Genes

8 pages, 236 KiB

Open AccessReview

The Influence of Diet and Obesity on Gene Expression in SLE

by Antonio La Cava

Genes 2019, 10(5), 405; https://doi.org/10.3390/genes10050405 - 27 May 2019

Cited by 17 | Viewed by 4125

This review provides an overview of the known effects of diet, obesity, and the intake of different nutrients on systemic lupus erythematosus (SLE). It summarizes and discusses the studies in rodents that identified how different diets can regulate gene expression in the disease, [...] Read more.

This review provides an overview of the known effects of diet, obesity, and the intake of different nutrients on systemic lupus erythematosus (SLE). It summarizes and discusses the studies in rodents that identified how different diets can regulate gene expression in the disease, together with a description of the effects of diet on lupus patients’ inflammatory state and disease severity. The identification of selected dietary candidates that can modulate SLE onset and progression is analyzed in relation to possible targeted approaches that could ultimately ameliorate the management and prognosis of this disease. Full article

(This article belongs to the Special Issue Gene-Diet Interactions in Obesity)

15 pages, 3509 KiB

Open AccessArticle

Biphenyl/PCB Degrading bph Genes of Ten Bacterial Strains Isolated from Biphenyl-Contaminated Soil in Kitakyushu, Japan: Comparative and Dynamic Features as Integrative Conjugative Elements (ICEs)

by Jun Hirose, Hidehiko Fujihara, Takahito Watanabe, Nobutada Kimura, Hikaru Suenaga, Taiki Futagami, Masatoshi Goto, Akiko Suyama and Kensuke Furukawa

Genes 2019, 10(5), 404; https://doi.org/10.3390/genes10050404 - 27 May 2019

Cited by 22 | Viewed by 4565

Abstract

We sequenced the entire genomes of ten biphenyl/PCB degrading bacterial strains (KF strains) isolated from biphenyl-contaminated soil in Kitakyushu, Japan. All the strains were Gram-negative bacteria belonging to β- and γ-proteobacteria. Out of the ten strains, nine strains carried a biphenyl catabolic bph [...] Read more.

We sequenced the entire genomes of ten biphenyl/PCB degrading bacterial strains (KF strains) isolated from biphenyl-contaminated soil in Kitakyushu, Japan. All the strains were Gram-negative bacteria belonging to β- and γ-proteobacteria. Out of the ten strains, nine strains carried a biphenyl catabolic bph gene cluster as integrative conjugative elements (ICEs), and they were classified into four groups based on the structural features of the bph genes. Group I (five strains) possessed bph genes that were very similar to the ones in Pseudomonas furukawaii KF707 (formerly Pseudomonas pseudoalcaligenes KF707), which is one of the best characterized biphenyl-utilizing strains. This group of strains carried salicylate catabolic sal genes that were approximately 6-kb downstream of the bph genes. Group II (two strains) possessed bph and sal genes similar to the ones in KF707, but these strains lacked the bphX region between bphC and bphD, which is involved in the downstream catabolism of biphenyl. These bph-sal clusters in groups I and II were located on an integrative conjugative element that was larger than 110 kb, and they were named ICE_bph-sal. Our previous study demonstrated that the ICE_bph-sal of Pseudomonas putida KF715 in group II existed both in an integrated form in the chromosome (referred to as ICE_bph-salKF715 (integrated)) and in a extrachromosomal circular form (referred to as ICE_bph-sal (circular)) (previously called pKF715A, 483 kb) in the stationary culture. The ICE_bph-sal was transferred from KF715 into P. putida AC30 and P. putida KT2440 with high frequency, and it was maintained stably as an extrachromosomal circular form. The ICE_bph-salKF715 (circular) in these transconjugants was further transferred to P. putida F39/D and then integrated into the chromosome in one or two copies. Meanwhile, group III (one strain) possessed bph genes, but not sal genes. The nucleotide sequences of the bph genes in this group were less conserved compared to the genes of the strains belonging to groups I and II. Currently, there is no evidence to indicate that the bph genes in group III are carried by a mobile element. Group IV (two strains) carried bph genes as ICEs (59–61 kb) that were similar to the genes found in Tn4371 from Cupriavidus oxalacticus A5 and ICE_KKS1024677 from the Acidovorax sp. strain KKS102. Our study found that bph gene islands have integrative functions, are transferred among soil bacteria, and are diversified through modification. Full article

(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)

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11 pages, 724 KiB

Open AccessArticle

Inter-Individual Variability in Xenobiotic-Metabolizing Enzymes: Implications for Human Aging and Longevity

by Paolina Crocco, Alberto Montesanto, Serena Dato, Silvana Geracitano, Francesca Iannone, Giuseppe Passarino and Giuseppina Rose

Genes 2019, 10(5), 403; https://doi.org/10.3390/genes10050403 - 27 May 2019

Cited by 19 | Viewed by 3717

Abstract

Xenobiotic-metabolizing enzymes (XME) mediate the body’s response to potentially harmful compounds of exogenous/endogenous origin to which individuals are exposed during their lifetime. Aging adversely affects such responses, making the elderly more susceptible to toxics. Of note, XME genetic variability was found to impact [...] Read more.

Xenobiotic-metabolizing enzymes (XME) mediate the body’s response to potentially harmful compounds of exogenous/endogenous origin to which individuals are exposed during their lifetime. Aging adversely affects such responses, making the elderly more susceptible to toxics. Of note, XME genetic variability was found to impact the ability to cope with xenobiotics and, consequently, disease predisposition. We hypothesized that the variability of these genes influencing the interaction with the exposome could affect the individual chance of becoming long-lived. We tested this hypothesis by screening a cohort of 1112 individuals aged 20–108 years for 35 variants in 23 XME genes. Four variants in different genes (CYP2B6/rs3745274-G/T, CYP3A5/rs776746-G/A, COMT/rs4680-G/A and ABCC2/rs2273697-G/A) differently impacted the longevity phenotype. In particular, the highest impact was observed in the age group 65–89 years, known to have the highest incidence of age-related diseases. In fact, genetic variability of these genes we found to account for 7.7% of the chance to survive beyond the age of 89 years. Results presented herein confirm that XME genes, by mediating the dynamic and the complex gene–environment interactions, can affect the possibility to reach advanced ages, pointing to them as novel genes for future studies on genetic determinants for age-related traits. Full article

(This article belongs to the Special Issue Genetic Determinants of Human Longevity)

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21 pages, 2054 KiB

Open AccessArticle

Complex Gene Regulation Underlying Mineral Nutrient Homeostasis in Soybean Root Response to Acidity Stress

by Qianqian Chen, Weiwei Wu, Tong Zhao, Wenqi Tan, Jiang Tian and Cuiyue Liang

Genes 2019, 10(5), 402; https://doi.org/10.3390/genes10050402 - 27 May 2019

Cited by 10 | Viewed by 3583

Abstract

Proton toxicity is one of the major environmental stresses limiting crop production and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrients accumulation, and global transcriptome changes in soybean (Glycine max) in response [...] Read more.

