scholarly journals Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes

Marine Drugs ◽  
2021 ◽  
Vol 19 (7) ◽  
pp. 392
Author(s):  
Haomiao Cheng ◽  
Chris Bowler ◽  
Xiaohui Xing ◽  
Vincent Bulone ◽  
Zhanru Shao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Full Length ◽  
Biosynthetic Pathways ◽  
Glycosidic Linkage ◽  
Thalassiosira Weissflogii ◽  
Ecological Value ◽  
Pacbio Sequencing ◽  
Non Coding Rnas ◽  
Chitin And Chitosan ◽  
Simple Sequence

β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.

scholarly journals Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis

Life ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 287
Author(s):  
Kunyuan Guo ◽  
Jie Chen ◽  
Yan Niu ◽  
Xianming Lin
Keyword(s):  
Average Length ◽  
Flavonoid Biosynthesis ◽  
Full Length ◽  
Marker Assisted Breeding ◽  
Pacbio Rs Ii ◽  
Secondary Metabolite Biosynthesis ◽  
Non Coding Rnas ◽  
First Time ◽  
Flavonoid Biosynthesis Pathway ◽  
Simple Sequence

One of the most commonly utilized medicinal plants in China is Fritillaria hupehensis (Hsiao et K.C. Hsia). However, due to a lack of genomic resources, little is known about the biosynthesis of relevant compounds, particularly the flavonoid biosynthesis pathway. A PacBio RS II sequencing generated a total of 342,044 reads from the bulb, leaf, root, and stem, of which 316,438 were full-length (FL) non-redundant reads with an average length of 1365 bp and a N50 of 1888 bp. There were also 38,607 long non-coding RNAs and 7914 simple sequence repeats detected. To improve our understanding of processes implicated in regulating secondary metabolite biosynthesis in F. hupehensis tissues, we evaluated potential metabolic pathways. Overall, this study provides a repertoire of FL transcripts in F. hupehensis for the first time, and it will be a valuable resource for marker-assisted breeding and research into bioactive compounds for medicinal and pharmacological applications.

scholarly journals Functional Genomic Identification of Cadmium Resistance Genes from a High GC Clone Library by Coupling the Sanger and PacBio Sequencing Strategies

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 7
Author(s):  
Jinghao Chen ◽  
Chao Xing ◽  
Xin Zheng ◽  
Xiaofang Li
Keyword(s):  
High Throughput ◽  
Resistance Genes ◽  
Sanger Sequencing ◽  
Genomic Library ◽  
Full Length ◽  
Host Cells ◽  
Full Genome Sequence ◽  
Functional Screening ◽  
Functional Genomic ◽  
Pacbio Sequencing

Functional (meta) genomics allows the high-throughput identification of functional genes in a premise-free way. However, it is still difficult to perform Sanger sequencing for high GC DNA templates, which hinders the functional genomic exploration of a high GC genomic library. Here, we developed a procedure to resolve this problem by coupling the Sanger and PacBio sequencing strategies. Identification of cadmium (Cd) resistance genes from a small-insert high GC genomic library was performed to test the procedure. The library was generated from a high GC (75.35%) bacterial genome. Nineteen clones that conferred Cd resistance to Escherichia coli subject to Sanger sequencing directly. The positive clones were in parallel subject to in vivo amplification in host cells, from which recombinant plasmids were extracted and linearized by selected restriction endonucleases. PacBio sequencing was performed to obtain the full-length sequences. As the identities, partial sequences from Sanger sequencing were aligned to the full-length sequences from PacBio sequencing, which led to the identification of seven unique full-length sequences. The unique sequences were further aligned to the full genome sequence of the source strain. Functional screening showed that the identified positive clones were all able to improve Cd resistance of the host cells. The functional genomic procedure developed here couples the Sanger and PacBio sequencing methods and overcomes the difficulties in PCR approaches for high GC DNA. The procedure can be a promising option for the high-throughput sequencing of functional genomic libraries, and realize a cost-effective and time-efficient identification of the positive clones, particularly for high GC genetic materials.

Hydroxyproline-O-glycosidic Linkage of the Plant Cell Wall Glycoprotein Extensin

Nature ◽  
1967 ◽  
Vol 216 (5122) ◽  
pp. 1322-1324 ◽  
Author(s):  
DEREK T. A. LAMPORT
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Glycosidic Linkage

scholarly journals A metabolic dependency for host isoprenoids in the obligate intracellular pathogenRickettsia parkeriunderlies a sensitivity for the statin class of host-targeted therapeutics

2019 ◽  
Author(s):  
Vida Ahyong ◽  
Charles A. Berdan ◽  
Daniel K. Nomura ◽  
Matthew D. Welch
Keyword(s):  
Cell Wall ◽  
Host Cell ◽  
Bacterial Growth ◽  
Spotted Fever ◽  
Intracellular Pathogens ◽  
Biosynthetic Pathways ◽  
Targeted Therapeutics ◽  
Rickettsia Parkeri ◽  
Obligate Intracellular ◽  
Intracellular Parasites

