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Scientific Data Jun 2024Euphorbia, one of the largest genera of flowering plants, is well-known for containing many biofuel crops. Euphorbia tirucalli, an evergreen succulent mainly native to...
Euphorbia, one of the largest genera of flowering plants, is well-known for containing many biofuel crops. Euphorbia tirucalli, an evergreen succulent mainly native to the Africa continent but cultivated worldwide, is a promising petroleum plant with high tolerance to drought and salt stress. However, the exploration of such an important plant resource is severely hampered by the lack of a reference genome. Here, we present the chromosome-level genome assembly of E. tirucalli using PacBio HiFi sequencing and Hi-C technology. Its genome size was approximately 745.62 Mb, with a contig N50 of 74.16 Mb. A total of 743.63 Mb (99.73%) of the assembled sequences were anchored to 10 chromosomes with a complete BUSCO score of 97.80%. Genome annotation revealed 26,304 protein-coding genes, and 76.37% of the genome was identified as repeat elements. The high-quality genome provides valuable genetic resources that would be useful for unraveling the genetic mechanisms of biofuel synthesis and evolutionary adaptation of E. tirucalli.
Topics: Euphorbia; Genome, Plant; Chromosomes, Plant; Stress, Physiological; Molecular Sequence Annotation
PubMed: 38906925
DOI: 10.1038/s41597-024-03503-w -
Scientific Reports Jun 2024The complete cp genomes of Pedicularis chinensis (GenBank accession number: OQ587614) and Pedicularis kansuensis (GenBank accession number: OQ587613) were sequenced,...
The complete cp genomes of Pedicularis chinensis (GenBank accession number: OQ587614) and Pedicularis kansuensis (GenBank accession number: OQ587613) were sequenced, assembled, and annotated. Their chloroplast (cp) genome lengths were 146,452 bp, and 146,852 bp, respectively; 120 and 116 genes were identified, comprising 75 and 72 protein-coding genes (PCGs), 37 and 36 transfer RNA (tRNA) genes, and 8 and 8 ribosomal RNA (rRNA) genes, for P. chinensis and P. kansuensis, respectively. A simple sequence repeat (SSR) analysis revealed that the repetitive sequences were mainly composed of mononucleotide repeats (A/T motif) and dinucleotide repeats (AT/TA motif). Comparative genomics identified several variant genes (rpl22, rps19, rpl12, ycf1, trnH, psbA, and ndhH) and variant regions (trnS-GGA, trnV-UAC, ndhJ-trnV, ycf4-cemA, ndhE-nhdG, and rpl32-trnL) with a high Pi, indicating the potential to serve as deoxyribo nucleic acid (DNA) barcodes for Pedicularis species identification. The results show that the cp genomes of P. chinensis and P. kansuensis were the same as those of other plants in Pedicularis, with different degrees of AT preference for codons. Large differences in the number of SSRs and the expansion of the inverted repeat (IR) region showed strong variability and interspecific differentiation between these two species and other species represented in the genus Pedicularis. A phylogenetic analysis showed that P. kansuensis had the closest relationship with P. oliveriana, and P. chinensis had the closest relationship with P. aschistorhyncha. These results will facilitate the study of the phylogenetic classification and interspecific evolution of Pedicularis plants.
Topics: Phylogeny; Genome, Chloroplast; Pedicularis; Microsatellite Repeats; RNA, Transfer
PubMed: 38906909
DOI: 10.1038/s41598-024-63815-0 -
Developmental Cell Jun 2024Sexually reproducing eukaryotes employ a developmentally regulated cell division program-meiosis-to generate haploid gametes from diploid germ cells. To understand how...
Sexually reproducing eukaryotes employ a developmentally regulated cell division program-meiosis-to generate haploid gametes from diploid germ cells. To understand how gametes arise, we generated a proteomic census encompassing the entire meiotic program of budding yeast. We found that concerted waves of protein expression and phosphorylation modify nearly all cellular pathways to support meiotic entry, meiotic progression, and gamete morphogenesis. Leveraging this comprehensive resource, we pinpointed dynamic changes in mitochondrial components and showed that phosphorylation of the FF-ATP synthase complex is required for efficient gametogenesis. Furthermore, using cryoET as an orthogonal approach to visualize mitochondria, we uncovered highly ordered filament arrays of Ald4, a conserved aldehyde dehydrogenase that is highly expressed and phosphorylated during meiosis. Notably, phosphorylation-resistant mutants failed to accumulate filaments, suggesting that phosphorylation regulates context-specific Ald4 polymerization. Overall, this proteomic census constitutes a broad resource to guide the exploration of the unique sequence of events underpinning gametogenesis.
PubMed: 38906138
DOI: 10.1016/j.devcel.2024.05.025 -
Evidence that the cold- and menthol-sensing functions of the human TRPM8 channel evolved separately.Science Advances Jun 2024Transient receptor potential melastatin 8 (TRPM8) is a temperature- and menthol-sensitive ion channel that contributes to diverse physiological roles, including cold...
