Genes

20 pages, 5230 KiB

Open AccessReview

Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes

by Albert Jeltsch^*

, Julian Broche and Pavel Bashtrykov

Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany

Genes 2018, 9(11), 566; https://doi.org/10.3390/genes9110566 - 21 Nov 2018

Cited by 53 | Viewed by 8451

Abstract

DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes [...] Read more.

DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. After summarizing the impact of DNA methylation on genome evolution including CpG depletion, we describe the connection of DNA methylation with several important histone post-translational modifications, including methylation of H3K4, H3K9, H3K27, and H3K36, but also with nucleosome remodeling. Moreover, we present the mechanistic features of mammalian DNA methyltransferases and their associated factors that mediate the crosstalk between DNA methylation and chromatin modifications. Finally, we describe recent advances regarding the methylation of non-CpG sites, methylation of adenine residues in human cells and methylation of mitochondrial DNA. At several places, we highlight controversial findings or open questions demanding future experimental work. Full article

(This article belongs to the Special Issue Role of DNA Methyltransferases in the Epigenome)

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12 pages, 919 KiB

Open AccessReview

Coping with Reactive Oxygen Species to Ensure Genome Stability in Escherichia coli

by Belén Mendoza-Chamizo, Anders Løbner-Olesen

and Godefroid Charbon^*

Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark

Genes 2018, 9(11), 565; https://doi.org/10.3390/genes9110565 - 21 Nov 2018

Cited by 29 | Viewed by 5950

Abstract

The facultative aerobic bacterium Escherichia coli adjusts its cell cycle to environmental conditions. Because of its lifestyle, the bacterium has to balance the use of oxygen with the potential lethal effects of its poisonous derivatives. Oxidative damages perpetrated by molecules such as hydrogen [...] Read more.

The facultative aerobic bacterium Escherichia coli adjusts its cell cycle to environmental conditions. Because of its lifestyle, the bacterium has to balance the use of oxygen with the potential lethal effects of its poisonous derivatives. Oxidative damages perpetrated by molecules such as hydrogen peroxide and superoxide anions directly incapacitate metabolic activities relying on enzymes co-factored with iron and flavins. Consequently, growth is inhibited when the bacterium faces substantial reactive oxygen insults coming from environmental or cellular sources. Although hydrogen peroxide and superoxide anions do not oxidize DNA directly, these molecules feed directly or indirectly the generation of the highly reactive hydroxyl radical that damages the bacterial chromosome. Oxidized bases are normally excised and the single strand gap repaired by the base excision repair pathway (BER). This process is especially problematic in E. coli because replication forks do not sense the presence of damages or a stalled fork ahead of them. As consequence, single-strand breaks are turned into double-strand breaks (DSB) through replication. Since E. coli tolerates the presence of DSBs poorly, BER can become toxic during oxidative stress. Here we review the repair strategies that E. coli adopts to preserve genome integrity during oxidative stress and their relation to cell cycle control of DNA replication. Full article

(This article belongs to the Special Issue Chromosome Replication and Genome Integrity)

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20 pages, 2437 KiB

Open AccessReview

Molecular and Cellular Functions of the Warsaw Breakage Syndrome DNA Helicase DDX11

by Francesca M. Pisani^1,*

, Ettore Napolitano¹

, Luisa M. R. Napolitano² and Silvia Onesti^2,*

¹ Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, 80131 Napoli, Italy

² Elettra–Sincrotrone Trieste S.C.p.A., AREA Science Park Basovizza, 34149 Trieste, Italy

Genes 2018, 9(11), 564; https://doi.org/10.3390/genes9110564 - 21 Nov 2018

Cited by 26 | Viewed by 5830

Abstract

DDX11/ChlR1 (Chl1 in yeast) is a DNA helicase involved in sister chromatid cohesion and in DNA repair pathways. The protein belongs to the family of the iron–sulphur cluster containing DNA helicases, whose deficiencies have been linked to a number of diseases affecting genome [...] Read more.

DDX11/ChlR1 (Chl1 in yeast) is a DNA helicase involved in sister chromatid cohesion and in DNA repair pathways. The protein belongs to the family of the iron–sulphur cluster containing DNA helicases, whose deficiencies have been linked to a number of diseases affecting genome stability. Mutations of human DDX11 are indeed associated with the rare genetic disorder named Warsaw breakage syndrome, showing both chromosomal breakages and chromatid cohesion defects. Moreover, growing evidence of a potential role in oncogenesis further emphasizes the clinical relevance of DDX11. Here, we illustrate the biochemical and structural features of DDX11 and how it cooperates with multiple protein partners in the cell, acting at the interface of DNA replication/repair/recombination and sister chromatid cohesion to preserve genome stability. Full article

(This article belongs to the Special Issue Chromosome Replication and Genome Integrity)

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30 pages, 7160 KiB

Open AccessArticle

Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications

by Anna Szczepaniak¹, Michał Książkiewicz^1,*

, Jan Podkowiński²

, Katarzyna B. Czyż³

, Marek Figlerowicz² and Barbara Naganowska¹

¹ Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland

² Department of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland

³ Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland

Genes 2018, 9(11), 563; https://doi.org/10.3390/genes9110563 - 21 Nov 2018

Cited by 7 | Viewed by 4856

Abstract

Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain [...] Read more.

Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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18 pages, 3468 KiB

Open AccessArticle

Molecular Factors of Hypochlorite Tolerance in the Hypersaline Archaeon Haloferax volcanii

by Miguel Gomez^1,†, Whinkie Leung^1,†, Swathi Dantuluri¹, Alexander Pillai¹, Zyan Gani¹, Sungmin Hwang¹, Lana J. McMillan^1,2, Saija Kiljunen³

, Harri Savilahti⁴ and Julie A. Maupin-Furlow^1,2,*

¹ Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA

² Genetics Institute, University of Florida, Gainesville, FL 32611, USA

³ Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, 00014 Helsinki, Finland

⁴ Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland

^† These authors have contributed equally to this work.

Genes 2018, 9(11), 562; https://doi.org/10.3390/genes9110562 - 20 Nov 2018

Cited by 6 | Viewed by 5439

Abstract

Halophilic archaea thrive in hypersaline conditions associated with desiccation, ultraviolet (UV) irradiation and redox active compounds, and thus are naturally tolerant to a variety of stresses. Here, we identified mutations that promote enhanced tolerance of halophilic archaea to redox-active compounds using Haloferax volcanii [...] Read more.

Halophilic archaea thrive in hypersaline conditions associated with desiccation, ultraviolet (UV) irradiation and redox active compounds, and thus are naturally tolerant to a variety of stresses. Here, we identified mutations that promote enhanced tolerance of halophilic archaea to redox-active compounds using Haloferax volcanii as a model organism. The strains were isolated from a library of random transposon mutants for growth on high doses of sodium hypochlorite (NaOCl), an agent that forms hypochlorous acid (HOCl) and other redox acid compounds common to aqueous environments of high concentrations of chloride. The transposon insertion site in each of twenty isolated clones was mapped using the following: (i) inverse nested two-step PCR (INT-PCR) and (ii) semi-random two-step PCR (ST-PCR). Genes that were found to be disrupted in hypertolerant strains were associated with lysine deacetylation, proteasomes, transporters, polyamine biosynthesis, electron transfer, and other cellular processes. Further analysis revealed a ΔpsmA1 (α1) markerless deletion strain that produces only the α2 and β proteins of 20S proteasomes was hypertolerant to hypochlorite stress compared with wild type, which produces α1, α2, and β proteins. The results of this study provide new insights into archaeal tolerance of redox active compounds such as hypochlorite. Full article

(This article belongs to the Special Issue Genetics of Halophilic Microorganisms)

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11 pages, 563 KiB

Open AccessReview

The Plant Circadian Clock and Chromatin Modifications

by Ping Yang^1,2, Jianhao Wang^1,2, Fu-Yu Huang³

, Songguang Yang^1,* and Keqiang Wu^3,*

¹ Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China

² University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China

³ Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan

Genes 2018, 9(11), 561; https://doi.org/10.3390/genes9110561 - 20 Nov 2018

Cited by 9 | Viewed by 5380

Abstract

The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes. The circadian function depends on the precise regulation of rhythmic gene expression at the core of the oscillators. In addition to the well-characterized [...] Read more.

