201
|
Abstract
Non-canonical amino acids are finding increasing use in basic and applied research. Proteins that evolved naturally for biological function did so by exploiting the chemistries of the canonical amino acids; however, when proteins are repurposed for biomedical and pharmacological applications, they are often subject to conditions different from those characteristic of their original biological environments. Non-canonical amino acids can impart properties that are inaccessible within canonical protein sequence space, and can thereby lead to improved or new functionality. We describe simple methods for global replacement of canonical amino acids by their non-canonical counterparts in recombinant proteins made in high yield in bacterial expression hosts. These methods can be used to engineer both chemical and physical properties of recombinant proteins.
Collapse
Affiliation(s)
- Katharine Y Fang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Seth A Lieblich
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
202
|
Abstract
Sequence-specific nucleases (SSNs) are nowadays fundamental tools to generate mutants that impaired in genes of interest. The bioactive molecules screened in the chemical genomics studies affect specific physiological process by disrupting the function of its target protein(s). Mutation analysis of the gene(s) of target protein(s) of the screened chemical is necessary to resolve how the chemical works in plants. Clustered regularly interspersed short palindromic repeats (CRISPR) from Prevotella and Francisella 1 (Cpf1) are newly characterized RNA-directed endonuclease. Several papers have shown clearly that Cpf1 could be a versatile SSN in plant genome engineering. Cfp1 from Francisella novicida (FnCpf1) recognizes TTN as its protospacer adjacent motif (PAM). FnCpf1 utilizes a shorter PAM compared to other known Cpf1s such as AsCpf1 or LbCpf1, which use TTTN as PAM. Since PAM length can be a limiting factor in target selection, this feature of FnCpf1 is practical for targeted mutagenesis experiments. The application of FnCpf1-mediated targeted mutagenesis to the chemical genomics could accelerate to figure out the mechanism of action of screened chemicals. Here, we describe procedures for targeted mutagenesis in rice and tobacco using FnCpf1.
Collapse
Affiliation(s)
- Akira Endo
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
| |
Collapse
|
203
|
Abstract
Noncanonical amino acid mutagenesis via amber suppression provides the means to tailor proteins inside living cells. A wide range of noncanonical amino acids have been incorporated using the Methanococcus pyrrolysyl-tRNA synthetase/tRNACUA (PylRS/PylT) in mammalian cell systems in proof of principle experiments, for (1) minimal genetically encoded fluorescence or affinity tagging, (2) photo-control of enzymes, (3) genetically encoded posttranslational protein modifications. We have developed a general and efficient method to genomically integrate the PylRS/PylT amber suppression machinery using PiggyBac-mediated transposition. A general protocol for the generation of stable amber suppression cell lines is described here. Using the modular plasmid system, homogenous and highly efficient amber suppression in a wide range of cell lines can be achieved.
Collapse
Affiliation(s)
- Simon J Elsässer
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
204
|
Gardiner DM, Benfield AH, Stiller J, Stephen S, Aitken K, Liu C, Kazan K. A high-resolution genetic map of the cereal crown rot pathogen Fusarium pseudograminearum provides a near-complete genome assembly. Mol Plant Pathol 2018; 19:217-226. [PMID: 27888554 PMCID: PMC6638115 DOI: 10.1111/mpp.12519] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 05/18/2023]
Abstract
Fusarium pseudograminearum is an important pathogen of wheat and barley, particularly in semi-arid environments. Previous genome assemblies for this organism were based entirely on short read data and are highly fragmented. In this work, a genetic map of F. pseudograminearum has been constructed for the first time based on a mapping population of 178 individuals. The genetic map, together with long read scaffolding of a short read-based genome assembly, was used to give a near-complete assembly of the four F. pseudograminearum chromosomes. Large regions of synteny between F. pseudograminearum and F. graminearum, the related pathogen that is the primary causal agent of cereal head blight disease, were previously proposed in the core conserved genome, but the construction of a genetic map to order and orient contigs is critical to the validation of synteny and the placing of species-specific regions. Indeed, our comparative analyses of the genomes of these two related pathogens suggest that rearrangements in the F. pseudograminearum genome have occurred in the chromosome ends. One of these rearrangements includes the transposition of an entire gene cluster involved in the detoxification of the benzoxazolinone (BOA) class of plant phytoalexins. This work provides an important genomic and genetic resource for F. pseudograminearum, which is less well characterized than F. graminearum. In addition, this study provides new insights into a better understanding of the sexual reproduction process in F. pseudograminearum, which informs us of the potential of this pathogen to evolve.
Collapse
Affiliation(s)
- Donald M. Gardiner
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Aurelie H. Benfield
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Jiri Stiller
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Stuart Stephen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Karen Aitken
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Chunji Liu
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| |
Collapse
|
205
|
Abstract
Site-specific, genetic incorporation of unnatural amino acids (UAAs) into proteins in living cells using engineered orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs is a powerful tool for studying and manipulating protein structure and function. To date, UAA incorporation systems have been developed for several bacterial and eukaryotic model hosts. Due to the importance of Streptomyces as prolific producers of bioactive natural products and as model hosts for natural product biosynthesis and bioengineering studies, we have developed systems for the incorporation of the UAAs p-iodo-L-phenylalanine (pIPhe) and p-azido-L-phenylalanine (pAzPhe) into green fluorescent protein (GFP) in Streptomyces venezuelae ATCC 15439. Here, we describe the procedure for using this system to site-specifically incorporate pIPhe or pAzPhe into proteins of interest in S. venezuelae. The modular design of plasmids harboring UAA incorporation systems enables use of other aaRS or aaRS/tRNA pairs for the incorporation of other UAAs; and the vector backbone used allows the system to be transferred to diverse Streptomyces species via both protoplast transformation and conjugation.
Collapse
Affiliation(s)
- Jingxuan He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
| | - Charles E Melançon
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA.
- Department of Biology, Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM, USA.
| |
Collapse
|
206
|
Ghosh S, Liu JL. Genomic Tagging of AGO1 Using CRISPR/Cas9-Mediated Homologous Recombination. Methods Mol Biol 2018; 1680:217-235. [PMID: 29030852 DOI: 10.1007/978-1-4939-7339-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Tagging of genes at the endogenous loci is a powerful strategy for the analysis of protein function. We have developed a homologous recombination-based approach for inserting epitope tag into Drosophila AGO1 locus by employing the CRISPR/Cas9 technology. The methodology involves co-expression of sgRNA (containing 20-nucleotide AGO1 targeting sequence) and Cas9 protein, together with a donor template that has HA-AGO1 cassette flanked by sequences homologous to the AGO1 locus. The integration is efficient and readily monitored by immunostaining of the transgenic cell line. This method facilitates rapid generation of stable cell lines and allows insertion of any tag sequence into endogenous loci, thus accelerating characterization of the tagged proteins.
Collapse
Affiliation(s)
- Sanjay Ghosh
- Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
| | - Ji-Long Liu
- Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
207
|
Abstract
Site-specific incorporation of unnatural amino acids (UAAs) has greatly expanded the toolkit available to study biological phenomena in single cells. However, to address questions involving complex cellular interactions such as development, ageing, and the functions of the nervous system it is often necessary to use multicellular model organisms. The nematode Caenorhabditis elegans was the first organism to have its genetic code expanded. Due to its small size, ease of cultivation, and excellent UAA incorporation efficiency, C. elegans makes an ideal model organism to apply UAAs as tools to investigate the functioning of multicellular systems.Here, we describe methods to generate transgenic C. elegans capable of UAA incorporation, as well as how to deliver unnatural amino acids and test incorporation. Furthermore, we describe methods to uncage photosensitive unnatural amino acid derivatives.
Collapse
Affiliation(s)
- Lloyd Davis
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, UK
| | - Sebastian Greiss
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
208
|
Connolly LR, Erlendson AA, Fargo CM, Jackson KK, Pelker MMG, Mazzola JW, Geisler MS, Freitag M. Application of the Cre/lox System to Construct Auxotrophic Markers for Quantitative Genetic Analyses in Fusarium graminearum. Methods Mol Biol 2018; 1848:235-263. [PMID: 30182239 DOI: 10.1007/978-1-4939-8724-5_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The bacteriophage P1 Cre/lox system has been utilized in diverse fungi for marker recycling and exchange, generation of targeted chromosome translocations, and targeted deletion of interstitial chromosome segments. Here we show the application of this tool in the wheat and maize pathogen, Fusarium graminearum. We explored three different ways to introduce Cre into strains with floxed genes, namely transformation with an episomal or integrative plasmid (pLC28), fusion of protoplasts of strains carrying floxed genes with strains expressing Cre by forcing heterokaryons, and crosses between strains with floxed genes and strains expressing Cre to isolate progeny in which the target genes had been deleted during the cross. We used this system for the construction of strains bearing auxotrophic markers that were generated by gene replacement with positively selectable markers followed by Cre-mediated marker excision. In addition, updated protocols for transformation and crosses for F. graminearum are provided. In combination, strains and tools developed here add to the arsenal of methods that can be used to carry out molecular genetics with F. graminearum.
Collapse
Affiliation(s)
- Lanelle R Connolly
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Corinne M Fargo
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Kendra K Jackson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Morgan M G Pelker
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Jacob W Mazzola
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Mark S Geisler
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
| |
Collapse
|
209
|
Abstract
The comparison of genome structures across distinct species offers valuable insights into the species' phylogeny, genome organization, and gene associations. In this chapter, we review the family-free genome comparison tool FFGC which provides several methods for gene order analyses that do not require prior knowledge of evolutionary relationships between the genes across the studied genomes. Moreover, the tool features a complete workflow for genome comparison, requiring nothing but annotated genome sequences as input.
Collapse
Affiliation(s)
- Daniel Doerr
- School of Computer and Communication Sciences, EPFL, Lausanne, Switzerland
| | - Pedro Feijão
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jens Stoye
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.
| |
Collapse
|
210
|
Abstract
Phytophthora capsici is an important plant pathogen, which causes significant economic losses on multiple vegetable crops worldwide. It is an ideal model pathogen to study the role of important genes, plant-pathogen interactions, and fungicide resistance mechanisms etc. due to its wide range of hosts and genetic diversity. A more efficient gene editing tool is required to do these studies. Here, we describe a detailed experimental procedure using the CRISPR-Cas9 system to edit genes of interest in P. capsici, which has been proven to be an accurate and efficient gene editing method in P. capsici.
