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BMC Plant Biology Feb 2021The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar...
BACKGROUND
The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar.
RESULTS
On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations.
CONCLUSION
Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.
Topics: Chromosome Mapping; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Genome, Plant; Genome-Wide Association Study; Multigene Family; Phylogeny; Plant Proteins; Populus; Stress, Physiological
PubMed: 33627082
DOI: 10.1186/s12870-021-02872-3 -
Cancer Metastasis Reviews Dec 2020The name of the oncogene, ras, has its origin in studies of murine leukemia viruses in the 1960s by Jenny Harvey (H-ras) and by Werner Kirsten (K-ras) which, at high... (Review)
Review
The name of the oncogene, ras, has its origin in studies of murine leukemia viruses in the 1960s by Jenny Harvey (H-ras) and by Werner Kirsten (K-ras) which, at high doses, produced sarcomas in rats. Transforming retroviruses were isolated, and its oncogene was named ras after rat sarcoma. From 1979, cellular ras sequences with transforming properties were identified by transfection of tumor DNA initially by Robert Weinberg from rodent tumors, and the isolation of homologous oncogenes from human tumors soon followed, including HRAS and KRAS, and a new member of the family named NRAS. I review these discoveries, placing emphasis on the pioneering research of Christopher Marshall and Alan Hall, who subsequently made immense contributions to our understanding of the functions of RAS and related small GTPases to signal transduction pathways, cell structure, and the behavior of normal and malignant cells.
Topics: Animals; Genes, Tumor Suppressor; Genes, ras; Genetics; History, 20th Century; History, 21st Century; Humans; Neoplasms
PubMed: 32728828
DOI: 10.1007/s10555-020-09919-1 -
PLoS Genetics Feb 2023Structural variations (SVs) are a key type of cancer genomic alterations, contributing to oncogenesis and progression of many cancers, including colorectal cancer (CRC)....
Structural variations (SVs) are a key type of cancer genomic alterations, contributing to oncogenesis and progression of many cancers, including colorectal cancer (CRC). However, SVs in CRC remain difficult to be reliably detected due to limited SV-detection capacity of the commonly used short-read sequencing. This study investigated the somatic SVs in 21 pairs of CRC samples by Nanopore whole-genome long-read sequencing. 5200 novel somatic SVs from 21 CRC patients (494 SVs / patient) were identified. A 4.9-Mbp long inversion that silences APC expression (confirmed by RNA-seq) and an 11.2-kbp inversion that structurally alters CFTR were identified. Two novel gene fusions that might functionally impact the oncogene RNF38 and the tumor-suppressor SMAD3 were detected. RNF38 fusion possesses metastasis-promoting ability confirmed by in vitro migration and invasion assay, and in vivo metastasis experiments. This work highlighted the various applications of long-read sequencing in cancer genome analysis, and shed new light on how somatic SVs structurally alter critical genes in CRC. The investigation on somatic SVs via nanopore sequencing revealed the potential of this genomic approach in facilitating precise diagnosis and personalized treatment of CRC.
Topics: Humans; Genomics; Genes, Tumor Suppressor; Genome; Whole Genome Sequencing; Colorectal Neoplasms; Genomic Structural Variation; Ubiquitin-Protein Ligases
PubMed: 36812239
DOI: 10.1371/journal.pgen.1010514 -
International Journal of Molecular... Sep 2022Hox genes play a crucial role in morphogenesis, especially in anterior-posterior body axis patterning. The organization of Hox clusters in vertebrates is a result of... (Review)
Review
Hox genes play a crucial role in morphogenesis, especially in anterior-posterior body axis patterning. The organization of Hox clusters in vertebrates is a result of several genome duplications: two rounds of duplication in the ancestors of all vertebrates and a third round that was specific for teleost fishes. Teleostei cluster structure has been significantly modified in the evolutionary processes by Hox gene losses and co-options, while mammals show no such tendency. In mammals, the Hox gene number in a single cluster is stable and generally large, and the numbers are similar to those in the Chondrichthyes. Hox gene alternative splicing activity slightly differs between fishes and mammals. Fishes and mammals have differences in their known alternative splicing activity for Hox gene distribution along the anterior-posterior body axis. The analyzed fish groups-the Coelacanthiformes, Chondrichthyes, and Teleostei-all have higher known alternative mRNA numbers from the anterior and posterior regions, whereas mammals have a more uniform Hox transcript distribution along this axis. In fishes, most Hox transcripts produce functioning proteins, whereas mammals have significantly more known transcripts that do not produce functioning proteins.