AbstractGram-negative bacteria in the order Rickettsiales are obligate intracellular parasites that cause human diseases such typhus and spotted fever. They have evolved a dependence on essential nutrients and metabolites from the host cell as a consequence of extensive genome streamlining. However, it remains largely unknown which nutrients they require and whether their metabolic dependency can be exploited therapeutically. Here, we describe a genetic rewiring of bacterial isoprenoid biosynthetic pathways in the Rickettsiales that has resulted from reductive genome evolution. We further investigated whether the spotted fever groupRickettsiaspeciesRickettsia parkeriscavenges isoprenoid precursors directly from the host. Using targeted mass spectrometry in uninfected and infected cells, we found decreases in host isoprenoid products and concomitant increases in bacterial isoprenoid metabolites. Additionally, we report that bacterial growth is prohibited by inhibition of the host isoprenoid pathway with the statins class of drugs. We show that growth inhibition correlates with changes in bacterial size and shape that mimic those caused by antibiotics that inhibit peptidoglycan biosynthesis, suggesting statins inhibit cell wall synthesis. Altogether, our results describe an Achilles’ heel of obligate intracellular pathogens that can be exploited with host-targeted therapeutics that interfere with metabolic pathways required for bacterial growth.ImportanceObligate intracellular parasites, which include viruses as well as certain bacteria and eukaryotes, extract essential nutrients and metabolites from their host cell. As a result, these pathogens have often lost essential biosynthetic pathways and are metabolically dependent on the host. In this study, we describe a metabolic dependency of the bacterial pathogenRickettsia parkerion host isoprenoid molecules that are used in the biosynthesis of downstream products including cholesterol, steroid hormones, and heme. Bacteria make products from isoprenoids such as an essential lipid carrier for making the bacterial cell wall. We show that bacterial metabolic dependency can represent an Achilles’ heel, and that inhibiting host isoprenoid biosynthesis with the FDA-approved statin class of drugs inhibits bacterial growth by interfering with the integrity of the cell wall. This work highlights a potential to treat infections by obligate intracellular pathogens through inhibition of host biosynthetic pathways that are susceptible to parasitism.

scholarly journals Synthesis of Biotin-Tagged Chitosan Oligosaccharides and Assessment of Their Immunomodulatory Activity

2020 ◽  
Vol 8 ◽  
Author(s):  
Yury E. Tsvetkov ◽  
Ema Paulovičová ◽  
Lucia Paulovičová ◽  
Pavol Farkaš ◽  
Nikolay E. Nifantiev
Keyword(s):  
Cell Wall ◽  
Chain Elongation ◽  
High Yield ◽  
Raw 264.7 Cells ◽  
Immunomodulatory Activity ◽  
Raw 264.7 ◽  
Fungal Cell ◽  
Chitosan Oligosaccharides ◽  
Chitin And Chitosan

Chitin, a polymer of β-(1→4)-linked N-acetyl-d-glucosamine, is one of the main polysaccharide components of the fungal cell wall. Its N-deacetylated form, chitosan, is enzymatically produced in the cell wall by chitin deacetylases. It exerts immunomodulative, anti-inflammatory, anti-cancer, anti-bacterial, and anti-fungal activities with various medical applications. To study the immunobiological properties of chitosan oligosaccharides, we synthesized a series of β-(1→4)-linked N-acetyl-d-glucosamine oligomers comprising 3, 5, and 7 monosaccharide units equipped with biotin tags. The key synthetic intermediate employed for oligosaccharide chain elongation, a disaccharide thioglycoside, was prepared by orthogonal glycosylation of a 4-OH thioglycoside acceptor with a glycosyl trichloroacetimidate bearing the temporary 4-O-tert-butyldimethylsilyl group. The use of silyl protection suppressed aglycon transfer and provided a high yield for the target disaccharide donor. Using synthesized chitosan oligomers, as well as previously obtained chitin counterparts, the immunobiological relationship between these synthetic oligosaccharides and RAW 264.7 cells was studied in vitro. Evaluation of cell proliferation, phagocytosis, respiratory burst, and Th1, Th2, Th17, and Treg polarized cytokine expression demonstrated effective immune responsiveness and immunomodulation in RAW 264.7 cells exposed to chitin- and chitosan-derived oligosaccharides. Macrophage reactivity was accompanied by significant inductive dose- and structure-dependent protective Th1 and Th17 polarization, which was greater with exposure to chitosan- rather than chitin-derived oligosaccharides. Moreover, no antiproliferative or cytotoxic effects were observed, even following prolonged 48 h exposure. The obtained results demonstrate the potent immunobiological activity of these synthetically prepared chito-oligosaccharides.

scholarly journals Protective activity of the fungal polysaccharides against fusariosis