Collapse
Affiliation(s)
- Zhiwen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Brett M Tyler
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing, China.
| |
Collapse
|
211
|
Hohnholz R, Pohlmann KJ, Achstetter T. Impact of plasmid architecture on stability and yEGFP3 reporter gene expression in a set of isomeric multicopy vectors in yeast. Appl Microbiol Biotechnol 2017; 101:8455-8463. [PMID: 29052760 PMCID: PMC5694506 DOI: 10.1007/s00253-017-8558-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/21/2017] [Accepted: 09/27/2017] [Indexed: 11/25/2022]
Abstract
Multicopy episomal plasmids in yeast, used whenever elevated levels of foreign or homologous gene expression are necessary, are known to be less stable compared to the endogenous 2-μm plasmid they are based on, at least without selective pressure. Considering that rich medium favors growth rate and, simultaneously, is less expensive than selective medium, enhancing stability in non-selective medium is extremely desirable. In this study, we changed the architecture of a multicopy model expression plasmid, creating six isoforms (same size, same DNA content but different positions and orientations of the expression block) and studied mitotic stability, copy number, as well as reporter yEGFP3 expression between isoforms. With one isoform being significantly more stable than the others and another one exhibiting elevated plasmid copy numbers in rich medium, we show that consideration of the arrangement of the plasmid elements might be crucial for productivity employing Saccharomyces cerevisiae as a host. We strongly believe that the ideal architecture has to be assessed for each case and assembly strategy has to begin by evaluating the stability of the vector backbone before insertion of the desired gene. For the plasmid set studied, yEGFP3 reporter production depends more on mitotic stability than on elevated plasmid copy numbers in a small number of cells retaining the plasmid under non-selective conditions.
Collapse
Affiliation(s)
- Ruben Hohnholz
- City University of Applied Sciences Bremen, Neustadtswall 30, D-28199, Bremen, Germany.
- Jacobs University Bremen, Campus Ring 1, D-28759, Bremen, Germany.
| | | | - Tilman Achstetter
- City University of Applied Sciences Bremen, Neustadtswall 30, D-28199, Bremen, Germany
| |
Collapse
|
212
|
Su Y, Zhang Y, Feng S, He J, Zhao Z, Bai Z, Liu L, Zhang R, Li Z. The mitochondrial genome of the wolfberry fruit fly, Neoceratitis asiatica (Becker) (Diptera: Tephritidae) and the phylogeny of Neoceratitis Hendel genus. Sci Rep 2017; 7:16612. [PMID: 29192255 PMCID: PMC5709374 DOI: 10.1038/s41598-017-16929-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/20/2017] [Indexed: 11/09/2022] Open
Abstract
Neoceratitis asiatica (Becker) (Diptera: Tephritidae) is one of the most important fruit pestsof wolfberry which is a traditional Chinese medicinal herb. We characterized the complete mitochondrial genome of N. asiatica and described its organization in this study. This mitogenome had a total length of 15,481 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region (A + T-rich control region). The overall base composition of N. asiatica in descending order was 40.6% A, 8.5% G, 38.4% T and 12.6% C. The phylogenetic relationships shows that Ceratitis capitata and N. asiatica may be sister taxa. This is the first report of the complete mitochondrial genome of a member of the Neoceratitis Genus and the complete mitochondrial genome sequence may provide useful information for phylogenetic analysis and studies between the genera Ceratitis and Neoceratitis.
Collapse
Affiliation(s)
- Yun Su
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Yue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Shiqian Feng
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jia He
- The Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Zihua Zhao
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Zhenzhen Bai
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Lijun Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Rong Zhang
- The Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China.
| | - Zhihong Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
213
|
Jeong D, Yoo J, Lee P, Kepreotis SV, Lee A, Wahlquist C, Brown BD, Kho C, Mercola M, Hajjar RJ. miR-25 Tough Decoy Enhances Cardiac Function in Heart Failure. Mol Ther 2017; 26:718-729. [PMID: 29273502 DOI: 10.1016/j.ymthe.2017.11.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 11/17/2017] [Accepted: 11/22/2017] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs are promising therapeutic targets, because their inhibition has the potential to normalize gene expression in diseased states. Recently, our group found that miR-25 is a key SERCA2a regulating microRNA, and we showed that multiple injections of antagomirs against miR-25 enhance cardiac contractility and function through SERCA2a restoration in a murine heart failure model. However, for clinical application, a more stable suppressor of miR-25 would be desirable. Tough Decoy (TuD) inhibitors are emerging as a highly effective method for microRNA inhibition due to their resistance to endonucleolytic degradation, high miRNA binding affinity, and efficient delivery. We generated a miR-25 TuD inhibitor and subcloned it into a cardiotropic AAV9 vector to evaluate its efficacy. The AAV9 TuD showed selective inhibition of miR-25 in vitro cardiomyoblast culture. In vivo, AAV9-miR-25 TuD delivered to the murine pressure-overload heart failure model selectively decreased expression of miR-25, increased levels of SERCA2a protein, and ameliorated cardiac dysfunction and fibrosis. Our data indicate that miR-25 TuD is an effective long-term suppressor of miR-25 and a promising therapeutic candidate to treat heart failure.
Collapse
Affiliation(s)
- Dongtak Jeong
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jimeen Yoo
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Philyoung Lee
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sacha V Kepreotis
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ahyoung Lee
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christine Wahlquist
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Brian D Brown
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Changwon Kho
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mark Mercola
- Department of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Roger J Hajjar
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
214
|
Du Y, Zhang C, Dietrich CH, Zhang Y, Dai W. Characterization of the complete mitochondrial genomes of Maiestas dorsalis and Japananus hyalinus (Hemiptera: Cicadellidae) and comparison with other Membracoidea. Sci Rep 2017; 7:14197. [PMID: 29079765 PMCID: PMC5660246 DOI: 10.1038/s41598-017-14703-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/17/2017] [Indexed: 01/29/2023] Open
Abstract
Only six mitochondrial genomes (mitogenomes) have been previously published for Cicadellidae, the largest family of Hemiptera. This study provides complete, annotated mitogenomes of two additional cicadellid, species Maiestas dorsalis and Japananus hyalinus, and the first comparative mitogenome analysis across the superfamily Membracoidea. The mitogenomes of both sequenced species are similar to those of other studied hemipteran mitogenomes in organization and the lengths are 15,352 and 15,364 bp with an A + T content of 78.7% and 76.6%, respectively. In M. dorsalis, all sequenced genes are arranged in the putative ancestral insect gene arrangement, while the tRNA cluster trnW-trnC-trnY is rearranged to trnY-trnW-trnC in J. hyalinus, the first reported gene rearrangement in Membracoidea. Phylogenetic analyses of the 11 available membracoid mitogenomes and outgroups representing the other two cicadomorphan superfamilies supported the monophyly of Membracoidea, and indicated that treehoppers are a derived lineage of leafhoppers. ML and BI analyses yielded topologies that were congruent except for relationships among included representatives of subfamily Deltocephalinae. Exclusion of third codon positions of PCGs improved some node support values in ML analyses.
Collapse
Affiliation(s)
- Yimin Du
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunni Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Yalin Zhang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Wu Dai
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.
| |
Collapse
|
215
|
Chingandu N, Kouakou K, Aka R, Ameyaw G, Gutierrez OA, Herrmann HW, Brown JK. The proposed new species, cacao red vein virus, and three previously recognized badnavirus species are associated with cacao swollen shoot disease. Virol J 2017; 14:199. [PMID: 29052506 PMCID: PMC5649073 DOI: 10.1186/s12985-017-0866-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 10/11/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao swollen shoot Togo A virus (CSSTAV) cause cacao swollen shoot disease (CSSD) in West Africa. During 2000-2003, leaf and shoot-swelling symptoms and rapid tree death were observed in cacao in Cote d'Ivoire and Ghana. Molecular tests showed positive infection in only ~50-60% of symptomatic trees, suggesting the possible emergence of an unknown badnavirus. METHODS The DNA virome was determined from symptomatic cacao samples using Illumina-Hi Seq, and sequence accuracy was verified by Sanger sequencing. The resultant 14, and seven previously known, full-length badnaviral genomic and RT-RNase H sequences were analyzed by pairwise distance analysis to resolve species relationships, and by Maximum likelihood (ML) to reconstruct phylogenetic relationships. The viral coding and non-coding sequences, genome organization, and predicted conserved protein domains (CPDs) were identified and characterized at the species level. RESULTS The 21 CSSD-badnaviral genomes and RT-RNase H sequences shared 70-100% and 72-100% identity, respectively. The RT-RNase H analysis predicted four species, based on an ≥80% species cutoff. The ML genome sequence tree resolved three well-supported clades, with ≥70% bootstrap, whereas, the RT-RNase H phylogeny was poorly resolved, however, both trees grouped CSSD isolates within one large clade, including the newly discovered Cacao red vein virus (CRVV) proposed species. The genome arrangement of the four species consists of four, five, or six predicted open reading frames (ORFs), and the CPDs have similar architectures. By comparison, two New World cacao-infecting badnaviruses encode four ORFs, and harbor CPDs like the West African species. CONCLUSIONS Three previously recognized West African cacao-infecting badnaviral species were identified, and a fourth, previously unidentified species, CRVV, is described for the first time. The CRVV is a suspect causal agent of the rapid decline phenotype, however Koch's Postulates have not been proven. To reconcile viral evolutionary with epidemiology considerations, more detailed information about CSSD-genomic variability is essential. Also, the functional basis for the multiple genome arrangements and subtly distinct CPD architectures among cacao-infecting badnaviruses is poorly understood. New knowledge about functional relationships may help explain the diverse symptomatologies observed in affected cacao trees.
