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Rice (New York, N.Y.) Jun 2024Polyploid is considered an advantage that has evolved to be more environmentally adaptable than its diploid. To understand if doubled chromosome of diploid rice can...
Polyploid is considered an advantage that has evolved to be more environmentally adaptable than its diploid. To understand if doubled chromosome of diploid rice can improve drought tolerance, we evaluated the diploid (2X) and autotetraploid (4X) plants of three indica and three japonica varieties. Drought stress in the plastic bucket of four-leaf stage revealed that the drought tolerance of 4X plants was lower than that of its diploid donor plants. The assay of photosynthetic rate of all varieties showed that all 4X varieties had lower rates than their diploid donors. The capacity for reactive oxygen species production and scavenging varied among different 2X and 4X varieties. Further, transcriptomic analysis of 2X and 4X plants of four varieties under normal and drought condition showed that the wide variation of gene expression was caused by difference of varieties, not by chromosome ploidy. However, weighted gene co-expression network analysis (WGCNA) revealed that the severe interference of photosynthesis-related genes in tetraploid plants under drought stress is the primary reason for the decrease of drought tolerance in autotetraploid lines. Consistently, new transcripts analysis in autotetraploid revealed that the gene transcription related with mitochondrion and plastid of cell component was influenced most significantly. The results indicated that chromosome doubling of diploid rice weakened their drought tolerance, primarily due to disorder of photosynthesis-related genes in tetraploid plants under drought stress. Maintain tetraploid drought tolerance through chromosome doubling breeding in rice needs to start with the selection of parental varieties and more efforts.
PubMed: 38888627
DOI: 10.1186/s12284-024-00716-w -
The EMBO Journal Jun 2024Starvation in diploid budding yeast cells triggers a cell-fate program culminating in meiosis and spore formation. Transcriptional activation of early meiotic genes...
Starvation in diploid budding yeast cells triggers a cell-fate program culminating in meiosis and spore formation. Transcriptional activation of early meiotic genes (EMGs) hinges on the master regulator Ime1, its DNA-binding partner Ume6, and GSK-3β kinase Rim11. Phosphorylation of Ume6 by Rim11 is required for EMG activation. We report here that Rim11 functions as the central signal integrator for controlling Ume6 phosphorylation and EMG transcription. In nutrient-rich conditions, PKA suppresses Rim11 levels, while TORC1 retains Rim11 in the cytoplasm. Inhibition of PKA and TORC1 induces Rim11 expression and nuclear localization. Remarkably, nuclear Rim11 is required, but not sufficient, for Rim11-dependent Ume6 phosphorylation. In addition, Ime1 is an anchor protein enabling Ume6 phosphorylation by Rim11. Subsequently, Ume6-Ime1 coactivator complexes form and induce EMG transcription. Our results demonstrate how various signaling inputs (PKA/TORC1/Ime1) converge through Rim11 to regulate EMG expression and meiosis initiation. We posit that the signaling-regulatory network elucidated here generates robustness in cell-fate control.
PubMed: 38886580
DOI: 10.1038/s44318-024-00149-7 -
Scientific Reports Jun 2024In vitro evolution and whole genome analysis has proven to be a powerful method for studying the mechanism of action of small molecules in many haploid microbes but has...
In vitro evolution and whole genome analysis has proven to be a powerful method for studying the mechanism of action of small molecules in many haploid microbes but has generally not been applied to human cell lines in part because their diploid state complicates the identification of variants that confer drug resistance. To determine if haploid human cells could be used in MOA studies, we evolved resistance to five different anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel) using a near-haploid cell line (HAP1) and then analyzed the genomes of the drug resistant clones, developing a bioinformatic pipeline that involved filtering for high frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound. Applying the filter to sequences from 28 drug resistant clones identified a set of 21 genes which was strongly enriched for known resistance genes or known drug targets (TOP1, TOP2A, DCK, WDR33, SLCO3A1). In addition, some lines carried structural variants that encompassed additional known resistance genes (ABCB1, WWOX and RRM1). Gene expression knockdown and knockout experiments of 10 validation targets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, discovered and studied in an isogenic background.
Topics: Humans; Haploidy; Drug Resistance, Neoplasm; Antineoplastic Agents; Genome, Human; Whole Genome Sequencing; Cell Line
PubMed: 38886371
DOI: 10.1038/s41598-024-63943-7 -
Plant Communications Jun 2024E3 ligases are key enzymes required for protein degradation. Here we identified a C3H2C3 RING domain-containing E3 ubiquitin ligase gene named GhATL68b. It is...