2017 ◽  
Vol 38 (SI 2 - 6th Conf EFPP 2002) ◽  
pp. 617-619 ◽  
Author(s):  
A. Šrobárová ◽  
G. Kogan ◽  
L. Tamas ◽  
E. Machová
Keyword(s):  
Cell Wall ◽  
Antifungal Activity ◽  
Defense Mechanisms ◽  
Field Experiments ◽  
Plant Protection ◽  
Water Soluble ◽  
Protective Activity ◽  
Fresh Weight ◽  
Fungal Polysaccharides ◽  
Chitin And Chitosan

Most of the experiments carried out in the area of plant protection have used chitin and chitosan obtained from the crustacean chitin which production is rather expensive. In our study we have applied the chitin-glucan complex prepared from the waste mycelia of filamentous fungi, from baker’s yeast. Five different polysaccharides have been used for the preparation of water-soluble compounds and the assay of their antifungal activity against plant pathogen Fusarium oxysporum. In the field experiments, application of the polysaccharides led to the diminished infestation as well as to significantly increased productivity of fresh weight of the plants (tomato). The results demonstrated that application of the polysaccharides led to increased production of cell wall and some outher and intermembrane-bound proteins. Although the nature of the observed proteins has not been yet established, it can be speculated that they represent some enzymes involved in the antiinfective defense mechanisms in plants.

scholarly journals Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves of Gnetum (Gnetales)

2019 ◽  
Vol 20 (24) ◽  
pp. 6350 ◽  
Author(s):  
Nan Deng ◽  
Chen Hou ◽  
Fengfeng Ma ◽  
Caixia Liu ◽  
Yuxin Tian
Keyword(s):  
Single Molecule ◽  
Developmental Stages ◽  
Alternative Polyadenylation ◽  
Full Length ◽  
Stomatal Development ◽  
Rna Seq ◽  
Leaf Transcriptome ◽  
Long Read ◽  
Non Coding Rnas ◽  
A Site

The limitations of RNA sequencing make it difficult to accurately predict alternative splicing (AS) and alternative polyadenylation (APA) events and long non-coding RNAs (lncRNAs), all of which reveal transcriptomic diversity and the complexity of gene regulation. Gnetum, a genus with ambiguous phylogenetic placement in seed plants, has a distinct stomatal structure and photosynthetic characteristics. In this study, a full-length transcriptome of Gnetum luofuense leaves at different developmental stages was sequenced with the latest PacBio Sequel platform. After correction by short reads generated by Illumina RNA-Seq, 80,496 full-length transcripts were obtained, of which 5269 reads were identified as isoforms of novel genes. Additionally, 1660 lncRNAs and 12,998 AS events were detected. In total, 5647 genes in the G. luofuense leaves had APA featured by at least one poly(A) site. Moreover, 67 and 30 genes from the bHLH gene family, which play an important role in stomatal development and photosynthesis, were identified from the G. luofuense genome and leaf transcripts, respectively. This leaf transcriptome supplements the reference genome of G. luofuense, and the AS events and lncRNAs detected provide valuable resources for future studies of investigating low photosynthetic capacity of Gnetum.

scholarly journals Transcriptomic profile analysis of the halophyte Suaeda rigida response and tolerance under NaCl stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhan-Jiang Han ◽  
Yang Sun ◽  
Min Zhang ◽  
Jun-Tuan Zhai
Keyword(s):  
Cell Wall ◽  
Salt Tolerance ◽  
Protein Transport ◽  
Profile Analysis ◽  
Nitrogen Compound ◽  
Enrichment Analysis ◽  
Plant Type ◽  
Ecological Value ◽  
Annotation Database ◽  
Cell Wall Biogenesis

Abstract Suaeda rigida is a lignified, true haplotype that predominantly grows in the Tarim basin, China. It has significant economic and ecological value. Herein, with aim to determine the genes associated with salt tolerance, transcriptome sequencing was performed on its stem, leaves and root over three set NaCl gradients regimens at treatment intervals of 3 h and 5 days. From our findings, we identified 829,095 unigenes, with 331,394 being successfully matched to at least one annotation database. In roots, under 3 h treatment, no up-regulated DEGs were identified in 100 and 500 mM NaCl treated samples. Under 5 days treatment, 97, 60 and 242 up-regulated DEGs were identified in 100, 300, 500 mM NaCl treated samples, respectively. We identified 50, 22 and 255 down-regulated DEGs in 100, 300, 500 mM NaCl treated samples, respectively. GO biological process enrichment analysis established that down-regulated DEGs were associated with nitrogen compound transport, organic substance transport and intracellular protein transport while the up-regulated genes were enriched in cell wall biogenesis, such as plant-type cell wall biogenesis, cell wall assembly, extracellular matrix organization and plant-type cell wall organization. These findings provide valuable knowledge on genes associated with salt tolerance of Suaeda rigida, and can be applied in other downstream haplotype studies.

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