Research Progress in the Biosynthetic Mechanisms of Marine Polyether Toxins
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Mrna Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection
International Journal of Molecular Sciences Review mRNA Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection 1, 1, 2 1,3, Shuqin Xu y, Kunpeng Yang y, Rose Li and Lu Zhang * 1 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200438, China; [email protected] (S.X.); [email protected] (K.Y.) 2 M.B.B.S., School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; [email protected] 3 Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, China * Correspondence: [email protected]; Tel.: +86-13524278762 These authors contributed equally to this work. y Received: 30 July 2020; Accepted: 30 August 2020; Published: 9 September 2020 Abstract: Messenger ribonucleic acid (mRNA)-based drugs, notably mRNA vaccines, have been widely proven as a promising treatment strategy in immune therapeutics. The extraordinary advantages associated with mRNA vaccines, including their high efficacy, a relatively low severity of side effects, and low attainment costs, have enabled them to become prevalent in pre-clinical and clinical trials against various infectious diseases and cancers. Recent technological advancements have alleviated some issues that hinder mRNA vaccine development, such as low efficiency that exist in both gene translation and in vivo deliveries. mRNA immunogenicity can also be greatly adjusted as a result of upgraded technologies. In this review, we have summarized details regarding the optimization of mRNA vaccines, and the underlying biological mechanisms of this form of vaccines. Applications of mRNA vaccines in some infectious diseases and cancers are introduced. It also includes our prospections for mRNA vaccine applications in diseases caused by bacterial pathogens, such as tuberculosis. -
Small RNA Fragments Derived from Multiple RNA Classes – the Missing
Jackowiak et al. BMC Genomics (2017) 18:502 DOI 10.1186/s12864-017-3891-3 RESEARCHARTICLE Open Access Small RNA fragments derived from multiple RNA classes – the missing element of multi-omics characteristics of the hepatitis C virus cell culture model Paulina Jackowiak1, Anna Hojka-Osinska1, Anna Philips1, Agnieszka Zmienko1,2, Lucyna Budzko1, Patrick Maillard3, Agata Budkowska3,4 and Marek Figlerowicz1,2* Abstract Background: A pool of small RNA fragments (RFs) derived from diverse cellular RNAs has recently emerged as a rich source of functionally relevant molecules. Although their formation and accumulation has been connected to various stress conditions, the knowledge on RFs produced upon viral infections is very limited. Here, we applied the next generation sequencing (NGS) to characterize RFs generated in the hepatitis C virus (HCV) cell culture model (HCV-permissive Huh-7.5 cell line). Results: We found that both infected and non-infected cells contained a wide spectrum of RFs derived from virtually all RNA classes. A significant fraction of identified RFs accumulated to similar levels as miRNAs. Our analysis, focused on RFs originating from constitutively expressed non-coding RNAs, revealed three major patterns of parental RNA cleavage. We found that HCV infection induced significant changes in the accumulation of low copy number RFs, while subtly altered the levels of high copy number ones. Finally, the candidate RFs potentially relevant for host-virus interactions were identified. Conclusions: Our results indicate that RFs should be considered an important component of the Huh-7.5 transcriptome and suggest that the main factors influencing the RF biogenesis are the RNA structure and RNA protection by interacting proteins. -
Explore the RNA Universe!
