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Idola D, Mori H, Nagata Y, Nonaka L, Yano H. Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria. Mob DNA 2023; 14:7. [PMID: 37237359 DOI: 10.1186/s13100-023-00295-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague. RESULTS To corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an SE host. Then, the SE core genes were defined based on gene knockout experiments, and the synteny blocks of their distant homologs were searched for in the RefSeq complete genome sequence database using PSI-BLAST. A genomic DNA fractionation experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. Operonic structure of three conserved coding sequences (intA, tfp, intB) and srap located at the left end of SEs were identified as essential for attL × attR recombination. The synteny blocks of tfp and srap homologs were detected in 3.6% of the replicons of Gammaproteobacteria but not in other taxa, implying that SE movement is host-dependent. SEs have been discovered most frequently in the orders Vibrionales (19% of replicons), Pseudomonadales (18%), Alteromonadales (17%), and Aeromonadales (12%). Genomic comparisons revealed 35 new SE members with identifiable termini. SEs are present at 1 to 2 copies per replicon and have a median length of 15.7 kb. Three newly identified SE members carry antimicrobial resistance genes, like tmexCD-toprJ, mcr-9, and blaGMA-1. Further experiments validated that three new SE members possess the strand-biased attL × attR recombination activity. CONCLUSIONS This study suggested that transposition intermediates of SEs are double-stranded circular DNA. The main hosts of SEs are a subset of free-living Gammaproteobacteria; this represents a rather narrow host range compared to those of mobile DNA element groups discovered to date. As the host range, genetic organization, and movements are unique among the mobile DNA elements, SEs provide a new model system for host-mobile DNA element coevolution studies.
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Affiliation(s)
- Desmila Idola
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan
| | - Hiroshi Mori
- Department of Informatics, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan
| | - Lisa Nonaka
- Faculty of Human Life Sciences, Shokei University, 2-6-78 Kuhonji, Kumamoto, 862-8678, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan.
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aobacho, Higashimurayama, Tokyo, 189-0002, Japan.
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Luo X, Yin Z, Yu L, Zhang J, Hu D, Xu M, Wang P, Wang F, Feng J. Genomic analysis of chromosomal cointegrated bla NDM-1-carrying ICE and bla RSA-1-carrying IME from clinical multidrug resistant Aeromonas caviae. Front Cell Infect Microbiol 2023; 13:1131059. [PMID: 37033477 PMCID: PMC10076717 DOI: 10.3389/fcimb.2023.1131059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The objective of this study is to thoroughly analyze the detailed genomic characteristics of clinical strain 211703 of Aeromonas caviae, which co-carrying bla RSA-1 and bla NDM-1 genes. 211703 was isolated from the patient's cerebrospinal fluid drainage sample in a Chinese tertiary hospital. Methods Carbapenemase NDM was detected by the immunocolloidal gold technique. The MIC values were determined by VITEK2. The whole genome sequence of 211703 was analyzed using phylogenetics, genomic comparison, and extensive dissection. Results This study revealed that 211703 only contained a single 4.78 Mb chromosome (61.8% GC content), and no plasmids were discovered in 211703. 15 different types of resistant genes were detected in the genome of 211703, including bla RSA-1 harbored on integrative and mobilizable element (IME) Tn7413a, and bla NDM-1 harbored on integrative and conjugative element (ICE). The ICE and IME were all carried on the chromosome of 211703 (c211703). Detailed comparison of related IMEs/ICEs showed that they shared similar conserved backbone regions, respectively. Comprehensive annotation revealed that bla RSA-1 was carried by the gene cassette of a novel integron In2148 on Tn7413a, and bla NDM-1 was captured by an insertion sequence ISCR14-like on the ICE of 211703. We speculated that mobile genetic elements (MGEs) such as ICE and IME facilitated the spread of resistance genes such as bla RSA-1 and bla NDM-1. Discussion In conclusion, this study provides an overall understanding of the genomic characterization of clinically isolated A. caviae 211703, and an in-depth discussion of multiple acquisition methods of drug resistance genes in Aeromonas. To the best of our knowledge, this is the first report of A. caviae carrying bla RSA-1 even both bla RSA-1 and bla NDM-1, and this is the first bacterium carrying bla RSA-1 isolated from the clinical setting.