Transient receptor potential melastatin 8 (TRPM8) is a temperature- and menthol-sensitive ion channel that contributes to diverse physiological roles, including cold sensing and pain perception. Clinical trials targeting TRPM8 have faced repeated setbacks predominantly due to the knowledge gap in unraveling the molecular underpinnings governing polymodal activation. A better understanding of the molecular foundations between the TRPM8 activation modes may aid the development of mode-specific, thermal-neutral therapies. Ancestral sequence reconstruction was used to explore the origins of TRPM8 activation modes. By resurrecting key TRPM8 nodes along the human evolutionary trajectory, we gained valuable insights into the trafficking, stability, and function of these ancestral forms. Notably, this approach unveiled the differential emergence of cold and menthol sensitivity over evolutionary time, providing a fresh perspective on complex polymodal behavior. These studies provide a paradigm for understanding polymodal behavior in TRPM8 and other proteins with the potential to enhance our understanding of sensory receptor biology and pave the way for innovative therapeutic interventions.
Topics: TRPM Cation Channels; Humans; Menthol; Cold Temperature; Evolution, Molecular; Phylogeny; Thermosensing
PubMed: 38905339
DOI: 10.1126/sciadv.adm9228 -
MBio Jun 2024The injectisome encoded by pathogenicity island 2 (SPI-2) had been thought to translocate 28 effectors. Here, we used a proteomic approach to characterize the secretome...
UNLABELLED
The injectisome encoded by pathogenicity island 2 (SPI-2) had been thought to translocate 28 effectors. Here, we used a proteomic approach to characterize the secretome of a clinical strain of invasive non-typhoidal serovar Enteritidis that had been mutated to cause hyper-secretion of the SPI-2 injectisome effectors. Along with many known effectors, we discovered the novel SseM protein. is widely distributed among the five subspecies of is found in many clinically relevant serovars, and is co-transcribed with , a SPI-2 effector gene. The translocation of SseM required a functional SPI-2 injectisome. Following expression in human cells, SseM interacted with five components of the dystrophin-associated protein complex (DAPC), namely, β-2-syntrophin, utrophin/dystrophin, α-catulin, α-dystrobrevin, and β-dystrobrevin. The interaction between SseM and β-2-syntrophin and α-dystrobrevin was verified in Typhimurium-infected cells and relied on the postsynaptic density-95/discs large/zonula occludens-1 (PDZ) domain of β-2-syntrophin and a sequence corresponding to a PDZ-binding motif (PBM) in SseM. A Δ mutant strain had a small competitive advantage over the wild-type strain in the . Typhimurium/mouse model of systemic disease. This phenotype was complemented by a plasmid expressing wild-type SseM from . Typhimurium or . Enteritidis and was dependent on the PBM of SseM. Therefore, a PBM within a effector mediates interactions with the DAPC and modulates the systemic growth of bacteria in mice. Furthermore, the Δ mutant strain displayed enhanced replication in bone marrow-derived macrophages, demonstrating that SseM restrains intracellular bacterial growth to modulate virulence.
IMPORTANCE
In , the injectisome machinery encoded by pathogenicity island 2 (SPI-2) is conserved among the five subspecies and delivers proteins (effectors) into host cells, which are required for virulence. The identification and functional characterization of SPI-2 injectisome effectors advance our understanding of the interplay between and its host(s). Using an optimized method for preparing secreted proteins and a clinical isolate of the invasive non-typhoidal serovar Enteritidis strain D24359, we identified 22 known SPI-2 injectisome effectors and one new effector-SseM. SseM modulates bacterial growth during murine infection and has a sequence corresponding to a postsynaptic density-95/discs large/zonula occludens-1 (PDZ)-binding motif that is essential for interaction with the PDZ-containing host protein β-2-syntrophin and other components of the dystrophin-associated protein complex (DAPC). To our knowledge, SseM is unique among effectors in containing a functional PDZ-binding motif and is the first bacterial protein to target the DAPC.
PubMed: 38904384
DOI: 10.1128/mbio.01128-24 -
Wellcome Open Research 2024We present a genome assembly from an individual male (the Winter Shade; Arthropoda; None; Lepidoptera; Tortricidae). The genome sequence is 441.2 megabases in span....
We present a genome assembly from an individual male (the Winter Shade; Arthropoda; None; Lepidoptera; Tortricidae). The genome sequence is 441.2 megabases in span. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,280 protein coding genes.
PubMed: 38903871
DOI: 10.12688/wellcomeopenres.21494.1 -
Wellcome Open Research 2024We present a genome assembly from an individual female (the wood-carving leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 290.0...
We present a genome assembly from an individual female (the wood-carving leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 290.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 23.71 kilobases in length. Gene annotation of this assembly on Ensembl 11,722 protein coding genes.