Collapse
Affiliation(s)
| | - Koffie Kouakou
- Centre National de Recherche Agronomique (CNRA), Programme Cacao, Divo, Côte d’Ivoire
| | - Romain Aka
- Centre National de Recherche Agronomique (CNRA), Programme Cacao, Divo, Côte d’Ivoire
| | - George Ameyaw
- Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
| | - Osman A. Gutierrez
- USDA-ARS Subtropical Horticultural Research Station, Miami, FL 33158 USA
| | | | - Judith K. Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721 USA
| |
Collapse
|
216
|
Abstract
BACKGROUND Gene order changes, under rearrangements, insertions, deletions and duplications, have been used as a new type of data source for phylogenetic reconstruction. Because these changes are rare compared to sequence mutations, they allow the inference of phylogeny further back in evolutionary time. There exist many computational methods for the reconstruction of gene-order phylogenies, including widely used maximum parsimonious methods and maximum likelihood methods. However, both methods face challenges in handling large genomes with many duplicated genes, especially in the presence of whole genome duplication. METHODS In this paper, we present three simple yet powerful methods based on maximum-likelihood (ML) approaches that encode multiplicities of both gene adjacency and gene content information for phylogenetic reconstruction. RESULTS Extensive experiments on simulated data sets show that our new method achieves the most accurate phylogenies compared to existing approaches. We also evaluate our method on real whole-genome data from eleven mammals. The package is publicly accessible at http://www.geneorder.org . CONCLUSIONS Our new encoding schemes successfully incorporate the multiplicity information of gene adjacencies and gene content into an ML framework, and show promising results in reconstruct phylogenies for whole-genome data in the presence of massive duplications.
Collapse
Affiliation(s)
- Lingxi Zhou
- Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208 South Carolina USA
| | - Yu Lin
- Research School of Computer Science, Australian National University, Canberra, 2601 ACT Australia
| | - Bing Feng
- Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208 South Carolina USA
| | - Jieyi Zhao
- University of Texas School of Biomedical Informatics at Houston, Houston, 77030 Texas USA
| | - Jijun Tang
- School of Computer Science and Engineering, Tianjin University, Tianjin, 300072 China
- Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208 South Carolina USA
| |
Collapse
|
217
|
Zhang D, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Wang GT, Li WX. Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny. Parasit Vectors 2017; 10:462. [PMID: 29017532 PMCID: PMC5633893 DOI: 10.1186/s13071-017-2404-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/25/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paratetraonchoides inermis (Monogenea: Tetraonchoididae) is a flatworm parasitising the gills of uranoscopid fishes. Its morphological characteristics are ambiguous, and molecular data have never been used to study its phylogenetic relationships, which makes its taxonomic classification controversial. Also, several decades of unsuccessful attempts to resolve the relationships within the Monogenea present a strong indication that morphological datasets may not be robust enough to be used to infer evolutionary histories. As the use of molecular data is currently severely limited by their scarcity, we have sequenced and characterized the complete mitochondrial (mt) genome of P. inermis. To investigate its phylogenetic position, we performed phylogenetic analyses using Bayesian inference and maximum likelihood approaches using concatenated amino acid sequences of all 12 protein-coding genes on a dataset containing all available monogenean mt genomes. RESULTS The circular mt genome of P. inermis (14,654 bp) contains the standard 36 genes: 22 tRNAs, two rRNAs, 12 protein-encoding genes (PCGs; Atp8 is missing) and a major non-coding region (mNCR). All genes are transcribed from the same strand. The A + T content of the whole genome (82.6%), as well as its elements, is the highest reported among the monogeneans thus far. Three tRNA-like cloverleaf structures were found in mNCR. Several results of the phylogenomic analysis are in disagreement with previously proposed relationships: instead of being closely related to the Gyrodactylidea, Tetraonchidea exhibit a phylogenetic affinity with the Dactylogyridea + Capsalidea clade; and the order Capsalidea is neither basal within the subclass Monopisthocotylea, nor groups with the Gyrodactylidea, but instead forms a sister clade with the Dactylogyridea. The mt genome of P. inermis exhibits a unique gene order, with an extensive reorganization of tRNAs. Monogenea exhibit exceptional gene order plasticity within the Neodermata. CONCLUSIONS This study shows that gene order within monopisthocotylid mt genomes is evolving at uneven rates, which creates misleading evolutionary signals. Furthermore, our results indicate that all previous attempts to resolve the evolutionary history of the Monogenea may have produced at least partially erroneous relationships. This further corroborates the necessity to generate more molecular data for this group of parasitic animals.
Collapse
Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Shan G. Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, People’s Republic of China
| | - Gui T. Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Wen X. Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| |
Collapse
|
218
|
Abstract
In vivo loss-of-function studies are currently limited by the need for appropriate conditional knockout alleles. CRISPR/Cas9 is a powerful tool commonly used to induce loss-of-function mutations in vitro. However, CRISPR components have been difficult to deploy in vivo. To address this problem, we developed the CASAAV (CRISPR/Cas9/AAV-based somatic mutagenesis) platform, in which recombinant adeno-associated virus (AAV) is used to deliver tandem guide RNAs and Cre recombinase to Cre-dependent Cas9-P2A-GFP mice. Because Cre is under the control of a tissue-specific promoter, this system allows temporally controlled, cell type-selective knockout of virtually any gene to be obtained within a month using only one mouse line. Here, we focus on gene disruption in cardiomyocytes, but the system could easily be adapted to inactivate genes in other cell types transduced by AAV. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Nathan J. VanDusen
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115 USA
| | - Yuxuan Guo
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115 USA
| | - Weiliang Gu
- Department of Pharmacology, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115 USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02130, USA
| |
Collapse
|
219
|
Wang C, Ward ME, Chen R, Liu K, Tracy TE, Chen X, Xie M, Sohn PD, Ludwig C, Meyer-Franke A, Karch CM, Ding S, Gan L. Scalable Production of iPSC-Derived Human Neurons to Identify Tau-Lowering Compounds by High-Content Screening. Stem Cell Reports 2017; 9:1221-1233. [PMID: 28966121 PMCID: PMC5639430 DOI: 10.1016/j.stemcr.2017.08.019] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 01/16/2023] Open
Abstract
Lowering total tau levels is an attractive therapeutic strategy for Alzheimer's disease and other tauopathies. High-throughput screening in neurons derived from human induced pluripotent stem cells (iPSCs) is a powerful tool to identify tau-targeted therapeutics. However, such screens have been hampered by heterogeneous neuronal production, high cost and low yield, and multi-step differentiation procedures. We engineered an isogenic iPSC line that harbors an inducible neurogenin 2 transgene, a transcription factor that rapidly converts iPSCs to neurons, integrated at the AAVS1 locus. Using a simplified two-step protocol, we differentiated these iPSCs into cortical glutamatergic neurons with minimal well-to-well variability. We developed a robust high-content screening assay to identify tau-lowering compounds in LOPAC and identified adrenergic receptors agonists as a class of compounds that reduce endogenous human tau. These techniques enable the use of human neurons for high-throughput screening of drugs to treat neurodegenerative disease.
Collapse
Affiliation(s)
- Chao Wang
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA
| | - Michael E Ward
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA; National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, USA
| | - Robert Chen
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA
| | - Kai Liu
- Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Tara E Tracy
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA
| | - Xu Chen
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA
| | - Min Xie
- Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Peter Dongmin Sohn
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA
| | - Connor Ludwig
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA
| | - Anke Meyer-Franke
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA
| | - Celeste M Karch
- Department of Psychiatry, Washington University School of Medicine, 425 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Sheng Ding
- Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Li Gan
- Gladstone Institute of Neurological Disease, 1650 Owens Street, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA.
| |
Collapse
|
220
|
Wang YC, Wang CW, Lin WC, Tsai YJ, Chang CP, Lee YJ, Lin MJ, Li C. Identification, chromosomal arrangements and expression analyses of the evolutionarily conserved prmt1 gene in chicken in comparison with its vertebrate paralogue prmt8. PLoS One 2017; 12:e0185042. [PMID: 28934323 PMCID: PMC5608299 DOI: 10.1371/journal.pone.0185042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/04/2017] [Indexed: 01/22/2023] Open
Abstract
Nine protein arginine methyltransferases (PRMTs) are conserved in mammals and fish. Among these, PRMT1 is the major type I PRMT for asymmetric dimethylarginine (ADMA) formation and is the most conserved and widely distributed one. Two chicken prmt1 splicing variants were assembled and confirmed by RT-PCR experiments. However, only two scaffolds containing single separate prmt1 exon with high GC contents are present in the current chicken genome assembly. Besides, prmt1 exons are scattered in separate small scaffolds in most avian species. Complete prmt1 gene has only been predicted from two falcon species with few neighboring genes. Crocodilians are considered close to the common ancestor shared by crocodilians and birds. The gene arrangements around prmt1 in American alligator are different from that in birds but are largely conserved in human. Orthologues of genes in a large segment of human chromosomal 19 around PRMT1 are missing or not assigned to the current chicken chromosomes. In comparison, prmt8, the prmt1 paralogue, is on chicken chromosome 1 with the gene arrangements downstream of prmt8 highly conserved in birds, crocodilians, and human. However, the ones upstream vary greatly in birds. Biochemically, we found that though prmt1 transcripts were detected, limited or none PRMT1 protein was present in chicken tissues. Moreover, a much higher level of PRMT8 protein was detected in chicken brain than in mouse brain. While PRMT8 is brain specific in other vertebrate species studied, low level of PRMT8 was present in chicken but not mouse liver and muscle. We also showed that the ADMA level in chicken was similar to that in mouse. This study provides the critical information of chicken PRMT1 and PRMT8 for future analyses of the function of protein arginine methyltransferases in birds.
Collapse
Affiliation(s)
- Yi-Chun Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan, ROC
| | - Chien-Wen Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Yun-Jung Tsai
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chien-Ping Chang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Jen Lee
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Min-Jon Lin
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan, ROC
| | - Chuan Li
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan, ROC
- * E-mail:
| |
Collapse
|
221
|
Yamazaki T, Ichihara K, Suzuki R, Oshima K, Miyamura S, Kuwano K, Toyoda A, Suzuki Y, Sugano S, Hattori M, Kawano S. Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita. Sci Rep 2017; 7:11679. [PMID: 28916791 PMCID: PMC5601483 DOI: 10.1038/s41598-017-11677-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 08/29/2017] [Indexed: 01/08/2023] Open
Abstract
The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt- and mt+ strains identified highly rearranged MT loci of 1.0 and 1.5 Mb in size and containing 46 and 67 genes, respectively, including 23 gametologs. Molecular evolutionary analyses suggested that the MT loci diverged over a prolonged period in the individual mating types after their establishment in an ancestor. A gene encoding an RWP-RK domain-containing protein was found in the mt- MT locus but was not an ortholog of the chlorophycean mating type determination gene MID. Taken together, our results suggest that the genomic structure and its evolutionary history in the U. partita MT locus are similar to those on other UV chromosomes and that the MT locus genes are quite different from those of Chlorophyceae.