The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes. The circadian function depends on the precise regulation of rhythmic gene expression at the core of the oscillators. In addition to the well-characterized transcriptional feedback regulation of several clock components, additional regulatory mechanisms, such as alternative splicing, regulation of protein stability, and chromatin modifications are beginning to emerge. In this review, we discuss recent findings in the regulation of the circadian clock function in Arabidopsis thaliana. The involvement of chromatin modifications in the regulation of the core circadian clock genes is also discussed. Full article

(This article belongs to the Special Issue Genetic Regulation of Circadian Rhythm in Plants)

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14 pages, 1628 KiB

Open AccessArticle

Association of Candidate Genes with Response to Heat and Newcastle Disease Virus

by Kaylee Rowland¹, Perot Saelao², Ying Wang², Janet E. Fulton³, Grant N. Liebe³

, Amy M. McCarron³, Anna Wolc^1,3, Rodrigo A. Gallardo⁴, Terra Kelly⁴, Huaijun Zhou²

, Jack C. M. Dekkers¹ and Susan J. Lamont^1,*

¹ Department of Animal Science, Iowa State University, Ames, IA 50011, USA

² Department of Animal Science, University of California, Davis, CA 95615, USA

³ Hy-Line International, Dallas Center, IA 50063, USA

⁴ School of Veterinary Medicine, University of California, Davis, CA 95616, USA

Genes 2018, 9(11), 560; https://doi.org/10.3390/genes9110560 - 19 Nov 2018

Cited by 13 | Viewed by 4414

Abstract

Newcastle disease is considered the number one disease constraint to poultry production in low and middle-income countries, however poultry that is raised in resource-poor areas often experience multiple environmental challenges. Heat stress has a negative impact on production, and immune response to pathogens [...] Read more.

Newcastle disease is considered the number one disease constraint to poultry production in low and middle-income countries, however poultry that is raised in resource-poor areas often experience multiple environmental challenges. Heat stress has a negative impact on production, and immune response to pathogens can be negatively modulated by heat stress. Candidate genes and regions chosen for this study were based on previously reported associations with response to immune stimulants, pathogens, or heat, including: TLR3, TLR7, MX, MHC-B (major histocompatibility complex, gene complex), IFI27L2, SLC5A1, HSPB1, HSPA2, HSPA8, IFRD1, IL18R1, IL1R1, AP2A2, and TOLLIP. Chickens of a commercial egg-laying line were infected with a lentogenic strain of NDV (Newcastle disease virus); half the birds were maintained at thermoneutral temperature and the other half were exposed to high ambient temperature before the NDV challenge and throughout the remainder of the study. Phenotypic responses to heat, to NDV, or to heat + NDV were measured. Selected SNPs (single nucleotide polymorphisms) within 14 target genes or regions were genotyped; and genotype effects on phenotypic responses to NDV or heat + NDV were tested in each individual treatment group and the combined groups. Seventeen significant haplotype effects, among seven genes and seven phenotypes, were detected for response to NDV or heat or NDV + heat. These findings identify specific genetic variants that are associated with response to heat and/or NDV which may be useful in the genetic improvement of chickens to perform favorably when faced with pathogens and heat stress. Full article

(This article belongs to the Special Issue Genomics of Avian Viral Infections)

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14 pages, 8780 KiB

Open AccessArticle

Molecular Characterization of Annexin B2, B3 and B12 in Taenia multiceps

by Cheng Guo^1,†, Yue Xie^1,†, Yuchen Liu¹, Ning Wang¹, Jiafei Zhan¹, Xuan Zhou², Christiana Angel^1,3

, Xiaobin Gu¹, Weimin Lai¹, Xuerong Peng⁴ and Guangyou Yang^1,*

¹ Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China

² Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China

³ Department of Veterinary Parasitology, Faculty of Veterinary Sciences, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sindh 67210, Pakistan

⁴ Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Chengdu 611130, China

^† These authors contributed equally to the work.

Genes 2018, 9(11), 559; https://doi.org/10.3390/genes9110559 - 19 Nov 2018

Cited by 8 | Viewed by 3738

Abstract

Coenurus cerebralis, the metacestode of Taenia multiceps, causes coenurosis, a disease severely affecting goat, sheep, cattle and yak farming and resulting in huge economic losses annually. Annexins bind calcium ions and play an important role in flatworm parasite development. To explore [...] Read more.

Coenurus cerebralis, the metacestode of Taenia multiceps, causes coenurosis, a disease severely affecting goat, sheep, cattle and yak farming and resulting in huge economic losses annually. Annexins bind calcium ions and play an important role in flatworm parasite development. To explore potential functions of annexins in T. multiceps, three homologous genes, namely, TmAnxB2, TmAnxB3 and TmAnxB12, were screened from the transcriptome dataset, amplified from C. cerebralis cDNA and subjected to bioinformatics analysis. Then, polyclonal antibodies recognizing the recombinant TmAnxB2 (rTmAnxB2) and rTmAnxB3 were prepared for localization of TmAnxB2 and TmAnxB3 in different tissues and developmental stages by immunofluorescence. The transcription of all three genes was also measured by relative fluorescent quantitative PCR. The sizes of rTmAnxB2, rTmAnxB3 and rTmAnxB12 were 58.00, 53.06 and 53.51 kDa, respectively, and rTmAnxB12 was unstable. Both rTmAnxB2 and rTmAnxB3 were recognized by goat-positive T. multiceps sera in Western blots. Immunofluorescence revealed that TmAnxB2 and TmAnxB3 were localized in the protoscolex and cyst wall and TmAnxB3 was also detected in adult cortex. TmAnxB2 and TmAnxB12 mRNA levels were determined to be highest in oncospheres and protoscolex, whereas transcription of TmAnxB3 was highest in scolex and immature segments. Taken together, these findings indicate that TmAnxB2 and TmAnxB12 may play critical roles in T. multiceps larvae, while TmAnxB3 may have important functions in adults. These results will lay the foundation for functional research of annexins in T. multiceps. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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16 pages, 3638 KiB

Open AccessArticle

Fanconi Anaemia-Like Mph1 Helicase Backs up Rad54 and Rad5 to Circumvent Replication Stress-Driven Chromosome Bridges

by Jonay García-Luis^1,† and Félix Machín^1,2,*

¹ Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain

² Instituto de Tecnologías Biomédicas, Universidad de La Laguna, C/Sta María Soledad, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain

^† Present address: Cell Cycle Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK

Genes 2018, 9(11), 558; https://doi.org/10.3390/genes9110558 - 17 Nov 2018

Cited by 7 | Viewed by 5664

Abstract

Homologous recombination (HR) is a preferred mechanism to deal with DNA replication impairments. However, HR synapsis gives rise to joint molecules (JMs) between the nascent sister chromatids, challenging chromosome segregation in anaphase. Joint molecules are resolved by the actions of several structure-selective endonucleases [...] Read more.