Proton toxicity is one of the major environmental stresses limiting crop production and becomes increasingly serious because of anthropogenic activities. To understand acid tolerance mechanisms, the plant growth, mineral nutrients accumulation, and global transcriptome changes in soybean (Glycine max) in response to long-term acidity stress were investigated. Results showed that acidity stress significantly inhibited soybean root growth but exhibited slight effects on the shoot growth. Moreover, concentrations of essential mineral nutrients were significantly affected by acidity stress, mainly differing among soybean organs and mineral nutrient types. Concentrations of phosphorus (P) and molybdenum (Mo) in both leaves and roots, nitrogen (N), and potassium (K) in roots and magnesium (Mg) in leaves were significantly decreased by acidity stress, respectively. Whereas, concentrations of calcium (Ca), sulfate (S), and iron (Fe) were increased in both leaves and roots. Transcriptome analyses in soybean roots resulted in identification of 419 up-regulated and 555 down-regulated genes under acid conditions. A total of 38 differentially expressed genes (DEGs) were involved in mineral nutrients transportation. Among them, all the detected five GmPTs, four GmZIPs, two GmAMTs, and GmKUPs, together with GmIRT1, GmNramp5, GmVIT2.1, GmSKOR, GmTPK5, and GmHKT1, were significantly down-regulated by acidity stress. Moreover, the transcription of genes encoding transcription factors (e.g., GmSTOP2s) and associated with pH stat metabolic pathways was significantly up-regulated by acidity stress. Taken together, it strongly suggests that maintaining pH stat and mineral nutrient homeostasis are adaptive strategies of soybean responses to acidity stress, which might be regulated by a complex signaling network. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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19 pages, 2608 KiB

Open AccessArticle

Genome-Wide Identification of Na⁺/H⁺ Antiporter (NHX) Genes in Sugar Beet (Beta vulgaris L.) and Their Regulated Expression under Salt Stress

by Guo-Qiang Wu, Jin-Long Wang and Shan-Jia Li

Genes 2019, 10(5), 401; https://doi.org/10.3390/genes10050401 - 27 May 2019

Cited by 60 | Viewed by 5463

Abstract

Salinity is one of the major environment factors that limits the growth of plants and the productivity of crops worldwide. It has been shown that Na⁺ transporters play a central role in salt tolerance and development of plants. The objective of this [...] Read more.

Salinity is one of the major environment factors that limits the growth of plants and the productivity of crops worldwide. It has been shown that Na⁺ transporters play a central role in salt tolerance and development of plants. The objective of this study was to identify Na⁺/H⁺ antiporter (NHX) genes and investigate their expression patterns in sugar beet (Beta vulgaris L.) subjected to various concentrations of NaCl. A total of five putative NHX genes were identified and distributed on four chromosomes in sugar beet. Phylogenetic analysis revealed that these BvNHX genes are grouped into three major classes, viz Vac- (BvNHX1, -2 and -3), Endo- (BvNHX4), and PM-class NHX (BvNHX5/BvSOS1), and within each class the exon/intron structures are conserved. The amiloride-binding site is found in TM3 at N-terminus of Vac-class NHX proteins. Protein-protein interaction (PPI) prediction suggested that only BvNHX5 putatively interacts with calcineurin B-like proteins (CBL) and CBL-interacting protein kinases (CIPK), implying it might be the primary NHX involved in CBL-CIPK pathway under saline condition. It was also found that BvNHX5 contains one abscisic acid (ABA)-responsive element (ABRE), suggesting that BvNHX5 might be involved in ABA signal responsiveness. Additionally, the qRT-PCR analysis showed that all the BvNHX genes in both roots and leaves are significantly up-regulated by salt, and the transcription levels under high salinity are significantly higher than those under either low or moderate salinity. Taken together, this work gives a detailed overview of the BvNHX genes and their expression patterns under salt stress. Our findings also provide useful information for elucidating the molecular mechanisms of Na⁺ homeostasis and further functional identification of the BvNHX genes in sugar beet. Full article

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

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17 pages, 3421 KiB

Open AccessArticle

Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L.

by Intikhab Alam, Dong-Li Cui, Khadija Batool, Yan-Qing Yang and Yun-Hai Lu

Genes 2019, 10(5), 400; https://doi.org/10.3390/genes10050400 - 27 May 2019

Cited by 13 | Viewed by 3558

Abstract

The HECT-domain protein family is one of the most important classes of E3 ligases. While the roles of this family in human diseases have been intensively studied, the information for plant HECTs is limited. In the present study, we performed the identification of [...] Read more.

The HECT-domain protein family is one of the most important classes of E3 ligases. While the roles of this family in human diseases have been intensively studied, the information for plant HECTs is limited. In the present study, we performed the identification of HECT genes in Brassica rapa and Brassica oleracea, followed by analysis of phylogeny, gene structure, additional domains, putative cis-regulatory elements, chromosomal location, synteny, and expression. Ten and 13 HECT genes were respectively identified in B. rapa and B. oleracea and then resolved into seven groups along with their Arabidopsis orthologs by phylogenetic analysis. This classification is well supported by analyses of gene structure, motif composition within the HECT domain and additional protein domains. Ka/Ks ratio analysis showed that these HECT genes primarily underwent purifying selection with varied selection pressures resulting in different rates of evolution. RNA-Seq data analysis showed that the overwhelming majority of them were constitutively expressed in all tested tissues. qRT-PCR based expression analysis of the 10 B. rapa HECT genes under salt and drought stress conditions showed that all of them were responsive to the two stress treatments, which was consistent with their promoter sequence analysis revealing the presence of an important number of phytohormone-responsive and stress-related cis-regulatory elements. Our study provides useful information and lays the foundation for further functional determination of each HECT gene across the Brassica species. Full article

(This article belongs to the Section Population and Evolutionary Genetics and Genomics)

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16 pages, 2055 KiB

Open AccessTechnical Note

Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol

by Frédéric Sanchez, Solène Geffroy, Manon Norest, Sheree Yau, Hervé Moreau and Nigel Grimsley

Genes 2019, 10(5), 399; https://doi.org/10.3390/genes10050399 - 26 May 2019

Cited by 17 | Viewed by 10729

Abstract

Ostreococcus tauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13–22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced [...] Read more.

Ostreococcus tauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13–22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave >10⁴ transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20–40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome. Full article

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

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18 pages, 2022 KiB

Open AccessReview

Preserving Genome Integrity during the Early Embryonic DNA Replication Cycles

by Chames Kermi, Antoine Aze and Domenico Maiorano

Genes 2019, 10(5), 398; https://doi.org/10.3390/genes10050398 - 24 May 2019

Cited by 32 | Viewed by 6468

Abstract

During the very early stages of embryonic development chromosome replication occurs under rather challenging conditions, including a very short cell cycle, absence of transcription, a relaxed DNA damage response and, in certain animal species, a highly contracted S-phase. This raises the puzzling question [...] Read more.

