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Ludwig J, Mrázek J. OrthoRefine: automated enhancement of prior ortholog identification via synteny. BMC Bioinformatics 2024; 25:163. [PMID: 38664637 PMCID: PMC11044567 DOI: 10.1186/s12859-024-05786-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Identifying orthologs continues to be an early and imperative step in genome analysis but remains a challenging problem. While synteny (conservation of gene order) has previously been used independently and in combination with other methods to identify orthologs, applying synteny in ortholog identification has yet to be automated in a user-friendly manner. This desire for automation and ease-of-use led us to develop OrthoRefine, a standalone program that uses synteny to refine ortholog identification. RESULTS We developed OrthoRefine to improve the detection of orthologous genes by implementing a look-around window approach to detect synteny. We tested OrthoRefine in tandem with OrthoFinder, one of the most used software for identification of orthologs in recent years. We evaluated improvements provided by OrthoRefine in several bacterial and a eukaryotic dataset. OrthoRefine efficiently eliminates paralogs from orthologous groups detected by OrthoFinder. Using synteny increased specificity and functional ortholog identification; additionally, analysis of BLAST e-value, phylogenetics, and operon occurrence further supported using synteny for ortholog identification. A comparison of several window sizes suggested that smaller window sizes (eight genes) were generally the most suitable for identifying orthologs via synteny. However, larger windows (30 genes) performed better in datasets containing less closely related genomes. A typical run of OrthoRefine with ~ 10 bacterial genomes can be completed in a few minutes on a regular desktop PC. CONCLUSION OrthoRefine is a simple-to-use, standalone tool that automates the application of synteny to improve ortholog detection. OrthoRefine is particularly efficient in eliminating paralogs from orthologous groups delineated by standard methods.
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Affiliation(s)
- J Ludwig
- Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA.
| | - J Mrázek
- Department of Microbiology and Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA
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Kearney SK, Berger A, Baker E. Aon: a service to augment Alliance Genome Resource data with additional species. BMC Res Notes 2023; 16:297. [PMID: 37891644 PMCID: PMC10604687 DOI: 10.1186/s13104-023-06577-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
OBJECTIVE Cross-species comparative genomics requires access to accurate homology data across the entire range of annotated genes. The Alliance of Genome Resources (AGR) provides an open-source and comprehensive database of homology data calculated using a wide array of algorithms at differing stringencies to elucidate orthologous relationships. However, the current AGR application program interface (API) is limited to five homology endpoints for nine species. While AGR provides a robust resource for several canonical species, its utility can be greatly enhanced by increased filtering and data processing options and incorporating additional species. RESULTS Here, we describe a novel API tool, AON, that expands access to the AGR orthology resource by creating a data structure that supports 50 additional endpoints. More importantly, it provides users with a framework for adding bespoke endpoints, custom species, and additional orthology data. We demonstrate AON's functionality by incorporating the service into the GeneWeaver ecosystem for supporting cross-species data analysis.
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Affiliation(s)
- Sophie K Kearney
- Department of Computer Science, Baylor University, One Bear Place Box 97356, Waco, 76798, USA
| | | | - Erich Baker
- Department of Computer Science, Baylor University, One Bear Place Box 97356, Waco, 76798, USA.
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3
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Cao Y, Fan T, Wang L, Zhang L, Li Y. Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis. BMC Plant Biol 2023; 23:145. [PMID: 36927311 PMCID: PMC10022305 DOI: 10.1186/s12870-023-04163-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND MYB transcription factors are widely distributed in the plant kingdom and play key roles in regulatory networks governing plant metabolism and biochemical and physiological processes. RESULTS Here, we first determined the R2R3-MYB genes in five Euphorbiaceae genomes. The three Trp (W) residues from the first MYB domain (R2) were absolutely conserved, whereas the first W residue from the second MYB domain (R3) was preferentially mutated. The R2R3-MYBs were clustered into 48 functional subfamilies, of which 34 had both R2R3-MYBs of Euphorbiaceae species and AtMYBs, and four contained only Euphorbiaceae R2R3-MYBs. The whole-genome duplication (WGD) and/or segmental duplication (SD) played key roles in the expansion of the R2R3-MYB family. Unlike paralogous R2R3-MYB family members, orthologous R2R3-MYB members contained a higher selective pressure and were subject to a constrained evolutionary rate. VfMYB36 was specifically expressed in fruit, and its trend was consistent with the change in oil content, indicating that it might be involved in oil biosynthesis. Overexpression experiments showed that VfMYB36 could significantly provide linolenic acid (C18:3) content, which eventually led to a significant increase in oil content. CONCLUSION Our study first provides insight into understanding the evolution and expression of R2R3-MYBs in Euphorbiaceae species, and also provides a target for the production of biomass diesel and a convenient way for breeding germplasm resources with high linolenic acid content in the future.