Topics: Animals; Evolution, Molecular; Fishes; Gene Duplication; Genes, Homeobox; Mammals; Multigene Family; Phylogeny
PubMed: 36077385
DOI: 10.3390/ijms23179990 -
Trends in Molecular Medicine Nov 2021Enhancers are genomic sequences that play a key role in regulating tissue-specific gene expression levels. An increasing number of diseases are linked to impaired... (Review)
Review
Enhancers are genomic sequences that play a key role in regulating tissue-specific gene expression levels. An increasing number of diseases are linked to impaired enhancer function through chromosomal rearrangement, genetic variation within enhancers, or epigenetic modulation. Here, we review how these enhancer disruptions have recently been implicated in congenital disorders, cancers, and common complex diseases and address the implications for diagnosis and treatment. Although further fundamental research into enhancer function, target genes, and context is required, enhancer-targeting drugs and gene editing approaches show great therapeutic promise for a range of diseases.
Topics: Enhancer Elements, Genetic; Epigenomics; Gene Editing; Genomics; Humans
PubMed: 34420874
DOI: 10.1016/j.molmed.2021.07.012 -
International Journal of Molecular... Mar 2022YEATS (YAF9, ENL, AF9, TAF14, SAS5) family proteins recognize acylated histones and in turn regulate chromatin structure, gene transcription, and stress signaling. The...
YEATS (YAF9, ENL, AF9, TAF14, SAS5) family proteins recognize acylated histones and in turn regulate chromatin structure, gene transcription, and stress signaling. The chromosomal translocations of ENL and mixed lineage leukemia are considered oncogenic drivers in acute myeloid leukemia and acute lymphoid leukemia. However, known ENL YEATS domain inhibitors have failed to suppress the proliferation of 60 tested cancer cell lines. Herein, we identified four hits from the NMR fragment-based screening against the AF9 YEATS domain. Ten inhibitors of new chemotypes were then designed and synthesized guided by two complex structures and affinity assays. The complex structures revealed that these inhibitors formed an extra hydrogen bond to AF9, with respect to known ENL inhibitors. Furthermore, these inhibitors demonstrated antiproliferation activities in AF9-sensitive HGC-27 cells, which recapitulated the phenotype of the CRISPR studies against AF9. Our work will provide the basis for further structured-based optimization and reignite the campaign for potent AF9 YEATS inhibitors as a precise treatment for AF9-sensitive cancers.
Topics: Histones; Humans; Leukemia, Myeloid, Acute; Oncogenes; Protein Domains
PubMed: 35409252
DOI: 10.3390/ijms23073893 -
Journal of Natural Products May 2022The genome of entomopathogenic fungus Gams encodes 43 putative biosynthetic gene clusters for specialized metabolites, although genotype-phenotype linkages have been... (Review)
Review
The genome of entomopathogenic fungus Gams encodes 43 putative biosynthetic gene clusters for specialized metabolites, although genotype-phenotype linkages have been reported only for the cyclosporins and fumonisins. was cultured in defined minimal media, supplemented with or without one of nine different amino acids. Acquisition of LC-MS/MS data for molecular networking and manual analysis facilitated annotation of putative known and unknown metabolites. These data led us to target a family of peptaibols and guided the isolation and purification of tolypocladamide H (), which showed modest antibacterial activity and toxicity to mammalian cells at micromolar concentrations. HRMS/MS, NMR, and advanced Marfey's analysis were used to assign the structure of as a peptaibol containing 4-[()-2-butenyl]-4-methyl-l-threonine (Bmt), a hallmark structural motif of the cyclosporins. LC-MS detection of homologous tolypocladamide metabolites and phylogenomic analyses of peptaibol biosynthetic genes in other cultured species allowed assignment of a putative tolypocladamide nonribosomal peptide synthetase gene.