Homologous recombination (HR) is a preferred mechanism to deal with DNA replication impairments. However, HR synapsis gives rise to joint molecules (JMs) between the nascent sister chromatids, challenging chromosome segregation in anaphase. Joint molecules are resolved by the actions of several structure-selective endonucleases (SSEs), helicases and topoisomerases. Previously, we showed that yeast double mutants for the Mus81-Mms4 and Yen1 SSEs lead to anaphase bridges (ABs) after replication stress. Here, we have studied the role of the Mph1 helicase in preventing these anaphase aberrations. Mph1, the yeast ortholog of Fanconi anaemia protein M (FANCM), is involved in the removal of the D-loop, the first JM to arise in canonical HR. Surprisingly, the absence of Mph1 alone did not increase ABs; rather, it blocked cells in G2. Interestingly, in the search for genetic interactions with functionally related helicases and translocases, we found additive effects on the G2 block and post-G2 aberrations between mph1Δ and knockout mutants for Srs2, Rad54 and Rad5. Based on these interactions, we suggest that Mph1 acts coordinately with these helicases in the non-canonical HR-driven fork regression mechanism to bypass stalled replication forks. Full article

(This article belongs to the Special Issue Chromosome Replication and Genome Integrity)

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15 pages, 1662 KiB

Open AccessReview

Cyclic Peptides: Promising Scaffolds for Biopharmaceuticals

by Donghyeok Gang, Do Wook Kim and Hee-Sung Park^*

Department of Chemistry, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea

Genes 2018, 9(11), 557; https://doi.org/10.3390/genes9110557 - 16 Nov 2018

Cited by 83 | Viewed by 10095

Abstract

To date, small molecules and macromolecules, including antibodies, have been the most pursued substances in drug screening and development efforts. Despite numerous favorable features as a drug, these molecules still have limitations and are not complementary in many regards. Recently, peptide-based chemical structures [...] Read more.

To date, small molecules and macromolecules, including antibodies, have been the most pursued substances in drug screening and development efforts. Despite numerous favorable features as a drug, these molecules still have limitations and are not complementary in many regards. Recently, peptide-based chemical structures that lie between these two categories in terms of both structural and functional properties have gained increasing attention as potential alternatives. In particular, peptides in a circular form provide a promising scaffold for the development of a novel drug class owing to their adjustable and expandable ability to bind a wide range of target molecules. In this review, we discuss recent progress in methodologies for peptide cyclization and screening and use of bioactive cyclic peptides in various applications. Full article

(This article belongs to the Special Issue Synthetic DNA and RNA Programming)

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14 pages, 1244 KiB

Open AccessReview

Modular Proteoglycan Perlecan/HSPG2: Mutations, Phenotypes, and Functions

by Jerahme R. Martinez¹, Akash Dhawan^2,3 and Mary C. Farach-Carson^2,3,*

¹ Department of Mechanical Engineering, University of Delaware, Newark, DE 19716, USA

² Department of Bioengineering, Rice University, Houston, TX 77005, USA

³ Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX 77054, USA

Genes 2018, 9(11), 556; https://doi.org/10.3390/genes9110556 - 16 Nov 2018

Cited by 56 | Viewed by 8667

Abstract

Heparan sulfate proteoglycan 2 (HSPG2) is an essential, highly conserved gene whose expression influences many developmental processes including the formation of the heart and brain. The gene is widely expressed throughout the musculoskeletal system including cartilage, bone marrow and skeletal muscle. [...] Read more.

Heparan sulfate proteoglycan 2 (HSPG2) is an essential, highly conserved gene whose expression influences many developmental processes including the formation of the heart and brain. The gene is widely expressed throughout the musculoskeletal system including cartilage, bone marrow and skeletal muscle. The HSPG2 gene product, perlecan is a multifunctional proteoglycan that preserves the integrity of extracellular matrices, patrols tissue borders, and controls various signaling pathways affecting cellular phenotype. Given HSPG2’s expression pattern and its role in so many fundamental processes, it is not surprising that relatively few gene mutations have been identified in viable organisms. Mutations to the perlecan gene are rare, with effects ranging from a relatively mild condition to a more severe and perinatally lethal form. This review will summarize the important studies characterizing mutations and variants of HSPG2 and discuss how these genomic modifications affect expression, function and phenotype. Additionally, this review will describe the clinical findings of reported HSPG2 mutations and their observed phenotypes. Finally, the evolutionary aspects that link gene integrity to function are discussed, including key findings from both in vivo animal studies and in vitro systems. We also hope to facilitate discussion about perlecan/HSPG2 and its role in normal physiology, to explain how mutation can lead to pathology, and to point out how this information can suggest pathways for future mechanistic studies. Full article

(This article belongs to the Special Issue DNA Variations in Evolution and Human Diseases)

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15 pages, 3141 KiB

Open AccessArticle

Genetic Dissection of Azuki Bean Weevil (Callosobruchus chinensis L.) Resistance in Moth Bean (Vigna aconitifolia [Jaqc.] Maréchal)

by Prakit Somta^1,2,3,*

, Achara Jomsangawong⁴, Chutintorn Yundaeng¹, Xingxing Yuan¹, Jingbin Chen¹

, Norihiko Tomooka⁵ and Xin Chen^1,*

¹ Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China

² Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand

³ Center for Agricultural Biotechnology (AG-BIO/PEDRO-CHE), Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand

⁴ Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand

⁵ Genetic Resources Center, Gene Bank, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

Genes 2018, 9(11), 555; https://doi.org/10.3390/genes9110555 - 15 Nov 2018

Cited by 13 | Viewed by 4224

Abstract

The azuki bean weevil (Callosobruchus chinensis L.) is an insect pest responsible for serious postharvest seed loss in leguminous crops. In this study, we performed quantitative trait locus (QTL) mapping of seed resistance to C. chinensis in moth bean (Vigna aconitifolia [...] Read more.

The azuki bean weevil (Callosobruchus chinensis L.) is an insect pest responsible for serious postharvest seed loss in leguminous crops. In this study, we performed quantitative trait locus (QTL) mapping of seed resistance to C. chinensis in moth bean (Vigna aconitifolia [Jaqc.] Maréchal). An F₂ population of 188 plants developed by crossing resistant accession ‘TN67’ (wild type from India; male parent) and susceptible accession ‘IPCMO056’ (cultivated type from India; female parent) was used for mapping. Seeds of the F₂ population from 2014 and F_2:3 populations from 2016 and 2017 were bioassayed with C. chinensis, and the percentage of damaged seeds and progress of infestation severity were measured. Segregation analysis suggested that C. chinensis resistance in TN176 is controlled by a single dominant gene, designated as Rcc. QTL analysis revealed one principal and one modifying QTL for the resistance, named qVacBrc2.1 and qVacBrc5.1, respectively. qVacBrc2.1 was located on linkage group 2 between simple sequence repeat markers CEDG261 and DMB-SSR160 and accounted for 50.41% to 64.23% of resistance-related traits, depending on the trait and population. Comparative genomic analysis suggested that qVacBrc2.1 is the same as QTL Brc2.1 conferring C. chinensis resistance in wild azuki bean (V. nepalensis Tateishi and Maxted). Markers CEDG261 and DMB-SSR160 should be useful for marker-assisted selection for C. chinensis resistance in moth bean. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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17 pages, 2000 KiB