E3 ligases are key enzymes required for protein degradation. Here we identified a C3H2C3 RING domain-containing E3 ubiquitin ligase gene named GhATL68b. It is preferentially and highly expressed in developing cotton fiber cells, and is more conserved in plants than in animals or in archaea. All four orthologs copies of this gene in various diploid cottons and eight in the allotetraploid G. hirsutum were found to originate from a single common ancestor that can be traced back to C. reinhardii at about 992 million years ago (MYA). Structural variations (SVs) occurred in the promoter regions of G. hirsutum, G. herbaceum, G. arboreum and G. raimondii correlated with significantly different methylation patterns. Homozygous CRISPR-Cas9 knock-out cotton lines produced significant poor fiber quality in terms of upper half mean length, elongation at break, uniformity and mature fiber weight. GhATL68b was shown to modulate the homeostasis of 2,4-dienoyl-CoA reductase (GhDECR), a rate-limiting enzyme for β-oxidation of polyunsaturated fatty acids (PUFAs) via the ubiquitin proteasome pathway through in vitro ubiquitination and cell-free protein degradation assays. Fiber cells harvested from these knockout mutants contained significantly lower levels of PUFAs important for glycerophospholipids production and also for plasma membrane fluidity regulations. Finally, the mutant fiber-growth defective phenotype can be fully compensated by adding linolenic acid (C18:3), the most abundant type of PUFA externally in ovule culture media. To our knowledge, this is the first experimentally characterized C3H2C3 type E3 ubiquitin ligase that is involved in regulating fiber cell elongation, and it may thus provide us with a new genetic target for improved cotton lint production.
PubMed: 38877704
DOI: 10.1016/j.xplc.2024.101003 -
Research Square May 2024Understanding the mechanisms of polyploidization in cardiomyocytes is crucial for advancing strategies to stimulate myocardial regeneration. Although endoreplication has...
Understanding the mechanisms of polyploidization in cardiomyocytes is crucial for advancing strategies to stimulate myocardial regeneration. Although endoreplication has long been considered the primary source of polyploid human cardiomyocytes, recent animal work suggests the potential for cardiomyocyte fusion. Moreover, the effects of polyploidization on the genomic-transcriptomic repertoire of human cardiomyocytes have not been studied previously. We applied single-nuclei whole genome sequencing, single nuclei RNA sequencing, and multiome ATAC + gene expression (from the same nuclei) techniques to nuclei isolated from 11 healthy hearts. Utilizing post-zygotic non-inherited somatic mutations occurring during development as "endogenous barcodes," to reconstruct lineage relationships of polyploid cardiomyocytes. Of 482 cardiomyocytes from multiple healthy donor hearts 75.7% can be sorted into several developmental clades marked by one or more somatic single-nucleotide variants (SNVs). At least ~10% of tetraploid cardiomyocytes contain cells from distinct clades, indicating fusion of lineally distinct cells, whereas 60% of higher-ploidy cardiomyocytes contain fused cells from distinct clades. Combined snRNA-seq and snATAC-seq revealed transcriptome and chromatin landscapes of polyploid cardiomyocytes distinct from diploid cardiomyocytes, and show some higher-ploidy cardiomyocytes with transcriptional signatures suggesting fusion between cardiomyocytes and endothelial and fibroblast cells. These observations provide the first evidence for cell and nuclear fusion of human cardiomyocytes, raising the possibility that cell fusion may contribute to developing or maintaining polyploid cardiomyocytes in the human heart.
PubMed: 38853931
DOI: 10.21203/rs.3.rs-4414468/v1 -
American Journal of Physiology. Heart... Jun 2024Factors responsible for cardiomyocyte proliferation could serve as potential therapeutics to stimulate endogenous myocardial regeneration following insult, such as...
