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Singh S, Anderson N, Chu D, Roy SW. Nematode histone H2A variant evolution reveals diverse histories of retention and loss and evidence for conserved core-like variant histone genes. PLoS One 2024; 19:e0300190. [PMID: 38814971 PMCID: PMC11139335 DOI: 10.1371/journal.pone.0300190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/22/2024] [Indexed: 06/01/2024] Open
Abstract
Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution.
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Affiliation(s)
- Swadha Singh
- Quantitative & Systems Biology, University of California, Merced, Merced, California, United States of America
| | - Noelle Anderson
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Diana Chu
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Scott W. Roy
- Quantitative & Systems Biology, University of California, Merced, Merced, California, United States of America
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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Chen Q, Zhu C, Guo L, Bu X, Yang W, Cheng S, Cong X, Xu F. Genome-wide identification of HMT gene family explores BpHMT2 enhancing selenium accumulation and tolerance in Broussonetia papyrifera. TREE PHYSIOLOGY 2024; 44:tpae030. [PMID: 38498335 DOI: 10.1093/treephys/tpae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024]
Abstract
Broussonetia papyrifera, a valuable feed resource, is known for its fast growth, wide adaptability, high protein content and strong selenium enrichment capacity. Selenomethionine (SeMet), the main selenium form in selenium fortification B. papyrifera, is safe for animals and this enhances its nutritional value as a feed resource. However, the molecular mechanisms underlying SeMet synthesis remain unclear. This study identified three homocysteine S-methyltransferase genes from the B. papyrifera genome. The phylogenetic tree demonstrated that BpHMTs were divided into two classes, and BpHMT2 in the Class 2-D subfamily evolved earlier and possesses more fundamental functions. On the basis of the correlation between gene expression levels and selenium content, BpHMT2 was identified as a key candidate gene associated with selenium tolerance. Subcellular localization experiments confirmed the targeting of BpHMT2 in nucleus, cell membrane and chloroplasts. Moreover, three BpHMT2 overexpression Arabidopsis thaliana lines were confirmed to enhance plant selenium tolerance and SeMet accumulation. Overall, our finding provides insights into the molecular mechanisms of selenium metabolism in B. papyrifera, highlighting the potential role of BpHMT2 in SeMet synthesis. This research contributes to our understanding of selenium-enriched feed resources, with increased SeMet content contributing to the improved nutritional value of B. papyrifera as a feed resource.
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Affiliation(s)
- Qiangwen Chen
- Enshi Se-Run Material Engineering Technology Co., Ltd, Enshi, Hubei 445000, China
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
| | - Changye Zhu
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
| | - Longfei Guo
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
| | - Xianchen Bu
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
| | - Wei Yang
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
- Hubei National Se-rich Technology Development Co., Ltd, Enshi 445000, China
| | - Shuiyuan Cheng
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan, Hubei 430023, China
- National Selenium Rich Product Quality Supervision and Inspection Center, Enshi, Hubei 445000, China
| | - Xin Cong
- Enshi Se-Run Material Engineering Technology Co., Ltd, Enshi, Hubei 445000, China
- National R&D Center for Se-rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan, Hubei 430023, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, JingZhou, Hubei 434025, China
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He S, Wang Y, Luo Y, Xue M, Wu M, Tan H, Peng Y, Wang K, Fang M. Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs. BMC Genomics 2024; 25:30. [PMID: 38178019 PMCID: PMC10765619 DOI: 10.1186/s12864-023-09925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Shaziling pig is a well-known indigenous breed in China who has superior meat quality traits. However, the genetic mechanism and genomic evidence underlying meat quality characteristics of Shaziling pigs are still unclear. To explore and investigate the germplasm characteristics of Shaziling pigs, we totally analyzed 67 individual's whole genome sequencing data for the first time (20 Shaziling pigs [S], 20 Dabasha pigs [DBS], 11 Yorkshire pigs [Y], 10 Berkshire pigs [BKX], 5 Basha pigs [BS] and 1 Warthog). RESULTS A total of 2,538,577 SNPs with high quality were detected and 9 candidate genes which was specifically selected in S and shared in S to DBS were precisely mined and screened using an integrated analysis strategy of identity-by-descent (IBD) and selective sweep. Of them, dickkopf WNT signaling pathway inhibitor 2 (DKK2), the antagonist of Wnt signaling pathway, was the most promising candidate gene which was not only identified an association of palmitic acid and palmitoleic acid quantitative trait locus in PigQTLdb, but also specifically selected in S compared to other 48 Chinese local pigs of 12 populations and 39 foreign pigs of 4 populations. Subsequently, a mutation at 12,726-bp of DKK2 intron 1 (g.114874954 A > C) was identified associated with intramuscular fat content using method of PCR-RFLP in 21 different pig populations. We observed DKK2 specifically expressed in adipose tissues. Overexpression of DKK2 decreased the content of triglyceride, fatty acid synthase and expression of relevant genes of adipogenic and Wnt signaling pathway, while interference of DKK2 got contrary effect during adipogenesis differentiation of porcine preadipocytes and 3T3-L1 cells. CONCLUSIONS Our findings provide an analysis strategy for mining functional genes of important economic traits and provide fundamental data and molecular evidence for improving pig meat quality traits and molecular breeding.
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Affiliation(s)
- Shuaihan He
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yubei Wang
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Yabiao Luo
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xue
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Maisheng Wu
- Xiangtan Bureau of Animal Husbandry and Veterinary Medicine and Aquatic Product, Xiangtan, 411102, China
| | - Hong Tan
- Xiangtan Bureau of Animal Husbandry and Veterinary Medicine and Aquatic Product, Xiangtan, 411102, China
| | - Yinglin Peng
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Meiying Fang
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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Liu D, Wu L, Wei H, Zhu C, Tian R, Zhu W, Xu Q. The SFT2D2 gene is associated with the autoimmune pathology of schizophrenia in a Chinese population. Front Neurol 2022; 13:1037777. [PMID: 36619926 PMCID: PMC9810986 DOI: 10.3389/fneur.2022.1037777] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Background The relative risk of GWAS-confirmed loci strongly associated with schizophrenia may be underestimated due to the decay of linkage disequilibrium between index SNPs and causal variants. This study is aimed to investigate schizophrenia-associated signals detected in the 1q24-25 region in order to identify a causal variant in LD with GWAS index SNPs, and the potential biological functions of the risk gene. Methods Re-genotyping analysis was performed in the 1q24-25 region that harbors three GWAS index SNPs associated with schizophrenia (rs10489202, rs11586522, and rs6670165) in total of 9801 case-control subjects of Chinese Han origin. Circulating autoantibody levels were assessed using an in-house ELISA against a protein derived fragment encoded by SFT2D2 in total of 682 plasma samples. Results A rare variant (rs532193193) in the SFT2D2 locus was identified to be strongly associated with schizophrenia. Compared with control subjects, patients with schizophrenia showed increased anti-SFT2D2 IgG levels. Receiver operating characteristic (ROC) analysis revealed an area under the ROC curve (AUC) of 0.803 with sensitivity of 28.57% against specificity of 95% for the anti-SFT2D2 IgG assay. Discussion Our findings indicate that SFT2D2 is a novel gene for risk of schizophrenia, while endogenous anti-SFT2D2 IgG may underlie the pathophysiology of the immunological aspects of schizophrenia.
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Affiliation(s)
- Duilin Liu
- State Key Laboratory of Medical Molecular Biology, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China
| | - Lin Wu
- State Key Laboratory of Medical Molecular Biology, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China,Laboratory of Molecular Diagnostics, Beijing Boren Hospital, Beijing, China
| | - Hui Wei
- State Key Laboratory of Medical Molecular Biology, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Caiyun Zhu
- State Key Laboratory of Medical Molecular Biology, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Runhui Tian
- Mental Health Center, The First Bethune Hospital of Jilin University, Changchun, China
| | - Wanwan Zhu
- State Key Laboratory of Medical Molecular Biology, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Qi Xu
- State Key Laboratory of Medical Molecular Biology, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, Beijing, China,Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, China,*Correspondence: Qi Xu
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Ren Y, Song Q, Shan S, Wang J, Ma S, Song Y, Ma L, Zhang G, Niu N. Genome-Wide Identification and Expression Analysis of TUA and TUB Genes in Wheat ( Triticum aestivum L.) during Its Development. PLANTS (BASEL, SWITZERLAND) 2022; 11:3495. [PMID: 36559605 PMCID: PMC9785050 DOI: 10.3390/plants11243495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Microtubules play a fundamental role in plant development, morphogenesis, and cytokinesis; they are assembled from heterodimers containing an α-tubulin (TUA) and a β-tubulin (TUB) protein. However, little research has been conducted on the TUA and TUB gene families in hexaploid wheat (Triticum aestivum L.). In this study, we identified 15 TaTUA and 28 TaTUB genes in wheat. Phylogenetic analysis showed that 15 TaTUA genes were divided into two major subfamilies, and 28 TaTUB genes were divided into five major subfamilies. Mostly, there were similar motif compositions and exon-intron structures among the same subfamilies. Segmental duplication of genes (WGD/segmental) is the main process of TaTUA and TaTUB gene family expansion in wheat. It was found that TaTUA and TaTUB genes presented specific temporal and spatial characteristics based on the expression profiles of 17 tissues during wheat development using publicly available RNA-seq data. It was worth noting, via qRT-PCR, that two TaTUA and five TaTUB genes were highly expressed in fertile anthers compared to male sterility. These were quite different between physiological male sterile lines and S-type cytoplasmic male sterile lines at different stages of pollen development. This study offers fundamental information on the TUA and TUB gene families during wheat development and provides new insights for exploring the molecular mechanism of wheat male sterility.
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Affiliation(s)
- Yang Ren
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
- College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Qilu Song
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Sicong Shan
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Junwei Wang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Shoucai Ma
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Yulong Song
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Lingjian Ma
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Gaisheng Zhang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Na Niu
- Key Laboratory of Crop Heterosis of Shaanxi Province, Wheat Breeding Engineering Research Center, Ministry of Education, College of Agronomy, Northwest A&F University, Yangling 712100, China
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Coates RJ, Young MT, Scofield S. Optimising expression and extraction of recombinant proteins in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1074531. [PMID: 36570881 PMCID: PMC9773421 DOI: 10.3389/fpls.2022.1074531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are of paramount importance for research, industrial and medical use. Numerous expression chassis are available for recombinant protein production, and while bacterial and mammalian cell cultures are the most widely used, recent developments have positioned transgenic plant chassis as viable and often preferential options. Plant chassis are easily maintained at low cost, are hugely scalable, and capable of producing large quantities of protein bearing complex post-translational modification. Several protein targets, including antibodies and vaccines against human disease, have been successfully produced in plants, highlighting the significant potential of plant chassis. The aim of this review is to act as a guide to producing recombinant protein in plants, discussing recent progress in the field and summarising the factors that must be considered when utilising plants as recombinant protein expression systems, with a focus on optimising recombinant protein expression at the genetic level, and the subsequent extraction and purification of target proteins, which can lead to substantial improvements in protein stability, yield and purity.
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Affiliation(s)
| | | | - Simon Scofield
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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Ma C, Wang M, Zhao M, Yu M, Zheng X, Tian Y, Sun Z, Liu X, Wang C. The Δ1-pyrroline-5-carboxylate synthetase family performs diverse physiological functions in stress responses in pear ( Pyrus betulifolia). FRONTIERS IN PLANT SCIENCE 2022; 13:1066765. [PMID: 36507426 PMCID: PMC9731112 DOI: 10.3389/fpls.2022.1066765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 05/24/2023]
Abstract
Δ1-Pyrroline-5-carboxylate synthetase (P5CS) acts as the rate-limiting enzyme in the biosynthesis of proline in plants. Although P5CS plays an essential role in plant responses to environmental stresses, its biological functions remain largely unclear in pear (Pyrus betulifolia). In the present study, 11 putative pear P5CSs (PbP5CSs) were identified by comprehensive bioinformatics analysis and classified into five subfamilies. Segmental and tandem duplications contributed to the expansion and evolution of the PbP5CS gene family. Various cis-acting elements associated with plant development, hormone responses, and/or stress responses were identified in the promoters of PbP5CS genes. To investigate the regulatory roles of PbP5CS genes in response to abiotic and biotic stresses, gene expression patterns in publicly available data were explored. The tissue-specific expressional dynamics of PbP5CS genes indicate potentially important roles in pear growth and development. Their spatiotemporal expression patterns suggest key functions in multiple environmental stress responses. Transcriptome and real-time quantitative PCR analyses revealed that most PbP5CS genes exhibited distinct expression patterns in response to drought, waterlogging, salinity-alkalinity, heat, cold, and infection by Alternaria alternate and Gymnosporangium haraeanum. The results provide insight into the versatile functions of the PbP5CS gene family in stress responses. The findings may assist further exploration of the physiological functions of PbP5CS genes for the development and enhancement of stress tolerance in pear and other fruits.