Collapse
Affiliation(s)
- Tomokazu Yamazaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Kensuke Ichihara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Ryogo Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenshiro Oshima
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Shinichi Miyamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazuyoshi Kuwano
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Masahira Hattori
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Shigeyuki Kawano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.
| |
Collapse
|
222
|
Kirk IK, Weinhold N, Brunak S, Belling K. The impact of the protein interactome on the syntenic structure of mammalian genomes. PLoS One 2017; 12:e0179112. [PMID: 28910296 PMCID: PMC5598925 DOI: 10.1371/journal.pone.0179112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 05/10/2017] [Indexed: 02/06/2023] Open
Abstract
Conserved synteny denotes evolutionary preserved gene order across species. It is not well understood to which degree functional relationships between genes are preserved in syntenic blocks. Here we investigate whether protein-coding genes conserved in mammalian syntenic blocks encode gene products that serve the common functional purpose of interacting at protein level, i.e. connectivity. High connectivity among protein-protein interactions (PPIs) was only moderately associated with conserved synteny on a genome-wide scale. However, we observed a smaller subset of 3.6% of all syntenic blocks with high-confidence PPIs that had significantly higher connectivity than expected by random. Additionally, syntenic blocks with high-confidence PPIs contained significantly more chromatin loops than the remaining blocks, indicating functional preservation among these syntenic blocks. Conserved synteny is typically defined by sequence similarity. In this study, we also examined whether a functional relationship, here PPI connectivity, can identify syntenic blocks independently of orthology. While orthology-based syntenic blocks with high-confident PPIs and the connectivity-based syntenic blocks largely overlapped, the connectivity-based approach identified additional syntenic blocks that were not found by conventional sequence-based methods alone. Additionally, the connectivity-based approach enabled identification of potential orthologous genes between species. Our analyses demonstrate that subsets of syntenic blocks are associated with highly connected proteins, and that PPI connectivity can be used to detect conserved synteny even if sequence conservation drifts beyond what orthology algorithms normally can identify.
Collapse
Affiliation(s)
- Isa Kristina Kirk
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nils Weinhold
- Memorial Sloan Kettering Cancer Center, Computational Biology Program, New York, NY, United States of America
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kirstine Belling
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| |
Collapse
|
223
|
Martinez-Gil M, Goh KGK, Rackaityte E, Sakamoto C, Audrain B, Moriel DG, Totsika M, Ghigo JM, Schembri MA, Beloin C. YeeJ is an inverse autotransporter from Escherichia coli that binds to peptidoglycan and promotes biofilm formation. Sci Rep 2017; 7:11326. [PMID: 28900103 PMCID: PMC5595812 DOI: 10.1038/s41598-017-10902-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/16/2017] [Indexed: 02/08/2023] Open
Abstract
Escherichia coli is a commensal or pathogenic bacterium that can survive in diverse environments. Adhesion to surfaces is essential for E. coli colonization, and thus it is important to understand the molecular mechanisms that promote this process in different niches. Autotransporter proteins are a class of cell-surface factor used by E. coli for adherence. Here we characterized the regulation and function of YeeJ, a poorly studied but widespread representative from an emerging class of autotransporter proteins, the inverse autotransporters (IAT). We showed that the yeeJ gene is present in ~40% of 96 completely sequenced E. coli genomes and that YeeJ exists as two length variants, albeit with no detectable functional differences. We demonstrated that YeeJ promotes biofilm formation in different settings through exposition at the cell-surface. We also showed that YeeJ contains a LysM domain that interacts with peptidoglycan and thus assists its localization into the outer membrane. Additionally, we identified the Polynucleotide Phosphorylase PNPase as a repressor of yeeJ transcription. Overall, our work provides new insight into YeeJ as a member of the recently defined IAT class, and contributes to our understanding of how commensal and pathogenic E. coli colonise their environments.
Collapse
Affiliation(s)
- Marta Martinez-Gil
- Institut Pasteur, Unité de Génétique des Biofilms, 28 rue du Dr. Roux, 75724, Paris, CEDEX 15, France
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias. Universidad de Málaga, Málaga, Spain
| | - Kelvin G K Goh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Elze Rackaityte
- Institut Pasteur, Unité de Génétique des Biofilms, 28 rue du Dr. Roux, 75724, Paris, CEDEX 15, France
- University of California San Francisco, Department of Medicine, San Francisco, CA, USA
| | - Chizuko Sakamoto
- Institut Pasteur, Unité de Génétique des Biofilms, 28 rue du Dr. Roux, 75724, Paris, CEDEX 15, France
| | - Bianca Audrain
- Institut Pasteur, Unité de Génétique des Biofilms, 28 rue du Dr. Roux, 75724, Paris, CEDEX 15, France
| | - Danilo G Moriel
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- GSK Vaccines Institute for Global Health S.r.l., 53100, Siena, Italy
| | - Makrina Totsika
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute of Health and Biomedical Innovation, and School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia
| | - Jean-Marc Ghigo
- Institut Pasteur, Unité de Génétique des Biofilms, 28 rue du Dr. Roux, 75724, Paris, CEDEX 15, France
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Christophe Beloin
- Institut Pasteur, Unité de Génétique des Biofilms, 28 rue du Dr. Roux, 75724, Paris, CEDEX 15, France.
| |
Collapse
|
224
|
Barzago MM, Kurosaki M, Fratelli M, Bolis M, Giudice C, Nordio L, Cerri E, Domenici L, Terao M, Garattini E. Generation of a new mouse model of glaucoma characterized by reduced expression of the AP-2β and AP-2δ proteins. Sci Rep 2017; 7:11140. [PMID: 28894266 PMCID: PMC5593953 DOI: 10.1038/s41598-017-11752-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022] Open
Abstract
We generated 6 transgenic lines with insertion of an expression plasmid for the R883/M xanthine dehydrogenase (XDH) mutant protein. Approximately 20% of the animals deriving from one of the transgenic lines show ocular abnormalities and an increase in intra-ocular pressure which are consistent with glaucoma. The observed pathologic phenotype is not due to expression of the transgene, but rather the consequence of the transgene insertion site, which has been defined by genome sequencing. The insertion site maps to chromosome 1qA3 in close proximity to the loci encoding AP-2β and AP-2δ, two proteins expressed in the eye. The insertion leads to a reduction in AP-2β and AP-2δ levels. Down-regulation of AP-2β expression is likely to be responsible for the pathologic phenotype, as conditional deletion of the Tfap2b gene in the neural crest has recently been shown to cause defective development of the eye anterior segment and early-onset glaucoma. In these conditional knock-out and our transgenic mice, the morphological/histological features of the glaucomatous pathology are surprisingly similar. Our transgenic mouse represents a model of angle-closure glaucoma and a useful tool for the study of the pathogenesis and the development of innovative therapeutic strategies.
Collapse
Affiliation(s)
- Maria Monica Barzago
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Mami Kurosaki
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Marco Bolis
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy
| | - Chiara Giudice
- DIVET, Faculty of Veterinary Medicine, University of Milan, Italy, Via Celoria 10, 20113, Milano, Italy
| | - Laura Nordio
- DIVET, Faculty of Veterinary Medicine, University of Milan, Italy, Via Celoria 10, 20113, Milano, Italy
| | - Elisa Cerri
- Consiglio Nazionale delle Ricerche (CNR), Neuroscience Institute, Pisa, Italy
| | - Luciano Domenici
- Consiglio Nazionale delle Ricerche (CNR), Neuroscience Institute, Pisa, Italy
- Department of Applied Clinical Sciences and Biotechnology (DISCAB), University of L'Aquila, L'Aquila, Italy
| | - Mineko Terao
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy.
| | - Enrico Garattini
- Laboratory of Molecular Biology, IRCCS-Istituto di Ricerche Farmacologiche "Mario Negri", via La Masa 19, 20156, Milano, Italy.
| |
Collapse
|
225
|
Geng P, Tian S, Yuan Z, Hu X. Identification and genomic comparison of temperate bacteriophages derived from emetic Bacillus cereus. PLoS One 2017; 12:e0184572. [PMID: 28886124 PMCID: PMC5590980 DOI: 10.1371/journal.pone.0184572] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/25/2017] [Indexed: 01/21/2023] Open
Abstract
Cereulide-producing Bacillus cereus isolates can cause serious emetic (vomiting) syndrome and even acute lethality. As mobile genetic elements, the exploration of prophages derived from emetic B. cereus isolates will help in our understanding of the genetic diversity and evolution of these pathogens. In this study, five temperate phages derived from cereulide-producing B. cereus strains were induced, with four of them undergoing genomic sequencing. Sequencing revealed that they all belong to the Siphoviridae family, but presented in different forms in their hosts. PfNC7401 and PfIS075 have typical icosahedral heads, probably existing alone as phagemids in the host with self-replicating capability in the lysogenic state. PfEFR-4, PfEFR-5, and PfATCC7953 have elongated heads, with the genomes of the former two identified as linear dsDNA, which could be integrated into the host genome during the lysogenic state. Genomic comparison of the four phages with others also derived from emetic B. cereus isolates showed similar genome structures and core genes, thus displaying host spectrum specificity. In addition, phylogenic analysis based on the complete genome and conserved tail fiber proteins of 36 Bacillus species-derived phages confirmed that the phages derived from emetic B. cereus strains were highly similar. Furthermore, one endolysin LysPfEFR-4 was cloned and showed lytic activity against all tested emetic B. cereus strains and cross-lytic activity against some other pathogenic bacteria, implying a potential to control bacterial contamination in the food supply.
Collapse
Affiliation(s)
- Peiling Geng
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Shen Tian
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (XH); (ZY)
| | - Xiaomin Hu
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (XH); (ZY)
| |
Collapse
|
226
|
Fernández-Pérez J, Nantón A, Ruiz-Ruano FJ, Camacho JPM, Méndez J. First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order. PLoS One 2017; 12:e0184464. [PMID: 28886105 PMCID: PMC5590976 DOI: 10.1371/journal.pone.0184464] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Four species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management. PRINCIPAL FINDINGS The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic. CONCLUSIONS Sequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource.
Collapse
Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | | | - Juan Pedro M. Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| |
Collapse
|
227
|
Festa S, Coppotelli BM, Madueño L, Loviso CL, Macchi M, Neme Tauil RM, Valacco MP, Morelli IS. Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches. PLoS One 2017; 12:e0184505. [PMID: 28886166 PMCID: PMC5591006 DOI: 10.1371/journal.pone.0184505] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/27/2017] [Indexed: 11/18/2022] Open
Abstract
The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31–43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).