Explore the RNA Universe! Circulating cell-free RNA (ccfRNA) Exosomes Exosomal RNA (exRNA) Ribonuclease P (RNase P) Small (short) interfering RNA (siRNA) Pre-miRNA Small nucleolar RNA Exportin-5 (snoRNA) MicroRNA (miRNA) Drosha Pri-miRNA RISC DGCR8 Ribosomal RNA (rRNA) Small nuclear RNA Ribonuclease MRP Y RNA (snRNA) (RNase MRP) Long non-coding RNA Messenger RNA (mRNA) (IncRNA) Transfer RNA (tRNA) Telomerase RNA Ribosomes Signal recognition particle RNA (SRP RNA) Mitochondria Piwi-interacting RNA (piRNA) Sample to Insight Explore the RNA Universe! RNA function RNA type Detailed role in the cell Protein synthesis Messenger RNA (mRNA) Carrying the genetic information copied from DNA in the form of three-nucleotide bases “codon,” each specifying a particular amino acid for protein synthesis at the ribosomes. Purify with: RNeasy® Plus Kits*, RNeasy Kits*, QIAamp® RNA Blood Kit*, QIAcube® Assay using: QuantiNova® Kits, RT2 Profiler™ PCR Assays and Arrays, Rotor-Gene® Q , QIAseq™ Targeted RNA Panels, QIAseq Stranded mRNA Select Library Kit, QIAseq UPX 3' Targeted RNA Panel, QIAseq UPX 3' Transcriptome RNA Library Kit, QIAseq Targeted RNAscan Panels, QIAseq FX Single Cell RNA Library Kit Transfer RNA Adapter molecule bringing the amino acid corresponding to a specific mRNA codon to the ribosome. Having an anticodon (complementary to the codon), a site (tRNA) binding a specific amino acid and a site binding aminoacyl-tRNA synthetase (enzyme catalyzing amino acid-tRNA binding). Ribosomal RNA (rRNA) RNA component of the ribosome, where protein is translated. Ribosomes align the anticodon of tRNA with the mRNA codon and are required for the peptidyl transferase activity catalyzing the assembly of amino acids into protein chains. -
Revealing the Missing Expressed Genes Beyond the Human Reference
Chen et al. BMC Genomics 2011, 12:590 http://www.biomedcentral.com/1471-2164/12/590 RESEARCH ARTICLE Open Access Revealing the missing expressed genes beyond the human reference genome by RNA-Seq Geng Chen1, Ruiyuan Li2, Leming Shi3, Junyi Qi1, Pengzhan Hu1, Jian Luo1, Mingyao Liu1 and Tieliu Shi1,4* Abstract Background: The complete and accurate human reference genome is important for functional genomics researches. Therefore, the incomplete reference genome and individual specific sequences have significant effects on various studies. Results: we used two RNA-Seq datasets from human brain tissues and 10 mixed cell lines to investigate the completeness of human reference genome. First, we demonstrated that in previously identified ~5 Mb Asian and ~5 Mb African novel sequences that are absent from the human reference genome of NCBI build 36, ~211 kb and ~201 kb of them could be transcribed, respectively. Our results suggest that many of those transcribed regions are not specific to Asian and African, but also present in Caucasian. Then, we found that the expressions of 104 RefSeq genes that are unalignable to NCBI build 37 in brain and cell lines are higher than 0.1 RPKM. 55 of them are conserved across human, chimpanzee and macaque, suggesting that there are still a significant number of functional human genes absent from the human reference genome. Moreover, we identified hundreds of novel transcript contigs that cannot be aligned to NCBI build 37, RefSeq genes and EST sequences. Some of those novel transcript contigs are also conserved among human, chimpanzee and macaque. By positioning those contigs onto the human genome, we identified several large deletions in the reference genome. -
Coding RNA Genes
Review A guide to naming human non-coding RNA genes Ruth L Seal1,2,* , Ling-Ling Chen3, Sam Griffiths-Jones4, Todd M Lowe5, Michael B Mathews6, Dawn O’Reilly7, Andrew J Pierce8, Peter F Stadler9,10,11,12,13, Igor Ulitsky14 , Sandra L Wolin15 & Elspeth A Bruford1,2 Abstract working on non-coding RNA (ncRNA) nomenclature in the mid- 1980s with the approval of initial gene symbols for mitochondrial Research on non-coding RNA (ncRNA) is a rapidly expanding field. transfer RNA (tRNA) genes. Since then, we have worked closely Providing an official gene symbol and name to ncRNA genes brings with experts in the ncRNA field to develop symbols for many dif- order to otherwise potential chaos as it allows