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Affiliation(s)
- Changqing Ma
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, China
| | - Mengqi Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, China
| | - Mingrui Zhao
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, China
| | - Mengyuan Yu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, China
| | - Xiaodong Zheng
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, China
| | - Yike Tian
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, China
| | - Zhijuan Sun
- College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xiaoli Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, China
| | - Caihong Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticulture Plants, Qingdao, China
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Yu H, Lin Y, Xu Y, Chen K, Wang Y, Fu L, Zhou H, Pi L, Che D, Qiu X, Gu X. Association between Rab31/rs9965664 polymorphism and immunoglobulin therapy resistance in patients with Kawasaki disease. Front Cardiovasc Med 2022; 9:944508. [PMID: 36329997 PMCID: PMC9623048 DOI: 10.3389/fcvm.2022.944508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
Background Kawasaki disease (KD) is an acute febrile systemic vasculitis affecting infants and young children. A high dose of intravenous immunoglobulin (IVIG) is the first-line strategy for patients with KD to reduce persistent inflammation and the risk of coronary artery aneurysm (CAA) formation. Unfortunately, 10–20% of the patients showed no response to the treatment and were defined as resistant to IVIG. Rab31 has been reported to regulate innate immunity in several human diseases. However, whether single nucleotide polymorphism (SNP) in Rab31 gene could predispose to IVIG therapy response in KD was uncovered. Methods Rab31/rs9965664 polymorphism was genotyped in 1,024 Chinese patients with KD through TaqMan assay. The odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the strength of association between Rab31/rs9965664 polymorphism and IVIG therapeutic effects. Results Our results showed that Rab31/rs9965664 AA/GA genotype was significantly associated with an increased risk of IVIG resistance compared to GG genotype (GA vs. GG: p = 0.0249; AA vs. GG: p = 0.0016; AA/GA vs. GG: p = 0.0039; and AA vs. GG/GA: p = 0.0072). Moreover, the KD individuals carrying the rs9965664 A allele displayed lower Rab31 protein levels, and the expression level of Rab31 in the IVIG-resistant group was decreased significantly when compared to that observed in the response group. A mechanical study demonstrated that Rab31 modulated IVIG response through NLRP3 and p38 pathways. Conclusion These results suggested that Rab31/rs9965664 polymorphism might be associated with an increased risk of IVIG resistance in southern Chinese patients with KD. The possible mechanism is that Rab31 regulates the NLRP3 pathway negatively to inhibit IVIG response.
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Affiliation(s)
- Hongyan Yu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yueling Lin
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yufen Xu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Kaining Chen
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yishuai Wang
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lanyan Fu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huazhong Zhou
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lei Pi
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Di Che
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiantao Qiu
- Department of Clinical Lab, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Xiantao Qiu
| | - Xiaoqiong Gu
- Department of Clinical Biological Resource Bank, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- Department of Blood Transfusion and Clinical Lab, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
- Xiaoqiong Gu
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Identification, Phylogeny, Divergence, Structure, and Expression Analysis of A20/AN1 Zinc Finger Domain Containing Stress-Associated Proteins (SAPs) Genes in Jatropha curcas L. Genes (Basel) 2022; 13:genes13101766. [PMID: 36292651 PMCID: PMC9601316 DOI: 10.3390/genes13101766] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/18/2022] [Accepted: 09/27/2022] [Indexed: 11/04/2022] Open
Abstract
Jatropha is a small woody perennial biofuel-producing shrub. Stress-associated proteins (SAPs) are novel stress regulatory zinc-finger proteins and are mainly associated with tolerance against various environmental abiotic stresses in Jatropha. In the present study, the JcSAP gene family were analyzed comprehensively in Jatropha curcas and 11 JcSAP genes were identified. Phylogenetic analysis classified the JcSAP genes into four groups based on sequence similarity, similar gene structure features, conserved A20 and/or AN1 domains, and their responsive motifs. Moreover, the divergence analysis further evaluated the evolutionary aspects of the JcSAP genes with the predicted time of divergence from 9.1 to 40 MYA. Furthermore, a diverse range of cis-elements including light-responsive elements, hormone-responsive elements, and stress-responsive elements were detected in the promoter region of JcSAP genes while the miRNA target sites predicted the regulation of JcSAP genes via a candid miRNA mediated post-transcriptional regulatory network. In addition, the expression profiles of JcSAP genes in different tissues under stress treatment indicated that many JcSAP genes play functional developmental roles in different tissues, and exhibit significant differential expression under stress treatment. These results collectively laid a foundation for the functional diversification of JcSAP genes.
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Yi X, Sun X, Tian R, Li K, Ni M, Ying J, Xu L, Liu L, Wang Y. Genome-Wide Characterization of the Aquaporin Gene Family in Radish and Functional Analysis of RsPIP2-6 Involved in Salt Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:860742. [PMID: 35909741 PMCID: PMC9337223 DOI: 10.3389/fpls.2022.860742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Aquaporins (AQPs) constitute a highly diverse family of channel proteins that transport water and neutral solutes. AQPs play crucial roles in plant development and stress responses. However, the characterization and biological functions of RsAQPs in radish (Raphanus sativus L.) remain elusive. In this study, 61 non-redundant members of AQP-encoding genes were identified from the radish genome database and located on nine chromosomes. Radish AQPs (RsAQPs) were divided into four subfamilies, including 21 plasma membrane intrinsic proteins (PIPs), 19 tonoplast intrinsic proteins (TIPs), 16 NOD-like intrinsic proteins (NIPs), and 5 small basic intrinsic proteins (SIPs), through phylogenetic analysis. All RsAQPs contained highly conserved motifs (motifs 1 and 4) and transmembrane regions, indicating the potential transmembrane transport function of RsAQPs. Tissue- and stage-specific expression patterns of AQP gene analysis based on RNA-seq data revealed that the expression levels of PIPs were generally higher than TIPs, NIPs, and SIPs in radish. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) revealed that seven selected RsPIPs, according to our previous transcriptome data (e.g., RsPIP1-3, 1-6, 2-1, 2-6, 2-10, 2-13, and 2-14), exhibited significant upregulation in roots of salt-tolerant radish genotype. In particular, the transcriptional levels of RsPIP2-6 dramatically increased after 6 h of 150 mM NaCl treatment during the taproot thickening stage. Additionally, overexpression of RsPIP2-6 could enhance salt tolerance by Agrobacterium rhizogenes-mediated transgenic radish hairy roots, which exhibited the mitigatory effects of plant growth reduction, leaf relative water content (RWC) reduction and alleviation of O2- in cells, as shown by nitro blue tetrazolium (NBT) staining, under salt stress. These findings are helpful for deeply dissecting the biological function of RsAQPs on the salt stress response, facilitating practical application and genetic improvement of abiotic stress resistance in radish.
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Affiliation(s)
- Xiaofang Yi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaochuan Sun
- College of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai’an, China
| | - Rong Tian
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kexin Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Meng Ni
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiali Ying
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China), Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Chen DTL, Cheng SW, Chen T, Chang JPC, Hwang BF, Chang HH, Chuang EY, Chen CH, Su KP. Identification of Genetic Variations in the NAD-Related Pathways for Patients with Major Depressive Disorder: A Case-Control Study in Taiwan. J Clin Med 2022; 11:3622. [PMID: 35806906 PMCID: PMC9267440 DOI: 10.3390/jcm11133622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 12/10/2022] Open
Abstract
Background and Objectives: Nicotinamide adenine dinucleotide (NAD) is an important coenzyme in various physiological processes, including sirtuins (SIRTs) and kynurenine pathway (KP). Previous studies have shown that lower NAD levels can be indicative of increased risks of cancer and psychiatric disorders. However, there has been no prior study exploring the link between NAD homeostasis and psychiatric disorders from a genetic perspective. Therefore, we aimed to investigate the association of genetic polymorphism in the pathways of NAD biosynthesis with major depressive disorder (MDD). Methods: A total of 317 patients were included in the case group and were compared with sex-matched control group of 1268 participants (1:4 ratio) from Taiwan Biobank (TWB). All subjects in the control group were over 65 years old, which is well past the average age of onset of MDD. Genomic DNA extracted from patients' blood buffy coat was analyzed using the Affymetrix TWB array. Full-model tests were conducted for the analysis of single nucleotide polymorphism (SNPs) in all candidate genes. We focused on genes within the NAD-related candidate pathways, including 15 in KP, 12 in nicotinate metabolism, 7 in SIRTs, and 19 in aldehyde dehydrogenases (ALDHs). A total of 508 SNPs were analyzed in this study. After significant SNPs were determined, 5000 genome-wide max(T) permutations were performed in Plink. Finally, we built a predictive model with logistic regression and assessed the interactions of SNPs with the haplotype association tests. Results: We found three SNPs that were significantly associated with MDD in our NAD-related candidate pathways, one within the KP (rs12622574 in ACMSD) and two within the nicotinate metabolism (rs28532698 in BST1 and rs3733593 in CD38). The observed association with MDD was significant in the dominant model of inheritance with marital status, education level, and body mass index (BMI) adjusted as covariates. Lastly, in haplotype analysis, the three associated SNPs consisted of one haploblock in ACMSD, four haploblocks in BST1, and two haploblocks in CD38. Conclusions: This study provides the first evidence that genetic variations involved in NAD homeostasis in the KP and nicotinate metabolism may be associated with the occurrence of MDD.
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Affiliation(s)
- Daniel Tzu-Li Chen
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 404, Taiwan;
- Department of Psychiatry and Mind-Body Interface Laboratory (MBI-Lab), China Medical University Hospital, Taichung 404, Taiwan; (S.-W.C.); (T.C.); (J.P.-C.C.)
- Graduate Institute of Biomedicine, College of Medicine, China Medical University, Taichung 404, Taiwan
| | - Szu-Wei Cheng
- Department of Psychiatry and Mind-Body Interface Laboratory (MBI-Lab), China Medical University Hospital, Taichung 404, Taiwan; (S.-W.C.); (T.C.); (J.P.-C.C.)
- School of Medicine, College of Medicine, China Medical University, Taichung 404, Taiwan
| | - Tiffany Chen
- Department of Psychiatry and Mind-Body Interface Laboratory (MBI-Lab), China Medical University Hospital, Taichung 404, Taiwan; (S.-W.C.); (T.C.); (J.P.-C.C.)
- College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Jane Pei-Chen Chang
- Department of Psychiatry and Mind-Body Interface Laboratory (MBI-Lab), China Medical University Hospital, Taichung 404, Taiwan; (S.-W.C.); (T.C.); (J.P.-C.C.)
- School of Medicine, College of Medicine, China Medical University, Taichung 404, Taiwan
| | - Bing-Fang Hwang
- Department of Occupational Safety and Health, College of Public Health, China Medical University, Taichung 404, Taiwan;
| | - Hen-Hong Chang
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, and Chinese Medicine Research Center, China Medical University, Taichung 404, Taiwan; (H.-H.C.); (C.-H.C.)
- Department of Chinese Medicine, China Medical University Hospital, Taichung 404, Taiwan
| | - Eric Y. Chuang
- Master Program for Biomedical Engineering, China Medical University, Taichung 404, Taiwan;
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 100, Taiwan
| | - Che-Hong Chen
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, and Chinese Medicine Research Center, China Medical University, Taichung 404, Taiwan; (H.-H.C.); (C.-H.C.)
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kuan-Pin Su
- Department of Psychiatry and Mind-Body Interface Laboratory (MBI-Lab), China Medical University Hospital, Taichung 404, Taiwan; (S.-W.C.); (T.C.); (J.P.-C.C.)