During the very early stages of embryonic development chromosome replication occurs under rather challenging conditions, including a very short cell cycle, absence of transcription, a relaxed DNA damage response and, in certain animal species, a highly contracted S-phase. This raises the puzzling question of how the genome can be faithfully replicated in such a peculiar metabolic context. Recent studies have provided new insights into this issue, and unveiled that embryos are prone to accumulate genetic and genomic alterations, most likely due to restricted cellular functions, in particular reduced DNA synthesis quality control. These findings may explain the low rate of successful development in mammals and the occurrence of diseases, such as abnormal developmental features and cancer. In this review, we will discuss recent findings in this field and put forward perspectives to further study this fascinating question. Full article

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

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11 pages, 1459 KiB

Open AccessArticle

Detecting Schisandrae Chinensis Fructus and Its Chinese Patent Medicines with a Nucleotide Signature

by Wenjun Jiang, Li Ren, Mengyue Guo, Nitin Mantri, Sha Zhao and Xiaohui Pang

Genes 2019, 10(5), 397; https://doi.org/10.3390/genes10050397 - 22 May 2019

Cited by 10 | Viewed by 3891

Abstract

Schisandrae Chinensis Fructus (Wuweizi) is often adulterated with Schisandrae Sphenantherae Fructus (Nanwuweizi) in the herbal market. This adulteration is a threat to clinical treatment and safety. In this study, we aimed to develop a nucleotide signature for the identification of Wuweizi and its [...] Read more.

Schisandrae Chinensis Fructus (Wuweizi) is often adulterated with Schisandrae Sphenantherae Fructus (Nanwuweizi) in the herbal market. This adulteration is a threat to clinical treatment and safety. In this study, we aimed to develop a nucleotide signature for the identification of Wuweizi and its Chinese patent medicines based on the mini-DNA barcoding technique. We collected 49 samples to obtain internal transcribed spacer 2 (ITS2) sequences and developed a 26-bp nucleotide signature (5′-CGCTTTGCGACGCTCCCCTCCCTCCC-3′) on the basis of a single nucleotide polymorphism (SNP) site within the ITS2 region that is unique to Wuweizi. Then, using the nucleotide signature, we investigated 27 batches of commercial crude drug samples labeled as Wuweizi and eight batches of Chinese patent medicines containing Wuweizi. Results showed that eight commercial crude drug samples were adulterants and one of the Chinese patent medicines contained adulterants. The nucleotide signature can serve as an effective tool for identifying Wuweizi and its Chinese patent medicines and can thus be used to ensure clinical drug safety. Full article

(This article belongs to the Special Issue DNA Barcoding and Metabarcoding of Complex Matrices)

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16 pages, 2020 KiB

Open AccessArticle

Protein Changes in Response to Lead Stress of Lead-Tolerant and Lead-Sensitive Industrial Hemp Using SWATH Technology

by Cheng Xia, Li Hong, Yang Yang, Xu Yanping, Huang Xing and Deng Gang

Genes 2019, 10(5), 396; https://doi.org/10.3390/genes10050396 - 22 May 2019

Cited by 22 | Viewed by 3759

Abstract

Hemp is a Pb-tolerant and Pb-accumulating plant and the study of its tolerance mechanisms could facilitate the breeding of hemp with enhanced Pb tolerance and accumulation. In the present study, we took advantage of sequential window acquisition of all theoretical mass spectra (SWATH) [...] Read more.

Hemp is a Pb-tolerant and Pb-accumulating plant and the study of its tolerance mechanisms could facilitate the breeding of hemp with enhanced Pb tolerance and accumulation. In the present study, we took advantage of sequential window acquisition of all theoretical mass spectra (SWATH) technology to study the difference in proteomics between the leaves of Pb-tolerant seed-type hemp variety Bamahuoma (BM) and the Pb-sensitive fiber-type hemp variety Yunma 1 (Y1) under Pb stress (3 g/kg soil). A total of 63 and 372 proteins differentially expressed under Pb stress relative to control conditions were identified with liquid chromatography electro spray ionization tandem mass spectrometry in BM and Y1, respectively; with each of these proteins being classified into 14 categories. Hemp adapted to Pb stress by: accelerating adenosine triphosphate (ATP) metabolism; enhancing respiration, light absorption and light energy transfer; promoting assimilation of intercellular nitrogen (N) and carbon (C); eliminating reactive oxygen species; regulating stomatal development and closure; improving exchange of water and CO₂ in leaves; promoting intercellular transport; preventing aggregation of unfolded proteins; degrading misfolded proteins; and increasing the transmembrane transport of ATP in chloroplasts. Our results provide an important reference protein and gene information for future molecular studies into the resistance and accumulation of Pb in hemp. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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15 pages, 1291 KiB

Open AccessArticle

Heat Stress-Responsive Transcriptome Analysis in the Liver Tissue of Hu Sheep

by Yaokun Li, Lingxuan Kong, Ming Deng, Zhiquan Lian, Yinru Han, Baoli Sun, Yongqing Guo, Guangbin Liu and Dewu Liu

Genes 2019, 10(5), 395; https://doi.org/10.3390/genes10050395 - 22 May 2019

Cited by 29 | Viewed by 4241

Abstract

Heat stress has a severe effect on animal health and can reduce the productivity and reproductive efficiency; it is therefore necessary to explore the molecular mechanism involved in heat stress response, which is helpful for the cultivation of an animal breed with resistance [...] Read more.

Heat stress has a severe effect on animal health and can reduce the productivity and reproductive efficiency; it is therefore necessary to explore the molecular mechanism involved in heat stress response, which is helpful for the cultivation of an animal breed with resistance to heat stress. However, little research about heat stress-responsive molecular analysis has been reported in sheep. Therefore, in this study, RNA sequencing (RNA-Seq) was used to investigate the transcriptome profiling in the liver of Hu sheep with and without heat stress. In total, we detected 520 and 22 differentially expressed mRNAs and lncRNAs, respectively. The differentially expressed mRNAs were mainly associated with metabolic processes, the regulation of biosynthetic processes, and the regulation of glucocorticoid; additionally, they were significantly enriched in the heat stress related pathways, including the carbon metabolism, the PPAR signaling pathway, and vitamin digestion and absorption. The co-located differentially expressed lncRNA Lnc_001782 might positively influence the expression of the corresponding genes APOA4 and APOA5, exerting co-regulative effects on the liver function. Thus, we made the hypothesis that Lnc_001782, APOA4 and APOA5 might function synergistically to regulate the anti-heat stress ability in Hu sheep. This study provides a catalog of Hu sheep liver mRNAs and lncRNAs, and will contribute to a better understanding of the molecular mechanism underlying heat stress responses. Full article

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

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15 pages, 3304 KiB

Open AccessArticle

Three New Integration Vectors and Fluorescent Proteins for Use in the Opportunistic Human Pathogen Streptococcus pneumoniae

by Lance E. Keller, Anne-Stéphanie Rueff, Jun Kurushima and Jan-Willem Veening

Genes 2019, 10(5), 394; https://doi.org/10.3390/genes10050394 - 22 May 2019

Cited by 22 | Viewed by 6018

Abstract

Here, we describe the creation of three integration vectors, pPEPX, pPEPY and pPEPZ, for use with the opportunistic human pathogen Streptococcus pneumoniae. The constructed vectors, named PEP for Pneumococcal Engineering Platform (PEP), employ an IPTG-inducible promoter and BglBrick and BglFusion compatible multiple [...] Read more.