Open AccessArticle

Cryptic Diversity Hidden within the Leafminer Genus Liriomyza (Diptera: Agromyzidae)

by Antonio Carapelli^1,*

, Abir Soltani², Chiara Leo¹

, Matteo Vitale¹

, Moez Amri³

and Jouda Mediouni-Ben Jemâa⁴

¹ Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy

² Faculté des Sciences de Bizerte, Université de Carthage, 7021 Zarzouna Bizerte, Tunisia

³ Biodiversity and Crop Improvement Program (BCI), International Center for Agricultural Research in the Dry Areas (ICARDA), 10112 Rabat-institutes, Morocco

⁴ Laboratoire de Biotechnologie Appliquée à l’Agriculture, INRAT, Université de Carthage, Rue Hedi Karray, 2080 Ariana, Tunisia

Genes 2018, 9(11), 554; https://doi.org/10.3390/genes9110554 - 15 Nov 2018

Cited by 8 | Viewed by 5098

Abstract

Leafminer insects of the genus Liriomyza are small flies whose larvae feed on the internal tissue of some of the most important crop plants for the human diet. Several of these pest species are highly uniform from the morphological point of view, meaning [...] Read more.

Leafminer insects of the genus Liriomyza are small flies whose larvae feed on the internal tissue of some of the most important crop plants for the human diet. Several of these pest species are highly uniform from the morphological point of view, meaning molecular data represents the only reliable taxonomic tool useful to define cryptic boundaries. In this study, both mitochondrial and nuclear molecular markers have been applied to investigate the population genetics of some Tunisian populations of the polyphagous species Liriomyza cicerina, one of the most important pest of chickpea cultivars in the whole Mediterranean region. Molecular data have been collected on larvae isolated from chickpea, faba bean, and lentil leaves, and used for population genetics, phylogenetics, and species delimitation analyses. Results point toward high differentiation levels between specimens collected on the three different legume crops, which, according to the species delimitation methods, are also sufficient to define incipient species differentiation and cryptic species occurrence, apparently tied up with host choice. Genetic data have also been applied for a phylogenetic comparison among Liriomyza species, further confirming their decisive role in the systematic studies of the genus. Full article

(This article belongs to the Special Issue Tools for Population and Evolutionary Genetics)

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15 pages, 3876 KiB

Open AccessArticle

Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains

by Joseph B. Ahrens, Jordon Rahaman and Jessica Siltberg-Liberles^*

Department of Biological Sciences, Florida International University, Miami, FL 33199, USA

Genes 2018, 9(11), 553; https://doi.org/10.3390/genes9110553 - 14 Nov 2018

Cited by 10 | Viewed by 4483

Abstract

Various structural and functional constraints govern the evolution of protein sequences. As a result, the relative rates of amino acid replacement among sites within a protein can vary significantly. Previous large-scale work on Metazoan (Animal) protein sequence alignments indicated that amino acid replacement [...] Read more.

Various structural and functional constraints govern the evolution of protein sequences. As a result, the relative rates of amino acid replacement among sites within a protein can vary significantly. Previous large-scale work on Metazoan (Animal) protein sequence alignments indicated that amino acid replacement rates are partially driven by a complex interaction among three factors: intrinsic disorder propensity; secondary structure; and functional domain involvement. Here, we use sequence-based predictors to evaluate the effects of these factors on site-specific sequence evolutionary rates within four eukaryotic lineages: Metazoans; Plants; Saccharomycete Fungi; and Alveolate Protists. Our results show broad, consistent trends across all four Eukaryote groups. In all four lineages, there is a significant increase in amino acid replacement rates when comparing: (i) disordered vs. ordered sites; (ii) random coil sites vs. sites in secondary structures; and (iii) inter-domain linker sites vs. sites in functional domains. Additionally, within Metazoans, Plants, and Saccharomycetes, there is a strong confounding interaction between intrinsic disorder and secondary structure—alignment sites exhibiting both high disorder propensity and involvement in secondary structures have very low average rates of sequence evolution. Analysis of gene ontology (GO) terms revealed that in all four lineages, a high fraction of sequences containing these conserved, disordered-structured sites are involved in nucleic acid binding. We also observe notable differences in the statistical trends of Alveolates, where intrinsically disordered sites are more variable than in other Eukaryotes and the statistical interactions between disorder and other factors are less pronounced. Full article

(This article belongs to the Special Issue Evolution and Structure of Proteins and Proteomes)

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21 pages, 1319 KiB

Open AccessReview

The Emerging Role of Epitranscriptomics in Cancer: Focus on Urological Tumors

by João Lobo^1,2,3

, Daniela Barros-Silva¹

, Rui Henrique^1,2,3

and Carmen Jerónimo^1,3,*

¹ Cancer Biology and Epigenetics Group, Research Center of Portuguese Oncology Institute of Porto (GEBC CI-IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal

² Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal

³ Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal

Genes 2018, 9(11), 552; https://doi.org/10.3390/genes9110552 - 13 Nov 2018

Cited by 63 | Viewed by 6832

Abstract

Epitranscriptomics has gained ground in recent years, especially after the advent of techniques for accurately studying these mechanisms. Among all modifications occurring in RNA molecules, N6-methyladenosine (m⁶A) is the most frequent, especially among mRNAs. m⁶A has been demonstrated to [...] Read more.

Epitranscriptomics has gained ground in recent years, especially after the advent of techniques for accurately studying these mechanisms. Among all modifications occurring in RNA molecules, N6-methyladenosine (m⁶A) is the most frequent, especially among mRNAs. m⁶A has been demonstrated to play important roles in many physiological processes and several disease states, including various cancer models (from solid to liquid tumors). Tumor cells’ epitranscriptome is indeed disrupted in a way to promote cancer-prone features, by means of up/downregulating m⁶A-related players: the so-called writers, readers and erasers. These proteins modulate m⁶A establishment, removal and determine mRNAs fate, acting in a context-dependent manner, so that a single player may act as an oncogenic signal in one tumor model (methyltransferase like 3 (METTL3) in lung cancer) and as a tumor suppressor in another context (METTL3 in glioblastoma). Despite recent advances, however, little attention has been directed towards urological cancer. By means of a thorough analysis of the publicly available TCGA (The Cancer Genome Atlas) database, we disclosed the most relevant players in four major urogenital neoplasms—kidney, bladder, prostate and testicular cancer—for prognostic, subtype discrimination and survival purposes. In all tumor models assessed, the most promising player was shown to be Vir like m⁶A methyltransferase associated (VIRMA), which could constitute a potential target for personalized therapies. Full article

(This article belongs to the Special Issue The Epitranscriptome in Human Disease)

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17 pages, 936 KiB

Open AccessArticle

Unintentional Genomic Changes Endow Cupriavidus metallidurans with an Augmented Heavy-Metal Resistance

by Felipe A. Millacura¹, Paul J. Janssen²

, Pieter Monsieurs², Ann Janssen², Ann Provoost², Rob Van Houdt²

and Luis A. Rojas^3,*

¹ School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JQ, UK

² Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK•CEN, 2400 Mol, Belgium

³ Chemistry Department, Faculty of Sciences, Universidad Católica del Norte, UCN, Antofagasta 1240000, Chile

Genes 2018, 9(11), 551; https://doi.org/10.3390/genes9110551 - 13 Nov 2018

Cited by 12 | Viewed by 5452

Abstract

For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To [...] Read more.