- Graduate Institute of Biomedicine, College of Medicine, China Medical University, Taichung 404, Taiwan
- An-Nan Hospital, China Medical University, Tainan 709, Taiwan
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Mallick B, Kumari M, Pradhan SK, C P, Acharya GC, Naresh P, Das B, Shashankar P. Genome-wide analysis and characterization of heat shock transcription factors (Hsfs) in common bean (Phaseolus vulgaris L.). Funct Integr Genomics 2022; 22:743-756. [PMID: 35718806 DOI: 10.1007/s10142-022-00875-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Heat shock transcription factors (Hsfs) play an essential role as transcriptional regulatory proteins against heat stress by controlling the expression of heat-responsive genes. Common bean is a highly thermosensitive crop, and, therefore, its genome sequence information is segregated, characterized here in terms of heat shock transcription factors and its evolutionary significance. In this study, a complete comprehensive set of 29 non-redundant full-length Hsf genes were identified and characterized from Phaseolus vulgaris L. (PvHsf) genome sequence. Detailed gene information such as chromosomal localization, domain position, motif organization, and exon-intron identification were analyzed. All the 29 PvHsf genes were mapped on 8 out of 11 chromosomes, indicating the gene duplication occurred in the common bean genome. Motif analysis and exon-intron structure were conserved in each group, which showed that the cytoplasmic proteins highly influence the conserved structure of PvHsfs and heat-induced response. The HSF genes were grouped into three classes, i.e., A to C and 14 groups, based on structural features and phylogenetic relationships. Only one pair of paralog sequences suggests that it may be derived from the duplication event during evolution. A comparative genomics study indicated the influence of whole-genome duplication and purifying selection on the common bean genome during development. In silico expression analysis showed the active role of class A and B family during abiotic stress conditions and higher expression in floral organs. The qRT-PCR analysis revealed PvHSFA8 as the master regulator and PvHSFB1A and PvHSFB2A induction during heat exposure in French beans.
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Affiliation(s)
- B Mallick
- Department of Bioinformatics, Orissa University of Agriculture & Technology, Bhubaneswar, India
| | - M Kumari
- ICAR-Research Complex for Eastern Region, RS, Ranchi, India. .,Central Horticultural Experiment Station (ICAR-IIHR), Bhubaneswar, India.
| | - S K Pradhan
- Department of Bioinformatics, Orissa University of Agriculture & Technology, Bhubaneswar, India
| | - Parmeswaran C
- Division of Biotechnology, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - G C Acharya
- Central Horticultural Experiment Station (ICAR-IIHR), Bhubaneswar, India
| | - P Naresh
- Central Horticultural Experiment Station (ICAR-IIHR), Bhubaneswar, India
| | - Bishnupriya Das
- Central Horticultural Experiment Station (ICAR-IIHR), Bhubaneswar, India
| | - P Shashankar
- Division of Biotechnology, ICAR-National Rice Research Institute, Cuttack, Odisha, India
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Lin Y, Sun H, Shaukat A, Deng T, Abdel-Shafy H, Che Z, Zhou Y, Hu C, Li H, Wu Q, Yang L, Hua G. Novel Insight Into the Role of ACSL1 Gene in Milk Production Traits in Buffalo. Front Genet 2022; 13:896910. [PMID: 35734439 PMCID: PMC9207818 DOI: 10.3389/fgene.2022.896910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic mechanisms underlying milk production traits contribute to improving the production potential of dairy animals. Long-chain acyl-CoA synthetase 1 (ACSL1) plays a key role in fatty acid metabolism and was highly expressed in the lactating mammary gland epithelial cells (MGECs). The objectives of the present study were to detect the polymorphisms within ACSL1 in Mediterranean buffalo, the genetic effects of these mutations on milk production traits, and understand the gene regulatory effects on MGECs. A total of twelve SNPs were identified by sequencing, including nine SNPs in the intronic region and three in the exonic region. Association analysis showed that nine SNPs were associated with one or more traits. Two haplotype blocks were identified, and among these haplotypes, the individuals carrying the H2H2 haplotype in block 1 and H5H1 in block 2 were superior to those of other haplotypes in milk production traits. Immunohistological staining of ACSL1 in buffalo mammary gland tissue indicated its expression and localization in MGECs. Knockdown of ACSL1 inhibited cell growth, diminished MGEC lipid synthesis and triglyceride secretion, and downregulated CCND1, PPARγ, and FABP3 expression. The overexpression of ACSL1 promoted cell growth, enhanced the triglyceride secretion, and upregulated CCND1, PPARγ, SREBP1, and FABP3. ACSL1 was also involved in milk protein regulation as indicated by the decreased or increased β-casein concentration and CSN3 expression in the knockdown or overexpression group, respectively. In summary, our present study depicted that ACSL1 mutations were associated with buffalo milk production performance. This may be related to its positive regulation roles on MGEC growth, milk fat, and milk protein synthesis. The current study showed the potential of the ACSL1 gene as a candidate for milk production traits and provides a new understanding of the physiological mechanisms underlying milk production regulation.
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Affiliation(s)
- Yuxin Lin
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui Sun
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Aftab Shaukat
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tingxian Deng
- Guangxi Key Laboratory of Buffalo Genetice, Breeding and Reproduxtion, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Guangxi, China
| | - Hamdy Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Zhaoxuan Che
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Zhou
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huazhao Li
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qipeng Wu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR); Frontiers Science Center for Animal Breeding and Sustainable Production; Key Laboratory of Smart Farming for Agricultural Animals, Huazhong Agricultural University, Wuhan, China
| | - Guohua Hua
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR); Frontiers Science Center for Animal Breeding and Sustainable Production; Key Laboratory of Smart Farming for Agricultural Animals, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Guohua Hua,
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Schäfer GG, Grebe LJ, Schinkel R, Lieb B. The Evolution of Hemocyanin Genes in Caenogastropoda: Gene Duplications and Intron Accumulation in Highly Diverse Gastropods. J Mol Evol 2021; 89:639-655. [PMID: 34757470 PMCID: PMC8599328 DOI: 10.1007/s00239-021-10036-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022]
Abstract
Hemocyanin is the oxygen transport protein of most molluscs and represents an important physiological factor that has to be well-adapted to their environments because of the strong influences of abiotic factors on its oxygen affinity. Multiple independent gene duplications and intron gains have been reported for hemocyanin genes of Tectipleura (Heterobranchia) and the caenogastropod species Pomacea canaliculata, which contrast with the uniform gene architectures of hemocyanins in Vetigastropoda. The goal of this study was to analyze hemocyanin gene evolution within the diverse group of Caenogastropoda in more detail. Our findings reveal multiple gene duplications and intron gains and imply that these represent general features of Apogastropoda hemocyanins. Whereas hemocyanin exon–intron structures are identical within different Tectipleura lineages, they differ strongly within Caenogastropoda among phylogenetic groups as well as between paralogous hemocyanin genes of the same species. Thus, intron accumulation took place more gradually within Caenogastropoda but finally led to a similar consequence, namely, a multitude of introns. Since both phenomena occurred independently within Heterobranchia and Caenogastropoda, the results support the hypothesis that introns may contribute to adaptive radiation by offering new opportunities for genetic variability (multiple paralogs that may evolve differently) and regulation (multiple introns). Our study indicates that adaptation of hemocyanin genes may be one of several factors that contributed to the evolution of the large diversity of Apogastropoda. While questions remain, this hypothesis is presented as a starting point for the further study of hemocyanin genes and possible correlations between hemocyanin diversity and adaptive radiation.
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Affiliation(s)
- Gabriela Giannina Schäfer
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Lukas Jörg Grebe
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Robin Schinkel
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Bernhard Lieb
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany.
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To JPC, Davis IW, Marengo MS, Shariff A, Baublite C, Decker K, Galvão RM, Gao Z, Haragutchi O, Jung JW, Li H, O'Brien B, Sant A, Elich TD. Expression Elements Derived From Plant Sequences Provide Effective Gene Expression Regulation and New Opportunities for Plant Biotechnology Traits. FRONTIERS IN PLANT SCIENCE 2021; 12:712179. [PMID: 34745155 PMCID: PMC8569612 DOI: 10.3389/fpls.2021.712179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plant biotechnology traits provide a means to increase crop yields, manage weeds and pests, and sustainably contribute to addressing the needs of a growing population. One of the key challenges in developing new traits for plant biotechnology is the availability of expression elements for efficacious and predictable transgene regulation. Recent advances in genomics, transcriptomics, and computational tools have enabled the generation of new expression elements in a variety of model organisms. In this study, new expression element sequences were computationally generated for use in crops, starting from native Arabidopsis and maize sequences. These elements include promoters, 5' untranslated regions (5' UTRs), introns, and 3' UTRs. The expression elements were demonstrated to drive effective transgene expression in stably transformed soybean plants across multiple tissues types and developmental stages. The expressed transcripts were characterized to demonstrate the molecular function of these expression elements. The data show that the promoters precisely initiate transcripts, the introns are effectively spliced, and the 3' UTRs enable predictable processing of transcript 3' ends. Overall, our results indicate that these new expression elements can recapitulate key functional properties of natural sequences and provide opportunities for optimizing the expression of genes in future plant biotechnology traits.
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Affiliation(s)
- Jennifer P. C. To
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Ian W. Davis
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Matthew S. Marengo
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Aabid Shariff
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
- Pairwise Plants, Durham, NC, United States
| | | | - Keith Decker
- Bayer Crop Science, Chesterfield, MO, United States
| | - Rafaelo M. Galvão
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Zhihuan Gao
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Olivia Haragutchi
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Jee W. Jung
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
- Duke University, Office for Translation and Commercialization, Durham, NC, United States
| | - Hong Li
- Bayer Crop Science, Chesterfield, MO, United States
| | - Brent O'Brien
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Anagha Sant
- Bayer Crop Science, Chesterfield, MO, United States
| | - Tedd D. Elich
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
- LifeEDIT Therapeutics, Durham, NC, United States
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Autoimmune Regulator Gene Polymorphisms in Egyptian Systemic Lupus Erythematosus Patients: Preliminary Results. Int J Rheumatol 2021; 2021:5546639. [PMID: 34621318 PMCID: PMC8492237 DOI: 10.1155/2021/5546639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/23/2021] [Accepted: 08/14/2021] [Indexed: 12/01/2022] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a systemic autoimmune disease. The autoimmune regulator (AIRE) is a master regulator of self-tolerance development. AIRE mutations lead to the development of autoimmune polyglandular syndrome type 1 while AIRE polymorphisms have been linked to organ-specific autoimmunity. The study is aimed at addressing the association between AIRE polymorphisms, rs2075876 (G > A) and rs760426 (A > G), and SLE susceptibility and expression in Egyptian patients. Methods Ninety-nine patients were included. One hundred and ten, and 123 control subjects were genotyped for rs2075876 and rs760426, respectively. Lupus severity was assessed using the Lupus Severity of Disease Index and Lupus Severity Index (LSI). Systemic Lupus International Collaborating Clinics (SLICC)/American College of Rheumatology (ACR) damage index was considered. Genotyping was done using StepOne Real-Time PCR. Results. AIRE rs760426 GG was more frequent in the patients under the genotype level (14.1% vs. 4.9%, p = 0.032) and recessive model (14.1% vs. 4.9%, p = 0.017, OR = 3.2 (1.2-8.7)). Musculoskeletal involvement and nephritis were associated with AIRE rs2075876 under the dominant (97.9% vs. 80.8%, p = 0.009, OR = 11 (1.3-89.2)) and recessive models (100% vs. 69.3%, p = 0.032), respectively; and both were linked to AIRE rs2075876 at the allelic level: 98.3% vs. 85%, p = 0.005, OR = 10.1 (1.3-76.6) and 82.8% vs. 68.6, p = 0.041, OR = 2.2 (1-4.7), respectively. Patients with AIRE rs2075876 A alleles had a higher damage index ( 1 ± 1.3 vs. 0.6 ± 1.1, p = 0.045) while the LSI was greater in patients with AIRE rs2075876 (8.5 ± 0.5 vs. 7.8 ± 1.3, p = 0.002) and rs760426 (8.6 ± 11 vs. 7.8 ± 1.2, p = 0.031) under the recessive models. Conclusion. AIRE rs760426 could share in SLE susceptibility while AIRE rs2075876 could influence the disease expression and burden in Egyptian patients.
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García S. A, Casamayor JC. On how to generalize species-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome. BMC Bioinformatics 2021; 22:353. [PMID: 34592923 PMCID: PMC8482561 DOI: 10.1186/s12859-021-04237-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and idiosyncrasy of genomic use cases mean that conceptual modeling techniques are used to generate conceptual schemes that focus on too specific scenarios (i.e., they are species-specific conceptual schemes). Our research group developed two different conceptual schemes. The first one is the Conceptual Schema of the Human Genome, which is intended to improve Precision Medicine and genetic diagnosis. The second one is the Conceptual Schema of the Citrus Genome, which is intended to identify the genetic cause of relevant phenotypes in the agri-food field. METHODS Our two conceptual schemes have been ontologically compared to identify their similarities and differences. Based on this comparison, several changes have been performed in the Conceptual Schema of the Human Genome in order to obtain the first version of a species-independent Conceptual Schema of the Genome. Identifying the different genome information items used in each genomic case study has been essential in achieving our goal. The changes needed to provide an expanded, more generic version of the Conceptual Schema of the Human Genome are analyzed and discussed. RESULTS This work presents a new CS called the Conceptual Schema of the Genome that is ready to be adapted to any specific working genome-based context (i.e., species-independent). CONCLUSION The generated Conceptual Schema of the Genome works as a global, generic element from which conceptual views can be created in order to work with any specific species. This first working version can be used in the human use case, in the citrus use case, and, potentially, in more use cases of other species.