Collapse
Affiliation(s)
- Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
- * E-mail:
| | - Bibiana Marina Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | - Laura Madueño
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | | | - Marianela Macchi
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
| | - Ricardo Martin Neme Tauil
- Centro de Estudios Químicos y Biológicos por Espectrometría de Masa- CEQUIBIEM, Facultad de Ciencias Exactas y Naturales, UBA, IQUIBICEN, CONICET
| | - María Pía Valacco
- Centro de Estudios Químicos y Biológicos por Espectrometría de Masa- CEQUIBIEM, Facultad de Ciencias Exactas y Naturales, UBA, IQUIBICEN, CONICET
| | - Irma Susana Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
| |
Collapse
|
228
|
Huang H, Zhu CT, Skuja LL, Hayden DJ, Hart AC. Genome-Wide Screen for Genes Involved in Caenorhabditis elegans Developmentally Timed Sleep. G3 (Bethesda) 2017; 7:2907-2917. [PMID: 28743807 PMCID: PMC5592919 DOI: 10.1534/g3.117.300071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/21/2017] [Indexed: 12/24/2022]
Abstract
In Caenorhabditis elegans, Notch signaling regulates developmentally timed sleep during the transition from L4 larval stage to adulthood (L4/A) . To identify core sleep pathways and to find genes acting downstream of Notch signaling, we undertook the first genome-wide, classical genetic screen focused on C. elegans developmentally timed sleep. To increase screen efficiency, we first looked for mutations that suppressed inappropriate anachronistic sleep in adult hsp::osm-11 animals overexpressing the Notch coligand OSM-11 after heat shock. We retained suppressor lines that also had defects in L4/A developmentally timed sleep, without heat shock overexpression of the Notch coligand. Sixteen suppressor lines with defects in developmentally timed sleep were identified. One line carried a new allele of goa-1; loss of GOA-1 Gαo decreased C. elegans sleep. Another line carried a new allele of gpb-2, encoding a Gβ5 protein; Gβ5 proteins have not been previously implicated in sleep. In other scenarios, Gβ5 GPB-2 acts with regulators of G protein signaling (RGS proteins) EAT-16 and EGL-10 to terminate either EGL-30 Gαq signaling or GOA-1 Gαo signaling, respectively. We found that loss of Gβ5 GPB-2 or RGS EAT-16 decreased L4/A sleep. By contrast, EGL-10 loss had no impact. Instead, loss of RGS-1 and RGS-2 increased sleep. Combined, our results suggest that, in the context of L4/A sleep, GPB-2 predominantly acts with EAT-16 RGS to inhibit EGL-30 Gαq signaling. These results confirm the importance of G protein signaling in sleep and demonstrate that these core sleep pathways function genetically downstream of the Notch signaling events promoting sleep.
Collapse
Affiliation(s)
- Huiyan Huang
- Department of Neuroscience, Brown University, Providence, Rhode Island 02912
| | - Chen-Tseh Zhu
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Lukas L Skuja
- Department of Neuroscience, Brown University, Providence, Rhode Island 02912
| | - Dustin J Hayden
- Department of Neuroscience, Brown University, Providence, Rhode Island 02912
| | - Anne C Hart
- Department of Neuroscience, Brown University, Providence, Rhode Island 02912
| |
Collapse
|
229
|
Burnight ER, Gupta M, Wiley LA, Anfinson KR, Tran A, Triboulet R, Hoffmann JM, Klaahsen DL, Andorf JL, Jiao C, Sohn EH, Adur MK, Ross JW, Mullins RF, Daley GQ, Schlaeger TM, Stone EM, Tucker BA. Using CRISPR-Cas9 to Generate Gene-Corrected Autologous iPSCs for the Treatment of Inherited Retinal Degeneration. Mol Ther 2017; 25:1999-2013. [PMID: 28619647 PMCID: PMC5589061 DOI: 10.1016/j.ymthe.2017.05.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 01/20/2023] Open
Abstract
Patient-derived induced pluripotent stem cells (iPSCs) hold great promise for autologous cell replacement. However, for many inherited diseases, treatment will likely require genetic repair pre-transplantation. Genome editing technologies are useful for this application. The purpose of this study was to develop CRISPR-Cas9-mediated genome editing strategies to target and correct the three most common types of disease-causing variants in patient-derived iPSCs: (1) exonic, (2) deep intronic, and (3) dominant gain of function. We developed a homology-directed repair strategy targeting a homozygous Alu insertion in exon 9 of male germ cell-associated kinase (MAK) and demonstrated restoration of the retinal transcript and protein in patient cells. We generated a CRISPR-Cas9-mediated non-homologous end joining (NHEJ) approach to excise a major contributor to Leber congenital amaurosis, the IVS26 cryptic-splice mutation in CEP290, and demonstrated correction of the transcript and protein in patient iPSCs. Lastly, we designed allele-specific CRISPR guides that selectively target the mutant Pro23His rhodopsin (RHO) allele, which, following delivery to both patient iPSCs in vitro and pig retina in vivo, created a frameshift and premature stop that would prevent transcription of the disease-causing variant. The strategies developed in this study will prove useful for correcting a wide range of genetic variants in genes that cause inherited retinal degeneration.
Collapse
Affiliation(s)
- Erin R Burnight
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Manav Gupta
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 01451, USA
| | - Luke A Wiley
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Kristin R Anfinson
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Audrey Tran
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 01451, USA
| | - Robinson Triboulet
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 01451, USA
| | - Jeremy M Hoffmann
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Darcey L Klaahsen
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Jeaneen L Andorf
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Chunhua Jiao
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Elliott H Sohn
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Malavika K Adur
- Department of Animal Sciences, Iowa State University, Ames, IA 50011, USA
| | - Jason W Ross
- Department of Animal Sciences, Iowa State University, Ames, IA 50011, USA
| | - Robert F Mullins
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - George Q Daley
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 01451, USA
| | - Thorsten M Schlaeger
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 01451, USA
| | - Edwin M Stone
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA
| | - Budd A Tucker
- Stephen A. Wynn Institute for Vision Research and Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52241, USA.
| |
Collapse
|
230
|
Hansmeier N, Miskiewicz K, Elpers L, Liss V, Hensel M, Sterzenbach T. Functional expression of the entire adhesiome of Salmonella enterica serotype Typhimurium. Sci Rep 2017; 7:10326. [PMID: 28871183 PMCID: PMC5583245 DOI: 10.1038/s41598-017-10598-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/10/2017] [Indexed: 12/21/2022] Open
Abstract
Adhesins are crucial virulence factors of pathogenic bacteria involved in colonization, transmission and pathogenesis. Many bacterial genomes contain the information for a surprisingly large number of diverse adhesive structures. One prominent example is the invasive and facultative intracellular pathogen Salmonella enterica with an adhesiome of up to 20 adhesins. Such large repertoire of adhesins contributes to colonization of a broad range of host species and may allow adaptation to various environments within the host, as well as in non-host environments. For S. enterica, only few members of the adhesiome are functionally expressed under laboratory conditions, and accordingly the structural and functional understanding of the majority of adhesins is sparse. We have devised a simple and versatile approach to functionally express all adhesins of S. enterica serotype Typhimurium, either within Salmonella or within heterologous hosts such as Escherichia coli. We demonstrate the surface expression of various so far cryptic adhesins and show ultrastructural features using atomic force microscopy and transmission electron microscopy. In summary, we report for the first time the expression of the entire adhesiome of S. enterica serotype Typhimurium.
Collapse
Affiliation(s)
- Nicole Hansmeier
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, Barbarastr. 11, 49076, Osnabrück, Germany
| | - Katarzyna Miskiewicz
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, Barbarastr. 11, 49076, Osnabrück, Germany
| | - Laura Elpers
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, Barbarastr. 11, 49076, Osnabrück, Germany
| | - Viktoria Liss
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, Barbarastr. 11, 49076, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, Barbarastr. 11, 49076, Osnabrück, Germany.
| | - Torsten Sterzenbach
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, Barbarastr. 11, 49076, Osnabrück, Germany.
| |
Collapse
|
231
|
Park I, Kim WJ, Yang S, Yeo SM, Li H, Moon BC. The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species. PLoS One 2017; 12:e0184257. [PMID: 28863163 PMCID: PMC5581188 DOI: 10.1371/journal.pone.0184257] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 08/21/2017] [Indexed: 11/18/2022] Open
Abstract
Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC–trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species.
Collapse
Affiliation(s)
- Inkyu Park
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Wook-jin Kim
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Sungyu Yang
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Sang-Min Yeo
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Hulin Li
- Department of Agronomy, Yanbian University Agriculture College, Yanji, China
| | - Byeong Cheol Moon
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
- * E-mail:
| |
Collapse
|
232
|
Zhou J, Chen X, Cui Y, Sun W, Li Y, Wang Y, Song J, Yao H. Molecular Structure and Phylogenetic Analyses of Complete Chloroplast Genomes of Two Aristolochia Medicinal Species. Int J Mol Sci 2017; 18:E1839. [PMID: 28837061 PMCID: PMC5618488 DOI: 10.3390/ijms18091839] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/15/2017] [Accepted: 08/20/2017] [Indexed: 12/13/2022] Open
Abstract
The family Aristolochiaceae, comprising about 600 species of eight genera, is a unique plant family containing aristolochic acids (AAs). The complete chloroplast genome sequences of Aristolochia debilis and Aristolochia contorta are reported here. The results show that the complete chloroplast genomes of A. debilis and A. contorta comprise circular 159,793 and 160,576 bp-long molecules, respectively and have typical quadripartite structures. The GC contents of both species were 38.3% each. A total of 131 genes were identified in each genome including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene (ycf1). The simple-sequence repeat sequences mainly comprise A/T mononucletide repeats. Phylogenetic analyses using maximum parsimony (MP) revealed that A. debilis and A. contorta had a close phylogenetic relationship with species of the family Piperaceae, as well as Laurales and Magnoliales. The data obtained in this study will be beneficial for further investigations on A. debilis and A. contorta from the aspect of evolution, and chloroplast genetic engineering.