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Affiliation(s)
- Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 430074 Wuhan, China
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China
- Forestry College, Central South University of Forestry and Technology, 410004 Changsha, Hunan China
| | - Tingting Fan
- Forestry College, Central South University of Forestry and Technology, 410004 Changsha, Hunan China
| | - Lihu Wang
- College of Landscape and Ecological Engineering, Hebei University of Engineering, 056009 Handan, China
| | - Lin Zhang
- School of Health and Nursing, Wuchang University of Technology, Wuhan, China
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, 430065 Wuhan, China
| | - Yanli Li
- Forestry College, Central South University of Forestry and Technology, 410004 Changsha, Hunan China
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Mittal V, Reid RW, Machado DJ, Mashanov V, Janies DA. EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms. BMC Genom Data 2022; 23:75. [PMID: 36274129 PMCID: PMC9590158 DOI: 10.1186/s12863-022-01090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity. RESULTS The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling. CONCLUSION EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
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Affiliation(s)
- Varnika Mittal
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA.
| | - Robert W Reid
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
| | - Vladimir Mashanov
- Wake Forest Institute for Regenerative Medicine, 91 Technology Way NE, Winston-Salem, NC, 27101, USA
| | - Daniel A Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA
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Nam MK, Moon JM, Kim GY, Kim SM, Rhim H. The novel human HtrA2 ortholog in zebrafish: New molecular insight and challenges into the imbalance of homeostasis. Gene 2022; 819:146263. [PMID: 35121025 DOI: 10.1016/j.gene.2022.146263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/17/2022] [Accepted: 01/27/2022] [Indexed: 11/28/2022]
Abstract
High temperature requirement A2 (HtrA2) contributes to regulating mitochondrial quality control and maintaining the balance between the death and survival of cells and living organisms. However, the molecular mechanism of HtrA2 in physiological and pathophysiological processes remains unclear. HtrA2 exhibits multifaceted characteristics according to the expression levels and acts opposite functions depending on its subcellular localization. Thus, innovative technologies and systems that can be freely manipulated at the quantitative, biochemical, molecular and cellular levels are needed to address not only the challenges faced by HtrA2 research but also the general obstacles to protein research. Here, we are the first to identify zebrafish HtrA2 (zHtrA2) as the true ortholog of human HtrA2 (hHtrA2), by in silico sequence analysis of genomic DNA and molecular biological techniques, which is highly conserved structurally and functionally as a serine protease and cell death regulator. The zHtrA2 protein is primarily localized in the mitochondria, where alanine-exposed mature zHtrA2 ((A)-zHtrA2) is generated by removing 111 residues at the N-terminus of pro-zHtrA2. The (A)-zHtrA2 released from the mitochondria into the cytosol induces the caspase cascade by binding to and inhibiting hXIAP, a cognate partner of hHtrA2. Notably, zHtrA2 has well conserved properties of serine protease that specifically cleaves hParkin, a cognate substrate of hHtrA2. Interestingly, cytosolic (M)-zHtrA2, which does not bind hXIAP, induces atypical cell death in a serine protease-dependent manner, as occurs in hHtrA2. Thus, the zebrafish-zHtrA2 system can be used to clarify the crucial role of HtrA2 in maintaining the survival of living organisms and provide an opportunity to develop novel therapeutics for HtrA2-associated diseases, such as neurodegenerative diseases and cancer, which are caused by dysregulation of HtrA2.
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Affiliation(s)
- Min-Kyung Nam
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seocho-gu, Seoul 06591, Republic of Korea.
| | - Jeong-Mi Moon
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seocho-gu, Seoul 06591, Republic of Korea
| | - Goo-Young Kim
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seocho-gu, Seoul 06591, Republic of Korea
| | - Sung Min Kim
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seocho-gu, Seoul 06591, Republic of Korea
| | - Hyangshuk Rhim
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, Seocho-gu, Seoul 06591, Republic of Korea; Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seocho-gu, Seoul 06591, Republic of Korea.