For the past three decades, Cupriavidus metallidurans has been one of the major model organisms for bacterial tolerance to heavy metals. Its type strain CH34 contains at least 24 gene clusters distributed over four replicons, allowing for intricate and multilayered metal responses. To gain organic mercury resistance in CH34, broad-spectrum mer genes were introduced in a previous work via conjugation of the IncP-1β plasmid pTP6. However, we recently noted that this CH34-derived strain, MSR33, unexpectedly showed an increased resistance to other metals (i.e., Co²⁺, Ni²⁺, and Cd²⁺). To thoroughly investigate this phenomenon, we resequenced the entire genome of MSR33 and compared its DNA sequence and basal gene expression profile to those of its parental strain CH34. Genome comparison identified 11 insertions or deletions (INDELs) and nine single nucleotide polymorphisms (SNPs), whereas transcriptomic analysis displayed 107 differentially expressed genes. Sequence data implicated the transposition of IS1088 in higher Co²⁺ and Ni²⁺ resistances and altered gene expression, although the precise mechanisms of the augmented Cd²⁺ resistance in MSR33 remains elusive. Our work indicates that conjugation procedures involving large complex genomes and extensive mobilomes may pose a considerable risk toward the introduction of unwanted, undocumented genetic changes. Special efforts are needed for the applied use and further development of small nonconjugative broad-host plasmid vectors, ideally involving CRISPR-related and advanced biosynthetic technologies. Full article

(This article belongs to the Special Issue Genomics of Bacterial Metal Resistance)

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14 pages, 2742 KiB

Open AccessArticle

Root-Specific Expression of a Jacalin Lectin Family Protein Gene Requires a Transposable Element Sequence in the Promoter

by Qiong Wu^1,2, Neil A. Smith², Daai Zhang², Changyong Zhou^1,* and Ming-Bo Wang^2,*

¹ Citrus Research Institute, Southwest University, Chongqing 400716, China

² Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT 2601, Australia

Genes 2018, 9(11), 550; https://doi.org/10.3390/genes9110550 - 13 Nov 2018

Cited by 5 | Viewed by 4283

Abstract

Transposable elements (TEs) are widespread in the plant genome and can impact on the expression of neighbouring genes. Our previous studies have identified a number of DNA demethylase-regulated defence-related genes that contain TE sequences in the promoter and show tissue-specific expression in Arabidopsis. [...] Read more.

Transposable elements (TEs) are widespread in the plant genome and can impact on the expression of neighbouring genes. Our previous studies have identified a number of DNA demethylase-regulated defence-related genes that contain TE sequences in the promoter and show tissue-specific expression in Arabidopsis. In this study we investigated the role of the promoter TE insertions in the root-specific expression of a DNA demethylase-regulated gene, AT5G38550, encoding a Jacalin lectin family protein. Using a promoter:GUS fusion reporter gene approach, we first demonstrated that the full-length promoter fragment, carrying four TE sequences, contained the essential regulatory information required for root-specific expression and DNA demethylase regulation in Arabidopsis. By successive deletion of the four TE sequences, we showed that one of the four TE insertions, a 201-bp TE fragment of the hAT DNA transposon family, was required for root-specific expression: Deletion of this TE, but not the first two TE sequences, converted the root-specific expression pattern to a constitutive expression pattern in Arabidopsis plants. Our study provides an example indicating an important role of TE insertions in tissue-specific expression of plant defence-related genes. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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3 pages, 169 KiB

Open AccessEditorial

Special Issue: Coevolution of Hosts and Their Microbiome

by Morten T. Limborg^1,*

and Philipp Heeb^2,*

¹ Natural History Museum of Denmark, University of Copenhagen, 1165 Copenhagen, Denmark

² Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier, 31330 Toulouse, France

Genes 2018, 9(11), 549; https://doi.org/10.3390/genes9110549 - 13 Nov 2018

Cited by 14 | Viewed by 4094

Abstract

The evolution of life-history traits in plants and animals has taken place in the midst of complex microbial communities. [...] Full article

(This article belongs to the Special Issue Coevolution of Hosts and their Microbiome)

33 pages, 1447 KiB

Open AccessReview

De-Extinction

by Ben Jacob Novak^1,2,3

¹ Revive & Restore, Sausalito, CA 94965, USA

² Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia

³ Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organization, Newcomb, Victoria 3220, Australia

Genes 2018, 9(11), 548; https://doi.org/10.3390/genes9110548 - 13 Nov 2018

Cited by 48 | Viewed by 57006

Abstract

De-extinction projects for species such as the woolly mammoth and passenger pigeon have greatly stimulated public and scientific interest, producing a large body of literature and much debate. To date, there has been little consistency in descriptions of de-extinction technologies and purposes. In [...] Read more.

De-extinction projects for species such as the woolly mammoth and passenger pigeon have greatly stimulated public and scientific interest, producing a large body of literature and much debate. To date, there has been little consistency in descriptions of de-extinction technologies and purposes. In 2016, a special committee of the International Union for the Conservation of Nature (IUCN) published a set of guidelines for de-extinction practice, establishing the first detailed description of de-extinction; yet incoherencies in published literature persist. There are even several problems with the IUCN definition. Here I present a comprehensive definition of de-extinction practice and rationale that expounds and reconciles the biological and ecological inconsistencies in the IUCN definition. This new definition brings together the practices of reintroduction and ecological replacement with de-extinction efforts that employ breeding strategies to recover unique extinct phenotypes into a single “de-extinction” discipline. An accurate understanding of de-extinction and biotechnology segregates the restoration of certain species into a new classification of endangerment, removing them from the purview of de-extinction and into the arena of species’ recovery. I term these species as “evolutionarily torpid species”; a term to apply to species falsely considered extinct, which in fact persist in the form of cryopreserved tissues and cultured cells. For the first time in published literature, all currently active de-extinction breeding programs are reviewed and their progress presented. Lastly, I review and scrutinize various topics pertaining to de-extinction in light of the growing body of peer-reviewed literature published since de-extinction breeding programs gained public attention in 2013. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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16 pages, 2217 KiB

Open AccessArticle

Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes

by Shuaibin Wang^1,2,3, Qingwei Song^1,2,3, Shanshan Li^1,2,3, Zhigang Hu⁴, Gangqiang Dong⁵, Chi Song⁶, Hongwen Huang¹ and Yifei Liu^4,*

¹ Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China

² Guangdong Provincial Key Laboratory of Applied Botany, Guangzhou 510650, China

³ University of Chinese Academy of Sciences, Beijing 100049, China

⁴ College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China

⁵ Amway (China) Botanical R&D Center, Wuxi 214115, China

⁶ Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China

Genes 2018, 9(11), 547; https://doi.org/10.3390/genes9110547 - 12 Nov 2018

Cited by 31 | Viewed by 5841

Abstract

Diversity in structure and organization is one of the main features of angiosperm mitochondrial genomes (mitogenomes). The ultra-long reads of Oxford Nanopore Technology (ONT) provide an opportunity to obtain a complete mitogenome and investigate the structural variation in unprecedented detail. In this study, [...] Read more.