Factors responsible for cardiomyocyte proliferation could serve as potential therapeutics to stimulate endogenous myocardial regeneration following insult, such as ischemic injury. A previously published forward genetics approach on cardiomyocyte cell cycle and ploidy led us to the transcription factor, RUNX1. Here, we examine the effect of on cardiomyocyte cell cycle during postnatal development and cardiac regeneration using cardiomyocyte-specific gain- and loss-of-function mouse models. RUNX1 is expressed in cardiomyocytes during early postnatal life, decreases to negligible levels by 3 weeks of age, and increases upon myocardial injury, all consistent with observed rates of cardiomyocyte cell cycle activity. Loss of transiently stymied cardiomyocyte cell cycle activity during normal postnatal development, a result that corrected itself and did not extend to the context of neonatal heart regeneration. On the other hand, cardiomyocyte-specific overexpression resulted in an expansion of diploid cardiomyocytes in uninjured hearts and expansion of 4N cardiomyocytes in the context of neonatal cardiac injury, suggesting overexpression is sufficient to induce cardiomyocyte cell cycle responses. Persistent overexpression of for >1 month continued to promote cardiomyocyte cell cycle activity resulting in substantial hyperpolyploidization (≥8N DNA content). This persistent cell cycle activation was accompanied by ventricular dilation and adverse remodeling, raising the concern that continued cardiomyocyte cell cycling can have detrimental effects.
PubMed: 38847758
DOI: 10.1152/ajpheart.00782.2023 -
Indian Journal of Public Health Jan 2024Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Immunophenotype (IPT) and cytogenetics are essential for diagnosis, risk stratification, and...
BACKGROUND
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Immunophenotype (IPT) and cytogenetics are essential for diagnosis, risk stratification, and management for ALL.
OBJECTIVES
Evaluating the burden of immunophenotypic and cytogenetic profile of pediatric ALL patients.
MATERIALS AND METHODS
A descriptive cross-sectional study was conducted on 100 patients of ALL (1-18 completed years) attending a tertiary-care center in Kolkata, Eastern India.
RESULTS
Ninety-six percent of patients had B-cell ALL (94.00% pre-B ALL and 2.00% Pro-B ALL) and 4.0% had T-ALL. 60% B-cell ALL were CD19/CD10 positive, 10% were CD79a positive, 9% were only CD19 positive, and 7% were only CD10 positive. Thirty-three percent of T-ALL were CD3+, whereas 22% were positive each for CD4 and CD7. 51.0% of patients had diploid, 46.0% hyperdiploid, and 3.0% hypodiploid karyotype. Among hyperdiploids, 98% had good prednisolone response and 89% had measurable residual disease (MRD) <0.01.
CONCLUSION
The most commonly diagnosed ALL by IPT was pre-B ALL. Among the detectable cytogenetic abnormalities, t(12; 21) ETV6-RUNX1 was the most common. ZNF-384 gene arrangement was also detected in our study. t(12;21) ETV6-RUNX1 had a good treatment response, while t(9;22) BCR-ABL, t(1;19) TCF3-PBX1, iAMP-21, MLL gene rearrangement, and ZNF-384 gene arrangement had poor treatment response in terms of MRD.
Topics: Humans; India; Child; Male; Female; Child, Preschool; Adolescent; Cross-Sectional Studies; Precursor Cell Lymphoblastic Leukemia-Lymphoma; Immunophenotyping; Infant; Cytogenetic Analysis
PubMed: 38847628
DOI: 10.4103/ijph.ijph_889_23 -
ELife Jun 2024Facultative parthenogenesis (FP) has historically been regarded as rare in vertebrates, but in recent years incidences have been reported in a growing list of fish,...
Facultative parthenogenesis (FP) has historically been regarded as rare in vertebrates, but in recent years incidences have been reported in a growing list of fish, reptile, and bird species. Despite the increasing interest in the phenomenon, the underlying mechanism and evolutionary implications have remained unclear. A common finding across many incidences of FP is either a high degree of homozygosity at microsatellite loci or low levels of heterozygosity detected in next-generation sequencing data. This has led to the proposal that second polar body fusion following the meiotic divisions restores diploidy and thereby mimics fertilization. Here, we show that FP occurring in the gonochoristic species and results in genome-wide homozygosity, an observation inconsistent with polar body fusion as the underlying mechanism of restoration. Instead, a high-quality reference genome for and analysis of whole-genome sequencing from multiple FP and control animals reveals that a post-meiotic mechanism gives rise to homozygous animals from haploid, unfertilized oocytes. Contrary to the widely held belief that females need to be isolated from males to undergo FP, females housed with conspecific and heterospecific males produced unfertilized eggs that underwent spontaneous development. In addition, offspring arising from both fertilized eggs and parthenogenetic development were observed to arise from a single clutch. Strikingly, our data support a mechanism for facultative parthenogenesis that removes all heterozygosity in a single generation. Complete homozygosity exposes the genetic load and explains the high rate of congenital malformations and embryonic mortality associated with FP in many species. Conversely, for animals that develop normally, FP could potentially exert strong purifying selection as all lethal recessive alleles are purged in a single generation.