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Affiliation(s)
- Alberto García S.
- PROS Research Center, Universitat Politècnica de València, Camino de Vera, Valencia, Spain
| | - Juan Carlos Casamayor
- PROS Research Center, Universitat Politècnica de València, Camino de Vera, Valencia, Spain
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Dwyer K, Agarwal N, Gega A, Ansari A. Proximity to the Promoter and Terminator Regions Regulates the Transcription Enhancement Potential of an Intron. Front Mol Biosci 2021; 8:712639. [PMID: 34291091 PMCID: PMC8287100 DOI: 10.3389/fmolb.2021.712639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/25/2021] [Indexed: 11/15/2022] Open
Abstract
An evolutionarily conserved feature of introns is their ability to enhance expression of genes that harbor them. Introns have been shown to regulate gene expression at the transcription and post-transcription level. The general perception is that a promoter-proximal intron is most efficient in enhancing gene expression and the effect diminishes with the increase in distance from the promoter. Here we show that the intron regains its positive influence on gene expression when in proximity to the terminator. We inserted ACT1 intron into different positions within IMD4 and INO1 genes. Transcription Run-On (TRO) analysis revealed that the transcription of both IMD4 and INO1 was maximal in constructs with a promoter-proximal intron and decreased with the increase in distance of the intron from the promoter. However, activation was partially restored when the intron was placed close to the terminator. We previously demonstrated that the promoter-proximal intron stimulates transcription by affecting promoter directionality through gene looping-mediated recruitment of termination factors in the vicinity of the promoter region. Here we show that the terminator-proximal intron also enhances promoter directionality and results in compact gene architecture with the promoter and terminator regions in close physical proximity. Furthermore, we show that both the promoter and terminator-proximal introns facilitate assembly or stabilization of the preinitiation complex (PIC) on the promoter. On the basis of these findings, we propose that proximity to both the promoter and the terminator regions affects the transcription regulatory potential of an intron, and the terminator-proximal intron enhances transcription by affecting both the assembly of preinitiation complex and promoter directionality.
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Affiliation(s)
| | | | | | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States
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Liu J, Deng Z, Liang C, Sun H, Li D, Song J, Zhang S, Wang R. Genome-Wide Analysis of RAV Transcription Factors and Functional Characterization of Anthocyanin-Biosynthesis-Related RAV Genes in Pear. Int J Mol Sci 2021; 22:ijms22115567. [PMID: 34070296 PMCID: PMC8197526 DOI: 10.3390/ijms22115567] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 11/28/2022] Open
Abstract
Related to ABSCISIC ACID INSENSITIVE3/VIVIPAROUS1 (ABI3/VP1, RAV), transcription factors (TFs) belonging to the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) TF family play critical roles in plant growth, development, and responses to abiotic and biotic stress. In this study, 11 novel RAV TFs were identified in pear (Pyrus bretschneideri Rehd). A phylogenetic analysis revealed that the TFs clustered into three groups with 10 conserved motifs, some of which were group- or subgroup-specific, implying that they are important for the functions of the RAVs in these clades. RAVs in Pyrus and Malus were closely related, and the former showed a collinear relationship. Analysis of their expression patterns in different tissues and at various growth stages and their responses to abiotic and biotic stress suggested that PbRAV6 and PbRAV7 play important roles in drought stress and salt stress, respectively. We investigated the function of RAVs in pear peel coloration using two red pear varieties with different color patterns and applying data from transcriptome analyses. We found that PbRAV6 participates in the regulation of pericarp color. These findings provide insight into a new TF family in pear and a basis for further studies on the response to drought stress and fruit coloration in this commercially important crop.
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Affiliation(s)
- Jianlong Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (J.L.); (Z.D.); (H.S.); (D.L.); (J.S.)
| | - Zhiwei Deng
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (J.L.); (Z.D.); (H.S.); (D.L.); (J.S.)
| | - Chenglin Liang
- Haidu College, Qingdao Agricultural University, Laiyang 265200, China;
| | - Hongwei Sun
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (J.L.); (Z.D.); (H.S.); (D.L.); (J.S.)
| | - Dingli Li
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (J.L.); (Z.D.); (H.S.); (D.L.); (J.S.)
| | - Jiankun Song
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (J.L.); (Z.D.); (H.S.); (D.L.); (J.S.)
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China;
| | - Ran Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China; (J.L.); (Z.D.); (H.S.); (D.L.); (J.S.)
- Correspondence:
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20
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Wang L, Liu Y, Chai M, Chen H, Aslam M, Niu X, Qin Y, Cai H. Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple ( Ananas comosus). PeerJ 2021; 9:e11329. [PMID: 33987013 PMCID: PMC8086565 DOI: 10.7717/peerj.11329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/31/2021] [Indexed: 11/28/2022] Open
Abstract
Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family.
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Affiliation(s)
- Lulu Wang
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Yanhui Liu
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Mengnan Chai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Huihuang Chen
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Mohammad Aslam
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
| | - Xiaoping Niu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yuan Qin
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Hanyang Cai
- State Key Lab of Ecological Pest Control for Fujian and Taiwan Crops; Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology, College of Life Sciences, Fuji, Fuzhou, Fujian, China
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21
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Gu XX, Tang ZZ, He YL, Zeng ZN, Shi WX, Qiao YC, Wei YS. A Functional Polymorphism in HIF-3α Is Related to an Increased Risk of Ischemic Stroke. J Mol Neurosci 2021; 71:1061-1069. [PMID: 33226577 PMCID: PMC8064973 DOI: 10.1007/s12031-020-01728-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023]
Abstract
Hypoxia-inducible factor-3α (HIF-3α), a member of HIF family, can mediate adaptive responses to low oxygen and ischemia. It is believed that HIF plays crucial roles in stroke-related diseases. However, there are no reports on the association between HIF-3α genetic variants and ischemic stroke (IS) susceptibility. Therefore, we examined the association between HIF-3α gene polymorphisms (rs3826795, rs2235095, and rs3764609) and IS risk. The study population included 302 controls and 310 patients with ischemic stroke. Three polymorphisms in HIF-3α (rs3826795, rs2235095, and rs3764609) were genotyped using SNPscan technique. Our study showed a strong association of rs3826795 in HIF-3α with the risk of IS. The genotype and allele frequencies were shown to differ between the two groups. The rs3826795 in an intron of HIF-3α was related to a prominent increased IS risk (AA vs GG adjusted odd ratio [OR], 2.21; 95% confidence intervals [95% CI], 1.10-4.44; P = 0.03; AA vs AG/GG OR = 1.74, 95% CI, 1.02-2.97, P = 0.04; A vs G OR = 1.48, 95% CI, 1.05-2.07, P = 0.02). Logistic regression analysis suggested that rs3826795 posed a risk factor for IS in addition to common factors. Furthermore, when compared to controls, increased levels of homocysteic acid and level of non-esterified fatty acid were found in the cases (P < 0.01). However, no significant association was found between rs2235095 or rs3264609 and IS risk. These findings indicated that the rs3826795 polymorphism may be a potential target for predicting the risk of IS.
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Affiliation(s)
- Xi-Xi Gu
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi China
| | | | - Yong-Ling He
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi China
| | - Zhi-Neng Zeng
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi China
| | - Wu-Xiang Shi
- Guilin Medical University, Guilin, Guangxi China
| | - Yong-Chao Qiao
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi China
| | - Ye-Sheng Wei
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi China
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Re-evaluation of single nucleotide variants and identification of structural variants in a cohort of 45 sudden unexplained death cases. Int J Legal Med 2021; 135:1341-1349. [PMID: 33895855 PMCID: PMC8205883 DOI: 10.1007/s00414-021-02580-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/16/2021] [Indexed: 12/30/2022]
Abstract
Sudden unexplained death (SUD) takes up a considerable part in overall sudden death cases, especially in adolescents and young adults. During the past decade, many channelopathy- and cardiomyopathy-associated single nucleotide variants (SNVs) have been identified in SUD studies by means of postmortem molecular autopsy, yet the number of cases that remain inconclusive is still high. Recent studies had suggested that structural variants (SVs) might play an important role in SUD, but there is no consensus on the impact of SVs on inherited cardiac diseases. In this study, we searched for potentially pathogenic SVs in 244 genes associated with cardiac diseases. Whole-exome sequencing and appropriate data analysis were performed in 45 SUD cases. Re-analysis of the exome data according to the current ACMG guidelines identified 14 pathogenic or likely pathogenic variants in 10 (22.2%) out of the 45 SUD cases, whereof 2 (4.4%) individuals had variants with likely functional effects in the channelopathy-associated genes SCN5A and TRDN and 1 (2.2%) individual in the cardiomyopathy-associated gene DTNA. In addition, 18 structural variants (SVs) were identified in 15 out of the 45 individuals. Two SVs with likely functional impairment were found in the coding regions of PDSS2 and TRPM4 in 2 SUD cases (4.4%). Both were identified as heterozygous deletions, which were confirmed by multiplex ligation-dependent probe amplification. In conclusion, our findings support that SVs could contribute to the pathology of the sudden death event in some of the cases and therefore should be investigated on a routine basis in suspected SUD cases.
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Dwyer K, Agarwal N, Pile L, Ansari A. Gene Architecture Facilitates Intron-Mediated Enhancement of Transcription. Front Mol Biosci 2021; 8:669004. [PMID: 33968994 PMCID: PMC8097089 DOI: 10.3389/fmolb.2021.669004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/31/2021] [Indexed: 12/28/2022] Open
Abstract
Introns impact several vital aspects of eukaryotic organisms like proteomic plasticity, genomic stability, stress response and gene expression. A role for introns in the regulation of gene expression at the level of transcription has been known for more than thirty years. The molecular basis underlying the phenomenon, however, is still not entirely clear. An important clue came from studies performed in budding yeast that indicate that the presence of an intron within a gene results in formation of a multi-looped gene architecture. When looping is defective, these interactions are abolished, and there is no enhancement of transcription despite normal splicing. In this review, we highlight several potential mechanisms through which looping interactions may enhance transcription. The promoter-5′ splice site interaction can facilitate initiation of transcription, the terminator-3′ splice site interaction can enable efficient termination of transcription, while the promoter-terminator interaction can enhance promoter directionality and expedite reinitiation of transcription. Like yeast, mammalian genes also exhibit an intragenic interaction of the promoter with the gene body, especially exons. Such promoter-exon interactions may be responsible for splicing-dependent transcriptional regulation. Thus, the splicing-facilitated changes in gene architecture may play a critical role in regulation of transcription in yeast as well as in higher eukaryotes.
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Affiliation(s)
- Katherine Dwyer
- Department of Biological Science, Wayne State University, Detroit, MI, United States
| | - Neha Agarwal
- Department of Biological Science, Wayne State University, Detroit, MI, United States
| | - Lori Pile
- Department of Biological Science, Wayne State University, Detroit, MI, United States
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States
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Polymorphisms of the ACSL1 Gene Influence Milk Production Traits and Somatic Cell Score in Chinese Holstein Cows. Animals (Basel) 2020; 10:ani10122282. [PMID: 33287296 PMCID: PMC7761635 DOI: 10.3390/ani10122282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Milk production traits of cows are important economic indicators of the livestock industry. Many dairy farms strive to improve the quality of their milk. Long-chain acyl-CoA synthetase 1 (ACSL1) is a gene related to lipid metabolism. It is widely found in various organisms and can affect fat content and protein content in milk. Single nucleotide polymorphisms (SNP) refers to the polymorphism of DNA sequence caused by a single nucleotide variation at the gene level, which plays a vital function in the genetic study of milk production traits in dairy cows. Our study identified six SNPs of the ACSL1 gene in Chinese Holstein cows, which were related to milk yield, milk fat content, milk protein content and somatic cell score (SCS) to some extent. In summary, the pleiotropic effects of bovine ACSL1 for milk production traits were found in this paper, which will provide a reference for Chinese Holstein cow breeding selection and high economic benefits. Abstract Improving the quality of milk is a challenge for zootechnicians and dairy farms across the globe. Long-chain acyl-CoA synthetase 1 (ACSL1) is a significant member of the long-chain acyl-CoA synthetase gene family. It is widely found in various organisms and influences the lactation performance of cows, including fat percentage, milk protein percentage etc. Our study was aimed to investigate the genetic effects of single nucleotide polymorphisms (SNPs) in ACSL1 on milk production traits. Twenty Chinese Holstein cows were randomly selected to extract DNA from their blood samples for PCR amplification and sequencing to identify SNPs of the bovine ACSL1 gene, and six SNPs (5’UTR-g.20523C>G, g.35446C>T, g.35651G>A, g.35827C>T, g.35941G>A and g.51472C>T) were discovered. Then, Holstein cow genotyping (n = 992) was performed by Sequenom MassARRAY based on former SNP information. Associations between SNPs and milk production traits and somatic cell score (SCS) were analyzed by the least-squares method. The results showed that SNP g.35827C>T was in high linkage disequilibrium with g.35941G>A. Significant associations were found between SNPs and test-day milk yield (TDMY), fat content (FC), protein content (PC) and SCS (p < 0.05). Among these SNPs, SNP 5’UTR-g.20523C>G showed an extremely significant effect on PC and SCS (p < 0.01). The SNP g.35446C>T showed a statistically significant effect on FC, PC, and SCS (p < 0.01), and also TDMY (p < 0.05). The SNP g.35651G>A had a statistically significant effect on PC (p < 0.01). The SNP g.35827C>T showed a highly significant effect on TDMY, FC, and SCS (p < 0.01) and significantly influenced PC (p < 0.05). Lastly, SNP g.51472C>T was significantly associated with TDMY, FC, and SCS (p < 0.05). In summary, the pleiotropic effects of bovine ACSL1 for milk production traits were found in this paper, but further investigation will be required on the intrinsic correlation to provide a theoretical basis for the research on molecular genetics of milk quality traits of Holstein cows.