Here, we describe the creation of three integration vectors, pPEPX, pPEPY and pPEPZ, for use with the opportunistic human pathogen Streptococcus pneumoniae. The constructed vectors, named PEP for Pneumococcal Engineering Platform (PEP), employ an IPTG-inducible promoter and BglBrick and BglFusion compatible multiple cloning sites allowing for fast and interchangeable cloning. PEP plasmids replicate in Escherichia coli and harbor integration sites that have homology in a large set of pneumococcal strains, including recent clinical isolates. In addition, several options of antibiotic resistance markers are available, even allowing for selection in multidrug resistant clinical isolates. The transformation efficiency of these PEP vectors as well as their ability to be expressed simultaneously was tested. Two of the three PEP vectors share homology of the integration regions with over half of the S. pneumoniae genomes examined. Transformation efficiency varied among PEP vectors based on the length of the homology regions, but all were highly transformable and can be integrated simultaneously in strain D39V. Vectors used for pneumococcal cloning are an important tool for researchers for a wide range of uses. The PEP vectors described are of particular use because they have been designed to allow for easy transfer of genes between vectors as well as integrating into transcriptionally silent areas of the chromosome. In addition, we demonstrate the successful production of several new spectrally distinct fluorescent proteins (mTurquoise2, mNeonGreen and mScarlet-I) from the PEP vectors. The PEP vectors and newly described fluorescent proteins will expand the genetic toolbox for pneumococcal researchers and aid future discoveries. Full article

(This article belongs to the Special Issue Evolutionary Genetics of Streptococcus pneumoniae)

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17 pages, 3250 KiB

Open AccessArticle

Expansion and Functional Divergence of Inositol Polyphosphate 5-Phosphatases in Angiosperms

by Zaibao Zhang, Yuting Li, Zhaoyi Luo, Shuwei Kong, Yilin Zhao, Chi Zhang, Wei Zhang, Hongyu Yuan and Lin Cheng

Genes 2019, 10(5), 393; https://doi.org/10.3390/genes10050393 - 22 May 2019

Cited by 11 | Viewed by 3608

Abstract

Inositol polyphosphate 5-phosphatase (5PTase), a key enzyme that hydrolyzes the 5′ position of the inositol ring, has essential functions in growth, development, and stress responses in plants, yeasts, and animals. However, the evolutionary history and patterns of 5PTases have not been examined systematically. [...] Read more.

Inositol polyphosphate 5-phosphatase (5PTase), a key enzyme that hydrolyzes the 5′ position of the inositol ring, has essential functions in growth, development, and stress responses in plants, yeasts, and animals. However, the evolutionary history and patterns of 5PTases have not been examined systematically. Here, we report a comprehensive molecular evolutionary analysis of the 5PTase gene family and define four groups. These four groups are different from former classifications, which were based on in vitro substrate specificity. Most orthologous groups appear to be conserved as single or low-copy genes in all lineages in Groups II–IV, whereas 5PTase genes in Group I underwent several duplication events in angiosperm, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for 5PTase duplications in angiosperm. Plant 5PTases have more members than that of animals, and most plant 5PTase genes appear to have evolved under strong purifying selection. The paralogs have diverged in substrate specificity and expression pattern, showing evidence of selection pressure. Meanwhile, the increase in 5PTases and divergences in sequence, expression, and substrate might have contributed to the divergent functions of 5PTase genes, allowing the angiosperms to successfully adapt to a great number of ecological niches. Full article

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

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15 pages, 5582 KiB

Open AccessArticle

Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes

by Gabriel Damasco, Vikram S. Shivakumar, Tracy M. Misciewicz, Douglas C. Daly and Paul V. A. Fine

Genes 2019, 10(5), 392; https://doi.org/10.3390/genes10050392 - 22 May 2019

Cited by 5 | Viewed by 3550

Abstract

Plants in the Burseraceae are globally recognized for producing resins and essential oils with medicinal properties and have economic value. In addition, most of the aromatic and non-aromatic components of Burseraceae resins are derived from a variety of terpene and terpenoid chemicals. Although [...] Read more.

Plants in the Burseraceae are globally recognized for producing resins and essential oils with medicinal properties and have economic value. In addition, most of the aromatic and non-aromatic components of Burseraceae resins are derived from a variety of terpene and terpenoid chemicals. Although terpene genes have been identified in model plant crops (e.g., Citrus, Arabidopsis), very few genomic resources are available for non-model groups, including the highly diverse Burseraceae family. Here we report the assembly of a leaf transcriptome of Protium copal, an aromatic tree that has a large distribution in Central America, describe the functional annotation of putative terpene biosynthetic genes and compare terpene biosynthetic genes found in P. copal with those identified in other Burseraceae taxa. The genomic resources of Protium copal can be used to generate novel sequencing markers for population genetics and comparative phylogenetic studies, and to investigate the diversity and evolution of terpene genes in the Burseraceae. Full article

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

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19 pages, 2625 KiB

Open AccessArticle

Comparative Transcriptome Analysis in Oilseed Rape (Brassica napus) Reveals Distinct Gene Expression Details between Nitrate and Ammonium Nutrition

by Weijie Tang, Xin He, Lunwen Qian, Feng Wang, Zhenhua Zhang, Chao Sun, Liangbin Lin and Chunyun Guan

Genes 2019, 10(5), 391; https://doi.org/10.3390/genes10050391 - 22 May 2019

Cited by 12 | Viewed by 4156

Abstract

Nitrate (NO₃⁻) and ammonium (NH₄⁺) are the main inorganic nitrogen (N) sources absorbed by oilseed rape, a plant that exhibits genotypic differences in N efficiency. In our previous study, the biomass, N accumulation, and root architecture of [...] Read more.