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Affiliation(s)
- Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Jin Zhang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Dakang Hu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Mengqiao Xu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fengling Wang
- Nanxiang Branch of Ruijin Hospital, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Jiao Feng, ; Fengling Wang,
| | - Jiao Feng
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- *Correspondence: Jiao Feng, ; Fengling Wang,
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Wang J, Qi K, Bai X, Wu Z, Kang W, Liang P, Zheng H, Xu J. Characterization of integrative and conjugative elements carrying antibiotic resistance genes of Streptococcus suis isolated in China. Front Microbiol 2022; 13:1074844. [PMID: 36620002 PMCID: PMC9815147 DOI: 10.3389/fmicb.2022.1074844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Streptococcus suis, an emerging zoonotic pathogen, is important reservoirs of antibiotic resistance genes that play critical roles in the horizontal transfer of corresponding resistances. In the present study, 656 antibiotic resistance (AR) genes were detected in 154 of 155 genomes of S. suis strains isolated from the nasopharynx of slaughtered pigs and the lungs of diseased pigs in China. The AR genes were clustered into 11 categories, consisting of tetracycline, macrolides, lincosamide, streptogramin, aminoglycoside, trimethoprim, amphenicols, nucleoside, quinupristin/dalfopristin, glycopeptide, and oxazolidinones resistance genes. In order to investigate the transmission patterns of the AR genes, AR genes-associated the mobile genetic elements (MGEs) were extracted and investigated. Twenty ICEs, one defective ICE, one tandem ICE, and ten prophages were found, which mainly carried tetracycline, macrolides/lincosamides/streptogramin (MLS), and aminoglycosides resistance genes. Three types of DNA cargo with AR genes were integrated into specific sites of ICEs: integrative mobilizable elements (IMEs), cis-IMEs (CIMEs), and transposon Tn916. Obvious differences in AR gene categories were found among the three cargo types. IMEs mainly harbored tetracycline and MLS resistance genes. CIMEs mainly carried aminoglycoside resistance genes, while transposon Tn916 carried only the tet (M) gene. Nearly all AR genes in ICEs were carried by IMEs and CIMEs. IMEs were prevalent and were also detected in additional 29 S. suis genomes. The horizontal transfer of IMEs and CIMEs may play critical role in ICE evolution and AR gene transmission in the S. suis population. Our findings provide novel insights into the transmission patterns of AR genes and the evolutionary mechanisms of ICEs in S. suis.
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Affiliation(s)
- Jianping Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kexin Qi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuemei Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zongfu Wu
- OIE Reference Lab for Swine Streptococcosis, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Weiming Kang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Pujun Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,*Correspondence: Han Zheng, ✉
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Berbel D, González-Díaz A, López de Egea G, Càmara J, Ardanuy C. An Overview of Macrolide Resistance in Streptococci: Prevalence, Mobile Elements and Dynamics. Microorganisms 2022; 10:2316. [PMID: 36557569 PMCID: PMC9783990 DOI: 10.3390/microorganisms10122316] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Streptococcal infections are usually treated with beta-lactam antibiotics, but, in case of allergic patients or reduced antibiotic susceptibility, macrolides and fluoroquinolones are the main alternatives. This work focuses on studying macrolide resistance rates, genetic associated determinants and antibiotic consumption data in Spain, Europe and also on a global scale. Macrolide resistance (MR) determinants, such as ribosomal methylases (erm(B), erm(TR), erm(T)) or active antibiotic efflux pumps and ribosomal protectors (mef(A/E)-mrs(D)), are differently distributed worldwide and associated with different clonal lineages and mobile genetic elements. MR rates vary together depending on clonal dynamics and on antibiotic consumption applying selective pressure. Among Streptococcus, higher MR rates are found in the viridans group, Streptococcus pneumoniae and Streptococcus agalactiae, and lower MR rates are described in Streptococcus pyogenes. When considering different geographic areas, higher resistance rates are usually found in East-Asian countries and milder or lower in the US and Europe. Unfortunately, the availability of data varies also between countries; it is scarce in low- and middle- income countries from Africa and South America. Thus, surveillance studies of macrolide resistance rates and the resistance determinants involved should be promoted to complete global knowledge among macrolide resistance dynamics.