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Brain-related genes are specifically enriched with long phase 1 introns. PLoS One 2020; 15:e0233978. [PMID: 32470086 PMCID: PMC7259759 DOI: 10.1371/journal.pone.0233978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/16/2020] [Indexed: 11/19/2022] Open
Abstract
Intronic gene regions are mostly considered in the scope of gene expression regulation, such as alternative splicing. However, relations between basic statistical properties of introns are much rarely studied in detail, despite vast available data. Particularly, little is known regarding the relationship between the intron length and the intron phase. Intron phase distribution is significantly different at different intron length thresholds. In this study, we performed GO enrichment analysis of gene sets with a particular intron phase at varying intron length thresholds using a list of 13823 orthologous human-mouse gene pairs. We found a specific group of 153 genes with phase 1 introns longer than 50 kilobases that were specifically expressed in brain, functionally related to synaptic signaling, and strongly associated with schizophrenia and other mental disorders. We propose that the prevalence of long phase 1 introns arises from the presence of the signal peptide sequence and is connected with 1–1 exon shuffling.
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Murata H, Tanaka S, Tsuzuki-Nakao T, Kido T, Kakita-Kobayashi M, Kida N, Hisamatsu Y, Tsubokura H, Hashimoto Y, Kitada M, Okada H. The transcription factor HAND2 up-regulates transcription of the IL15 gene in human endometrial stromal cells. J Biol Chem 2020; 295:9596-9605. [PMID: 32444497 DOI: 10.1074/jbc.ra120.012753] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/18/2020] [Indexed: 12/26/2022] Open
Abstract
Cyclic changes of the human endometrium, such as proliferation, secretion, and decidualization, occur during regular menstrual cycles. Heart- and neural crest derivatives-expressed transcript 2 (HAND2) is a key transcription factor in progestin-induced decidualization of human endometrial stromal cells (ESCs). It has been suggested that HAND2 regulates interleukin 15 (IL15), a key immune factor required for the activation and survival of uterine natural killer (uNK) cells. Activated uNK cells can promote spiral artery remodeling and secrete cytokines to induce immunotolerance. To date, no studies have evaluated the transcription factors that regulate IL15 expression in human ESCs. In the present study, we examined whether HAND2 controls IL15 transcriptional regulation in human ESCs. Quantitative RT-PCR and histological analyses revealed that HAND2 and IL15 levels increase considerably in the secretory phase of human endometrium tissues. Results from ChIP-quantitative PCR suggested that HAND2 binds to a putative HAND2 motif, which we identified in the upstream region of the human IL15 gene through in silico analysis. Using a luciferase reporter assay, we found that the upstream region of the human IL15 gene up-regulates reporter gene activities in response to estradiol and a progestin representative (medroxyprogesterone) in ESCs. The upstream region of the human IL15 gene also exhibited increasing responsiveness to transfection with a HAND2 expression vector. Of note, deletion and substitution variants of the putative HAND2 motif in the upstream region of IL15 did not respond to HAND2 transfection. These findings confirm that HAND2 directly up-regulates human IL15 transcription in ESCs.
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Affiliation(s)
- Hiromi Murata
- Department of Obstetrics and Gynecology, Kansai Medical University, Osaka, Japan
| | - Susumu Tanaka
- Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Tomoko Tsuzuki-Nakao
- Department of Obstetrics and Gynecology, Kansai Medical University, Osaka, Japan
| | - Takeharu Kido
- Department of Obstetrics and Gynecology, Kansai Medical University, Osaka, Japan
| | | | - Naoko Kida
- Department of Obstetrics and Gynecology, Kansai Medical University, Osaka, Japan
| | - Yoji Hisamatsu
- Department of Obstetrics and Gynecology, Kansai Medical University, Osaka, Japan
| | - Hiroaki Tsubokura
- Department of Obstetrics and Gynecology, Kansai Medical University, Osaka, Japan
| | - Yoshiko Hashimoto
- Department of Obstetrics and Gynecology, Kansai Medical University, Osaka, Japan
| | - Masaaki Kitada
- Department of Anatomy, Kansai Medical University, Osaka, Japan
| | - Hidetaka Okada
- Department of Obstetrics and Gynecology, Kansai Medical University, Osaka, Japan
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Tai A, Zhu M, Qilimuge H, Rong H, He X, Bai M, Jin T. Genetic polymorphisms of IL1RN were associated with lumbar disk herniation risk in a Chinese Han population. Mol Genet Genomic Med 2020; 8:e1247. [PMID: 32319224 PMCID: PMC7284030 DOI: 10.1002/mgg3.1247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/07/2020] [Accepted: 02/24/2020] [Indexed: 01/27/2023] Open
Abstract
Background Interleukin (IL)‐1 is a cytokine superfamily, which involved in the inflammatory process and immune response in human body. IL‐1 receptor antagonist (IL1RN) has been found to be associated with risk of lumbar disk herniation (LDH) in Finland samples. However, to date, there was no investigation focus on the polymorphisms of IL1RN in Chinese Han LDH patient. Materials and Methods We conducted a case–control study based on 498 LDH patients and 463 controls. Five single‐nucleotide polymorphisms (SNPs) in IL1RN were genotyped. Results As a result, we found that the AG and GG genotypes of rs3181052 were associated with decreased risk LDH under the dominant model (OR = 0.74, 95%CI: 0.57–0.96, p = .025). In the stratification analysis, the frequency of the “A” allele of rs17042888 was significantly lower in elder LDH cases than in controls (OR = 0.723, 95%CI: 0.544–0.961, p = .025). In addition, the AG and AA genotypes of rs17042888 were associated with decreased risk of LDH in elder group under the dominant model (OR = 0.69, 95%CI: 0.49–0.98, p = .038). The GG genotype of rs315919 was identified have correlation with decreased risk of LDH in elder group under the recessive model (OR = 0.60, 95%CI: 0.37–0.97, p = .034). Conclusions Our data showed that IL1RN may be a susceptibility gene for risk of LDH in Chinese Han population.
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Affiliation(s)
- Ariga Tai
- Department of rehabilitation medicine, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Ming Zhu
- College of Mongolian medicine, Inner Mongolia Medical University, Hohhot, China
| | - Han Qilimuge
- College of Mongolian medicine, Inner Mongolia Medical University, Hohhot, China
| | - Hao Rong
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China.,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China.,Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Xue He
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China.,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China.,Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Mei Bai
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China.,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China.,Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Tianbo Jin
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China.,Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, China.,Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, China
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Sharma H, Bhandawat A, Rahim MS, Kumar P, Choudhoury MP, Roy J. Novel intron length polymorphic (ILP) markers from starch biosynthesis genes reveal genetic relationships in Indian wheat varieties and related species. Mol Biol Rep 2020; 47:3485-3500. [PMID: 32281056 DOI: 10.1007/s11033-020-05434-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/03/2020] [Indexed: 11/28/2022]
Abstract
Introns experience lesser selection pressure, thus are liable for higher polymorphism. Intron Length Polymorphic (ILP) markers designed from exon-flanking introns exploits this polymorphic potential and have been proved to be a robust co-dominant marker in eukaryotes. Wheat is among the most consumed cereal crop by majority of the word population. It is a rich source of calories in the form of stored starch. In the current study, starch biosynthesis genes were mined for development of ILP markers and their subsequent utilization for genetic characterization of popular Indian wheat varieties and transferability to wild relatives. Sixty-one markers generated 122 alleles and showed 77-88.5% transferability (mean PIC: 0.36) to the related species. A subset of markers showed clear genetic distinctions (Avg. genetic dissimilarity = 0.42) among Indian wheat varieties, signifying the importance of novel ILPs. 'Kenphad25' showed maximum genetic dissimilarity with 'K 8962' (0.82), while maximum genetic similarity was observed between 'Safed Lerma' and 'RAJ 4037' (0.1). This is the first report of ILP markers in wheat and will be a useful genomic resource for future germplasm conservation and molecular breeding studies.
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Affiliation(s)
- Himanshu Sharma
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Abhishek Bhandawat
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Mohammed Saba Rahim
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Pankaj Kumar
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Mohini Pal Choudhoury
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Joy Roy
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, India.
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Ye J, Yang X, Hu G, Liu Q, Li W, Zhang L, Song X. Genome-Wide Investigation of Heat Shock Transcription Factor Family in Wheat ( Triticum aestivum L.) and Possible Roles in Anther Development. Int J Mol Sci 2020; 21:E608. [PMID: 31963482 PMCID: PMC7013567 DOI: 10.3390/ijms21020608] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 01/19/2023] Open
Abstract
Heat shock transcription factors (HSFs) play crucial roles in resisting heat stress and regulating plant development. Recently, HSFs have been shown to play roles in anther development. Thus, investigating the HSF family members and identifying their protective roles in anthers are essential for the further development of male sterile wheat breeding. In the present study, 61 wheat HSF genes (TaHsfs) were identified in the whole wheat genome and they are unequally distributed on 21 chromosomes. According to gene structure and phylogenetic analyses, the 61 TaHsfs were classified into three categories and 12 subclasses. Genome-wide duplication was identified as the main source of the expansion of the wheat HSF gene family based on 14 pairs of homeologous triplets, whereas only a very small number of TaHsfs were derived by segmental duplication and tandem duplication. Heat shock protein 90 (HSP90), HSP70, and another class of chaperone protein called htpG were identified as proteins that interact with wheat HSFs. RNA-seq analysis indicated that TaHsfs have obvious period- and tissue-specific expression patterns, and the TaHsfs in classes A and B respond to heat shock, whereas the C class TaHsfs are involved in drought regulation. qRT-PCR identified three TaHsfA2bs with differential expression in sterile and fertile anthers, and they may be candidate genes involved in anther development. This comprehensive analysis provides novel insights into TaHsfs, and it will be useful for understanding the mechanism of plant fertility conversion.
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Affiliation(s)
| | | | | | | | | | | | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China; (J.Y.); (X.Y.); (G.H.); (Q.L.); (W.L.); (L.Z.)