Collapse
Affiliation(s)
- Jianguo Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Xinlian Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Yingxian Cui
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Yonghua Li
- Department of Pharmacy, Guangxi Traditional Chinese Medicine University, Nanning 530200, China.
| | - Yu Wang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
| |
Collapse
|
233
|
Huang X, Zhuang C, Zhuang C, Xiong T, Li Y, Gui Y. An enhanced hTERT promoter-driven CRISPR/Cas9 system selectively inhibits the progression of bladder cancer cells. Mol Biosyst 2017; 13:1713-1721. [PMID: 28702647 DOI: 10.1039/c7mb00354d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The current therapies for treating tumors are lacking in efficacy and specificity. Synthetic biology principles may bring some new possible methods for curing cancer. Here we present a synthetic logic circuit based on the CRISPR/Cas9 system. The CRISPR/Cas9 technology has been applied in many biological fields, including cancer research. In this study, the expression of Cas9 nuclease was controlled indirectly by an enhanced hTERT promoter using the GAL4/upstream activating sequence (UAS) binding system. Cas9 was driven by 5XUAS, single guide RNA (sgRNA) was used to target mutant or wild-type HRAS, and the fusion gene GAL4-P65 was driven by the enhanced hTERT promoter. The system was tested in bladder cancer cells (T24 and 5637) and the results showed that the enhanced hTERT promoter could drive the expression of GAL4-P65 in these bladder cancer cell lines. Then all these devices were packed into lentivirus and the results of quantitative real-time PCR showed that the mRNA expression level of HRAS was selectively inhibited in the T24 and 5637 cells. The results of functional experiments suggested that the proliferation, cell migration and invasion were selectively suppressed, and that the apoptosis rate was increased in bladder cancer cells but not in human foreskin fibroblasts (HFF). In conclusion, we successfully constructed an enhanced hTERT promoter-driven CRISPR/Cas9 system and data showed that it could selectively suppress the progression of bladder cancer cells.
Collapse
Affiliation(s)
- Xinbo Huang
- Graduate School, Anhui Medical University, HeFei, Anhui 230032, China.
| | | | | | | | | | | |
Collapse
|
234
|
Abstract
Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.
Collapse
Affiliation(s)
- Jiangxing Ruan
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300308, China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| |
Collapse
|
235
|
Shen X, Wu M, Liao B, Liu Z, Bai R, Xiao S, Li X, Zhang B, Xu J, Chen S. Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua. Molecules 2017; 22:molecules22081330. [PMID: 28800082 PMCID: PMC6152406 DOI: 10.3390/molecules22081330] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 07/31/2017] [Accepted: 08/08/2017] [Indexed: 12/17/2022] Open
Abstract
The complete chloroplast genome of Artemisia annua (Asteraceae), the primary source of artemisinin, was sequenced and analyzed. The A. annua cp genome is 150,995 bp, and harbors a pair of inverted repeat regions (IRa and IRb), of 24,850 bp each that separate large (LSC, 82,988 bp) and small (SSC, 18,267 bp) single-copy regions. Our annotation revealed that the A. annua cp genome contains 113 genes and 18 duplicated genes. The gene order in the SSC region of A. annua is inverted; this fact is consistent with the sequences of chloroplast genomes from three other Artemisia species. Fifteen (15) forward and seventeen (17) inverted repeats were detected in the genome. The existence of rich SSR loci in the genome suggests opportunities for future population genetics work on this anti-malarial medicinal plant. In A. annua cpDNA, the rps19 gene was found in the LSC region rather than the IR region, and the rps19 pseudogene was absent in the IR region. Sequence divergence analysis of five Asteraceae species indicated that the most highly divergent regions were found in the intergenic spacers, and that the differences between A. annua and A. fukudo were very slight. A phylogenetic analysis revealed a sister relationship between A. annua and A. fukudo. This study identified the unique characteristics of the A. annua cp genome. These results offer valuable information for future research on Artemisia species identification and for the selective breeding of A. annua with high pharmaceutical efficacy.
Collapse
Affiliation(s)
- Xiaofeng Shen
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Mingli Wu
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, Hubei, China.
| | - Baosheng Liao
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhixiang Liu
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Rui Bai
- College of Pharmacy and Chemistry, Dali University, Dali 671000, Yunnan, China.
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Xiwen Li
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Boli Zhang
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Jiang Xu
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| |
Collapse
|
236
|
Hao YJ, Zou YL, Ding YR, Xu WY, Yan ZT, Li XD, Fu WB, Li TJ, Chen B. Complete mitochondrial genomes of Anopheles stephensi and An. dirus and comparative evolutionary mitochondriomics of 50 mosquitoes. Sci Rep 2017; 7:7666. [PMID: 28794438 PMCID: PMC5550476 DOI: 10.1038/s41598-017-07977-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/06/2017] [Indexed: 01/09/2023] Open
Abstract
To better understand the phylogeny and evolution of mosquitoes, the complete mitochondrial genome (mitogenome) of Anopheles stephensi and An. dirus were sequenced and annotated, and a total of 50 mosquito mitogenomes were comparatively analyzed. The complete mitogenome of An. stephensi and An. dirus is 1,5371 bp and 1,5406 bp long, respectively. The main features of the 50 mosquito mitogenomes are conservative: 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, positive AT-skew and negative GC-skew. The gene order trnA-trnR in ancestral insects is rearranged. All tRNA genes have the typical clover leaf secondary structure but tRNA Ser . The control regions are highly variable in size. PCGs show signals of purifying selection, but evidence for positive selection in ND2, ND4 and ND6 is found. Bayesian and Maximum Likelihood phylogenetic analyses based on all PCG nucleotides produce an identical tree topology and strongly support the monophyly of subgenera Cellia, Anopheles, Keterszia and Nyssorhynchus, the sister relationship of the subgenera Nyssorhynchus and Keterszia, and Cellia and Anopheles. The most recent ancestor of the genus Anopheles and Culicini + Aedini exited ~145 Mya ago. This is the first comprehensive study of mosquito mitogenomes, which are effective for mosquito phylogeny at various taxonomic levels.
Collapse
Affiliation(s)
- You-Jin Hao
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Yi-Lin Zou
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Yi-Ran Ding
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Wen-Yue Xu
- The Department of Pathogenic Biology, Third Military Medical University, Chongqing, 400038, China
| | - Zhen-Tian Yan
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Xu-Dong Li
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Wen-Bo Fu
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Ting-Jing Li
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China
| | - Bin Chen
- Chongqing Key Laboratory of Vector Insects; Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing, 401331, China.
| |
Collapse
|
237
|
Asaf S, Khan AL, Khan MA, Waqas M, Kang SM, Yun BW, Lee IJ. Chloroplast genomes of Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea: Structures and comparative analysis. Sci Rep 2017; 7:7556. [PMID: 28790364 PMCID: PMC5548756 DOI: 10.1038/s41598-017-07891-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 07/05/2017] [Indexed: 11/26/2022] Open
Abstract
We investigated the complete chloroplast (cp) genomes of non-model Arabidopsis halleri ssp. gemmifera and Arabidopsis lyrata ssp. petraea using Illumina paired-end sequencing to understand their genetic organization and structure. Detailed bioinformatics analysis revealed genome sizes of both subspecies ranging between 154.4~154.5 kbp, with a large single-copy region (84,197~84,158 bp), a small single-copy region (17,738~17,813 bp) and pair of inverted repeats (IRa/IRb; 26,264~26,259 bp). Both cp genomes encode 130 genes, including 85 protein-coding genes, eight ribosomal RNA genes and 37 transfer RNA genes. Whole cp genome comparison of A. halleri ssp. gemmifera and A. lyrata ssp. petraea, along with ten other Arabidopsis species, showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. The location and distribution of repeat sequences were determined, and sequence divergences of shared genes were calculated among related species. Comparative phylogenetic analysis of the entire genomic data set and 70 shared genes between both cp genomes confirmed the previous phylogeny and generated phylogenetic trees with the same topologies. The sister species of A. halleri ssp. gemmifera is A. umezawana, whereas the closest relative of A. lyrata spp. petraea is A. arenicola.
Collapse
Affiliation(s)
- Sajjad Asaf
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Abdul Latif Khan
- Chair of Oman's Medicinal Plants & Marine Natural Products, University of Nizwa, Nizwa, 616, Oman
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Muhammad Waqas
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sang-Mo Kang
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Byung-Wook Yun
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| |
Collapse
|
238
|
Komor AC, Zhao KT, Packer MS, Gaudelli NM, Waterbury AL, Koblan LW, Kim YB, Badran AH, Liu DR. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity. Sci Adv 2017; 3:eaao4774. [PMID: 28875174 PMCID: PMC5576876 DOI: 10.1126/sciadv.aao4774] [Citation(s) in RCA: 470] [Impact Index Per Article: 67.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/04/2017] [Indexed: 05/17/2023]
Abstract
We recently developed base editing, the programmable conversion of target C:G base pairs to T:A without inducing double-stranded DNA breaks (DSBs) or requiring homology-directed repair using engineered fusions of Cas9 variants and cytidine deaminases. Over the past year, the third-generation base editor (BE3) and related technologies have been successfully used by many researchers in a wide range of organisms. The product distribution of base editing-the frequency with which the target C:G is converted to mixtures of undesired by-products, along with the desired T:A product-varies in a target site-dependent manner. We characterize determinants of base editing outcomes in human cells and establish that the formation of undesired products is dependent on uracil N-glycosylase (UNG) and is more likely to occur at target sites containing only a single C within the base editing activity window. We engineered CDA1-BE3 and AID-BE3, which use cytidine deaminase homologs that increase base editing efficiency for some sequences. On the basis of these observations, we engineered fourth-generation base editors (BE4 and SaBE4) that increase the efficiency of C:G to T:A base editing by approximately 50%, while halving the frequency of undesired by-products compared to BE3. Fusing BE3, BE4, SaBE3, or SaBE4 to Gam, a bacteriophage Mu protein that binds DSBs greatly reduces indel formation during base editing, in most cases to below 1.5%, and further improves product purity. BE4, SaBE4, BE4-Gam, and SaBE4-Gam represent the state of the art in C:G-to-T:A base editing, and we recommend their use in future efforts.