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Affiliation(s)
- Dàmaris Berbel
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Aida González-Díaz
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Guillem López de Egea
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Jordi Càmara
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, IDIBELL-UB, 08907 Barcelona, Spain
- Research Network for Respiratory Diseases (CIBERES), ISCIII, 28020 Madrid, Spain
- Department of Pathology and Experimental Therapeutics, School of Medicine, University of Barcelona, 08007 Barcelona, Spain
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Ni L, Cao J, Yuan C, Zhou LT, Wu X. Expression of Ferroptosis-Related Genes is Correlated with Immune Microenvironment in Diabetic Kidney Disease. Diabetes Metab Syndr Obes 2022; 15:4049-4064. [PMID: 36597492 PMCID: PMC9805740 DOI: 10.2147/dmso.s388724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/26/2022] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE This study aims to explore the correlation between ferroptosis and immune microenvironment (IME) in diabetic kidney disease (DKD) to provide a new clue for exploring the underlying molecular mechanisms. METHODS Corresponding RNA data of DKD patients were downloaded from GEO databases. The weighted gene co-expression network analysis (WGCNA) was used to construct the network, and the selected hub genes, then, overlapped with ferroptosis-related genes (FRGs) from FerrDb. Consensus clustering was performed to identify new molecular subgroups. ESTIMATE, TIMER and ssGSEA analyses were applied to determinate the IME and immune status. Functional analyses including GO, KEGG and GSEA were conducted to elucidate the underlying mechanisms. RESULTS Two molecular subtypes were identified based on the expression of FRGs. ESTIMATE algorithm revealed that there were significant differences in ESTIMATE score between these two clusters of DKD patients, with no significant difference found in stromal score and immune score. In addition, TIMER algorithm indicated there was a significant difference in the degree of T cell infiltration. The ssGSEA algorithm showed immunity was mainly concentrated in thick ascending limb and distal convoluted tubule in adult kidney. GO, KEGG and GSEA analyses revealed that the differentially expressed genes (DEGs) were mainly enriched in immune and metabolism associated pathways. CONCLUSION The ferroptosis may be induced by dysregulation of IME, thereby accelerating the progression of DKD. Our work could be applied to provide a new clue for exploring the underlying molecular mechanisms and sheds novel light on the therapy strategy of DKD.
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Affiliation(s)
- Lihua Ni
- Department of Nephrology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Jingyuan Cao
- The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, People’s Republic of China
| | - Cheng Yuan
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
| | - Le-Ting Zhou
- Department of Nephrology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, People’s Republic of China
| | - Xiaoyan Wu
- Department of Nephrology, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Correspondence: Xiaoyan Wu; Le-Ting Zhou, Email ;
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Colombi E, Perry BJ, Sullivan JT, Bekuma AA, Terpolilli JJ, Ronson CW, Ramsay JP. Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium. Microb Genom 2021; 7. [PMID: 34605762 PMCID: PMC8627217 DOI: 10.1099/mgen.0.000657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSymR7A.