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30
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Wang PH, Kumar S, Zeng J, McEwan R, Wright TR, Gupta M. Transcription Terminator-Mediated Enhancement in Transgene Expression in Maize: Preponderance of the AUGAAU Motif Overlapping With Poly(A) Signals. FRONTIERS IN PLANT SCIENCE 2020; 11:570778. [PMID: 33178242 PMCID: PMC7591816 DOI: 10.3389/fpls.2020.570778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/11/2020] [Indexed: 05/08/2023]
Abstract
The selection of transcription terminators (TTs) for pairing with high expressing constitutive promoters in chimeric constructs is crucial to deliver optimal transgene expression in plants. In this study, the use of the native combinations of four polyubiquitin gene promoters and corresponding TTs resulted in up to >3-fold increase in transgene expression in maize. Of the eight polyubiquitin promoter and TT regulatory elements utilized, seven were novel and identified from the polyubiquitin genes of Brachypodium distachyon, Setaria italica, and Zea mays. Furthermore, gene expression driven by the Cassava mosaic virus promoter was studied by pairing the promoter with distinct TTs derived from the high expressing genes of Arabidopsis. Of the three TTs studied, the polyubiquitin10 gene TT produced the highest transgene expression in maize. Polyadenylation patterns and mRNA abundance from eight distinct TTs were analyzed using 3'-RACE and next-generation sequencing. The results exhibited one to three unique polyadenylation sites in the TTs. The poly(A) site patterns for the StPinII TT were consistent when the same TT was deployed in chimeric constructs irrespective of the reporter gene and promoter used. Distal to the poly(A) sites, putative polyadenylation signals were identified in the near-upstream regions of the TTs based on previously reported mutagenesis and bioinformatics studies in rice and Arabidopsis. The putative polyadenylation signals were 9 to 11 nucleotides in length. Six of the eight TTs contained the putative polyadenylation signals that were overlaps of either canonical AAUAAA or AAUAAA-like polyadenylation signals and AUGAAU, a top-ranking-hexamer of rice and Arabidopsis gene near-upstream regions. Three of the polyubiquitin gene TTs contained the identical 9-nucleotide overlap, AUGAAUAAG, underscoring the functional significance of such overlaps in mRNA 3' end processing. In addition to identifying new combinations of regulatory elements for high constitutive trait gene expression in maize, this study demonstrated the importance of TTs for optimizing gene expression in plants. Learning from this study could be applied to other dicotyledonous and monocotyledonous plant species for transgene expression. Research on TTs is not limited to transgene expression but could be extended to the introduction of appropriate mutations into TTs via genome editing, paving the way for expression modulation of endogenous genes.
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Affiliation(s)
- Po-Hao Wang
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
| | - Sandeep Kumar
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
- *Correspondence: Sandeep Kumar,
| | - Jia Zeng
- Data Science & Informatics, Corteva Agriscience, Indianapolis, IN, United States
| | - Robert McEwan
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
| | - Terry R. Wright
- Trait Discovery, Corteva Agriscience, Indianapolis, IN, United States
| | - Manju Gupta
- Trait Product Development, Dow Agrosciences, Indianapolis, IN, United States
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Shi H, Yang M, Mo C, Xie W, Liu C, Wu B, Ma X. Complete chloroplast genomes of two Siraitia Merrill species: Comparative analysis, positive selection and novel molecular marker development. PLoS One 2019; 14:e0226865. [PMID: 31860647 PMCID: PMC6924677 DOI: 10.1371/journal.pone.0226865] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/05/2019] [Indexed: 11/18/2022] Open
Abstract
Siraitia grosvenorii fruit, known as Luo-Han-Guo, has been used as a traditional Chinese medicine for many years, and mogrosides are its primary active ingredients. Unfortunately, Siraitia siamensis, its wild relative, might be misused due to its indistinguishable appearance, not only threatening the reliability of the medication but also partly exacerbating wild resource scarcity. Therefore, high-resolution genetic markers must be developed to discriminate between these species. Here, the complete chloroplast genomes of S. grosvenorii and S. siamensis were assembled and analyzed for the first time; they were 158,757 and 159,190 bp in length, respectively, and possessed conserved quadripartite circular structures. Both contained 134 annotated genes, including 8 rRNA, 37 tRNA and 89 protein-coding genes. Twenty divergences (Pi > 0.03) were found in the intergenic regions. Nine protein-coding genes, accD, atpA, atpE, atpF, clpP, ndhF, psbH, rbcL, and rpoC2, underwent selection within Cucurbitaceae. Phylogenetic relationship analysis indicated that these two species originated from the same ancestor. Finally, four pairs of molecular markers were developed to distinguish the two species. The results of this study will be beneficial for taxonomic research, identification and conservation of Siraitia Merrill wild resources in the future.
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Affiliation(s)
- Hongwu Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Changming Mo
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, China
| | | | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail: (BW); (XM)
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- * E-mail: (BW); (XM)
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32
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Good News for Nuclear Transgene Expression in Chlamydomonas. Cells 2019; 8:cells8121534. [PMID: 31795196 PMCID: PMC6952782 DOI: 10.3390/cells8121534] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
Chlamydomonas reinhardtii is a well-established model system for basic research questions ranging from photosynthesis and organelle biogenesis, to the biology of cilia and basal bodies, to channelrhodopsins and photoreceptors. More recently, Chlamydomonas has also been recognized as a suitable host for the production of high-value chemicals and high-value recombinant proteins. However, basic and applied research have suffered from the inefficient expression of nuclear transgenes. The combined efforts of the Chlamydomonas community over the past decades have provided insights into the mechanisms underlying this phenomenon and have resulted in mutant strains defective in some silencing mechanisms. Moreover, many insights have been gained into the parameters that affect nuclear transgene expression, like promoters, introns, codon usage, or terminators. Here I critically review these insights and try to integrate them into design suggestions for the construction of nuclear transgenes that are to be expressed at high levels.
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Li W, Wan XL, Yu JY, Wang KL, Zhang J. Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation ( Dianthus caryophyllus). Int J Mol Sci 2019; 20:ijms20205233. [PMID: 31652538 PMCID: PMC6829504 DOI: 10.3390/ijms20205233] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 01/26/2023] Open
Abstract
Heat shock transcription factors (Hsfs) are a class of important transcription factors (TFs) which play crucial roles in the protection of plants from damages caused by various abiotic stresses. The present study aimed to characterize the Hsf genes in carnation (Dianthus caryophyllus), which is one of the four largest cut flowers worldwide. In this study, a total of 17 non-redundant Hsf genes were identified from the D. caryophyllus genome. Specifically, the gene structure and motifs of each DcaHsf were comprehensively analyzed. Phylogenetic analysis of the DcaHsf family distinctly separated nine class A, seven class B, and one class C Hsf genes. Additionally, promoter analysis indicated that the DcaHsf promoters included various cis-acting elements that were related to stress, hormones, as well as development processes. In addition, cis-elements, such as STRE, MYB, and ABRE binding sites, were identified in the promoters of most DcaHsf genes. According to qRT-PCR data, the expression of DcaHsfs varied in eight tissues and six flowering stages and among different DcaHsfs, even in the same class. Moreover, DcaHsf-A1, A2a, A9a, B2a, B3a revealed their putative involvement in the early flowering stages. The time-course expression profile of DcaHsf during stress responses illustrated that all the DcaHsfs were heat- and drought-responsive, and almost all DcaHsfs were down-regulated by cold, salt, and abscisic acid (ABA) stress. Meanwhile, DcaHsf-A3, A7, A9a, A9b, B3a were primarily up-regulated at an early stage in response to salicylic acid (SA). This study provides an overview of the Hsf gene family in D. caryophyllus and a basis for the breeding of stress-resistant carnation.
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Affiliation(s)
- Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Xue-Li Wan
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Jia-Yu Yu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Kui-Ling Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266000, China.
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Sá JM, Kaslow SR, Moraes Barros RR, Brazeau NF, Parobek CM, Tao D, Salzman RE, Gibson TJ, Velmurugan S, Krause MA, Melendez-Muniz V, Kite WA, Han PK, Eastman RT, Kim A, Kessler EG, Abebe Y, James ER, Chakravarty S, Orr-Gonzalez S, Lambert LE, Engels T, Thomas ML, Fasinu PS, Serre D, Gwadz RW, Walker L, DeConti DK, Mu J, Bailey JA, Sim BKL, Hoffman SL, Fay MP, Dinglasan RR, Juliano JJ, Wellems TE. Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross. Nat Commun 2019; 10:4300. [PMID: 31541097 PMCID: PMC6754410 DOI: 10.1038/s41467-019-12256-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 08/26/2019] [Indexed: 12/30/2022] Open
Abstract
Mainstay treatment for Plasmodium vivax malaria has long relied on chloroquine (CQ) against blood-stage parasites plus primaquine against dormant liver-stage forms (hypnozoites), however drug resistance confronts this regimen and threatens malaria control programs. Understanding the basis of P. vivax chloroquine resistance (CQR) will inform drug discovery and malaria control. Here we investigate the genetics of P. vivax CQR by a cross of parasites differing in drug response. Gametocytogenesis, mosquito infection, and progeny production are performed with mixed parasite populations in nonhuman primates, as methods for P. vivax cloning and in vitro cultivation remain unavailable. Linkage mapping of progeny surviving >15 mg/kg CQ identifies a 76 kb region in chromosome 1 including pvcrt, an ortholog of the Plasmodium falciparum CQR transporter gene. Transcriptional analysis supports upregulated pvcrt expression as a mechanism of CQR.
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Affiliation(s)
- Juliana M Sá
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sarah R Kaslow
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Roberto R Moraes Barros
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nicholas F Brazeau
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian M Parobek
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dingyin Tao
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Rebecca E Salzman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tyler J Gibson
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Michael A Krause
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Viviana Melendez-Muniz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Whitney A Kite
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul K Han
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Richard T Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Adam Kim
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Evan G Kessler
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | | | | | - Sachy Orr-Gonzalez
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lynn E Lambert
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Theresa Engels
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marvin L Thomas
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pius S Fasinu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Robert W Gwadz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Larry Walker
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
| | - Derrick K DeConti
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jeffrey A Bailey
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Campbell University, Buies Creek, NC, 27506, USA
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | | | | | - Michael P Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Rhoel R Dinglasan
- W Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Emerging Pathogens Institute, Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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35
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Han L, Husaiyin S, Ma C, Niyazi M. Association study between the polymorphisms of angiogenesis-related genes and cervical cancer susceptibility in Chinese Uygur population. Mol Genet Genomic Med 2019; 7:e00899. [PMID: 31478352 PMCID: PMC6785432 DOI: 10.1002/mgg3.899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Cervical cancer is the second most common malignant tumor in women, and its invasion and metastasis are regulated by tumor angiogenic growth factors and their cognate receptors. In this study, we explored the relationship between genetic polymorphisms of angiogenesis-related genes (VEGF-C, VEGFR-2, and VEGFR-3) and the risk of cervical cancer in Chinese Uygur population. METHODS We investigated four single-nucleotide polymorphisms (SNPs) in 342 cervical cancer cases and 498 controls to evaluate their association with the risk of cervical cancer. Their correlations were evaluated by chi-squared test, Fisher's exact test, t test, and genetic model analyses. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated using unconditional logistic regression. RESULTS We observed that rs12646659 in VEGF-C was associated with a lower cervical cancer risk in allele, dominant, and log-additive models (allele: p = .017; dominant: p = .018; log-additive: p = .018). For the individuals older than 43, rs4604006 (VEGF-C) was related to an increased cervical cancer risk under codominant model (p = .035), and rs12646659 was significantly associated with a reduced cervical cancer risk in allele, dominant, log-additive models (allele: p = .028; codominant: p = .037; log-additive: p = .037) However, there were no significant correlation of rs1000611 (VEGFR-2) and rs1195571 (VEGFR-3) with cervical cancer risk in Chinese Uygur population. CONCLUSION Our study firstly provided evidence that rs4604006 and rs12646659 of VEGF-C gene were related to the susceptibility of cervical cancer in Chinese Uygur population.
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Affiliation(s)
- Lili Han
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Sulaiya Husaiyin
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Chunhua Ma
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Mayinuer Niyazi
- Department of Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
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36
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Gao Y, Ma J, Zheng JC, Chen J, Chen M, Zhou YB, Fu JD, Xu ZS, Ma YZ. The Elongation Factor GmEF4 Is Involved in the Response to Drought and Salt Tolerance in Soybean. Int J Mol Sci 2019; 20:E3001. [PMID: 31248195 PMCID: PMC6627591 DOI: 10.3390/ijms20123001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 06/11/2019] [Accepted: 06/17/2019] [Indexed: 11/23/2022] Open
Abstract
Growing evidence indicates that elongation factor 1α (EF1α) is involved in responses to various abiotic stresses in several plant species. Soybean EF1α proteins include three structural domains: one GTP-binding domain and two oligonucleotide binding domains that are also called as domain 2 and domain 3. In this study, 10 EF1α genes were identified in the soybean genome. We predicted structures of different domains and analyzed gene locations, gene structures, phylogenetic relationships, various cis-elements, and conserved domains of soybean EF1αs. The expression patterns of 10 EF1α genes were analyzed by quantitative real-time PCR (qRT-PCR). Under drought stress, soybean EF1α genes were upregulated in varying degrees. In particular, GmEF4 was upregulated under drought and salt treatments. Compared to the drought- and salt-treated empty vector (EV)-control plants, drought- and salt-treated GmEF4-overexpressing (OE) plants had significantly delayed leaf wilting, longer root, higher biomass, higher proline (Pro) content, and lower H2O2, O2-, and malondialdehyde (MDA) contents. Thus, this study provides a foundation for further functional genomics research about this important family under abiotic stress.
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Affiliation(s)
- Yuan Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China.
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China.
| | - Jia-Cheng Zheng
- Anhui Science and Technology University, Fengyang 233100, Anhui, China.