unambiguous ferent kinds of ncRNA genes. communication about each gene. The HUGO Gene Nomenclature The number of genes that the HGNC has named per ncRNA class Committee (HGNC, www.genenames.org) is the only group with is shown in Fig 1, and ranges in number from over 4,500 long the authority to approve symbols for human genes. The HGNC ncRNA (lncRNA) genes and over 1,900 microRNA genes, to just four works with specialist advisors for different classes of ncRNA to genes in the vault and Y RNA classes. Every gene symbol has a ensure that ncRNA nomenclature is accurate and informative, Symbol Report on our website, www.genenames.org, which where possible. Here, we review each major class of ncRNA that is displays the gene symbol, gene name, chromosomal location and currently annotated in the human genome and describe how each also includes links to key resources such as Ensembl (Zerbino et al, class is assigned a standardised nomenclature. -
Long Noncoding Rnas Involvement in Epstein-Barr Virus Infection And
Zhang et al. Virology Journal (2020) 17:51 https://doi.org/10.1186/s12985-020-01308-y REVIEW Open Access Long noncoding RNAs involvement in Epstein-Barr virus infection and tumorigenesis Jing Zhang1,2,3, Xiaohan Li1,2,3, Jingjin Hu1,2,3, Pengfei Cao2, Qijia Yan1,2, Siwei Zhang1,2,3, Wei Dang1,2,3 and Jianhong Lu1,2* Abstract The Epstein-Barr virus (EBV) is a ubiquitous γ-herpesvirus related to various types of cancers, including epithelial nasopharyngeal carcinoma, gastric carcinoma, and lymphoma. Long noncoding RNAs (lncRNAs) are expressed extensively in mammalian cells and play crucial roles in regulating various cellular processes and multiple cancers. Cellular lncRNAs can be differentially expressed induced by EBV infection. The dysregulated lncRNAs probably modulate the host immune response and other biological functions. At present, lncRNAs have been found to be significantly increased or decreased in EBV-infected cells, exosomes and EBV-associated cancers, suggesting their potential function and clinical application as biomarkers. In addition, EBV-encoded lncRNAs, BART and BHLF1 lncRNAs, may play roles in the viral oncogenesis. Analysis of the specific lncRNAs involved in interactions with the EBV machinery will provide information on their potential mechanism of action during multiple steps of EBV tumorigenesis. Here, we review the current knowledge regarding EBV- related lncRNAs and their possible roles in the pathogenesis of EBV-associated cancers. Keywords: Long noncoding RNA, Epstein-Barr virus, Tumorigenesis, Epithelial cancer, Lymphoma Background lymphoma, nasopharyngeal carcinoma (NPC), gastric can- Epstein-Barr virus (EBV) is a ubiquitous γ-herpesvirus, cer (GC), Hodgkin’s disease and breast cancer [1, 2]. -
FMB Ch05-Gerwick.Indd
PB Marine Cyanobacteria Ramaswamy et al. 175 5 The Secondary Metabolites and Biosynthetic Gene Clusters of Marine Cyanobacteria. Applications in Biotechnology Aishwarya V. Ramaswamy, Patricia M. Flatt, Daniel J. Edwards, T. Luke Simmons, Bingnan Han and William H. Gerwick* Abstract Marine cyanobacteria have proven to be one of the most versatile marine producers of secondary metabolites. Many of these metabolites demonstrate antiproliferative activity (e.g. curacin A, dolastatins), acute cytotoxic activity (e.g. apratoxin, hectochlorin) or have specific neurotoxic activity (e.g. kalkitoxin, antillatoxin), making them invaluable as potential therapeutic leads or pharmacological tools. The predominant biogenetic theme in cyanobacterial natural products chemistry is the integration of polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS) along with a variety of unusual tailoring or modifying enzymes, and accounts for the tremendous structural diversity of their metabolites. Only recently has the genetic architecture of several cyanobacterial biosynthetic gene clusters been determined, and studies to understand and exploit this biosynthentic machinery present an exciting new frontier. This chapter will summarize the properties of several notable metabolites from marine cyanobacteria that have clinical or pharmacological applications followed by a detailed account of their biosyntheses at the molecular genetic level and their potential applications in biotechnology. 1. Introduction Cyanobacteria, also known as blue-green algae, are ancient (ca. 2 x 109 years) photosynthetic prokaryotes which inhabit a wide diversity of habitats including *For correspondence email [email protected] 176 Marine Cyanobacteria Ramaswamy et al. 177 open oceans, tropical reefs, shallow water environments, terrestrial substrates, aerial environments such as in trees and rock faces, and fresh water ponds, streams and puddles (Whitton and Potts, 2000) . -