Nitrate (NO₃⁻) and ammonium (NH₄⁺) are the main inorganic nitrogen (N) sources absorbed by oilseed rape, a plant that exhibits genotypic differences in N efficiency. In our previous study, the biomass, N accumulation, and root architecture of two oilseed rape cultivars, Xiangyou 15 (high N efficiency, denoted “15”) and 814 (low N efficiency, denoted “814”), were inhibited under NH₄⁺ nutrition, though both cultivars grew normally under NO₃⁻ nutrition. To gain insight into the underlying molecular mechanisms, transcriptomic changes were investigated in the roots of 15 and 814 plants subjected to nitrogen-free (control, CK), NO₃⁻ (NT), and NH₄⁺ (AT) treatments at the seedling stage. A total of 14,355 differentially expressed genes (DEGs) were identified. Among the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway categories of these DEGs, carbohydrate metabolism, lipid metabolism, protein metabolism, and cell wall biogenesis were inhibited by AT treatment. Interestingly, DEGs such as N transporters, genes involved in N assimilation and CESA genes related to cellulose synthase were also mostly downregulated in the AT treatment group. This downregulation of genes related to crucial metabolic pathways resulted in inhibition of oilseed rape growth after AT treatment. Full article

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

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18 pages, 5269 KiB

Open AccessArticle

Functional Characterization of Date Palm Aquaporin Gene PdPIP1;2 Confers Drought and Salinity Tolerance to Yeast and Arabidopsis

by Himanshu V. Patankar, Ibtisam Al-Harrasi, Rashid Al-Yahyai and Mahmoud W. Yaish

Genes 2019, 10(5), 390; https://doi.org/10.3390/genes10050390 - 22 May 2019

Cited by 33 | Viewed by 4382

Abstract

Recent studies on salinity tolerance in date palm revealed the discovery of salt-responsive genes including PdPIP1;2, a highly conserved aquaporin gene in plants, which was functionally characterized in this study to investigate its precise role in drought and salinity tolerance. Immunoblot assay [...] Read more.

Recent studies on salinity tolerance in date palm revealed the discovery of salt-responsive genes including PdPIP1;2, a highly conserved aquaporin gene in plants, which was functionally characterized in this study to investigate its precise role in drought and salinity tolerance. Immunoblot assay showed a high level of PIP1 protein accumulation only in the leaves of date palm plants when grown under drought, an observation which may imply the involvement of PIP1;2 in CO₂ uptake. Heterologous overexpression of PdPIP1;2 in yeast (Saccharomyces cerevisiae) improved tolerance to salinity and oxidative stress. While, heterologous overexpression of PdPIP1;2 in Arabidopsis had significantly (p < 0.05) increased biomass, chlorophyll content, and root length under drought and salinity. In addition, a significantly (p < 0.05) higher percentage of transgenic plants could be recovered by rewatering after drought stress, indicating the ability of the transgenic plants to maintain water and viability under drought. Transgenic plants under drought and salinity maintained significantly (p < 0.05) higher K⁺/Na⁺ ratios than wild type (WT) plants, an observation which may represent an efficient tolerance mechanism controlled by the transgene. Collectively, this study provided an insight on the mechanism by which PdPIP1;2 conferred tolerance to salt and drought stresses in date palm. Full article

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

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13 pages, 1514 KiB

Open AccessArticle

Correlation Analysis of Lignin Accumulation and Expression of Key Genes Involved in Lignin Biosynthesis of Ramie (Boehmeria nivea)

by Yinghong Tang, Fang Liu, Hucheng Xing, Kaiquan Mao, Guo Chen, Qingquan Guo and Jianrong Chen

Genes 2019, 10(5), 389; https://doi.org/10.3390/genes10050389 - 22 May 2019

Cited by 33 | Viewed by 3707

Abstract

The phloem of the stem of ramie (Boehmeria nivea) is an important source of natural fiber for the textile industry. However, the lignin content in the phloem affects the quality of ramie phloem fiber. In this study, the lignin content and [...] Read more.

The phloem of the stem of ramie (Boehmeria nivea) is an important source of natural fiber for the textile industry. However, the lignin content in the phloem affects the quality of ramie phloem fiber. In this study, the lignin content and related key gene expression levels were analyzed in the phloem and xylem at different developmental periods. The results showed that the relative expression levels of lignin synthesis-related key genes in the xylem and phloem of the stem gradually decreased from the fast-growing period to the late maturation period, but the corresponding lignin content increased significantly. However, the relative expression levels of a few genes were the highest during the maturation period. During all three periods, the lignin content in ramie stems was positively correlated with the expression of genes, including PAL, C4H and 4CL1 in the phenylpropanoid pathway, F5H and CCoAOMT in the lignin-specific synthetic pathway, and CAD in the downstream pathway of lignin synthesis, but the lignin content was negatively correlated with the expression of genes including 4CL3 in the phenylpropanoid pathway and UDP-GT in the shunt pathway of lignin monomer synthesis. The ramie 4CL3 recombinant protein prefers cinnamic acid as a substrate during catalysis, and it negatively regulates lignin synthesis. It is speculated that ramie 4CL3 is mainly involved in the synthesis of ramie flavonoid compounds, and that 4CL1 is mainly involved in lignin synthesis. Full article

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

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2 pages, 697 KiB

Open AccessErratum

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

by Albert Jeltsch, Julian Broche and Pavel Bashtrykov

Genes 2019, 10(5), 388; https://doi.org/10.3390/genes10050388 - 21 May 2019

Cited by 8 | Viewed by 3364

Abstract

The authors wish to make the following correction to their paper [...] Full article

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

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17 pages, 1693 KiB

Open AccessReview

Gene and Base Editing as a Therapeutic Option for Cystic Fibrosis—Learning from Other Diseases

by Karen Mention, Lúcia Santos and Patrick T. Harrison

Genes 2019, 10(5), 387; https://doi.org/10.3390/genes10050387 - 21 May 2019

Cited by 23 | Viewed by 9038

Abstract

Cystic fibrosis (CF) is a monogenic autosomal recessive disorder caused by mutations in the CFTR gene. There are at least 346 disease-causing variants in the CFTR gene, but effective small-molecule therapies exist for only ~10% of them. One option to treat all mutations [...] Read more.

Cystic fibrosis (CF) is a monogenic autosomal recessive disorder caused by mutations in the CFTR gene. There are at least 346 disease-causing variants in the CFTR gene, but effective small-molecule therapies exist for only ~10% of them. One option to treat all mutations is CFTR cDNA-based therapy, but clinical trials to date have only been able to stabilise rather than improve lung function disease in patients. While cDNA-based therapy is already a clinical reality for a number of diseases, some animal studies have clearly established that precision genome editing can be significantly more effective than cDNA addition. These observations have led to a number of gene-editing clinical trials for a small number of such genetic disorders. To date, gene-editing strategies to correct CFTR mutations have been conducted exclusively in cell models, with no in vivo gene-editing studies yet described. Here, we highlight some of the key breakthroughs in in vivo and ex vivo gene and base editing in animal models for other diseases and discuss what might be learned from these studies in the development of editing strategies that may be applied to cystic fibrosis as a potential therapeutic approach. There are many hurdles that need to be overcome, including the in vivo delivery of editing machinery or successful engraftment of ex vivo-edited cells, as well as minimising potential off-target effects. However, a successful proof-of-concept study for gene or base editing in one or more of the available CF animal models could pave the way towards a long-term therapeutic strategy for this disease. Full article

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

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9 pages, 1408 KiB

Open AccessArticle

Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs

by Benoit Hédan, Edouard Cadieu, Nadine Botherel, Caroline Dufaure de Citres, Anna Letko, Maud Rimbault, Cord Drögemüller, Vidhya Jagannathan, Thomas Derrien, Sheila Schmutz, Tosso Leeb and Catherine André

Genes 2019, 10(5), 386; https://doi.org/10.3390/genes10050386 - 21 May 2019

Cited by 19 | Viewed by 12234

Abstract

White coat color in mammals has been selected several times during the domestication process. Numerous dog breeds are fixed for one form of white coat color that involves darkly pigmented skin. The genetic basis of this color, due to the absence of pigment [...] Read more.