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Oh Y, Lee WJ, Hur JK, Song WJ, Lee Y, Kim H, Gwon LW, Kim YH, Park YH, Kim CH, Lim KS, Song BS, Huh JW, Kim SU, Jun BH, Jung C, Lee SH. Expansion of the prime editing modality with Cas9 from Francisella novicida. Genome Biol 2022; 23:92. [PMID: 35410288 PMCID: PMC8996390 DOI: 10.1186/s13059-022-02644-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 02/28/2022] [Indexed: 11/27/2022] Open
Abstract
Prime editing can induce a desired base substitution, insertion, or deletion in a target gene using reverse transcriptase after nick formation by CRISPR nickase. In this study, we develop a technology that can be used to insert or replace external bases in the target DNA sequence by linking reverse transcriptase to the Francisella novicida Cas9, which is a CRISPR-Cas9 ortholog. Using FnCas9(H969A) nickase, the targeting limitation of existing Streptococcus pyogenes Cas9 nickase [SpCas9(H840A)]-based prime editing is dramatically extended, and accurate prime editing is induced specifically for the target genes in human cell lines.
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Affiliation(s)
- Yeounsun Oh
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea.,Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Wi-Jae Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea.,Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Junho K Hur
- Department of Genetics, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea.,Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea.,Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Woo Jeung Song
- Department of Medicine, Major in Medical Genetics, Graduate School, Hanyang University, Seoul, 04763, Republic of Korea
| | - Youngjeon Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Hanseop Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea.,School of Life Sciences and Biotechnology, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Lee Wha Gwon
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea.,Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Gajeong-dong, Yuseong-gu, Daejeon, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Young-Ho Park
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Chan Hyoung Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea.,Department of Biological Sciences, Chungnam National University, Daejeon, Korea
| | - Kyung-Seob Lim
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Bong-Seok Song
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Jae-Won Huh
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Sun-Uk Kim
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Cheulhee Jung
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.
| | - Seung Hwan Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea. .,Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea. .,Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Gajeong-dong, Yuseong-gu, Daejeon, Republic of Korea.
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Wang J, Sheng J, Zhu J, Hu Z, Diao Y. Comparative transcriptome analysis and identification of candidate adaptive evolution genes of Miscanthus lutarioriparius and Miscanthus sacchariflorus. Physiol Mol Biol Plants 2021; 27:1499-1512. [PMID: 34366592 PMCID: PMC8295449 DOI: 10.1007/s12298-021-01030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Miscanthus species are perennial C4 grasses that are considered promising energy crops because of their high biomass yields, excellent adaptability and low management costs. Miscanthus lutarioriparius and Miscanthus sacchariflorus are closely related subspecies that are distributed in different habitats. However, there are only a few reports on the mechanisms by which Miscanthus adapts to different environments. Here, comparative transcriptomic and morphological analyses were used to study the evolutionary adaptation of M. lutarioriparius and M. sacchariflorus to different habitats. In total, among 7586 identified orthologs, 2060 orthologs involved in phenylpropanoid biosynthesis and plant hormones were differentially expressed between the two species. Through an analysis of the Ka/Ks ratios of the orthologs, we estimated that the divergence time between the two species was approximately 4.37 Mya. In addition, 37 candidate positively selected orthologs (PSGs) that played important roles in the adaptation of these species to different habitats were identified. Then, the expression levels of 20 PSGs in response to flooding and drought stress were analyzed, and the analysis revealed significant changes in their expression levels. These results facilitate our understanding of the evolutionary adaptation to habitats and the speciation of M. lutarioriparius and M. sacchariflorus. We hypothesise that lignin synthesis genes are the main cause of the morphological differences between the two species. In summary, the plant nonspecific phospholipase C gene family and the receptor-like protein kinase gene family played important roles in the evolution of these two species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01030-1.