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Affiliation(s)
- Elena Colombi
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Benjamin J Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Amanuel A Bekuma
- Centre for Rhizobium Studies, Food Futures Institute, Murdoch University, Perth, WA, Australia, Murdoch University, Perth, WA, Australia.,Present address: Western Australian Department of Primary Industries and Regional Development, Research and Industry Innovation, South Perth, WA, Australia
| | - Jason J Terpolilli
- Centre for Rhizobium Studies, Food Futures Institute, Murdoch University, Perth, WA, Australia, Murdoch University, Perth, WA, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Joshua P Ramsay
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
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Kim S, Song H, Hur Y. Intron-retained radish (Raphanus sativus L.) RsMYB1 transcripts found in colored-taproot lines enhance anthocyanin accumulation in transgenic Arabidopsis plants. Plant Cell Rep 2021; 40:1735-1749. [PMID: 34308490 DOI: 10.1007/s00299-021-02735-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Overexpression of the naturally occurring intron-retained (IR) forms of radish RsMYB1 and RsTT8 transcripts in Arabidopsis causes a substantial increase in anthocyanin accumulation. The production of anthocyanins in plants is tightly controlled by the MYB-bHLH-WD40 (MBW) complex. In this study, analysis of four radish (Raphanus sativus L.) inbred lines with different colored taproots revealed that regulatory genes of anthocyanin biosynthesis, RsMYB1 and RsTT8, produce three transcripts, one completely spliced and two intron retention (IR1 and IR2) forms. Transcripts RsMYB1-IR1 and RsMYB1-IR2 retained the 1st (380 nt) and 2nd (149 nt) introns, respectively; RsTT8-IR1 retained the 4th intron (113 nt); RsTT8-IR2 retained both the 3rd (128 nt) and 4th introns. Levels of most IR forms were substantially low in radish samples, but the RsTT8-IR2 level was higher than RsTT8 in red skin/red flesh (RsRf) root. Since all IR forms contained a stop codon within the intron, they were predicted to encode truncated proteins with defective interaction domains, resulting in the inability to form the MBW complex in vivo. However, tobacco leaves transiently co-expressing RsMYB1-IRs and RsTT8-IRs showed substantially higher anthocyanin accumulation than those co-expressing their spliced forms. Consistently, co-expression of constructs encoding truncated proteins with spliced or IR forms of their interaction partner in tobacco leaves did not result in anthocyanin accumulation. Compared with RsMYB1, the overexpression of RsMYB1-IRs in Arabidopsis pap1 mutant increased anthocyanin accumulation by > sevenfold and upregulated the expression of Arabidopsis flavonoid biosynthesis genes including AtTT8. Our results suggest that the stable co-expression of RsMYB1-IRs in fruit trees and vegetable crops could be used to increase their anthocyanin contents.
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Affiliation(s)
- Soyun Kim
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hayoung Song
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yoonkang Hur
- Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Doulberis M, Pierre NT, Manzini G, Papaefthymiou A, Kountouras J, Klukowska-Rötzler J, Polyzos SA, Srivastava S, Exadaktylos AK, Knuchel J, Kuntzen T, Srivastava DS. Helicobacter pylori-Related Metabolic Parameters and Premalignant Gastric Mucosa Histological Lesions in Swiss Bariatric Patients. Microorganisms 2021; 9:microorganisms9071361. [PMID: 34201748 PMCID: PMC8303942 DOI: 10.3390/microorganisms9071361] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 02/08/2023] Open
Abstract
Obesity, as a major risk factor of metabolic syndrome (MetS), represents a pandemic, especially in Western societies, and is considered a risk factor for malignancies. Helicobacter pylori (Hp), is a definite carcinogen with global distribution. We aimed to investigate, for the first time in Switzerland, the main gastric mucosa premalignant histological lesions of bariatric patients in correlation with MetS components and Hp Infection (Hp-I). By reviewing retrospectively 94304 patient cases, a total of 116 eligible patients having undergone bariatric surgery were identified. The mean patient age was 48.66 years. Hp(+) patients were 24% (28/116). Presence of gastric mucosa atrophy was documented in 8/28 Hp(+) patients (29%) and (2/88) Hp(-) ones (2%) (p = 0.006). Gastric mucosa intestinal metaplasia was observed in 14/28 (50%) Hp(+) patients versus 3/88 (3.4%) of Hp(-) group (p < 0.0001). Hp(+) patients exhibited statistically higher arterial hypertension (p = 0.033). The homeostatic model of assessment insulin resistance was also statistically significantly higher for the Hp(+) group (p < 0.001). In a multivariate analysis, including arterial hypertension, gastric mucosa atrophy, and intestinal metaplasia as variables, statistical significance remained only for intestinal metaplasia (p = 0.001). In conclusion, Hp-I is associated with premalignant gastric mucosa histologic lesions and MetS components, including arterial hypertension and IR. Further large-scale prospective studies are required to confirm these findings.
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Affiliation(s)
- Michael Doulberis
- Emergency Department, University Hospital Inselspital of Bern, 3010 Bern, Switzerland; (N.T.P.); (J.K.-R.); (A.K.E.); (D.S.S.)
- Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, 5001 Aarau, Switzerland; (J.K.); (T.K.)
- Second Medical Clinic, School of Medicine, Aristotle University of Thessaloniki, Ippokration Hospital, 54642 Thessaloniki, Macedonia, Greece; (A.P.); (J.K.)
- First Laboratory of Pharmacology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece;
- Correspondence:
| | - Noah Thierry Pierre
- Emergency Department, University Hospital Inselspital of Bern, 3010 Bern, Switzerland; (N.T.P.); (J.K.-R.); (A.K.E.); (D.S.S.)
- Private Practice, 4704 Niederbipp, Switzerland
| | - Giulia Manzini
- Department of General and Visceral Surgery, Kantonsspital Aarau, 5001 Aarau, Switzerland;
| | - Apostolis Papaefthymiou
- Second Medical Clinic, School of Medicine, Aristotle University of Thessaloniki, Ippokration Hospital, 54642 Thessaloniki, Macedonia, Greece; (A.P.); (J.K.)
- First Laboratory of Pharmacology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece;
- Department of Gastroenterology, University Hospital of Larisa, Mezourlo, 41110 Larisa, Thessaly, Greece
| | - Jannis Kountouras
- Second Medical Clinic, School of Medicine, Aristotle University of Thessaloniki, Ippokration Hospital, 54642 Thessaloniki, Macedonia, Greece; (A.P.); (J.K.)
| | - Jolanta Klukowska-Rötzler
- Emergency Department, University Hospital Inselspital of Bern, 3010 Bern, Switzerland; (N.T.P.); (J.K.-R.); (A.K.E.); (D.S.S.)
| | - Stergios A. Polyzos
- First Laboratory of Pharmacology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Macedonia, Greece;
| | | | - Aristomenis K. Exadaktylos
- Emergency Department, University Hospital Inselspital of Bern, 3010 Bern, Switzerland; (N.T.P.); (J.K.-R.); (A.K.E.); (D.S.S.)
| | - Jürg Knuchel
- Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, 5001 Aarau, Switzerland; (J.K.); (T.K.)
| | - Thomas Kuntzen
- Division of Gastroenterology and Hepatology, Medical University Department, Kantonsspital Aarau, 5001 Aarau, Switzerland; (J.K.); (T.K.)
| | - David S. Srivastava
- Emergency Department, University Hospital Inselspital of Bern, 3010 Bern, Switzerland; (N.T.P.); (J.K.-R.); (A.K.E.); (D.S.S.)
- Department of General Internal Medicine, Kliniken Hirslanden Beau-Site, 3013 Bern, Switzerland
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Djemal R, Khoudi H. Combination of the endogenous promoter-intron significantly improves salt and drought tolerance conferred by TdSHN1 transcription factor in transgenic tobacco. Plant Physiol Biochem 2019; 139:435-445. [PMID: 30999131 DOI: 10.1016/j.plaphy.2019.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/27/2019] [Accepted: 04/09/2019] [Indexed: 05/08/2023]
Abstract
Recent years have witnessed a renewed interest in introns as a tool to increase gene expression. We previously isolated TdSHN1 gene encoding a transcription factor in durum wheat. Here we show that TdSHN1 intron contains many CT-stretches and the motif CGATT known to be important for IME. When subjected to bioinformatics analysis using IMEter software, TdSHN1 intron obtained a score of 17.04 which indicates that it can moderately enhance gene expression. TdSHN1 gene including its intron was placed under the control of TdSHN1 endogenous salt and drought-inducible promoter or the constitutive 35S promoter and transferred into tobacco. Transgenic lines were obtained and designated gD (with 35S promoter) and PI (with native promoter). A third construct was also used in which intron-less cDNA was driven by the 35S promoter (cD lines). Results showed that, gD lines exhibited lower stomatal density than cD lines. When subjected to drought and salt stresses, gD lines outperformed intron-less cD lines and WT. Indeed, gD lines exhibited longer roots, higher biomass production, retained more chlorophyll, produced less ROS and MDA and had higher antioxidant activity. qRT-PCR analysis revealed that gD lines had higher TdSHN1 expression levels than cD lines. In addition, expression of ROS-scavengering, stress-related and wax biosynthesis tobacco genes was higher in gD lines compared to cD lines and WT. Interestingly, under stress conditions, PI transgenic lines showed higher TdSHN1 expression levels and outperformed gD lines. These results suggest that TdSHN1 intron enhances gene expression when used alone or in combination with TdSHN1 endogenous promoter.