Diversity in structure and organization is one of the main features of angiosperm mitochondrial genomes (mitogenomes). The ultra-long reads of Oxford Nanopore Technology (ONT) provide an opportunity to obtain a complete mitogenome and investigate the structural variation in unprecedented detail. In this study, we compared mitogenome assembly methods using Illumina and/or ONT sequencing data and obtained the complete mitogenome (208 kb) of Chrysanthemum nankingense based on the hybrid assembly method. The mitogenome encoded 19 transfer RNA genes, three ribosomal RNA genes, and 34 protein-coding genes with 21 group II introns disrupting eight intron-contained genes. A total of seven medium repeats were related to homologous recombination at different frequencies as supported by the long ONT reads. Subsequently, we investigated the variations in gene content and constitution of 28 near-complete mitogenomes from Asteraceae. A total of six protein-coding genes were missing in all Asteraceae mitogenomes, while four other genes were not detected in some lineages. The core fragments (~88 kb) of the Asteraceae mitogenomes had a higher GC content (~46.7%) than the variable and specific fragments. The phylogenetic topology based on the core fragments of the Asteraceae mitogenomes was highly consistent with the topologies obtained from the corresponding plastid datasets. Our results highlighted the advantages of the complete assembly of the C. nankingense mitogenome and the investigation of its structural variation based on ONT sequencing data. Moreover, the method based on local collinear blocks of the mitogenomes could achieve the alignment of highly rearrangeable and variable plant mitogenomes as well as construct a robust phylogenetic topology. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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17 pages, 1228 KiB

Open AccessArticle

Dissecting the Contribution of Release Factor Interactions to Amber Stop Codon Reassignment Efficiencies of the Methanocaldococcus jannaschii Orthogonal Pair

by David G. Schwark, Margaret A. Schmitt and John D. Fisk^*

Department of Chemistry, University of Colorado Denver, Campus Box 194, P.O. Box 173364, Denver, CO 80217-3364, USA

Genes 2018, 9(11), 546; https://doi.org/10.3390/genes9110546 - 12 Nov 2018

Cited by 21 | Viewed by 4264

Abstract

Non-canonical amino acids (ncAAs) are finding increasing use in basic biochemical studies and biomedical applications. The efficiency of ncAA incorporation is highly variable, as a result of competing system composition and codon context effects. The relative quantitative contribution of the multiple factors affecting [...] Read more.

Non-canonical amino acids (ncAAs) are finding increasing use in basic biochemical studies and biomedical applications. The efficiency of ncAA incorporation is highly variable, as a result of competing system composition and codon context effects. The relative quantitative contribution of the multiple factors affecting incorporation efficiency are largely unknown. This manuscript describes the use of green fluorescent protein (GFP) reporters to quantify the efficiency of amber codon reassignment using the Methanocaldococcus jannaschii orthogonal pair system, commonly employed for ncAA incorporation, and quantify the contribution of release factor 1 (RF1) to the overall efficiency of amino acid incorporation. The efficiencies of amber codon reassignments were quantified at eight positions in GFP and evaluated in multiple combinations. The quantitative contribution of RF1 competition to reassignment efficiency was evaluated through comparisons of amber codon suppression efficiencies in normal and genomically recoded Escherichia coli strains. Measured amber stop codon reassignment efficiencies for eight single stop codon GFP variants ranged from 51 to 117% in E. coli DH10B and 76 to 104% in the RF1 deleted E. coli C321.ΔA.exp. Evaluation of efficiency changes in specific sequence contexts in the presence and absence of RF1 suggested that RF1 specifically interacts with +4 Cs and that the RF1 interactions contributed approximately half of the observed sequence context-dependent variation in measured reassignment efficiency. Evaluation of multisite suppression efficiencies suggests that increasing demand for translation system components limits multisite incorporation in cells with competing RF1. Full article

(This article belongs to the Special Issue Synthetic DNA and RNA Programming)

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11 pages, 2878 KiB

Open AccessArticle

miRNA Mediated Noise Making of 3′UTR Mutations in Cancer

by Wei Wu^1,†

, Lingxiang Wu^1,†, Mengyan Zhu^1,†, Ziyu Wang¹, Min Wu¹, Pengping Li¹, Yumin Nie¹, Xue Lin¹, Jie Hu¹, Eskil Eskilsson², Qh Wang^1,3,4,5,6,*, Jiaofang Shao^1,*

and Sali Lyu^1,3,4,*

¹ Department of Bioinformatics, Nanjing Medical University, Nanjing 211166, China

² Independent, San Francisco, CA 94952, USA

³ Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing 211166, China

⁴ Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing 211166, China

⁵ Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 211166, China

⁶ State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China

^† These authors are considered as joint first authors.

Genes 2018, 9(11), 545; https://doi.org/10.3390/genes9110545 - 12 Nov 2018

Cited by 8 | Viewed by 4153

Abstract

Somatic mutations in 3′-untranslated regions (3′UTR) do not alter amino acids and are considered to be silent in cancers. We found that such mutations can promote tumor progression by altering microRNA (miRNA) targeting efficiency and consequently affecting miRNA–mRNA interactions. We identified 67,159 somatic [...] Read more.

Somatic mutations in 3′-untranslated regions (3′UTR) do not alter amino acids and are considered to be silent in cancers. We found that such mutations can promote tumor progression by altering microRNA (miRNA) targeting efficiency and consequently affecting miRNA–mRNA interactions. We identified 67,159 somatic mutations located in the 3′UTRs of messenger RNAs (mRNAs) which can alter miRNA–mRNA interactions (functional somatic mutations, funcMutations), and 69.3% of these funcMutations (the degree of energy change > 12 kcal/mol) were identified to significantly promote loss of miRNA-mRNA binding. By integrating mRNA expression profiles of 21 cancer types, we found that the expression of target genes was positively correlated with the loss of absolute affinity level and negatively correlated with the gain of absolute affinity level. Functional enrichment analysis revealed that genes carrying funcMutations were significantly enriched in the MAPK and WNT signaling pathways, and analysis of regulatory modules identified eighteen miRNA modules involved with similar cellular functions. Our findings elucidate a complex relationship between miRNA, mRNA, and mutations, and suggest that 3′UTR mutations may play an important role in tumor development. Full article

(This article belongs to the Special Issue Non-coding RNAs)

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19 pages, 1945 KiB

Open AccessArticle

Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls (Larus bulleri)

by Claudia Mischler^1,*, Andrew Veale², Tracey Van Stijn³, Rudiger Brauning³

, John C. McEwan³

, Richard Maloney⁴

and Bruce C. Robertson¹

¹ Department of Zoology, University of Otago, Great King Street, Dunedin 9016, New Zealand

² Department of Environmental and Animal Sciences, Unitec, 139 Carrington Road, Auckland 1025, New Zealand

³ AgResearch Limited, Invermay Agricultural Centre, Private Bag 50034, Mosgiel 9053, New Zealand

⁴ Department of Conservation, 161 Cashel Street, Christchurch 8011, New Zealand

Genes 2018, 9(11), 544; https://doi.org/10.3390/genes9110544 - 9 Nov 2018

Cited by 8 | Viewed by 5453

Abstract

Black-billed gulls (Larus bulleri) are endemic to New Zealand and are suspected to be undergoing substantial population declines. They primarily breed on open gravel beds in braided rivers of the South Island—a habitat that is diminishing and becoming increasingly modified. Although [...] Read more.