Topics: Animals; Chromatography, Liquid; Cyclosporins; Mammals; Molecular Structure; Multigene Family; Peptaibols; Tandem Mass Spectrometry
PubMed: 35500108
DOI: 10.1021/acs.jnatprod.2c00153 -
Scientific Reports Apr 2023Isoflavone reductase (IFR) is a key enzyme controlling isoflavone synthesis and widely involved in response to various stresses. In this study, the IFR genes in four...
Isoflavone reductase (IFR) is a key enzyme controlling isoflavone synthesis and widely involved in response to various stresses. In this study, the IFR genes in four Gossypium species and other 7 species were identified and analyzed in the whole genome, and the physicochemical properties, gene structures, cis-acting elements, chromosomal locations, collinearity relationships and expression patterns of IFR genes were systematically analyzed. 28, 28, 14 and 15 IFR genes were identified in Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii, respectively, which were divided into five clades according to the evolutionary tree and gene structure. Collinear analysis showed that segmental duplication and whole genome duplication were the main driving forces in the process of evolution, and most genes underwent pure selection. Gene structure analysis showed that IFR gene family was relatively conserved. Cis-element analysis of promoter showed that most GhIFR genes contain cis-elements related to abiotic stresses and plant hormones. Analysis of GhIFR gene expression under different stresses showed that GhIFR genes were involved in the response to drought, salt, heat and cold stresses through corresponding network mechanisms, especially GhIFR9A. Phenotypic analysis after silencing GhIFR9A gene by VIGS was shown that GhIFR9A gene was involved in the response to salt stress. This study laid a foundation for the subsequent functional study of cotton IFR genes.
Topics: Multigene Family; Gossypium; Chromosomes; Regulatory Sequences, Nucleic Acid; Stress, Physiological; Gene Expression Regulation, Plant; Phylogeny; Plant Proteins; Genome, Plant
PubMed: 37029187
DOI: 10.1038/s41598-023-32213-3 -
Genes May 2021Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved....
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of L. contained introns, and cp tRNA contained the anti-codon (C-A-U), which was generally the anti-codon of tRNA. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.
Topics: Codon; Evolution, Molecular; Genes, Chloroplast; Genomic Structural Variation; Gossypium; Phylogeny; RNA, Transfer
PubMed: 34071968
DOI: 10.3390/genes12060822 -
Biosensors & Bioelectronics Mar 2022In a published review entitled "COVID-19 diagnosis -A review of current methods", the authors considered hemagglutinin esterase as one of the structural proteins of... (Review)
Review
In a published review entitled "COVID-19 diagnosis -A review of current methods", the authors considered hemagglutinin esterase as one of the structural proteins of SARS-CoV-2 and also they did not represent ORF3b, ORF9b, and ORF9c in SARS-CoV-2 genome structure. However, according to the scientific evidence, among coronaviruses only some betacoronaviruses (Embecovirus subgenera) contain HE, and the genome of most of the coronaviruses such as SARS-CoV-2, SARS-CoV, and MERS-CoV lack the HE gene. In addition, the genome of SARS-CoV-2 contains several accessory proteins ORFs including ORF3a, ORF3b, ORF6, ORF7a, ORF7b, ORF8, ORF9b, ORF9c, and ORF10.
Topics: Biosensing Techniques; COVID-19; COVID-19 Testing; Humans; Open Reading Frames; SARS-CoV-2
PubMed: 34974265
DOI: 10.1016/j.bios.2021.113924