acidic stretches emanating from the core domain for histone interaction.

biophysics↗

bioRxiv2022

Using large soybean historical data to study genotype by environment variation and identify mega-environments with the integration of genetic and non-genetic factors

1Soybean (Glycine max (L.) Merr.) provides plant-based protein for global food production and is extensively bred to create cultivars with greater productivity in distinct environments. Plant breeders evaluate new soybean genotypes using multi-environment trials (MET). The application of MET assumes that trial locations provide representative environmental conditions that cultivars are likely to encounter when grown by farmers. In addition, MET are important to depict the patterns of genotype by environment interactions (GEI). To evaluate GEI for soybean seed yield and identify mega-environments (ME), a retrospective analysis of 39,006 data points from experimental soybean genotypes evaluated in preliminary and uniform field trials conducted by public plant breeders from 1989-2019 was considered. ME were identified from phenotypic information from the annual trials, geographic, soil, and meteorological records at the trial locations. Results indicate that yield variation was mostly explained by location and location by year interactions. The static portion of the GEI represented 26.30% of the total yield variance. Estimates of variance components derived from linear mixed models demonstrated that the phenotypic variation due to genotype by location interaction effects was greater than genotype by year interaction effects. A trend analysis indicated a two-fold increase in the genotypic variance between 1989-1995 and 1996-2019. Furthermore, the heterogeneous estimates of genotypic, genotype by location, genotype by year, and genotype by location by year variances, were encapsulated by distinct probability distributions. The observed target population of environments can be divided into at least two and at most three ME, thereby suggesting improvements in the response to selection can be achieved when selecting directly for clustered (i.e., regions, ME) versus selecting across regions. Clusters obtained using phenotypic data, latitude, and soil variables plus elevation, were the most effective. In addition, we published the R package SoyURT which contains the data sets used in this work. 2 HighlightsO_LIMega-environments can be identified with phenotypic, geographic, and meteorological data. C_LIO_LIReliable estimates of variances can be obtained with proper analyses of historical data. C_LIO_LIGenotype by location was more important than genotype by year variation for seed yield. C_LIO_LIThe trend in genotype by environment variances was captured in probability distributions. C_LI

genetics↗