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Affiliation(s)
- Jia Wang
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001 People’s Republic of China
| | - Jiajing Sheng
- College of Life Sciences, Nantong University, Nantong, 226019 People’s Republic of China
| | - Jianyong Zhu
- College of Forestry and Life Sciences, Chongqing University of Arts and Sciences, Chongqing, 402160 People’s Republic of China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Ying Diao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023 People’s Republic of China
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Ogita Y, Tamura K, Mawaribuchi S, Takamatsu N, Ito M. Independent pseudogenizations and losses of sox15 during amniote diversification following asymmetric ohnolog evolution. BMC Ecol Evol 2021; 21:134. [PMID: 34193037 PMCID: PMC8244163 DOI: 10.1186/s12862-021-01864-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/17/2021] [Indexed: 11/28/2022] Open
Abstract
Background Four ohnologous genes (sox1, sox2, sox3, and sox15) were generated by two rounds of whole-genome duplication in a vertebrate ancestor. In eutherian mammals, Sox1, Sox2, and Sox3 participate in central nervous system (CNS) development. Sox15 has a function in skeletal muscle regeneration and has little functional overlap with the other three ohnologs. In contrast, the frog Xenopus laevis and zebrafish orthologs of sox15 as well as sox1-3 function in CNS development. We previously reported that Sox15 is involved in mouse placental development as neofunctionalization, but is pseudogenized in the marsupial opossum. These findings suggest that sox15 might have evolved with divergent gene fates during vertebrate evolution. However, knowledge concerning sox15 in other vertebrate lineages than therian mammals, anuran amphibians, and teleost fish is scarce. Our purpose in this study was to clarify the fate and molecular evolution of sox15 during vertebrate evolution. Results We searched for sox15 orthologs in all vertebrate classes from agnathans to mammals by significant sequence similarity and synteny analyses using vertebrate genome databases. Interestingly, sox15 was independently pseudogenized at least twice during diversification of the marsupial mammals. Moreover, we observed independent gene loss of sox15 at least twice during reptile evolution in squamates and crocodile-bird diversification. Codon-based phylogenetic tree and selective analyses revealed an increased dN/dS ratio for sox15 compared to the other three ohnologs during jawed vertebrate evolution. Conclusions The findings revealed an asymmetric evolution of sox15 among the four ohnologs during vertebrate evolution, which was supported by the increased dN/dS values in cartilaginous fishes, anuran amphibians, and amniotes. The increased dN/dS value of sox15 may have been caused mainly by relaxed selection. Notably, independent pseudogenizations and losses of sox15 were observed during marsupial and reptile evolution, respectively. Both might have been caused by strong relaxed selection. The drastic gene fates of sox15, including neofunctionalization and pseudogenizations/losses during amniote diversification, might be caused by a release from evolutionary constraints. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01864-z.
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Affiliation(s)
- Yusaku Ogita
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa, 252-0373, Japan
| | - Kei Tamura
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa, 252-0373, Japan
| | - Shuuji Mawaribuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Nobuhiko Takamatsu
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa, 252-0373, Japan
| | - Michihiko Ito
- Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa, 252-0373, Japan.
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9
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Banerjee SM, Stoll JA, Allen CD, Lynch JM, Harris HS, Kenyon L, Connon RE, Sterling EJ, Naro-Maciel E, McFadden K, Lamont MM, Benge J, Fernandez NB, Seminoff JA, Benson SR, Lewison RL, Eguchi T, Summers TM, Hapdei JR, Rice MR, Martin S, Jones TT, Dutton PH, Balazs GH, Komoroske LM. Species and population specific gene expression in blood transcriptomes of marine turtles. BMC Genomics 2021; 22:346. [PMID: 33985425 PMCID: PMC8117300 DOI: 10.1186/s12864-021-07656-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations. RESULTS We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance. CONCLUSIONS Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.
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Affiliation(s)
- Shreya M Banerjee
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Jamie Adkins Stoll
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Camryn D Allen
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Jennifer M Lynch
- Chemical Sciences Division, National Institute of Standards and Technology, Hawai'i Pacific University, Waimanalo, HI, USA
| | - Heather S Harris
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Lauren Kenyon
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Richard E Connon
- Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Eleanor J Sterling
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, USA
| | | | - Kathryn McFadden
- School of Agricultural, Forest, and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Margaret M Lamont
- United States Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - James Benge
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Nadia B Fernandez
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Jeffrey A Seminoff
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Scott R Benson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Moss Landing, CA, 95039, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, 95039, USA
| | - Rebecca L Lewison
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Tomoharu Eguchi
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | | | - Jessy R Hapdei
- Jessy's Tag Services, Saipan, Commonwealth of the Northern Mariana Islands, USA
| | - Marc R Rice
- Hawai'i Preparatory Academy, Kamuela, HI, USA
| | - Summer Martin
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - T Todd Jones
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - Peter H Dutton
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | | | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA. .,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
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10
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Li HZ, Shao XX, Shou LL, Li N, Liu YL, Xu ZG, Guo ZY. Unusual orthologs shed new light on the binding mechanism of ghrelin to its receptor GHSR1a. Arch Biochem Biophys 2021; 704:108872. [PMID: 33857472 DOI: 10.1016/j.abb.2021.108872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/23/2021] [Accepted: 04/06/2021] [Indexed: 01/18/2023]
Abstract
The gastric peptide ghrelin has important functions in energy metabolism and cellular homeostasis by activating growth hormone secretagogue receptor type 1a (GHSR1a). The N-terminal residues of ghrelin orthologs from all vertebrates are quite conserved; however, in orthologs from Cavia porcellus and Phyllostomus discolor, Ser2 and Leu5 are replaced by a smaller Ala and a positively charged Arg, respectively. In the present study, we first demonstrated that the hydrophobic Leu5 is essential for the function of human ghrelin, because Ala replacement caused an approximately 100-fold decrease in activity. However, replacement of Leu5 by an Arg residue caused much less disruption; further replacement of Ser2 by Ala almost restored full activity, although the [S2A] mutation itself showed slight detriments, implying that the positively charged Arg5 in the [S2A,L5R] mutant might form alternative interactions with certain receptor residues to compensate for the loss of the essential Leu5. To identify the responsible receptor residues, we screened GHSR1a mutants in which all conserved negatively charged residues in the extracellular regions and all aromatic residues in the ligand-binding pocket were mutated separately. According to the decrease in selectivity of the mutant receptors towards [S2A,L5R]ghrelin, we deduced that the positively charged Arg5 of the ghrelin mutant primarily interacts with the essential aromatic Phe286 at the extracellular end of the sixth transmembrane domain of GHSR1a by forming cation-π and π-π interactions. The present study provided new insights into the binding mechanism of ghrelin with its receptor, and thus would facilitate the design of novel ligands for GHSR1a.