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China.
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China.
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China.
| | - Jin-Dong Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China.
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China.
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China.
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Intron-mediated regulation of β-tubulin genes expression affects the sensitivity to carbendazim in Fusarium graminearum. Curr Genet 2019; 65:1057-1069. [DOI: 10.1007/s00294-019-00960-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/13/2019] [Accepted: 03/26/2019] [Indexed: 12/20/2022]
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Zhang XZ, Zheng WJ, Cao XY, Cui XY, Zhao SP, Yu TF, Chen J, Zhou YB, Chen M, Chai SC, Xu ZS, Ma YZ. Genomic Analysis of Stress Associated Proteins in Soybean and the Role of GmSAP16 in Abiotic Stress Responses in Arabidopsis and Soybean. FRONTIERS IN PLANT SCIENCE 2019; 10:1453. [PMID: 31803204 PMCID: PMC6876671 DOI: 10.3389/fpls.2019.01453] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/18/2019] [Indexed: 05/22/2023]
Abstract
Stress associated proteins (SAPs) containing A20/AN1 zinc finger domains have emerged as novel regulators of stress responses. In this study, 27 SAP genes were identified in soybean. The phylogenetic relationships, exon-intron structure, domain structure, chromosomal localization, putative cis-acting elements, and expression patterns of SAPs in various tissues under abiotic stresses were analyzed. Among the soybean SAP genes, GmSAP16 was significantly induced by water deficit stress, salt, and abscisic acid (ABA) and selected for further analysis. GmSAP16 was located in the nucleus and cytoplasm. The overexpression of GmSAP16 in Arabidopsis improved drought and salt tolerance at different developmental stages and increased ABA sensitivity, as indicated by delayed seed germination and stomatal closure. The GmSAP16 transgenic Arabidopsis plants had a higher proline content and a lower water loss rate and malondialdehyde (MDA) content than wild type (WT) plants in response to stresses. The overexpression of GmSAP16 in soybean hairy roots enhanced drought and salt tolerance of soybean seedlings, with higher proline and chlorophyll contents and a lower MDA content than WT. RNA inference (RNAi) of GmSAP16 increased stress sensitivity. Stress-related genes, including GmDREB1B;1, GmNCED3, GmRD22, GmDREB2, GmNHX1, and GmSOS1, showed significant expression alterations in GmSAP16-overexpressing and RNAi plants under stress treatments. These results indicate that soybean SAP genes play important roles in abiotic stress responses.
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Affiliation(s)
- Xiang-Zhan Zhang
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Wei-Jun Zheng
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Xin-You Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement, Jinan, China
| | - Xi-Yan Cui
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Shu-Ping Zhao
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Tai-Fei Yu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Shou-Cheng Chai
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China
- *Correspondence: Shou-Cheng Chai ; Zhao-Shi Xu,
| | - Zhao-Shi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
- *Correspondence: Shou-Cheng Chai ; Zhao-Shi Xu,
| | - You-Zhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
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Xiong W, Wu Z, Liu Y, Li Y, Su K, Bai Z, Guo S, Hu Z, Zhang Z, Bao Y, Sun J, Yang G, Fu C. Mutation of 4-coumarate: coenzyme A ligase 1 gene affects lignin biosynthesis and increases the cell wall digestibility in maize brown midrib5 mutants. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:82. [PMID: 31007716 PMCID: PMC6456989 DOI: 10.1186/s13068-019-1421-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/29/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Maize brown midrib (bm) mutants associated with impaired lignin biosynthesis are a potential source for the breed of novel germplasms with improved cell wall digestibility. The spontaneous bm5 mutants had been identified since 2008. However, the gene responsible for the bm5 locus, and the comprehensive effects of bm5 mutation on lignin biosynthesis, soluble phenolics accumulation, and cell wall degradation have yet to be elucidated. RESULTS The bm5 locus was identified to encode a major 4-coumarate: coenzyme A ligase (Zm4CL1) through analyzing MutMap-assisted gene mapping data. Two alleles of Zm4CL1 isolated from bm5 mutants contained two transposons inserted in the first exon and the second intron, respectively, and consequently, the activities of 4CLs in the crude enzyme extracts from bm5 midribs were reduced by 51-62% compared with the wild type. Furthermore, five 4CLs were retrieved from maize genome, and Zm4CL1 was the most highly expressed one in the lignified tissues. Mutation of Zm4CL1 mainly impeded the biosynthesis of guaiacyl (G) lignins and increased the level of soluble feruloyl derivatives without impacting maize growth and development. Moreover, both neutral detergent fiber digestibility and saccharification efficiency of cell walls were significantly elevated in the bm5 mutant. CONCLUSIONS Zm4CL1 was identified as the Bm5 gene, since two independent alleles of Zm4CL1 were associated with the same mutant phenotype. Mutation of Zm4CL1 mainly affected G lignin biosynthesis and soluble feruloyl derivatives accumulation in maize lignified tissues. The reduced recalcitrance of the bm5 mutant suggests that Zm4CL1 is an elite target for cell wall engineering, and genetic manipulation of this gene will facilitate the utilization of crop straw and stover that have to be dealt with for environmental protection.
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Affiliation(s)
- Wangdan Xiong
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Zhenying Wu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Yuchen Liu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Yu Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Kunlong Su
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Zetao Bai
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Siyi Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, 475001 China
| | - Zhubing Hu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng, 475001 China
| | - Zhiming Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
| | - Yan Bao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Juan Sun
- School of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- School of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
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Rigau M, Juan D, Valencia A, Rico D. Intronic CNVs and gene expression variation in human populations. PLoS Genet 2019; 15:e1007902. [PMID: 30677042 PMCID: PMC6345438 DOI: 10.1371/journal.pgen.1007902] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022] Open
Abstract
Introns can be extraordinarily large and they account for the majority of the DNA sequence in human genes. However, little is known about their population patterns of structural variation and their functional implication. By combining the most extensive maps of CNVs in human populations, we have found that intronic losses are the most frequent copy number variants (CNVs) in protein-coding genes in human, with 12,986 intronic deletions, affecting 4,147 genes (including 1,154 essential genes and 1,638 disease-related genes). This intronic length variation results in dozens of genes showing extreme population variability in size, with 40 genes with 10 or more different sizes and up to 150 allelic sizes. Intronic losses are frequent in evolutionarily ancient genes that are highly conserved at the protein sequence level. This result contrasts with losses overlapping exons, which are observed less often than expected by chance and almost exclusively affect primate-specific genes. An integrated analysis of CNVs and RNA-seq data showed that intronic loss can be associated with significant differences in gene expression levels in the population (CNV-eQTLs). These intronic CNV-eQTLs regions are enriched for intronic enhancers and can be associated with expression differences of other genes showing long distance intron-promoter 3D interactions. Our data suggests that intronic structural variation of protein-coding genes makes an important contribution to the variability of gene expression and splicing in human populations.
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Affiliation(s)
- Maria Rigau
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - David Juan
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Daniel Rico
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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J J, Vanisree AJ, Ravisankar S, K R. Site specific hypermethylation of CpGs in Connexin genes 30, 26 and 43 in different grades of glioma and attenuated levels of their mRNAs. Int J Neurosci 2018; 129:273-282. [PMID: 30280947 DOI: 10.1080/00207454.2018.1526802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
AIM Gliomas, the intracranial tumours are considered the deadliest malignancies. The gap junctional Connexins (Cxs) that maintain cellular homeostasis perform a unique function in glial tumour suppression. However, the differential methylation patterns of Cxs were not revealed in glioma so far. The current study attempts to categorise promoter methylation of Cx30 and Cx26 and intron methylation of Cx43 in different grades of human glioma. MATERIALS AND METHODS About 85 glioma patients with pathologically confirmed grades and 15 control brain tissues were recruited in the study. Bisulphite-PCR-Single Stranded Conformation analysis(SSCA), Bisulphite sequencing and MeDIP-qPCR were carried out to assess methylation status and Cx mRNA levels were also analysed to evaluate the effect of methylation. RESULTS We found that promoter CpG islands(CpGs) reside in Sp1 and Ap2 sites of Cx30 and 26 were hypermethylated in high grades (HG) of glioma rather than low grades. The input % of both was significantly increased (p < 0.03) in progressive grades. Interestingly, Cx43 could exhibit a significant increase (p < 0.05) in input % only in grade IV. While, Cx30 and 26 mRNAs were downregulated according to their methylation status in progressive fashion with grades, Cx43 was downregulated irrespective of intron methylation. CONCLUSION Thus, we suggest that the sites and extent of methylation of Cxs (30 and 26 but not in 43) are found to be altered. In different grades of glioma can provide better appreciation of the grade of the patient and might help in strategies based on epigenetic approaches.
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Affiliation(s)
- Jayalakshmi J
- a Department of Biochemistry , University of Madras , Chennai , Tamilnadu , India
| | | | - Shantha Ravisankar
- b Department of Neuropathology , Tamilnadu Multispeciality Hospital , Chennai , Tamilnadu , India
| | - Rama K
- c Department of Neuropathology , Madras Medical College and Government General hospital , Chennai , Tamilnadu , India
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Yu TF, Zhao WY, Fu JD, Liu YW, Chen M, Zhou YB, Ma YZ, Xu ZS, Xi YJ. Genome-Wide Analysis of CDPK Family in Foxtail Millet and Determination of SiCDPK24 Functions in Drought Stress. FRONTIERS IN PLANT SCIENCE 2018; 9:651. [PMID: 30093908 PMCID: PMC6071576 DOI: 10.3389/fpls.2018.00651] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/27/2018] [Indexed: 05/22/2023]
Abstract
Plant calcium-dependent protein kinases (CDPKs) were reported to play important roles in plant resistance to abiotic stress. Foxtail millet cultivation "H138" was used for RNA-seq analysis. The data from drought-induced de novo transcriptomic sequences of foxtail millet showed that CDPKs were up- or down-regulated by drought to different degrees. In this study, 29 foxtail millet CDPKs were classified into four subgroups. These genes were unevenly distributed on nine foxtail millet chromosomes, and chromosomes 2, 3, and 9 contained the most SiCDPK members. Analysis of putative cis-acting elements showed that most foxtail millet CDPK genes contained the ABRE, LTR, HSE, MYB, MYC, DRE, CGTCA-motif, and TGACG-motif cis-acting elements, which could be activated by abiotic stresses. Real-time PCR analysis indicated that 29 SiCDPK genes experienced different degrees of induction under drought and ABA stresses. SiCDPK24 had the highest expression levels at 6 and 12 h of drought treatment and was chosen for further analysis. SiCDPK24 localized to the cell membrane and the nucleus of Arabidopsis mesophyll protoplasts. Western blot analysis showed that SiCDPK24 protein had autophosphorylation activity. Overexpression of SiCDPK24 in Arabidopsis enhanced drought resistance and improved the survival rate under drought stress. It also activated the expressions of nine stress-related genes, namely RD29A, RD29B, RD22, KIN1, COR15, COR47, LEA14, CBF3/DREB1A, and DREB2A. These genes are involved in resistance to abiotic stresses in Arabidopsis. These results indicate that foxtail millet CDPK genes play important roles in resisting drought stress.
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Affiliation(s)
- Tai-Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest Agricultural and Forestry University, Yangling, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Wan-Ying Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest Agricultural and Forestry University, Yangling, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Jin-Dong Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Wei Liu
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ya-Jun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest Agricultural and Forestry University, Yangling, China
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Pydiura N, Pirko Y, Galinousky D, Postovoitova A, Yemets A, Kilchevsky A, Blume Y. Genome‐wide identification, phylogenetic classification, and exon–intron structure characterization of the tubulin and actin genes in flax (Linum usitatissimum). Cell Biol Int 2018; 43:1010-1019. [DOI: 10.1002/cbin.11001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 05/31/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Nikolay Pydiura
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Dmitry Galinousky
- Institute of Genetics and CytologyNational Academy of Sciences of BelarusMinsk Akademicheskaya st., 27220072 Belarus
| | - Anastasiia Postovoitova
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Aleksandr Kilchevsky
- Institute of Genetics and CytologyNational Academy of Sciences of BelarusMinsk Akademicheskaya st., 27220072 Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
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Anastasiadi D, Esteve-Codina A, Piferrer F. Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. Epigenetics Chromatin 2018; 11:37. [PMID: 29958539 PMCID: PMC6025724 DOI: 10.1186/s13072-018-0205-1] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is one of the main epigenetic mechanisms for the regulation of gene expression in eukaryotes. In the standard model, methylation in gene promoters has received the most attention since it is generally associated with transcriptional silencing. Nevertheless, recent studies in human tissues reveal that methylation of the region downstream of the transcription start site is highly informative of gene expression. Also, in some cell types and specific genes it has been found that methylation of the first intron, a gene feature typically rich in enhancers, is linked with gene expression. However, a genome-wide, tissue-independent, systematic comparative analysis of the relationship between DNA methylation in the first intron and gene expression across vertebrates has not been explored yet. RESULTS The most important findings of this study are: (1) using different tissues from a modern fish, we show a clear genome-wide, tissue-independent quasi-linear inverse relationship between DNA methylation of the first intron and gene expression. (2) This relationship is conserved across vertebrates, since it is also present in the genomes of a model pufferfish, a model frog and different human tissues. Among the gene features, tissues and species interrogated, the first intron's negative correlation with the gene expression was most consistent. (3) We identified more tissue-specific differentially methylated regions (tDMRs) in the first intron than in any other gene feature. These tDMRs have positive or negative correlation with gene expression, indicative of distinct mechanisms of tissue-specific regulation. (4) Lastly, we identified CpGs in transcription factor binding motifs, enriched in the first intron, the methylation of which tended to increase with the distance from the first exon-first intron boundary, with a concomitant decrease in gene expression. CONCLUSIONS Our integrative analysis clearly reveals the important and conserved role of the methylation level of the first intron and its inverse association with gene expression regardless of tissue and species. These findings not only contribute to our basic understanding of the epigenetic regulation of gene expression but also identify the first intron as an informative gene feature regarding the relationship between DNA methylation and gene expression where future studies should be focused.