White coat color in mammals has been selected several times during the domestication process. Numerous dog breeds are fixed for one form of white coat color that involves darkly pigmented skin. The genetic basis of this color, due to the absence of pigment in the hairs, was suggested to correspond to extreme dilution of the phaeomelanin, by both the expression of only phaeomelanin (locus E) and its extreme dilution (locus I). To go further, we performed genome-wide association studies (GWAS) using a multiple breed approach. The first GWAS, using 34 white dogs and 128 non-white dogs, including White Shepherds, Poodles, Cotons de Tulear and Bichons allowed us to identify two significantly associated loci on the locus E and a novel locus on chromosome 20. A second GWAS using 15 other breeds presenting extreme phaeomelanin dilution confirmed the position of locus I on the chromosome 20 (position 55 Mb p_corrected = 6 × 10⁻¹³). Using whole-genome sequencing, we identified a missense variant in the first exon of MFSD12, a gene recently identified to be involved in human, mouse and horse pigmentation. We confirmed the role of this variant in phaeomelanin dilution of numerous canine breeds, and the conserved role of MFSD12 in mammalian pigmentation. Full article

(This article belongs to the Special Issue Canine Genetics)

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17 pages, 2565 KiB

Open AccessArticle

Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration

by Rebekkah J. Hitti, James A. C. Oliver, Ellen C. Schofield, Anina Bauer, Maria Kaukonen, Oliver P. Forman, Tosso Leeb, Hannes Lohi, Louise M. Burmeister, David Sargan and Cathryn S. Mellersh

Genes 2019, 10(5), 385; https://doi.org/10.3390/genes10050385 - 21 May 2019

Cited by 8 | Viewed by 9103

Abstract

Canine progressive retinal atrophies (PRA) are genetically heterogeneous diseases characterized by retinal degeneration and subsequent blindness. PRAs are untreatable and affect multiple dog breeds, significantly impacting welfare. Three out of seven Giant Schnauzer (GS) littermates presented with PRA around four years of age. [...] Read more.

Canine progressive retinal atrophies (PRA) are genetically heterogeneous diseases characterized by retinal degeneration and subsequent blindness. PRAs are untreatable and affect multiple dog breeds, significantly impacting welfare. Three out of seven Giant Schnauzer (GS) littermates presented with PRA around four years of age. We sought to identify the causal variant to improve our understanding of the aetiology of this form of PRA and to enable development of a DNA test. Whole genome sequencing of two PRA-affected full-siblings and both unaffected parents was performed. Variants were filtered based on those segregating appropriately for an autosomal recessive disorder and predicted to be deleterious. Successive filtering against 568 canine genomes identified a single nucleotide variant in the gene encoding NECAP endocytosis associated 1 (NECAP1): c.544G>A (p.Gly182Arg). Five thousand one hundred and thirty canids of 175 breeds, 10 cross-breeds and 3 wolves were genotyped for c.544G>A. Only the three PRA-affected GS were homozygous (allele frequency in GS, excluding proband family = 0.015). In addition, we identified heterozygotes belonging to Spitz and Dachshund varieties, demonstrating c.544G>A segregates in other breeds of German origin. This study, in parallel with the known retinal expression and role of NECAP1 in clathrin mediated endocytosis (CME) in synapses, presents NECAP1 as a novel candidate gene for retinal degeneration in dogs and other species. Full article

(This article belongs to the Special Issue Canine Genetics)

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21 pages, 1305 KiB

Open AccessArticle

Novel Polymorphisms in RAPGEF6 Gene Associated with Egg-Laying Rate in Chinese Jing Hong Chicken using Genome-Wide SNP Scan

by Syed Ali Azmal, Ali Akbar Bhuiyan, Abdullah Ibne Omar, Shuai Ma, Chenghao Sun, Zhongdong Han, Meikuen Zhang, Shuhong Zhao and Shijun Li

Genes 2019, 10(5), 384; https://doi.org/10.3390/genes10050384 - 20 May 2019

Cited by 13 | Viewed by 5247

Abstract

The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern [...] Read more.

The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern in the poultry industry. In this study, we calculated the egg-laying rate at weeks 61–69 (60 days) of Jing Hong chickens parent generation as the phenotype, and the genotype were detected by the chicken 600K Affymetrix Axiom High Density (HD) Single Nucleotide Polymorphisms (SNP)-array. The Genome-Wide Association Study (GWAS) result showed that the egg production trait is significantly associated with five SNPs (AX-75745366, AX-75745380, AX-75745340, AX-75745388, and AX-75745341), which are in the rap guanine nucleotide exchange factor 6 (RAPGEF6) gene on chicken chromosome 13. A total of 1676 Chinese commercial Jing Hong laying hens—including two populations, P1 population (858 hens) and P2 population (818 hens)—were genotyped using the Polymerase Chain Reaction-Restriction Fragments Length Polymorphisms (PCR-RFLP) method for the association analysis of egg-laying rates for the verification of the GWAS results. Genotypic and allelic frequencies of five SNPs were inconsistent with Hardy–Weinberg equilibrium, and the average population genetics parameters considering all the SNP values; i.e., gene homozygosity (Ho), gene heterozygosity (He), the effective number of alleles (Ne), and the polymorphism information content (PIC) were 0.75, 0.25, 1.40, and 0.20 in P1; 0.71, 0.29, 1.46, and 0.24 in P2; and 0.73, 0.27, 1.43, and 0.22 in P1 + P2 populations, respectively. The association analysis results revealed that out of the five polymorphisms, three of them (AX-75745366, AX-75745340, and AX-75745341; Patent applying No: 201810428916.5) had highly significant effects on egg-laying rates according to the GWAS results. Population-specific association analyses also showed similar significant association effects with this trait. Four haplotypes (AAGG, AAAG, AGGG, and AGAG) were inferred based on significant loci (AX-75745340 and AX-75745341) and also showed significant associations with the egg-laying rate, where haplotype AAGG had the highest egg-laying rate, with the exception of the egg-laying rate in P1 population, followed by other haplotypes. Furthermore, genotypes TT, AA, and GG showed the highest egg-laying rate compared to the corresponding genotypes at AX-75745366, AX-75745340, and AX-75745341 SNP loci in P1+P2, respectively. A similar result was found in the population-specific analysis except for the P1 population, in which TC genotype showed the highest egg-laying rate. No significant association was found in the egg-laying rate during the 60 days laying period for the SNPs (AX-75745380 and AX-75745388) in any group of population (p ≥ 0.05). Collectively, we report for the first time that 3 SNPs in the RAPGEF6 gene were significantly associated with the egg-laying rate during the later stage of egg production, which could be used as the potential candidate molecular genetic markers that would be able to facilitate in the selection and improvement of egg production traits through chicken breeding. Full article

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

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3 pages, 200 KiB

Open AccessEditorial

Advances in Genetics of Regeneration in Metabesity

by Benoit R. Gauthier and Francisco J. Bermúdez-Silva

Genes 2019, 10(5), 383; https://doi.org/10.3390/genes10050383 - 20 May 2019

Cited by 2 | Viewed by 2715

Abstract

‘Metabesity’ is a recent term comprising a wide range of diseases with underlying metabolic disarrangements at its root, and whose aetiology lies in complex relationships among genes and the obesogenic environment to which individuals are currently exposed in most countries. Of note, epigenetic [...] Read more.