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Affiliation(s)
- Hao-Zheng Li
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiao-Xia Shao
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Li-Li Shou
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ning Li
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ya-Li Liu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zeng-Guang Xu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhan-Yun Guo
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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11
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Ahrens JB, Teufel AI, Siltberg-Liberles J. A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs. J Mol Evol 2020; 88:720-730. [PMID: 33118098 DOI: 10.1007/s00239-020-09969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
Heterotachy-the change in sequence evolutionary rate over time-is a common feature of protein molecular evolution. Decades of studies have shed light on the conditions under which heterotachy occurs, and there is evidence that site-specific evolutionary rate shifts are correlated with changes in protein function. Here, we present a large-scale, computational analysis using thousands of protein sequence alignments from animal and plant proteomes, representing genes related either by orthology (speciation events) or paralogy (gene duplication), to compare sequence divergence patterns in orthologous vs. paralogous sequence alignments. We use sequence-based phylogenetic analyses to infer overall sequence divergence (tree length/number of sequences) and to fit site-specific rates to a discrete gamma distribution with a shape parameter α. This inference method is applied to real protein sequence alignments, as well as alignments simulated under various models of protein sequence evolution. Our simulations indicate that sequence divergence and the α parameter are positively correlated when sequences evolve with heterotachy, meaning that inferred site rate distributions appear more uniform as sequences diverge. Divergence and α are also positively correlated in both orthologous and paralogous genes, but the average increase in α (as a function of divergence) is significantly higher in paralogous protein alignments than in orthologous alignments. This result is consistent with the widely held view that recently duplicated proteins initially evolve under relaxed selective pressure, promoting functional divergence by accumulation of amino acid replacements, and hence experience more evolutionary rate fluctuations than orthologous proteins. We discuss these findings in the context of the ortholog conjecture, a long-standing assumption in molecular evolution, which posits that protein sequences related by orthology tend to be more functionally conserved than paralogous proteins.
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Affiliation(s)
- Joseph B Ahrens
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL, USA. .,Department of Biochemistry and Molecular Genetics, Computational Bioscience Program, University of Colorado Denver, Aurora, CO, USA.
| | - Ashley I Teufel
- Department of Integrative Biology, The University of Texas At Austin, Austin, TX, USA.,Santa Fe Institute, Santa Fe, NM, USA
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
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12
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David KT, Oaks JR, Halanych KM. Patterns of gene evolution following duplications and speciations in vertebrates. PeerJ 2020; 8:e8813. [PMID: 32266119 PMCID: PMC7120047 DOI: 10.7717/peerj.8813] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/27/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Eukaryotic genes typically form independent evolutionary lineages through either speciation or gene duplication events. Generally, gene copies resulting from speciation events (orthologs) are expected to maintain similarity over time with regard to sequence, structure and function. After a duplication event, however, resulting gene copies (paralogs) may experience a broader set of possible fates, including partial (subfunctionalization) or complete loss of function, as well as gain of new function (neofunctionalization). This assumption, known as the Ortholog Conjecture, is prevalent throughout molecular biology and notably plays an important role in many functional annotation methods. Unfortunately, studies that explicitly compare evolutionary processes between speciation and duplication events are rare and conflicting. METHODS To provide an empirical assessment of ortholog/paralog evolution, we estimated ratios of nonsynonymous to synonymous substitutions (ω = dN/dS) for 251,044 lineages in 6,244 gene trees across 77 vertebrate taxa. RESULTS Overall, we found ω to be more similar between lineages descended from speciation events (p < 0.001) than lineages descended from duplication events, providing strong support for the Ortholog Conjecture. The asymmetry in ω following duplication events appears to be largely driven by an increase along one of the paralogous lineages, while the other remains similar to the parent. This trend is commonly associated with neofunctionalization, suggesting that gene duplication is a significant mechanism for generating novel gene functions.