Collapse
Affiliation(s)
- Alexis C. Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin T. Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S. Packer
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicole M. Gaudelli
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda L. Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Luke W. Koblan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Y. Bill Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmed H. Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R. Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Corresponding author.
| |
Collapse
|
239
|
Mongiardini EJ, Quelas JI, Dardis C, Althabegoiti MJ, Lodeiro AR. Transcriptional Control of the Lateral-Flagellar Genes of Bradyrhizobium diazoefficiens. J Bacteriol 2017; 199:e00253-17. [PMID: 28533217 PMCID: PMC5512216 DOI: 10.1128/jb.00253-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 05/16/2017] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium diazoefficiens, a soybean N2-fixing symbiont, possesses a dual flagellar system comprising a constitutive subpolar flagellum and inducible lateral flagella. Here, we analyzed the genomic organization and biosynthetic regulation of the lateral-flagellar genes. We found that these genes are located in a single genomic cluster, organized in two monocistronic transcriptional units and three operons, one possibly containing an internal transcription start site. Among the monocistronic units is blr6846, homologous to the class IB master regulators of flagellum synthesis in Brucella melitensis and Ensifer meliloti and required for the expression of all the lateral-flagellar genes except lafA2, whose locus encodes a single lateral flagellin. We therefore named blr6846 lafR (lateral-flagellar regulator). Despite its similarity to two-component response regulators and its possession of a phosphorylatable Asp residue, lafR behaved as an orphan response regulator by not requiring phosphorylation at this site. Among the genes induced by lafR is flbTL , a class III regulator. We observed different requirements for FlbTL in the synthesis of each flagellin subunit. Although the accumulation of lafA1, but not lafA2, transcripts required FlbTL, the production of both flagellin polypeptides required FlbTL Moreover, the regulation cascade of this lateral-flagellar regulon appeared to be not as strictly ordered as those found in other bacterial species.IMPORTANCE Bacterial motility seems essential for the free-living style in the environment, and therefore these microorganisms allocate a great deal of their energetic resources to the biosynthesis and functioning of flagella. Despite energetic costs, some bacterial species possess dual flagellar systems, one of which is a primary system normally polar or subpolar, and the other is a secondary, lateral system that is produced only under special circumstances. Bradyrhizobium diazoefficiens, an N2-fixing symbiont of soybean plants, possesses dual flagellar systems, including the lateral system that contributes to swimming in wet soil and competition for nodulation and is expressed under high energy availability, as well as under requirement for high torque by the flagella. The structural organization and transcriptional regulation of the 41 genes that comprise this secondary flagellar system seem adapted to adjust bacterial energy expenditures for motility to the soil's environmental dynamics.
Collapse
Affiliation(s)
- Elías J Mongiardini
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| | - J Ignacio Quelas
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| | - Carolina Dardis
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| | - M Julia Althabegoiti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| | - Aníbal R Lodeiro
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT-La Plata, CONICET, La Plata, Argentina
| |
Collapse
|
240
|
Xin ZZ, Yu Liu, Zhu XY, Wang Y, Zhang HB, Zhang DZ, Zhou CL, Tang BP, Liu QN. Mitochondrial Genomes of Two Bombycoidea Insects and Implications for Their Phylogeny. Sci Rep 2017; 7:6544. [PMID: 28747720 PMCID: PMC5529375 DOI: 10.1038/s41598-017-06930-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/22/2017] [Indexed: 11/21/2022] Open
Abstract
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogenetics. As such, the two complete mt genomes of Ampelophaga rubiginosa and Rondotia menciana were sequenced and annotated. The two circular genomes of A. rubiginosa and R. menciana are 15,282 and 15,636 bp long, respectively, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. The nucleotide composition of the A. rubiginosa mt genome is A + T rich (81.5%) but is lower than that of R. menciana (82.2%). The AT skew is slightly positive and the GC skew is negative in these two mt genomes. Except for cox1, which started with CGA, all other 12PCGs started with ATN codons. The A + T-rich regions of A. rubiginosa and R. menciana were 399 bp and 604 bp long and consist of several features common to Bombycoidea insects. The order and orientation of A. rubiginosa and R. menciana mitogenomes with the order trnM-trnI-trnQ-nad2 is different from the ancestral insects in which trnM is located between trnQ and nad2 (trnI-trnQ-trnM-nad2). Phylogenetic analyses indicate that A. rubiginosa belongs in the Sphingidae family, and R. menciana belongs in the Bombycidae family.
Collapse
Affiliation(s)
- Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Ying Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China.
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China.
| |
Collapse
|
241
|
Pie MR, Ströher PR, Belmonte-Lopes R, Bornschein MR, Ribeiro LF, Faircloth BC, McCormack JE. Phylogenetic relationships of diurnal, phytotelm-breeding Melanophryniscus (Anura: Bufonidae) based on mitogenomic data. Gene 2017; 628:194-199. [PMID: 28720533 DOI: 10.1016/j.gene.2017.07.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 06/20/2017] [Accepted: 07/14/2017] [Indexed: 11/19/2022]
Abstract
Melanophryniscus is a bufonid frog genus with a broad geographic distribution over southeastern South America. In recent years, several new species of Melanophryniscus have been discovered in southern Brazil showing a distinctive life-history strategy for the genus - breeding in phytotelmata - as well as a strong association with high-altitude regions. In this study, we use mitogenomic data to infer the phylogenetic relationships among diurnal, phytotelm-breeding Melanophryniscus and to determine the timing of their divergence. We obtained the mitochondrial genomes (not including the control region) for eight individuals of Melanophryniscus representing all three described species (M. alipioi, M. milanoi, and M. xanthostomus), as well as some recently-discovered and potentially new species. Gene order was conserved in all species and corresponded to the general order found in bufonids. Although the phylogenetic relationships among the studied species was poorly supported, dating confirmed that they diverged during the Pleistocene, suggesting that phytotelm breeding could have arisen during drier periods in the glacial/interglacial cycles due to a decrease in the availability of permanent streams or ephemeral/temporary streams or ponds in which Melanophryniscus species commonly breed.
Collapse
Affiliation(s)
- Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, CEP 81531-980 Curitiba, Paraná, Brazil; Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil.
| | - Patrícia R Ströher
- Departamento de Zoologia, Universidade Federal do Paraná, CEP 81531-980 Curitiba, Paraná, Brazil
| | - Ricardo Belmonte-Lopes
- Departamento de Zoologia, Universidade Federal do Paraná, CEP 81531-980 Curitiba, Paraná, Brazil; Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil
| | - Marcos R Bornschein
- Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil; Instituto de Biociências, Universidade Estadual Paulista, Praça Infante Dom Henrique s/no, Parque Bitaru, CEP 11330-900 São Vicente, São Paulo, Brazil
| | - Luiz F Ribeiro
- Mater Natura - Instituto de Estudos Ambientais, CEP 80250-020 Curitiba, Paraná, Brazil; Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Brant C Faircloth
- Dept. of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - John E McCormack
- Moore Laboratory of Zoology, Occidental College, 1600 Campus Road, Los Angeles, CA 90041, USA
| |
Collapse
|
242
|
Guo S, Wong SM. Deep sequencing analysis reveals a TMV mutant with a poly(A) tract reduces host defense responses in Nicotiana benthamiana. Virus Res 2017; 239:126-135. [PMID: 28082213 DOI: 10.1016/j.virusres.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/07/2017] [Accepted: 01/08/2017] [Indexed: 12/24/2022]
Abstract
Tobacco mosaic virus (TMV) possesses an upstream pseudoknotted domain (UPD), which is important for replication. After substituting the UPD with an internal poly(A) tract (43 nt), a mutant TMV-43A was constructed. TMV-43A replicated slower than TMV and induced a non-lethal mosaic symptom in Nicotiana benthamiana. In this study, deep sequencing was performed to detect the differences of small RNA profiles between TMV- and TMV-43A-infected N. benthamiana. The results showed that TMV-43A produced lesser amount of virus-derived interfering RNAs (vsiRNAs) than that of TMV. However, the distributions of vsiRNAs generation hotspots between TMV and TMV-43A were similar. Expression of genes related to small RNA biogenesis in TMV-43A-infected N. benthamiana was significantly lower than that of TMV, which leads to generation of lesser vsiRNAs. The expressions of host defense response genes were up-regulated after TMV infection, as compared to TMV-43A-infected plants. Host defense response to TMV-43A infection was lower than that to TMV. The absence of UPD might contribute to the reduced host response to TMV-43A. Our study provides valuable information in the role of the UPD in eliciting host response genes after TMV infection in N. benthamiana. (187 words).
Collapse
Affiliation(s)
- Song Guo
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Republic of Singapore; Temasek Life Sciences Laboratory, Singapore, Republic of Singapore; National University of Singapore Research Institute in Suzhou, Jiangsu, People's Republic of China.
| |
Collapse
|
243
|
Marandino A, Tomás G, Panzera Y, Greif G, Parodi-Talice A, Hernández M, Techera C, Hernández D, Pérez R. Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages. Infect Genet Evol 2017; 54:245-250. [PMID: 28705717 PMCID: PMC7106025 DOI: 10.1016/j.meegid.2017.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 01/28/2023]
Abstract
Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants. Genomic analysis was performed in two main lineages of Infectious bronchitis virus. Lineages differ in their S1 sequences but are similar in the rest of the genome. Genomic similarity between both lineages arise by inter-lineage recombination. Inter-lineage recombination occurred in South America between European/Asiatic and local strain. Recombinant forms have persisted in the continent for several years with wide geographic distribution.
Collapse
Affiliation(s)
- Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Greif
- Unidad de Biología Molecular, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Adriana Parodi-Talice
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Unidad de Biología Molecular, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Martín Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Claudia Techera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Diego Hernández
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
| |
Collapse
|
244
|
Donohoe BS, Wei H, Mittal A, Shollenberger T, Lunin VV, Himmel ME, Brunecky R. Towards an Understanding of Enhanced Biomass Digestibility by In Planta Expression of a Family 5 Glycoside Hydrolase. Sci Rep 2017; 7:4389. [PMID: 28663545 PMCID: PMC5491509 DOI: 10.1038/s41598-017-04502-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 05/17/2017] [Indexed: 12/21/2022] Open
Abstract
In planta expression of a thermophilic endoglucanase (AcCel5A) reduces recalcitrance by creating voids and other irregularities in cell walls of Arabidopsis thaliana that increase enzyme accessibility without negative impacts on plant growth or cell wall composition. Our results suggest that cellulose β-1-4 linkages can be cut sparingly in the assembling wall and that these minimal changes, made at the proper time, have an impact on plant cell wall recalcitrance without negative effects on overall plant development.