Black-billed gulls (Larus bulleri) are endemic to New Zealand and are suspected to be undergoing substantial population declines. They primarily breed on open gravel beds in braided rivers of the South Island—a habitat that is diminishing and becoming increasingly modified. Although management of this species is increasing, little has been published on their movements and demographics. In this study, both mitochondrial DNA (mtDNA) control region domain I and nuclear single nucleotide polymorphisms (SNPs) were examined to help understand the connectivity and population structure of black-billed gulls across the country and to help inform management decisions. Mitochondrial DNA showed no population structure, with high haplotype and low nucleotide diversity, and analyses highlighted mitochondrial introgression with the closely related red-billed gulls (Larus novaehollandiae scopulinus). Nuclear DNA analyses, however, identified two groups, with Rotorua birds in the North Island being distinct from the rest of New Zealand, and isolation-by-distance evident across the South Island populations. Gene flow primarily occurs between nearby colonies with a stepwise movement across the landscape. The importance from a genetic perspective of the more isolated North Island birds (1.6% of total population) needs to be further evaluated. From our results, we infer that the South Island black-billed gull management should focus on maintaining several populations within each region rather than focusing on single specific colonies or river catchments. Future study is needed to investigate the genetic structure of populations at the northern limit of the species’ range, and identify the mechanisms behind, and extent of, the hybridisation between red-billed and black-billed gulls. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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15 pages, 4698 KiB

Open AccessArticle

The MAPKKK CgMck1 Is Required for Cell Wall Integrity, Appressorium Development, and Pathogenicity in Colletotrichum gloeosporioides

by Yu-Lan Fang, Li-Ming Xia, Ping Wang, Li-Hua Zhu, Jian-Ren Ye and Lin Huang^*

Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China

Genes 2018, 9(11), 543; https://doi.org/10.3390/genes9110543 - 8 Nov 2018

Cited by 40 | Viewed by 5125

Abstract

Mitogen-activated protein kinase (MAPK) signaling pathway plays key roles in sensing extracellular signals and transmitting them from the cell membrane to the nucleus in response to various environmental stimuli. A MAPKKK protein CgMck1 in Colletotrichum gloeosporioides was characterized. Phenotypic analyses of the ∆ [...] Read more.

Mitogen-activated protein kinase (MAPK) signaling pathway plays key roles in sensing extracellular signals and transmitting them from the cell membrane to the nucleus in response to various environmental stimuli. A MAPKKK protein CgMck1 in Colletotrichum gloeosporioides was characterized. Phenotypic analyses of the ∆Cgmck1 mutant showed that the CgMck1 was required for vegetative growth, fruiting body development, and sporulation. Additionally, the CgMCK1 deletion mutant showed significant defects in cell wall integrity, and responses to osmotic stresses. The mutant abolished the ability to develop appressorium, and lost pathogenicity to host plants. The ∆Cgmck1 mutant also exhibited a higher sensitivity to antifungal bacterium agent Bacillus velezensis. The deletion mutants of downstream MAPK cascades components CgMkk1 and CgMps1 showed similar defects to the ∆Cgmck1 mutant. In conclusion, CgMck1 is involved in the regulation of vegetative growth, asexual development, cell wall integrity, stresses resistance, and infection morphogenesis in C. gloeosporioides. Full article

(This article belongs to the Section Microbial Genetics and Genomics)

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16 pages, 1173 KiB

Open AccessReview

Harnessing Rhizobia to Improve Heavy-Metal Phytoremediation by Legumes

by Camilla Fagorzi¹, Alice Checcucci^1,*

, George C. DiCenzo¹

, Klaudia Debiec-Andrzejewska²

, Lukasz Dziewit³

, Francesco Pini⁴

and Alessio Mengoni^1,*

¹ Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy

² Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland

³ Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland

⁴ Department of Agri-food Production and Environmental Science, University of Florence, 50144 Florence, Italy

Genes 2018, 9(11), 542; https://doi.org/10.3390/genes9110542 - 8 Nov 2018

Cited by 84 | Viewed by 9638

Abstract

Rhizobia are bacteria that can form symbiotic associations with plants of the Fabaceae family, during which they reduce atmospheric di-nitrogen to ammonia. The symbiosis between rhizobia and leguminous plants is a fundamental contributor to nitrogen cycling in natural and agricultural ecosystems. Rhizobial microsymbionts [...] Read more.

Rhizobia are bacteria that can form symbiotic associations with plants of the Fabaceae family, during which they reduce atmospheric di-nitrogen to ammonia. The symbiosis between rhizobia and leguminous plants is a fundamental contributor to nitrogen cycling in natural and agricultural ecosystems. Rhizobial microsymbionts are a major reason why legumes can colonize marginal lands and nitrogen-deficient soils. Several leguminous species have been found in metal-contaminated areas, and they often harbor metal-tolerant rhizobia. In recent years, there have been numerous efforts and discoveries related to the genetic determinants of metal resistance by rhizobia, and on the effectiveness of such rhizobia to increase the metal tolerance of host plants. Here, we review the main findings on the metal resistance of rhizobia: the physiological role, evolution, and genetic determinants, and the potential to use native and genetically-manipulated rhizobia as inoculants for legumes in phytoremediation practices. Full article

(This article belongs to the Special Issue Genomics of Bacterial Metal Resistance)

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16 pages, 2177 KiB

Open AccessReview

Epidemiology of Hepatitis B Virus Infection in Bangladesh: Prevalence among General Population, Risk Groups and Genotype Distribution

by Md. Hassan Uz-Zaman¹

, Ayesha Rahman² and Mahmuda Yasmin^3,*

¹ International Center for Diarrhoeal Disease Research, Mohakhali, Dhaka 1212, Bangladesh

² Department of Microbiology, Jagannath University, 9-10 Chittaranjan Ave, Dhaka 1100, Bangladesh

³ Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh

Genes 2018, 9(11), 541; https://doi.org/10.3390/genes9110541 - 8 Nov 2018

Cited by 20 | Viewed by 9846

Abstract

Despite a considerable body of published research on hepatitis B in Bangladesh, researchers continue to lament the lack of reliable information about hepatitis B virus (HBV) infection epidemiology. The present review aims to provide a comprehensive survey of the literature with particular focus [...] Read more.

Despite a considerable body of published research on hepatitis B in Bangladesh, researchers continue to lament the lack of reliable information about hepatitis B virus (HBV) infection epidemiology. The present review aims to provide a comprehensive survey of the literature with particular focus on a number of epidemiological questions, as well as a commentary on the trends of hepatitis B research as it has taken place in Bangladesh. The key themes to emerge from this review are: first, beyond noting a declining trend, it is difficult to provide conclusive estimates about HBV prevalence in the general population of Bangladesh. The majority of the studies, even the ones conducted on apparently healthy populations, fail to be adequately representative for the reasons explored in the article. Secondly, HBV infection in Bangladesh is sharply stratified across sociodemographic lines, which speaks to the role of awareness and risk exposure in HBV prevalence. Third, more research on occult infection rates is required to estimate the extent of risk posed by the current blood donation screening program, which relies exclusively on hepatitis B surface antigen as a biomarker. The same considerations apply for the comparative importance of vertical versus horizontal transmission and prevalence among particular risk groups like healthcare workers with high occupational exposure. Finally, while recent studies do allow us, albeit with some ambiguity, to draw conclusions about distribution of HBV genotypes in Bangladesh, there needs to be an added emphasis on molecular epidemiology. It is hoped that the present review, the first of its kind in Bangladesh, will serve as an up-to-date summary of the course HBV epidemiology research in Bangladesh has taken thus far, as well as crucial gaps to address going forward. Full article

(This article belongs to the Special Issue Hepatitis B Virus Infection: An Update on Epidemiology, Diagnosis, Treatment and Prevention)

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19 pages, 1265 KiB

Open AccessReview

Transcriptomic and Genomic Approaches for Unravelling Candida albicans Biofilm Formation and Drug Resistance—An Update

by Pei Pei Chong^1,*

, Voon Kin Chin¹, Won Fen Wong^2,*

, Priya Madhavan³

, Voon Chen Yong¹

and Chung Yeng Looi¹

¹ School of Biosciences, Faculty of Health and Medical Sciences, Taylor’s University Malaysia, Subang Jaya, 47500 Selangor, Malaysia

² Department of Medical Microbiology, Faculty of Medicine, University Malaya, 50603 Kuala Lumpur, Malaysia

³ School of Medicine, Faculty of Health and Medical Sciences, Taylor’s University Malaysia, Subang Jaya, 47500 Selangor, Malaysia

Genes 2018, 9(11), 540; https://doi.org/10.3390/genes9110540 - 7 Nov 2018

Cited by 41 | Viewed by 10532

Abstract

Candida albicans is an opportunistic fungal pathogen, which causes a plethora of superficial, as well as invasive, infections in humans. The ability of this fungus in switching from commensalism to active infection is attributed to its many virulence traits. Biofilm formation is a [...] Read more.