Topics: Animals; Parthenogenesis; Female; Lizards; Male; Meiosis; Homozygote
PubMed: 38847388
DOI: 10.7554/eLife.97035 -
BMC Genomics Jun 2024KNOXs, a type of homeobox genes that encode atypical homeobox proteins, play an essential role in the regulation of growth and development, hormonal response, and...
Genome-wide identification and expression analysis of the KNOX family and its diverse roles in response to growth and abiotic tolerance in sweet potato and its two diploid relatives.
KNOXs, a type of homeobox genes that encode atypical homeobox proteins, play an essential role in the regulation of growth and development, hormonal response, and abiotic stress in plants. However, the KNOX gene family has not been explored in sweet potato. In this study, through sequence alignment, genomic structure analysis, and phylogenetic characterization, 17, 12 and 11 KNOXs in sweet potato (I. batatas, 2n = 6x = 90) and its two diploid relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30) were identified. The protein physicochemical properties, chromosome localization, phylogenetic relationships, gene structure, protein interaction network, cis-elements of promoters, tissue-specific expression and expression patterns under hormone treatment and abiotic stresses of these 40 KNOX genes were systematically studied. IbKNOX4, -5, and - 6 were highly expressed in the leaves of the high-yield varieties Longshu9 and Xushu18. IbKNOX3 and IbKNOX8 in Class I were upregulated in initial storage roots compared to fibrous roots. IbKNOXs in Class M were specifically expressed in the stem tip and hardly expressed in other tissues. Moreover, IbKNOX2 and - 6, and their homologous genes were induced by PEG/mannitol and NaCl treatments. The results showed that KNOXs were involved in regulating growth and development, hormone crosstalk and abiotic stress responses between sweet potato and its two diploid relatives. This study provides a comparison of these KNOX genes in sweet potato and its two diploid relatives and a theoretical basis for functional studies.
Topics: Ipomoea batatas; Phylogeny; Stress, Physiological; Diploidy; Gene Expression Regulation, Plant; Plant Proteins; Multigene Family; Homeodomain Proteins; Genome, Plant; Gene Expression Profiling; Promoter Regions, Genetic
PubMed: 38844832
DOI: 10.1186/s12864-024-10470-4 -
BMC Plant Biology Jun 2024Non-hydraulic root source signaling (nHRS) is a unique positive response to soil drying in the regulation of plant growth and development. However, it is unclear how the...
Non-hydraulic root source signaling (nHRS) is a unique positive response to soil drying in the regulation of plant growth and development. However, it is unclear how the nHRS mediates the tradeoff between source and sink at the late growth stages and its adaptive mechanisms in primitive wheat. To address this issue, a root-splitting design was made by inserting solid partition in the middle of the pot culture to induce the occurrence of nHRS using four wheat cultivars (MO1 and MO4, diploid; DM22 and DM31, tetraploid) as materials. Three water treatments were designed as 1) both halves watered (CK), 2) holistic root system watered then droughted (FS), 3) one-half of the root system watered and half droughted (PS). FS and PS were designed to compare the role of the full root system and split root system to induce nHRS. Leaves samples were collected during booting and anthesis to compare the role of nHRS at both growth stages. The data indicated that under PS treatment, ABA concentration was significantly higher than FS and CK, demonstrating the induction of nHRS in split root design and nHRS decreased cytokinin (ZR) levels, particularly in the PS treatment. Soluble sugar and proline accumulation were higher in the anthesis stage as compared to the booting stage. POD activity was higher at anthesis, while CAT was higher at the booting stage. Increased ABA (nHRS) correlated with source-sink relationships and metabolic rate (i.e., leaf) connecting other stress signals. Biomass density showed superior resource acquisition and utilization capabilities in both FS and PS treatment as compared to CK in all plants. Our findings indicate that nHRS-induced alterations in phytohormones and their effect on source-sink relations were allied with the growth stages in primitive wheat.
Topics: Triticum; Tetraploidy; Plant Roots; Diploidy; Signal Transduction; Plant Shoots; Plant Growth Regulators; Abscisic Acid; Cytokinins; Plant Leaves
PubMed: 38831289
DOI: 10.1186/s12870-024-05046-z