Why Y Rnas? About Versatile Rnas and Their Functions
Biomolecules 2013, 3, 143-156; doi:10.3390/biom3010143 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Review Why Y RNAs? About Versatile RNAs and Their Functions Marcel Köhn, Nikolaos Pazaitis and Stefan Hüttelmaier * Martin-Luther-University Halle-Wittenberg, Institute of Molecular Medicine, Section Molecular Cell Biology, ZAMED, Heinrich-Damerow-Str.1, D-6120 Halle, Germany; E-Mails: [email protected] (M.K.) [email protected] (N.P.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +0049-(0)3455522860; Fax: +0049-(0)3455522894. Received: 31 December 2012; in revised form: 27 January 2013 / Accepted: 31 January 2013 / Published: 8 February 2013 Abstract: Y RNAs constitute a family of highly conserved small noncoding RNAs (in humans: 83-112 nt; Y1, Y3, Y4 and Y5). They are transcribed from individual genes by RNA-polymerase III and fold into conserved stem-loop-structures. Although discovered 30 years ago, insights into the cellular and physiological role of Y RNAs remains incomplete. In this review, we will discuss knowledge on the structural properties, associated proteins and discuss proposed functions of Y RNAs. We suggest Y RNAs to be an integral part of ribonucleoprotein networks within cells and could therefore have substantial influence on many different cellular processes. Putative functions of Y RNAs include small RNA quality control, DNA replication, regulation of the cellular stress response and proliferation. This suggests Y RNAs as essential regulators of cell fate and indicates future avenues of research, which will provide novel insights into the role of small noncoding RNAs in gene expression. -
UC San Diego Dissertation
UNIVERSITY OF CALIFORNIA, SAN DIEGO Enhancing Natural Products Structural Dereplication and Elucidation with Deep Learning Based Nuclear Magnetic Resonance Techniques A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in NanoEngineering by Chen Zhang Committee in charge: William H. Gerwick, Chair Garrison W. Cottrell, Co-Chair Gaurav Arya Seth M. Cohen Chambers C. Hughes Preston B. Landon Liangfang Zhang 2017 Copyright Chen Zhang, 2017 All rights reserved The Dissertation of Chen Zhang is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ____________________________________________ ____________________________________________ ____________________________________________ ____________________________________________ ____________________________________________ ____________________________________________ Co-Chair ____________________________________________ Chair University of California, San Diego 2017 iii DEDICATION I dedicate my dissertation work to my family and many friends. A special feeling of gratitude to my beloved parents, Jianping Zhao and Xiaojing Zhang whose words of encouragement and push for tenacity ring in my ears. My cousin Min Zhang has never left my side and is very special. I also dedicate this dissertation to my mentors who have shown me fascinating views of the world throughout the process, and those who have walked me through the valley of the shadow of frustration. I will always appreciate all they have done, especially Bill Gerwick, Gary Cottrell and Preston Landon for showing me the gate to new frontiers, Sylvia Evans, Pieter Dorrestein, Shu Chien, Liangfang Zhang, and Gaurav Arya for their great encouragement, and Wood Lee and Yezifeng for initially showing me the value of freedom, and continuously answering my questions regarding social sciences, humanities, literature, and arts. -
Cloning and Biochemical Characterization of the Hectochlorin Biosynthetic Gene Cluster from the Marine Cyanobacteriumlyngbya Majuscula