Candida albicans is an opportunistic fungal pathogen, which causes a plethora of superficial, as well as invasive, infections in humans. The ability of this fungus in switching from commensalism to active infection is attributed to its many virulence traits. Biofilm formation is a key process, which allows the fungus to adhere to and proliferate on medically implanted devices as well as host tissue and cause serious life-threatening infections. Biofilms are complex communities of filamentous and yeast cells surrounded by an extracellular matrix that confers an enhanced degree of resistance to antifungal drugs. Moreover, the extensive plasticity of the C. albicans genome has given this versatile fungus the added advantage of microevolution and adaptation to thrive within the unique environmental niches within the host. To combat these challenges in dealing with C. albicans infections, it is imperative that we target specifically the molecular pathways involved in biofilm formation as well as drug resistance. With the advent of the -omics era and whole genome sequencing platforms, novel pathways and genes involved in the pathogenesis of the fungus have been unraveled. Researchers have used a myriad of strategies including transcriptome analysis for C. albicans cells grown in different environments, whole genome sequencing of different strains, functional genomics approaches to identify critical regulatory genes, as well as comparative genomics analysis between C. albicans and its closely related, much less virulent relative, C. dubliniensis, in the quest to increase our understanding of the mechanisms underlying the success of C. albicans as a major fungal pathogen. This review attempts to summarize the most recent advancements in the field of biofilm and antifungal resistance research and offers suggestions for future directions in therapeutics development. Full article

(This article belongs to the Special Issue Fungal Pathogenesis in Humans: The Growing Threat)

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21 pages, 2746 KiB

Open AccessReview

Genome Instability Induced by Low Levels of Replicative DNA Polymerases in Yeast

by Dao-Qiong Zheng^1,*

and Thomas D. Petes^2,*

¹ Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China

² Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA

Genes 2018, 9(11), 539; https://doi.org/10.3390/genes9110539 - 7 Nov 2018

Cited by 21 | Viewed by 5751

Abstract

Most cells of solid tumors have very high levels of genome instability of several different types, including deletions, duplications, translocations, and aneuploidy. Much of this instability appears induced by DNA replication stress. As a model for understanding this type of instability, we have [...] Read more.

Most cells of solid tumors have very high levels of genome instability of several different types, including deletions, duplications, translocations, and aneuploidy. Much of this instability appears induced by DNA replication stress. As a model for understanding this type of instability, we have examined genome instability in yeast strains that have low levels of two of the replicative DNA polymerases: DNA polymerase α and DNA polymerase δ (Polα and Polδ). We show that low levels of either of these DNA polymerases results in greatly elevated levels of mitotic recombination, chromosome rearrangements, and deletions/duplications. The spectrum of events in the two types of strains, however, differs in a variety of ways. For example, a reduced level of Polδ elevates single-base alterations and small deletions considerably more than a reduced level of Polα. In this review, we will summarize the methods used to monitor genome instability in yeast, and how this analysis contributes to understanding the linkage between genome instability and DNA replication stress. Full article

(This article belongs to the Special Issue Chromosome Replication and Genome Integrity)

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23 pages, 2421 KiB

Open AccessReview

Cystic Fibrosis Gene Therapy: Looking Back, Looking Forward

by Ashley L. Cooney

, Paul B. McCray, Jr. and Patrick L. Sinn^*

Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA

Genes 2018, 9(11), 538; https://doi.org/10.3390/genes9110538 - 7 Nov 2018

Cited by 95 | Viewed by 28962

Abstract

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that encodes a cAMP-regulated anion channel. Although CF is a multi-organ system disease, most people with CF die of progressive lung [...] Read more.

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that encodes a cAMP-regulated anion channel. Although CF is a multi-organ system disease, most people with CF die of progressive lung disease that begins early in childhood and is characterized by chronic bacterial infection and inflammation. Nearly 90% of people with CF have at least one copy of the ΔF508 mutation, but there are hundreds of CFTR mutations that result in a range of disease severities. A CFTR gene replacement approach would be efficacious regardless of the disease-causing mutation. After the discovery of the CFTR gene in 1989, the in vitro proof-of-concept for gene therapy for CF was quickly established in 1990. In 1993, the first of many gene therapy clinical trials attempted to rescue the CF defect in airway epithelia. Despite the initial enthusiasm, there is still no FDA-approved gene therapy for CF. Here we discuss the history of CF gene therapy, from the discovery of the CFTR gene to current state-of-the-art gene delivery vector designs. While implementation of CF gene therapy has proven more challenging than initially envisioned; thanks to continued innovation, it may yet become a reality. Full article

(This article belongs to the Special Issue Cystic Fibrosis: Therapy and Genetics)

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15 pages, 1012 KiB

Open AccessReview

Versatility of Synthetic tRNAs in Genetic Code Expansion

by Kyle S. Hoffman¹

, Ana Crnković¹

and Dieter Söll^1,2,*

¹ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA

² Department of Chemistry, Yale University, New Haven, CT 06520, USA

Genes 2018, 9(11), 537; https://doi.org/10.3390/genes9110537 - 7 Nov 2018

Cited by 16 | Viewed by 7064

Abstract

Transfer RNA (tRNA) is a dynamic molecule used by all forms of life as a key component of the translation apparatus. Each tRNA is highly processed, structured, and modified, to accurately deliver amino acids to the ribosome for protein synthesis. The tRNA molecule [...] Read more.

Transfer RNA (tRNA) is a dynamic molecule used by all forms of life as a key component of the translation apparatus. Each tRNA is highly processed, structured, and modified, to accurately deliver amino acids to the ribosome for protein synthesis. The tRNA molecule is a critical component in synthetic biology methods for the synthesis of proteins designed to contain non-canonical amino acids (ncAAs). The multiple interactions and maturation requirements of a tRNA pose engineering challenges, but also offer tunable features. Major advances in the field of genetic code expansion have repeatedly demonstrated the central importance of suppressor tRNAs for efficient incorporation of ncAAs. Here we review the current status of two fundamentally different translation systems (TSs), selenocysteine (Sec)- and pyrrolysine (Pyl)-TSs. Idiosyncratic requirements of each of these TSs mandate how their tRNAs are adapted and dictate the techniques used to select or identify the best synthetic variants. Full article

(This article belongs to the Special Issue Synthetic DNA and RNA Programming)

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Genes, Volume 9, Issue 11 (November 2018) – 51 articles

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