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Affiliation(s)
- Kyle T. David
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Jamie R. Oaks
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
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13
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Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH. Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO). Virology 2019; 529:29-42. [PMID: 30660046 PMCID: PMC6502252 DOI: 10.1016/j.virol.2019.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/13/2022]
Abstract
We developed a computational approach called Domain-architecture Aware Inference of Orthologs (DAIO) for the analysis of protein orthology by combining phylogenetic and protein domain-architecture information. Using DAIO, we performed a systematic study of the proteomes of all human Herpesviridae species to define Strict Ortholog Groups (SOGs). In addition to assessing the taxonomic distribution for each protein based on sequence similarity, we performed a protein domain-architecture analysis for every protein family and computationally inferred gene duplication events. While many herpesvirus proteins have evolved without any detectable gene duplications or domain rearrangements, numerous herpesvirus protein families do exhibit complex evolutionary histories. Some proteins acquired additional domains (e.g., DNA polymerase), whereas others show a combination of domain acquisition and gene duplication (e.g., betaherpesvirus US22 family), with possible functional implications. This novel classification system of SOGs for human Herpesviridae proteins is available through the Virus Pathogen Resource (ViPR, www.viprbrc.org).
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Affiliation(s)
| | - David M Knipe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip E Pellett
- Department of Biochemistry, Microbiology & Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego, CA 92093, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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14
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Abstract
In daily practice of de novo genome assembly and gene prediction, it would be a natural urge to evaluate their products. Different programs and parameter settings give rise to variable outputs, which leaves a decision of which output to adopt for downstream analysis for addressing biological questions. Instead of superficial assessment of length-based statistics of output sequences (e.g., N50 scaffold length), completeness assessment by means of scoring the coverage of reference orthologs has been increasingly utilized.We previously launched a web service, gVolante ( https://gvolante.riken.jp /), to provide a user-friendly interface and a uniform environment for completeness assessment with the pipelines CEGMA and BUSCO. Completeness assessments performed on gVolante report scores based on not just the coverage of reference genes but also on sequence lengths, allowing quality control in multiple aspects. This chapter focuses on the procedure for such assessment and provides technical tips for higher accuracy.
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15
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Abstract
BACKGROUND WRKY transcription factors, so named because of the WRKYGQK heptapeptide at the N-terminal end, are widely distributed in plants and play an important role in physiological changes and response to biotic and abiotic stressors. Many previous studies have focused on the evolution of WRKY transcription factors in a given plant; however, little is known about WRKY evolution in legumes. The gene expression pattern of duplicated WRKY transcription factors remains unclear. RESULTS We first identified the WRKY proteins in 12 legumes. We found that the WRKYGQK heptapeptide tended to mutate into WRKYGKK. The Q site in WRKYGQK preferentially mutated, while W, K, and Y were conserved. The phylogenetic tree shows that the WRKY proteins in legumes have multiple origins, especially group IIc. For example, WRKY64 from Lupinus angustifolius (LaWRKY64) contains three WRKY domains, of which the first two clustered together in the N-terminal WRKY domain of the group I WRKY protein, and the third WRKY domain grouped in the C-terminal WRKY domain of the group I WRKY protein. Orthologous WRKY genes have a faster evolutionary rate and are subject to constrained selective pressure, unlike paralogous WRKY genes. Different gene features were observed between duplicated WRKY genes and singleton WRKY genes. Duplicated Glycine max WRKY genes with similar gene features have gene expression divergence. CONCLUSIONS We analyzed the WRKY number and type in 12 legumes, concluding that the WRKY proteins have multiple origins. A novel WRKY protein, LaWRKY64, was found in L. angustifolius. The first two WRKY domains of LaWRKY64 have the same origin. The orthologous and paralogous WRKY proteins have different evolutionary rates. Duplicated WRKY genes have gene expression divergence under normal growth conditions in G. max. These results provide insight into understanding WRKY evolution and expression.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Weihong Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
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16
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Kaur G, Guruprasad K, Temple BRS, Shirvanyants DG, Dokholyan NV, Pati PK. Structural complexity and functional diversity of plant NADPH oxidases. Amino Acids 2018; 50:79-94. [PMID: 29071531 PMCID: PMC6492275 DOI: 10.1007/s00726-017-2491-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
Abstract
Plant NADPH oxidases also known as respiratory burst oxidase homologs (Rbohs) are a family of membrane-bound enzymes that play diverse roles in the defense response and morphogenetic processes via regulated generation of reactive oxygen species. Rbohs are associated with a variety of functions, although the reason for this is not clear. To evaluate using bioinformatics, the possible mechanisms for the observed functional diversity within the plant kingdom, 127 Rboh protein sequences representing 26 plant species were analyzed. Multiple clusters were identified with gene duplications that were both dicot as well as monocot-specific. The N-terminal sequences were observed to be highly variable. The conserved cysteine (equivalent of Cys890) in C-terminal of AtRbohD suggested that the redox-based modification like S-nitrosylation may regulate the activity of other Rbohs. Three-dimensional models corresponding to the N-terminal domain for Rbohs from Arabidopsis thaliana and Oryza sativa were constructed and molecular dynamics studies were carried out to study the role of Ca2+ in the folding of Rboh proteins. Certain mutations indicated possibly affect the structure and function of the plant NADPH oxidases, thereby providing the rationale for further experimental validation.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India
- Bioinformatics, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Kunchur Guruprasad
- Bioinformatics, Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Brenda R S Temple
- R. L. Juliano Structural Bioinformatics Core Facility, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - David G Shirvanyants
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, India.