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Affiliation(s)
- Rania Djemal
- Laboratory of Plant Biotechnology and Improvement, University of Sfax, Center of Biotechnology of Sfax, Route Sidi Mansour, Km 6 B.P' 1177, 3018, Sfax, Tunisia
| | - Habib Khoudi
- Laboratory of Plant Biotechnology and Improvement, University of Sfax, Center of Biotechnology of Sfax, Route Sidi Mansour, Km 6 B.P' 1177, 3018, Sfax, Tunisia.
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Vexler K, Cymerman MA, Berezin I, Fridman A, Golani L, Lasnoy M, Saul H, Shaul O. The Arabidopsis NMD Factor UPF3 Is Feedback-Regulated at Multiple Levels and Plays a Role in Plant Response to Salt Stress. Front Plant Sci 2016; 7:1376. [PMID: 27746786 PMCID: PMC5040709 DOI: 10.3389/fpls.2016.01376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/29/2016] [Indexed: 05/22/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a eukaryotic RNA surveillance mechanism that degrades aberrant transcripts and controls the levels of many normal mRNAs. It was shown that balanced expression of the NMD factor UPF3 is essential for the maintenance of proper NMD homeostasis in Arabidopsis. UPF3 expression is controlled by a negative feedback loop that exposes UPF3 transcript to NMD. It was shown that the long 3' untranslated region (3' UTR) of UPF3 exposes its transcript to NMD. Long 3' UTRs that subject their transcripts to NMD were identified in several eukaryotic NMD factors. Interestingly, we show here that a construct that contains all the regulatory regions of the UPF3 gene except this long 3' UTR is also feedback-regulated by NMD. This indicates that UPF3 expression is feedback-regulated at multiple levels. UPF3 is constitutively expressed in different plant tissues, and its expression is equal in leaves of plants of different ages. This finding is in agreement with the possibility that UPF3 is ubiquitously operative in the Arabidopsis NMD pathway. Expression mediated by the regulatory regions of UPF3 is significantly induced by salt stress. We found that both a deficiency and a strong excess of UPF3 expression are detrimental to plant resistance to salt stress. This indicates that UPF3 plays a role in plant response to salt stress, and that balanced expression of the UPF3 gene is essential for coping with this stress.
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Jiang L, Huang C, Sun Q, Guo H, Cheng T, Peng Z, Dang Y, Liu W, Xu G, Xia Q. The 5'-UTR intron of the midgut-specific BmAPN4 gene affects the level and location of expression in transgenic silkworms. Insect Biochem Mol Biol 2015; 63:1-6. [PMID: 25982022 DOI: 10.1016/j.ibmb.2015.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/07/2015] [Accepted: 05/04/2015] [Indexed: 05/09/2023]
Abstract
Introns are important for regulating gene expression. BmAPN4, which has a 5'-UTR upstream intron (5 UI), is specifically expressed in the entire silkworm midgut. In our previous study, the promoter region upstream of the 5 UI of BmAPN4 was cloned and identified as the P3 promoter (P3P) with activity only in the anterior midgut. In this study, the sequence consisting of the P3P and the 5 UI was cloned and named as P3P+5 UI. A transgenic vector was constructed in which EGFP was controlled by P3P+5 UI. Transgenic P3+5 UI silkworms were generated by embryo microinjection. RT-PCR showed P3P+5 UI activity throughout the larval stage. Intense green fluorescence was seen only in the entire midgut of P3+5 UI silkworms and expression was confirmed by RT-PCR. qPCR revealed that expression of EGFP in the anterior midgut of P3+5 UI silkworms was 64% higher than in P3 silkworms, indicating the 5 UI sustained intron-mediated enhancement of gene expression. These results suggested that the BmAPN4 5 UI affected the level and site of expression. The 5 UI was cloned and added behind P2P, another specific promoter with activity only in the anterior midgut of silkworm, to construct the P2P+5 UI and transgenic P2+5 UI silkworms. Expression patterns were the same for P2P+5 UI and P2P, suggesting that the 5UI of BmAPN4 did not affect P2P. This study found that the BmAPN4 5 UI affected the amount and location of gene expression. Its influence appeared to be dependent on a specific promoter.