‘Metabesity’ is a recent term comprising a wide range of diseases with underlying metabolic disarrangements at its root, and whose aetiology lies in complex relationships among genes and the obesogenic environment to which individuals are currently exposed in most countries. Of note, epigenetic changes are increasingly being reported to play an outstanding role in carrying deleterious information that, together with susceptibility genes, boost the development of metabesity in subsequent generations. In this context, it is noteworthy to mention that the transition from the pre-industrial era to the current high-technology society and global economy, even after suffering two world wars, has been very fast. By contrast, evolution-driven processes, such as biological ones, are slow. In fact, there is a general consensus that at the metabolic level, adipogenic processes and thrifty pathways prevail over those promoting energy expenditure in a way that currently leads to metabolic diseases by excessive energy storage. In such an imbalanced social–biological scenario, genes that were beneficial in the past have shifted to becoming detrimental, i.e., favouring metabesity, which is quickly growing to reach pandemic proportions. Full article

(This article belongs to the Special Issue Advances in Genetics of Regeneration in Metabesity)

17 pages, 4244 KiB

Open AccessArticle

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations

by Himansu Kumar, Woncheol Park, Krishnamoorthy Srikanth, Bong-Hwan Choi, Eun-Seok Cho, Kyung-Tai Lee, Jun-Mo Kim, Kwangmin Kim, Junhyung Park, Dajeong Lim and Jong-Eun Park

Genes 2019, 10(5), 382; https://doi.org/10.3390/genes10050382 - 20 May 2019

Cited by 13 | Viewed by 4396

Abstract

The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative [...] Read more.

The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative analysis of cecum microbiota of crossbred Korean native pigs at two different growth stages (stage L = 10 weeks, and stage LD = 26 weeks) using 16S rRNA sequencing technology. Our results revealed remarkable differences in microbial composition, α and β diversity, and differential abundance between the two stages. Phylum composition analysis with respect to SILVA132 database showed Firmicutes to be present at 51.87% and 48.76% in stages L and LD, respectively. Similarly, Bacteroidetes were present at 37.28% and 45.98% in L and LD, respectively. The genera Prevotella, Anaerovibrio, Succinivibrio, Megasphaera were differentially enriched in stage L, whereas Clostridium, Terrisporobacter, Rikenellaceae were enriched in stage LD. Functional annotation of microbiome by level-three KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that glycine, serine, threonine, valine, leucine, isoleucine arginine, proline, and tryptophan metabolism were differentially enriched in stage L, whereas alanine, aspartate, glutamate, cysteine, methionine, phenylalanine, tyrosine, and tryptophan biosynthesis metabolism were differentially enriched in stage LD. Through machine-learning approaches such as LEfSe (linear discriminant analysis effect size), random forest, and Pearson’s correlation, we found pathways such as amino acid metabolism, transport systems, and genetic regulation of metabolism are commonly enriched in both stages. Our findings suggest that the bacterial compositions in cecum content of pigs are heavily involved in their nutrient digestion process. This study may help to meet the demand of human food and can play significant roles in medicinal application. Full article

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

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21 pages, 2090 KiB

Open AccessArticle

Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis

by Hakim Tafer, Caroline Poyntner, Ksenija Lopandic, Katja Sterflinger and Guadalupe Piñar

Genes 2019, 10(5), 381; https://doi.org/10.3390/genes10050381 - 20 May 2019

Cited by 15 | Viewed by 4413

Abstract

Salt mines are among the most extreme environments as they combine darkness, low nutrient availability, and hypersaline conditions. Based on comparative genomics and transcriptomics, we describe in this work the adaptive strategies of the true halophilic fungus Aspergillus salisburgensis, found in a [...] Read more.

Salt mines are among the most extreme environments as they combine darkness, low nutrient availability, and hypersaline conditions. Based on comparative genomics and transcriptomics, we describe in this work the adaptive strategies of the true halophilic fungus Aspergillus salisburgensis, found in a salt mine in Austria, and compare this strain to the ex-type halotolerant fungal strain Aspergillus sclerotialis. On a genomic level, A. salisburgensis exhibits a reduced genome size compared to A. sclerotialis, as well as a contraction of genes involved in transport processes. The proteome of A. sclerotialis exhibits an increased proportion of alanine, glycine, and proline compared to the proteome of non-halophilic species. Transcriptome analyses of both strains growing at 5% and 20% NaCl show that A. salisburgensis regulates three-times fewer genes than A. sclerotialis in order to adapt to the higher salt concentration. In A. sclerotialis, the increased osmotic stress impacted processes related to translation, transcription, transport, and energy. In contrast, membrane-related and lignolytic proteins were significantly affected in A. salisburgensis. Full article

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

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10 pages, 218 KiB

Open AccessConcept Paper

Impact of Acute Aerobic Exercise on Genome-Wide DNA-Methylation in Natural Killer Cells—A Pilot Study

by Alexander Schenk, Christine Koliamitra, Claus Jürgen Bauer, Robert Schier, Michal R. Schweiger, Wilhelm Bloch and Philipp Zimmer

Genes 2019, 10(5), 380; https://doi.org/10.3390/genes10050380 - 19 May 2019

Cited by 20 | Viewed by 4296

Abstract

Natural Killer (NK-) cells reveal a keen reaction to acute bouts of exercise, including changes of epigenetic modifications. So far, exercise-induced alterations in NK-cell DNA-methylation were shown for single genes only. Studies analyzing genome-wide DNA-methylation have used conglomerates like peripheral blood mononuclear cells [...] Read more.