Collapse
Affiliation(s)
- Bryon S Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Ashutosh Mittal
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Todd Shollenberger
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado, 80401, United States.
| |
Collapse
|
245
|
Basso A, Babbucci M, Pauletto M, Riginella E, Patarnello T, Negrisolo E. The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura. Sci Rep 2017; 7:4096. [PMID: 28642542 PMCID: PMC5481413 DOI: 10.1038/s41598-017-04168-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/11/2017] [Indexed: 11/09/2022] Open
Abstract
We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both α- and β-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the β-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis.
Collapse
Affiliation(s)
- Andrea Basso
- University of Padova, Department of Comparative Biomedicine and Food Science (BCA), 35020, Agripolis, Legnaro (PD), Italy
| | - Massimiliano Babbucci
- University of Padova, Department of Comparative Biomedicine and Food Science (BCA), 35020, Agripolis, Legnaro (PD), Italy
| | - Marianna Pauletto
- University of Padova, Department of Comparative Biomedicine and Food Science (BCA), 35020, Agripolis, Legnaro (PD), Italy
| | - Emilio Riginella
- University of Padova, Department of Biology, 35131, Padova, Italy
| | - Tomaso Patarnello
- University of Padova, Department of Comparative Biomedicine and Food Science (BCA), 35020, Agripolis, Legnaro (PD), Italy
| | - Enrico Negrisolo
- University of Padova, Department of Comparative Biomedicine and Food Science (BCA), 35020, Agripolis, Legnaro (PD), Italy.
| |
Collapse
|
246
|
Huang YY, Cho ST, Haryono M, Kuo CH. Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae. PLoS One 2017; 12:e0179055. [PMID: 28617867 PMCID: PMC5472289 DOI: 10.1371/journal.pone.0179055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 05/23/2017] [Indexed: 02/02/2023] Open
Abstract
Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp). The annotation contains a total of 128 predicted genes, including 82 protein-coding, 38 tRNA, and 8 rRNA genes. Additionally, our in silico analyses identified 10 sets of repeats longer than 20 bp and predicted the presence of 36 RNA editing sites. Overall, the chloroplast genome of common bermudagrass resembles those from other Poaceae lineages. Compared to most angiosperms, the accD gene and the introns of both clpP and rpoC1 genes are missing. Additionally, the ycf1, ycf2, ycf15, and ycf68 genes are pseudogenized and two genome rearrangements exist. Our phylogenetic analysis based on 47 chloroplast protein-coding genes supported the placement of common bermudagrass within Chloridoideae. Our phylogenetic character mapping based on the parsimony principle further indicated that the loss of the accD gene and clpP introns, the pseudogenization of four ycf genes, and the two rearrangements occurred only once after the most recent common ancestor of the Poaceae diverged from other monocots, which could explain the unusual long branch leading to the Poaceae when phylogeny is inferred based on chloroplast sequences.
Collapse
Affiliation(s)
- Ya-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
247
|
Gómez-Garzón C, Hernández-Santana A, Dussán J. A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials. PLoS One 2017; 12:e0179666. [PMID: 28604819 PMCID: PMC5467902 DOI: 10.1371/journal.pone.0179666] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/01/2017] [Indexed: 01/25/2023] Open
Abstract
The toxic lineage (TL) of Lysinibacillus sphaericus has been extensively studied because of its potential biotechnological applications in biocontrol of mosquitoes and bioremediation of toxic metals. We previously proposed that L. sphaericus TL should be considered as a novel species based on a comparative genomic analysis. In the current work, we constructed the first manually curated metabolic reconstruction for this species on the basis of the available genomes. We elucidated the central metabolism of the proposed species and, beyond confirming the reported experimental evidence with genomic a support, we found insights to propose novel applications and traits to be considered in further studies. The strains belonging to this lineage exhibit a broad repertory of genes encoding insecticidal factors, some of them remain uncharacterized. These strains exhibit other unexploited biotechnological important traits, such as lactonases (quorum quenching), toxic metal resistance, and potential for aromatic compound degradation. In summary, this study provides a guideline for further research aimed to implement this organism in biocontrol and bioremediation. Similarly, we highlighted the unanswered questions to be responded in order to gain a deeper understanding of the L. sphaericus TL biology.
Collapse
Affiliation(s)
- Camilo Gómez-Garzón
- Centro de investigaciones microbiológicas (CIMIC), Universidad de los Andes, Bogotá, Colombia
| | | | - Jenny Dussán
- Centro de investigaciones microbiológicas (CIMIC), Universidad de los Andes, Bogotá, Colombia
- * E-mail:
| |
Collapse
|
248
|
Xie J, Mao Q, Tai PWL, He R, Ai J, Su Q, Zhu Y, Ma H, Li J, Gong S, Wang D, Gao Z, Li M, Zhong L, Zhou H, Gao G. Short DNA Hairpins Compromise Recombinant Adeno-Associated Virus Genome Homogeneity. Mol Ther 2017; 25:1363-1374. [PMID: 28462820 PMCID: PMC5474962 DOI: 10.1016/j.ymthe.2017.03.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 02/05/2023] Open
Abstract
Short hairpin (sh)RNAs delivered by recombinant adeno-associated viruses (rAAVs) are valuable tools to study gene function in vivo and a promising gene therapy platform. Our data show that incorporation of shRNA transgenes into rAAV constructs reduces vector yield and produces a population of truncated and defective genomes. We demonstrate that sequences with hairpins or hairpin-like structures drive the generation of truncated AAV genomes through a polymerase redirection mechanism during viral genome replication. Our findings reveal the importance of genomic secondary structure when optimizing viral vector designs. We also discovered that shDNAs could be adapted to act as surrogate mutant inverted terminal repeats (mTRs), sequences that were previously thought to be required for functional self-complementary AAV vectors. The use of shDNAs as artificial mTRs opens the door to engineering a new generation of AAV vectors with improved potency, genetic stability, and safety for both preclinical studies and human gene therapy.
Collapse
Affiliation(s)
- Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Qin Mao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Thoracic Cancer, Cancer Center, West China Hospital, West China School of Clinical Medicine, Sichuan University, Chengdu, Sichuan 610000, China
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ran He
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jianzhong Ai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Urology Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ye Zhu
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Cardiovascular Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Hong Ma
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jia Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shoufang Gong
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zhen Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mengxin Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Li Zhong
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Heather Zhou
- Genetics and Pharmacogenomics, Merck Research Laboratory, Kenilworth, NJ 07033, USA.
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Viral Vector Core, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China.
| |
Collapse
|
249
|
Wee EG, Ondondo B, Berglund P, Archer J, McMichael AJ, Baltimore D, Ter Meulen JH, Hanke T. HIV-1 Conserved Mosaics Delivered by Regimens with Integration-Deficient DC-Targeting Lentiviral Vector Induce Robust T Cells. Mol Ther 2017; 25:494-503. [PMID: 28153096 PMCID: PMC5368423 DOI: 10.1016/j.ymthe.2016.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/19/2022] Open
Abstract
To be effective against HIV type 1 (HIV-1), vaccine-induced T cells must selectively target epitopes, which are functionally conserved (present in the majority of currently circulating and reactivated HIV-1 strains) and, at the same time, beneficial (responses to which are associated with better clinical status and control of HIV-1 replication), and rapidly reach protective frequencies upon exposure to the virus. Heterologous prime-boost regimens using virally vectored vaccines are currently the most promising vaccine strategies; nevertheless, induction of robust long-term memory remains challenging. To this end, lentiviral vectors induce high frequencies of memory cells due to their low-inflammatory nature, while typically inducing only low anti-vector immune responses. Here, we describe construction of novel candidate vaccines ZVex.tHIVconsv1 and ZVex.tHIVconsv2, which are based on an integration-deficient lentiviral vector platform with preferential transduction of human dendritic cells and express a bivalent mosaic of conserved-region T cell immunogens with a high global HIV-1 match. Each of the two mosaic vaccines was individually immunogenic. When administered together in heterologous prime-boost regimens with chimpanzee adenovirus and/or poxvirus modified vaccinia virus Ankara (MVA) vaccines to BALB/c and outbred CD1-Swiss mice, they induced a median frequency of over 6,000 T cells/106 splenocytes, which were plurifunctional, broadly specific, and cross-reactive. These results support further development of this vaccine concept.
Collapse
Affiliation(s)
- Edmund G Wee
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | | | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK; International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-8555, Japan.
| |
Collapse
|
250
|
Zhang X, Wang Z, Jan S, Yang Q, Wang M. Expression and functional analysis of the lysine decarboxylase and copper amine oxidase genes from the endophytic fungus Colletotrichum gloeosporioides ES026. Sci Rep 2017; 7:2766. [PMID: 28584293 PMCID: PMC5459845 DOI: 10.1038/s41598-017-02834-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/19/2017] [Indexed: 11/09/2022] Open
Abstract
Huperzine A (HupA) isolated from Huperzia serrata is an important compound used to treat Alzheimer's disease (AD). Recently, HupA was reported in various endophytic fungi, with Colletotrichum gloeosporioides ES026 previously isolated from H. serrata shown to produce HupA. In this study, we performed next-generation sequencing and de novo RNA sequencing of C. gloeosporioides ES026 to elucidate the molecular functions, biological processes, and biochemical pathways of these unique sequences. Gene ontology and Kyoto Encyclopedia of Genes and Genomes assignments allowed annotation of lysine decarboxylase (LDC) and copper amine oxidase (CAO) for their conversion of L-lysine to 5-aminopentanal during HupA biosynthesis. Additionally, we constructed a stable, high-yielding HupA-expression system resulting from the overexpression of CgLDC and CgCAO from the HupA-producing endophytic fungus C. gloeosporioides ES026 in Escherichia coli. Quantitative reverse transcription polymerase chain reaction analysis confirmed CgLDC and CgCAO expression, and quantitative determination of HupA levels was assessed by liquid chromatography high-resolution mass spectrometry, which revealed that elevated expression of CgLDC and CgCAO produced higher yields of HupA than those derived from C. gloeosporioides ES026. These results revealed CgLDC and CgCAO involvement in HupA biosynthesis and their key role in regulating HupA content in C. gloeosporioides ES026.
Collapse
Affiliation(s)
- Xiangmei Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Zhangqian Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, People's Republic of China
| | - Saad Jan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Qian Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Mo Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
| |
Collapse
|