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Affiliation(s)
- Liang Jiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Chunlin Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Qiang Sun
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Huizhen Guo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Tingcai Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Zhengwen Peng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Yinghui Dang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Weiqiang Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Guowen Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China.
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Akua T, Shaul O. The Arabidopsis thaliana MHX gene includes an intronic element that boosts translation when localized in a 5' UTR intron. J Exp Bot 2013; 64:4255-70. [PMID: 24006416 PMCID: PMC3808313 DOI: 10.1093/jxb/ert235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The mechanisms that underlie the ability of some introns to increase gene expression, a phenomenon called intron-mediated enhancement (IME), are not fully understood. It is also not known why introns localized in the 5'-untranslated region (5' UTR) are considerably longer than downstream eukaryotic introns. It was hypothesized that this extra length results from the presence of some functional intronic elements. However, deletion analyses studies carried out thus far were unable to identify specific intronic regions necessary for IME. Using deletion analysis and a gain-of-function approach, an internal element that considerably increases translational efficiency, without affecting splicing, was identified in the 5' UTR intron of the Arabidopsis thaliana MHX gene. Moreover, the ability of this element to enhance translation was diminished by a minor downstream shift in the position of introns containing it from the 5' UTR into the coding sequence. These data suggest that some of the extra length of 5' UTR introns results from the presence of elements that enhance translation, and, moreover, from the ability of 5' UTR introns to provide preferable platforms for such elements over downstream introns. The impact of the identified intronic element on translational efficiency was augmented upon removal of neighbouring intronic elements. Interference between different intronic elements had not been reported thus far. This interference may support the bioinformatics-based idea that some of the extra sequence of 5' UTR introns is also necessary for separating different functional intronic elements.
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Affiliation(s)
- Tsofit Akua
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Orit Shaul
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Gallois JL, Drouaud J, Lécureuil A, Guyon-Debast A, Bonhomme S, Guerche P. Functional characterization of the plant ubiquitin regulatory X (UBX) domain-containing protein AtPUX7 in Arabidopsis thaliana. Gene 2013; 526:299-308. [PMID: 23747397 DOI: 10.1016/j.gene.2013.05.056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 05/16/2013] [Accepted: 05/21/2013] [Indexed: 10/26/2022]
Abstract
p97/CDC48 is a major AAA-ATPase that acts in many cellular events such as ubiquitin-dependent degradation and membrane fusion. Its specificity depends on a set of adaptor proteins, most of them containing the ubiquitin regulatory X (UBX) domain. Using a differential hybridization system, we isolated a UBX-containing protein that is expressed during the early phase of male gametophyte development in the crop Brassica napus and isolated and characterized its closest Arabidopsis thaliana homolog, AtPUX7. The AtPUX7 gene is expressed broadly in both the sporophyte and gametophyte due to regulation inferred by its first intron. The subcellular localization of AtPUX7 was assigned mainly to the nucleus in both the sporophyte and in pollen, mirroring the AAA-ATPase AtCDC48A localization. Furthermore, AtPUX7 interacts specifically with AtCDC48A in yeast as well as in planta in the nucleus. This interaction was mediated through the AtPUX7 UBX domain, which is located at the protein C-terminus, while an N-terminal UBA domain mediated its interaction with ubiquitin. Consistent with those results, a yeast-three hybrid analysis showed that AtPUX7 can act as a bridge between AtCDC48A and ubiquitin, suggesting a role in targeted protein degradation. It is likely that AtPUX7 acts redundantly with other members of the Arabidopsis PUX family because a null Atpux7-1 mutant does not display obvious developmental defects.
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Affiliation(s)
- Jean-Luc Gallois
- INRA-UR 1052 Génétique et Amélioration des Fruits et Légumes (GAFL), Domaine St Maurice, CS 60094, F-84143 Montfavet Cedex, France.
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