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Affiliation(s)
- Dafni Anastasiadi
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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Qu G, Piazza CL, Smith D, Belfort M. Group II intron inhibits conjugative relaxase expression in bacteria by mRNA targeting. eLife 2018; 7:e34268. [PMID: 29905149 PMCID: PMC6003770 DOI: 10.7554/elife.34268] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/18/2018] [Indexed: 01/27/2023] Open
Abstract
Group II introns are mobile ribozymes that are rare in bacterial genomes, often cohabiting with various mobile elements, and seldom interrupting housekeeping genes. What accounts for this distribution has not been well understood. Here, we demonstrate that Ll.LtrB, the group II intron residing in a relaxase gene on a conjugative plasmid from Lactococcus lactis, inhibits its host gene expression and restrains the naturally cohabiting mobile element from conjugative horizontal transfer. We show that reduction in gene expression is mainly at the mRNA level, and results from the interaction between exon-binding sequences (EBSs) in the intron and intron-binding sequences (IBSs) in the mRNA. The spliced intron targets the relaxase mRNA and reopens ligated exons, causing major mRNA loss. Taken together, this study provides an explanation for the distribution and paucity of group II introns in bacteria, and suggests a potential force for those introns to evolve into spliceosomal introns.
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Affiliation(s)
- Guosheng Qu
- Department of Biological SciencesUniversity at AlbanyAlbanyUnited States
- RNA InstituteUniversity at AlbanyAlbanyUnited States
| | - Carol Lyn Piazza
- Department of Biological SciencesUniversity at AlbanyAlbanyUnited States
- RNA InstituteUniversity at AlbanyAlbanyUnited States
| | - Dorie Smith
- Department of Biological SciencesUniversity at AlbanyAlbanyUnited States
- RNA InstituteUniversity at AlbanyAlbanyUnited States
| | - Marlene Belfort
- Department of Biological SciencesUniversity at AlbanyAlbanyUnited States
- RNA InstituteUniversity at AlbanyAlbanyUnited States
- Department of Biomedical Sciences, School of Public HealthUniversity at AlbanyAlbanyUnited States
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46
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Gonzalez DO, Church JB, Robinson A, Connell JP, Sopko M, Rowland B, Woodall K, Larsen CM, Davies JP. Expression characterization of the herbicide tolerance gene Aryloxyalkanoate Dioxygenase (aad-1) controlled by seven combinations of regulatory elements. BMC PLANT BIOLOGY 2018; 18:14. [PMID: 29334902 PMCID: PMC5769356 DOI: 10.1186/s12870-018-1227-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
BACKGROUND Availability of well characterized maize regulatory elements for gene expression in a variety of tissues and developmental stages provides effective alternatives for single and multigene transgenic concepts. We studied the expression of the herbicide tolerance gene aryloxyalkanoate dioxygenase (aad-1) driven by seven different regulatory element construct designs including the ubiquitin promoters of maize and rice, the actin promoters of melon and rice, three different versions of the Sugarcane Bacilliform Badnavirus promoters in association with other regulatory elements of gene expression. RESULTS Gene expression of aad-1 was characterized at the transcript and protein levels in a collection of maize tissues and developmental stages. Protein activity against its target herbicide was characterized by herbicide dosage response. Although differences in transcript and protein accumulation were observed among the different constructs tested, all events were tolerant to commercially relevant rates of quizalafop-P-ethyl compared to non-traited maize under greenhouse conditions. DISCUSSION The data reported demonstrate how different regulatory elements affect transcript and protein accumulation and how these molecular characteristics translate into the level of herbicide tolerance. The level of transcript detected did not reflect the amount of protein quantified in a particular tissue since protein accumulation may be influenced not only by levels of transcript produced but also by translation rate, post-translational regulation mechanisms and protein stability. The amount of AAD-1 enzyme produced with all constructs tested showed sufficient enzymatic activity to detoxify the herbicide and prevent most herbicidal damage at field-relevant levels without having a negative effect on plant health. CONCLUSIONS Distinctive profiles of aad-1 transcript and protein accumulation were observed when different regulatory elements were utilized in the constructs under study. The ZmUbi and the SCBV constructs showed the most consistent robust tolerance, while the melon actin construct provided the lowest level of tolerance compared to the other regulatory elements used in this study. These data provide insights into the effects of differing levels of gene expression and how these molecular characteristics translate into the level of herbicide tolerance. Furthermore, these data provide valuable information to optimize future designs of single and multiple gene constructs for maize research and crop improvement.
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Affiliation(s)
| | - Jeff B. Church
- Dow AgroSciences, LLC, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | - Andrew Robinson
- Dow AgroSciences, LLC, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | - James P. Connell
- Current address: Purdue University College of Pharmacy, 575 Stadium Mall Drive, West Lafayette, IN 47907 USA
| | - Megan Sopko
- Dow AgroSciences, LLC, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | - Boyd Rowland
- Dow AgroSciences, LLC, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | - Kristina Woodall
- Dow AgroSciences, LLC, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | - Cory M. Larsen
- Dow AgroSciences, LLC, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
| | - John P. Davies
- Dow AgroSciences, LLC, 9330 Zionsville Rd, Indianapolis, IN 46268 USA
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Bessière C, Taha M, Petitprez F, Vandel J, Marin JM, Bréhélin L, Lèbre S, Lecellier CH. Probing instructions for expression regulation in gene nucleotide compositions. PLoS Comput Biol 2018; 14:e1005921. [PMID: 29293496 PMCID: PMC5766238 DOI: 10.1371/journal.pcbi.1005921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/12/2018] [Accepted: 12/10/2017] [Indexed: 01/22/2023] Open
Abstract
Gene expression is orchestrated by distinct regulatory regions to ensure a wide variety of cell types and functions. A challenge is to identify which regulatory regions are active, what are their associated features and how they work together in each cell type. Several approaches have tackled this problem by modeling gene expression based on epigenetic marks, with the ultimate goal of identifying driving regions and associated genomic variations that are clinically relevant in particular in precision medicine. However, these models rely on experimental data, which are limited to specific samples (even often to cell lines) and cannot be generated for all regulators and all patients. In addition, we show here that, although these approaches are accurate in predicting gene expression, inference of TF combinations from this type of models is not straightforward. Furthermore these methods are not designed to capture regulation instructions present at the sequence level, before the binding of regulators or the opening of the chromatin. Here, we probe sequence-level instructions for gene expression and develop a method to explain mRNA levels based solely on nucleotide features. Our method positions nucleotide composition as a critical component of gene expression. Moreover, our approach, able to rank regulatory regions according to their contribution, unveils a strong influence of the gene body sequence, in particular introns. We further provide evidence that the contribution of nucleotide content can be linked to co-regulations associated with genome 3D architecture and to associations of genes within topologically associated domains.
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Affiliation(s)
- Chloé Bessière
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - May Taha
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- IMAG, Univ. Montpellier, CNRS, Montpellier, France
| | - Florent Petitprez
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Jimmy Vandel
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- LIRMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Jean-Michel Marin
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- IMAG, Univ. Montpellier, CNRS, Montpellier, France
| | - Laurent Bréhélin
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- LIRMM, Univ. Montpellier, CNRS, Montpellier, France
| | - Sophie Lèbre
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- IMAG, Univ. Montpellier, CNRS, Montpellier, France
- Univ. Paul-Valéry-Montpellier 3, Montpellier, France
| | - Charles-Henri Lecellier
- IBC, Univ. Montpellier, CNRS, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
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Bérczi B, Gerencsér G, Farkas N, Hegyi P, Veres G, Bajor J, Czopf L, Alizadeh H, Rakonczay Z, Vigh É, Erőss B, Szemes K, Gyöngyi Z. Association between AIRE gene polymorphism and rheumatoid arthritis: a systematic review and meta-analysis of case-control studies. Sci Rep 2017; 7:14096. [PMID: 29074995 PMCID: PMC5658331 DOI: 10.1038/s41598-017-14375-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/09/2017] [Indexed: 12/31/2022] Open
Abstract
Autoimmune regulator (AIRE) is a transcription factor that functions as a novel player in immunological investigations. In the thymus, it has a pivotal role in the negative selection of naive T-cells during central tolerance. Experimental studies have shown that single nucleotide polymorphism (SNP) alters transcription of the AIRE gene. SNPs thereby provide a less efficient negative selection, propagate higher survival of autoimmune T-cells, and elevate susceptibility to autoimmune diseases. To date, only rheumatoid arthritis (RA) has been analysed by epidemiological investigations in relation to SNPs in AIRE. In our meta-analysis, we sought to encompass case-control studies and confirm that the association between SNP occurrence and RA. After robust searches of Embase, PubMed, Cochrane Library, and Web of Science databases, we found 19 articles that included five independent studies. Out of 11 polymorphisms, two (rs2075876, rs760426) were common in the five case-control studies. Thus, we performed a meta-analysis for rs2075876 (7145 cases and 8579 controls) and rs760426 (6696 cases and 8164 controls). Our results prove that rs2075876 and rs760426 are significantly associated with an increased risk of RA in allelic, dominant, recessive, codominant heterozygous, and codominant homozygous genetic models. These findings are primarily based on data from Asian populations.
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Affiliation(s)
- Bálint Bérczi
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Gellért Gerencsér
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Nelli Farkas
- Institute of Bioanalysis, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Hegyi
- MTA-SZTE Translational Gastroenterology Research Group, Szeged, Hungary
- Institute for Translational Medicine, University of Pécs, Pécs, Hungary
- Department of Translational Medicine, First Department of Medicine, University of Pécs, Pécs, Hungary
| | - Gábor Veres
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Judit Bajor
- Department of Gastroenterology, First Department of Medicine, University of Pécs, Pécs, Hungary
| | - László Czopf
- Division of Cardiology and Angiology, First Department of Medicine, University of Pécs, Pécs, Hungary
| | - Hussain Alizadeh
- Department of Haematology, First Department of Medicine, University of Pécs, Pécs, Hungary
| | - Zoltán Rakonczay
- Department of Pathophysiology, University of Szeged, Szeged, Hungary
| | - Éva Vigh
- Department of Radiology, Medical School, University of Pécs, Pécs, Hungary
| | - Bálint Erőss
- Institute for Translational Medicine, University of Pécs, Pécs, Hungary
| | - Kata Szemes
- Department of Gastroenterology, First Department of Medicine, University of Pécs, Pécs, Hungary
| | - Zoltán Gyöngyi
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary.
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Li Y, Luo S, Jia X, Zhu Y, Chen D, Duan Y, Hou Y, Zhou M. Regulatory roles of introns in fungicide sensitivity of Fusarium graminearum. Environ Microbiol 2017; 19:4140-4153. [DOI: 10.1111/1462-2920.13863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 06/10/2017] [Accepted: 07/14/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Yanjun Li
- College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Shunwen Luo
- College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Xiaojing Jia
- College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Yuanye Zhu
- College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Dongming Chen
- College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Yabing Duan
- College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Yiping Hou
- College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Mingguo Zhou
- College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
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Nepal MP, Andersen EJ, Neupane S, Benson BV. Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. Genes (Basel) 2017; 8:E249. [PMID: 28973974 PMCID: PMC5664099 DOI: 10.3390/genes8100249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.
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Affiliation(s)
- Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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