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Song H, Song J, Kim YJ, Jeong HH, Min HJ, Koh SS. DCPP1 is the mouse ortholog of human PAUF that possesses functional analogy in pancreatic cancer. Biochem Biophys Res Commun 2017; 493:1498-1503. [PMID: 28988106 DOI: 10.1016/j.bbrc.2017.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/03/2017] [Indexed: 11/15/2022]
Abstract
Pancreatic adenocarcinoma upregulated factor (PAUF) overexpressed in pancreatic ductal adenocarcinoma (PDAC) plays a major role in tumor progression and metastasis by autocrine and paracrine manners. However, underlying molecular mechanism of PAUF functioning in pancreatic cancer are not fully understood yet. The objective of this study was to evaluate the potential of demilune cell and parotid protein 1 (DCPP1) as a putative mouse ortholog of human PAUF by sequence alignment and functional studies. Overexpression of mouse DCPP1 in Chinese hamster ovary (CHO) cells or pancreatic cancer cells increased cell proliferation, migration, invasion, and adhesion ability in vitro. Treatment of human pancreatic cancer cells with recombinant mouse DCPP1 elevated cell growth, motility, invasiveness, and adhesiveness. Mouse DCPP1 exerted its function on pancreatic cancer cells by activating intracellular signaling pathways involved in aggressive cancer phenotype of human pancreatic cancer cells. Moreover, subcutaneous injection of mice with DCPP1-overexpressing CHO cells increased tumor sizes. Taken together, we conclude that mouse DCPP1 is a multifunctional promoter of tumor growth through functional activation of pancreatic cancer cells, suggesting it to be an ortholog of human PAUF.
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Affiliation(s)
- Hayne Song
- Department of Biological Sciences, Dong-A University, Busan, South Korea
| | - Jinhoi Song
- Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yeon Jeong Kim
- Department of Biological Sciences, Dong-A University, Busan, South Korea
| | - Hyeon Hee Jeong
- Department of Biological Sciences, Dong-A University, Busan, South Korea
| | - Hye Jin Min
- Aging Research Institute, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Sang Seok Koh
- Department of Biological Sciences, Dong-A University, Busan, South Korea.
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18
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Geithe C, Protze J, Kreuchwig F, Krause G, Krautwurst D. Structural determinants of a conserved enantiomer-selective carvone binding pocket in the human odorant receptor OR1A1. Cell Mol Life Sci 2017; 74:4209-4229. [PMID: 28656349 DOI: 10.1007/s00018-017-2576-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/29/2017] [Accepted: 06/16/2017] [Indexed: 12/17/2022]
Abstract
Chirality is a common phenomenon within odorants. Most pairs of enantiomers show only moderate differences in odor quality. One example for enantiomers that are easily discriminated by their odor quality is the carvones: humans significantly distinguish between the spearmint-like (R)-(-)-carvone and caraway-like (S)-(+)-carvone enantiomers. Moreover, for the (R)-(-)-carvone, an anosmia is observed in about 8% of the population, suggesting enantioselective odorant receptors (ORs). With only about 15% de-orphaned human ORs, the lack of OR crystal structures, and few comprehensive studies combining in silico and experimental approaches to elucidate structure-function relations of ORs, knowledge on cognate odorant/OR interactions is still sparse. An adjusted homology modeling approach considering OR-specific proline-caused conformations, odorant docking studies, single-nucleotide polymorphism (SNP) analysis, site-directed mutagenesis, and subsequent functional studies with recombinant ORs in a cell-based, real-time luminescence assay revealed 11 amino acid positions to constitute an enantioselective binding pocket necessary for a carvone function in human OR1A1 and murine Olfr43, respectively. Here, we identified enantioselective molecular determinants in both ORs that discriminate between minty and caraway odor. Comparison with orthologs from 36 mammalian species demonstrated a hominid-specific carvone binding pocket with about 100% conservation. Moreover, we identified loss-of-function SNPs associated with the carvone binding pocket of OR1A1. Given carvone enantiomer-specific receptor activation patterns including OR1A1, our data suggest OR1A1 as a candidate receptor for constituting a carvone enantioselective phenotype, which may help to explain mechanisms underlying a (R)-(-)-carvone-specific anosmia in humans.