PubMed: 38903870
DOI: 10.12688/wellcomeopenres.21002.1 -
Frontiers in Genetics 2024Mitochondria are semi-autonomous organelles in eukaryotic cells with their own genome. Plant mitogenomes differ from animal mitogenomes in size, structure, and...
Mitochondria are semi-autonomous organelles in eukaryotic cells with their own genome. Plant mitogenomes differ from animal mitogenomes in size, structure, and repetitive DNA sequences. Despite larger sizes, plant mitogenomes do not have significantly more genes. They exhibit diverse structures due to variations in size, repetitive DNA, recombination frequencies, low gene densities, and reduced nucleotide substitution rates. In this study, we analyzed the mitochondrial genome of using Nanopore and Illumina sequencing. assembly and annotation were conducted using Unicycler, Geseq, tRNAscan-SE and BLASTN, followed by codon usage, repeat sequence, RNA-editing, synteny, and phylogenetic analyses. mitogenome consisted of one linear contig and six circular contigs totaling 724,751 bp. It had 39 protein-coding genes, 27 tRNA genes, and 3 rRNA genes. Transfer of chloroplast sequences accounted for 13.14% of the mitogenome. Various analyses provided insights into genetic characteristics, evolutionary dynamics, and phylogenetic placement. Further investigations can explore transferred genes' functions and RNA-editing's role in mitochondrial gene expression in .
PubMed: 38903753
DOI: 10.3389/fgene.2024.1395805 -
Frontiers in Genetics 2024The recognition of DNA Binding Proteins (DBPs) plays a crucial role in understanding biological functions such as replication, transcription, and repair. Although...
The recognition of DNA Binding Proteins (DBPs) plays a crucial role in understanding biological functions such as replication, transcription, and repair. Although current sequence-based methods have shown some effectiveness, they often fail to fully utilize the potential of deep learning in capturing complex patterns. This study introduces a novel model, LGC-DBP, which integrates Long Short-Term Memory (LSTM), Gated Inception Convolution, and Improved Channel Attention mechanisms to enhance the prediction of DBPs. Initially, the model transforms protein sequences into Position Specific Scoring Matrices (PSSM), then processed through our deep learning framework. Within this framework, Gated Inception Convolution merges the concepts of gating units with the advantages of Graph Convolutional Network (GCN) and Dilated Convolution, significantly surpassing traditional convolution methods. The Improved Channel Attention mechanism substantially enhances the model's responsiveness and accuracy by shifting from a single input to three inputs and integrating three sigmoid functions along with an additional layer output. These innovative combinations have significantly improved model performance, enabling LGC-DBP to recognize and interpret the complex relationships within DBP features more accurately. The evaluation results show that LGC-DBP achieves an accuracy of 88.26% and a Matthews correlation coefficient of 0.701, both surpassing existing methods. These achievements demonstrate the model's strong capability in integrating and analyzing multi-dimensional data and mark a significant advancement over traditional methods by capturing deeper, nonlinear interactions within the data.
PubMed: 38903752
DOI: 10.3389/fgene.2024.1411847 -
Frontiers in Neuroscience 2024Recently a broad range of phenotypic abnormalities related to the neurodevelopmental and neurodegenerative disorder NEDAMSS (Neurodevelopmental Disorder with Regression,... (Review)
Review
Recently a broad range of phenotypic abnormalities related to the neurodevelopmental and neurodegenerative disorder NEDAMSS (Neurodevelopmental Disorder with Regression, Abnormal Movements, Loss of Speech, and Seizures) have been associated with rare single-nucleotide polymorphisms (SNPs) or insertion and deletion variants (Indel) in the intron-less gene IRF2BPL. Up to now, 34 patients have been identified through whole exome sequencing carrying different heterozygous pathogenic variants spanning the intron-less gene from the first polyglutamine tract at the N-terminus to the C3HC4 RING domain of the C-terminus of the protein. As a result, the phenotypic spectrum of the patients is highly heterogeneous and ranges from abnormal neurocognitive development to severe neurodegenerative courses with developmental and seizure-related encephalopathies. While the treatment of IRF2BPL-related disorders has focused on alleviating the patient's symptoms by symptomatic multidisciplinary management, there has been no prospect of entirely relieving the symptoms of the individual patients. Yet, the recent advancement of CRISPR-Cas9-derived gene editing tools, leading to the generation of base editors (BEs) and prime editors (PEs), provide an encouraging new therapeutic avenue for treating NEDAMSS and other neurodevelopmental and neurodegenerative diseases, which contain SNPs or smaller Indels in post-mitotic cell populations of the central nervous system, due to its ability to generate site-specific DNA sequence modifications without creating double-stranded breaks, and recruiting the non-homologous DNA end joining repair mechanism.
PubMed: 38903604
DOI: 10.3389/fnins.2024.1426177