Natural Killer (NK-) cells reveal a keen reaction to acute bouts of exercise, including changes of epigenetic modifications. So far, exercise-induced alterations in NK-cell DNA-methylation were shown for single genes only. Studies analyzing genome-wide DNA-methylation have used conglomerates like peripheral blood mononuclear cells (PBMCs) rather than specific subsets of immune cells. Therefore, the aim of this pilot-study was to generate first insights into the influence of a single bout of exercise on genome-wide DNA-methylation in isolated NK-cells to open the field for such analyses. Five healthy women performed an incremental step test and blood samples were taken before and after exercise. DNA was isolated from magnet bead sorted NK-cells and further analyzed for global DNA-methylation using the Infinium MethylationEPIC BeadChip. DNA-methylation was changed at 33 targets after acute exercise. These targets were annotated to 25 genes. Of the targets, 19 showed decreased and 14 increased methylation. The 25 genes with altered DNA-methylation have different roles in cell regulation and differ in their molecular functions. These data give new insights in the exercise induced regulation of NK-cells. By using isolated NK-cells, exercise induced differences in DNA-methylation could be shown. Whether or not these changes lead to functional adaptions needs to be elucidated. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Modulation of Cell Functions by Physical Exercise)

25 pages, 1854 KiB

Open AccessReview

Ontogenetic and Pathogenetic Views on Somatic Chromosomal Mosaicism

by Ivan Y. Iourov, Svetlana G. Vorsanova, Yuri B. Yurov and Sergei I. Kutsev

Genes 2019, 10(5), 379; https://doi.org/10.3390/genes10050379 - 19 May 2019

Cited by 46 | Viewed by 5679

Abstract

Intercellular karyotypic variability has been a focus of genetic research for more than 50 years. It has been repeatedly shown that chromosome heterogeneity manifesting as chromosomal mosaicism is associated with a variety of human diseases. Due to the ability of changing dynamically throughout [...] Read more.

Intercellular karyotypic variability has been a focus of genetic research for more than 50 years. It has been repeatedly shown that chromosome heterogeneity manifesting as chromosomal mosaicism is associated with a variety of human diseases. Due to the ability of changing dynamically throughout the ontogeny, chromosomal mosaicism may mediate genome/chromosome instability and intercellular diversity in health and disease in a bottleneck fashion. However, the ubiquity of negligibly small populations of cells with abnormal karyotypes results in difficulties of the interpretation and detection, which may be nonetheless solved by post-genomic cytogenomic technologies. In the post-genomic era, it has become possible to uncover molecular and cellular pathways to genome/chromosome instability (chromosomal mosaicism or heterogeneity) using advanced whole-genome scanning technologies and bioinformatic tools. Furthermore, the opportunities to determine the effect of chromosomal abnormalities on the cellular phenotype seem to be useful for uncovering the intrinsic consequences of chromosomal mosaicism. Accordingly, a post-genomic review of chromosomal mosaicism in the ontogenetic and pathogenetic contexts appears to be required. Here, we review chromosomal mosaicism in its widest sense and discuss further directions of cyto(post)genomic research dedicated to chromosomal heterogeneity. Full article

(This article belongs to the Special Issue Chromosomal Heterogeneity and Human Diseases)

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12 pages, 5008 KiB

Open AccessArticle

Role of D-GADD45 in JNK-Dependent Apoptosis and Regeneration in Drosophila

by Carlos Camilleri-Robles, Florenci Serras and Montserrat Corominas

Genes 2019, 10(5), 378; https://doi.org/10.3390/genes10050378 - 18 May 2019

Cited by 12 | Viewed by 4870

Abstract

The GADD45 proteins are induced in response to stress and have been implicated in the regulation of several cellular functions, including DNA repair, cell cycle control, senescence, and apoptosis. In this study, we investigate the role of D-GADD45 during Drosophila development and regeneration [...] Read more.

The GADD45 proteins are induced in response to stress and have been implicated in the regulation of several cellular functions, including DNA repair, cell cycle control, senescence, and apoptosis. In this study, we investigate the role of D-GADD45 during Drosophila development and regeneration of the wing imaginal discs. We find that higher expression of D-GADD45 results in JNK-dependent apoptosis, while its temporary expression does not have harmful effects. Moreover, D-GADD45 is required for proper regeneration of wing imaginal discs. Our findings demonstrate that a tight regulation of D-GADD45 levels is required for its correct function both, in development and during the stress response after cell death. Full article

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

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15 pages, 1039 KiB

Open AccessReview

Retinal miRNA Functions in Health and Disease

by Marta Zuzic, Jesus Eduardo Rojo Arias, Stefanie Gabriele Wohl and Volker Busskamp

Genes 2019, 10(5), 377; https://doi.org/10.3390/genes10050377 - 17 May 2019

Cited by 55 | Viewed by 8561

Abstract

The health and function of our visual system relies on accurate gene expression. While many genetic mutations are associated with visual impairment and blindness, we are just beginning to understand the complex interplay between gene regulation and retinal pathologies. MicroRNAs (miRNAs), a class [...] Read more.

The health and function of our visual system relies on accurate gene expression. While many genetic mutations are associated with visual impairment and blindness, we are just beginning to understand the complex interplay between gene regulation and retinal pathologies. MicroRNAs (miRNAs), a class of non-coding RNAs, are important regulators of gene expression that exert their function through post-transcriptional silencing of complementary mRNA targets. According to recent transcriptomic analyses, certain miRNA species are expressed in all retinal cell types, while others are cell type-specific. As miRNAs play important roles in homeostasis, cellular function, and survival of differentiated retinal cell types, their dysregulation is associated with retinal degenerative diseases. Thus, advancing our understanding of the genetic networks modulated by miRNAs is central to harnessing their potential as therapeutic agents to overcome visual impairment. In this review, we summarize the role of distinct miRNAs in specific retinal cell types, the current knowledge on their implication in inherited retinal disorders, and their potential as therapeutic agents. Full article

(This article belongs to the Special Issue Molecular Therapies for Inherited Retinal Diseases)

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15 pages, 2933 KiB

Open AccessArticle

Identification and Validation of Novel Reference Genes in Acute Lymphoblastic Leukemia for Droplet Digital PCR

by Vanessa Villegas-Ruíz, Karina Olmos-Valdez, Kattia Alejandra Castro-López, Victoria Estefanía Saucedo-Tepanecatl, Josselen Carina Ramírez-Chiquito, Eleazar Israel Pérez-López, Isabel Medina-Vera and Sergio Juárez-Méndez

Genes 2019, 10(5), 376; https://doi.org/10.3390/genes10050376 - 17 May 2019

Cited by 9 | Viewed by 4498

Abstract

Droplet digital PCR is the most robust method for absolute nucleic acid quantification. However, RNA is a very versatile molecule and its abundance is tissue-dependent. RNA quantification is dependent on a reference control to estimate the abundance. Additionally, in cancer, many cellular processes [...] Read more.

Droplet digital PCR is the most robust method for absolute nucleic acid quantification. However, RNA is a very versatile molecule and its abundance is tissue-dependent. RNA quantification is dependent on a reference control to estimate the abundance. Additionally, in cancer, many cellular processes are deregulated which consequently affects the gene expression profiles. In this work, we performed microarray data mining of different childhood cancers and healthy controls. We selected four genes that showed no gene expression variations (PSMB6, PGGT1B, UBQLN2 and UQCR2) and four classical reference genes (ACTB, GAPDH, RPL4 and RPS18). Gene expression was validated in 40 acute lymphoblastic leukemia samples by means of droplet digital PCR. We observed that PSMB6, PGGT1B, UBQLN2 and UQCR2 were expressed ~100 times less than ACTB, GAPDH, RPL4 and RPS18. However, we observed excellent correlations among the new reference genes (p < 0.0001). We propose that PSMB6, PGGT1B, UBQLN2 and UQCR2 are housekeeping genes with low expression in childhood cancer. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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