AN ABSTRACT OF THE DISSERTATION OF Aishwarya V. Ramaswamy for the degree of Doctor of Philosophy in Microbiology presented on June 02, 2005. Title: Cloning and Biochemical Characterization of the Hectochiorin Biosynthetic Gene Cluster from the Marine Cyanobacterium Lyngbya maluscula Abstract approved: Redacted for privacy William H. Gerwick Cyanobacteria are rich in biologically active secondary metabolites, many of which have potential application as anticancer or antimicrobial drugs or as useful probes in cell biology studies. A Jamaican isolate of the marine cyanobacterium, Lyngbya majuscula was the source of a novel antifungal and cytotoxic secondary metabolite, hectochlorin. The structure of hectochiorin suggested that it was derived from a hybid PKS/NIRPS system. Unique features of hectochlorin such as the presence of a gem dichloro functionality and two 2,3-dihydroxy isovaleric acid prompted efforts to clone and characterize the gene cluster involved in hectochiorin biosynthesis. Initial attempts to isolate the hectochlorin biosynthetic gene cluster led to the identification of a mixed PKS/NRPS gene cluster, LMcryl,whose genetic architecture did not substantiate its involvement in the biosynthesis of hectochlorin. This gene cluster was designated as a cryptic gene cluster because a corresponding metabolite remains as yet unidentified. The expression of thisgene cluster was successfully demonstrated using RT-PCR and these results form the basis for characterizing the metabolite using a novel interdisciplinary approach. A 38 kb region -
RNA Metabolism Guided by RNA Modifications
biomolecules Review RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control Lisa Lirussi 1,2 , Özlem Demir 3, Panpan You 1,2, Antonio Sarno 4,5 , Rommie E. Amaro 3 and Hilde Nilsen 1,2,* 1 Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; [email protected] (L.L.); [email protected] (P.Y.) 2 Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway 3 Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA; [email protected] (Ö.D.); [email protected] (R.E.A.) 4 Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway; [email protected] 5 SINTEF Ocean AS, 7010 Trondheim, Norway * Correspondence: [email protected]; Tel.: +47-67963922 Abstract: RNA modifications are essential for proper RNA processing, quality control, and matura- tion steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveil- lance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucle- oproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. -
Chicken Genome: Current Status and Future Opportunities
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Perspective Chicken genome: Current status and future opportunities David W. Burt Department of Genomics and Genetics, Roslin Institute (Edinburgh), Midlothian EH25 9PS, United Kingdom The chicken genome sequence is important for several reasons. First, the chicken shared a common ancestor with mammals ∼310 million years ago (Mya) at a phylogenetic distance not previously covered by other genome sequences. It therefore fills a gap in our knowledge and understanding of the evolution and conservation of genes, regulatory sequences, genomes, and karyotypes. The chicken is also a major source of protein in the world, with billions of birds used in meat and egg production each year. It is the first livestock species to be sequenced and so leads the way for others. The sequence and the 2.8 million genetic polymorphisms defined in a parallel project are expected to benefit agriculture and cast new light on animal domestication. Also, as the first bird to be sequenced, it is a model for the 9600 avian species thought to exist today. Many of the features of the chicken genome and its biology make it an ideal organism for studies in development and evolution, along with applications in agriculture and medicine. Avian genomics has its origins in genetic linkage mapping (Burt been an increase in the incidence of osteoporosis associated with and Cheng 1998), but our knowledge of the chicken genome has increased egg production. Given the possibility that genetic been transformed in recent years, mostly through the analysis of progress in egg and meat production will reach its limit within large numbers of partial cDNA sequences (Abdrakhmanov et al.