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Affiliation(s)
- Christiane Geithe
- Deutsche Forschungsanstalt für Lebensmittelchemie Leibniz Institut (DFA), Freising, Germany
| | - Jonas Protze
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Franziska Kreuchwig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Gerd Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Dietmar Krautwurst
- Deutsche Forschungsanstalt für Lebensmittelchemie Leibniz Institut (DFA), Freising, Germany.
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Qihong Z, Jie L, Xiao X, Qian X, Wei G, Jichen X. PicW orthologs from spruce with differential freezing tolerance expressed in Escherichia coli. Int J Biol Macromol 2017; 101:595-602. [PMID: 28315763 DOI: 10.1016/j.ijbiomac.2017.03.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
Abstract
Spruce can grow at an extra low temperature (LT), and is inferred with important antifreezing gene resources. The research here identified 4 different spruce varieties, named as PicW1, PicW2, PicM and PicK. Sequence alignment showed base-substitution and deficiency mutations among them with sequence identity between 97.61% and 99.25%. Each gene was transferred into E. coli, where protein was induced by IPTG (isopropyl-β-d-thiogalactoside). Strains cultured at -5°C showed the lethal dose 50% (LD-50) between 53h and 57h for the transgenic strains, but 35h for the control. Strains cultivated at -20°C showed the LD-50 between 38h and 44h for the transgenic strains, but 25h for the control. Further, the soluble gene proteins were extracted and purified for Differential Scanning Calorimeter (DSC) test, which showed characteristic thermal hysteresis (TH) value of 0.77°C (PicW1), 0.78°C (PicW2), 0.72°C (PicM), and 0.86°C (PicK) respectively, significantly higher than the value of 0.05°C of the control (BSA). Summarily, four homologous proteins showed good antifreeze property with the range from high to low as PicK>PicW2>PicW1>PicM. It suggested that they can be used as resources for genetic engineering of plant cold tolerance.
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Affiliation(s)
- Zhao Qihong
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
| | - Liu Jie
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
| | - Xu Xiao
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Xu Qian
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Gao Wei
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Xu Jichen
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
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Mustafin ZS, Lashin SA, Matushkin YG, Gunbin KV, Afonnikov DA. Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles. BMC Bioinformatics 2017; 18:1427. [PMID: 28466792 PMCID: PMC5333177 DOI: 10.1186/s12859-016-1427-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape (http://cytoscape.org/) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged ‘network evolution’ found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Results Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Conclusion Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1427-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sergey Alexandrovich Lashin
- Institute of Cytology and Genetics SB RAS, Lavrentiev Avenue 10, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090, Russia.
| | | | | | - Dmitry Arkadievich Afonnikov
- Institute of Cytology and Genetics SB RAS, Lavrentiev Avenue 10, Novosibirsk, 630090, Russia.,Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090, Russia
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Kudo T, Terashima S, Takaki Y, Nakamura Y, Kobayashi M, Yano K. Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza Sativa and Other Plant Species. Methods Mol Biol 2017; 1533:229-40. [PMID: 27987174 DOI: 10.1007/978-1-4939-6658-5_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of a gene expression network (GEN), which is constructed based on similarity of gene expression profiles, is a widely used approach to gain clues for new biological insights. The recent abundant availability of transcriptome data in public databases is enabling GEN analysis under various experimental conditions, and even comparative GEN analysis across species. To provide a platform to gain biological insights from public transcriptome data, valuable databases have been created and maintained. This chapter introduces the web database OryzaExpress, providing omics information on Oryza sativa (rice). The integrated database Plant Omics Data Center, supporting a wide variety of plant species, is also described to compare omics information among multiple plant species.
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22
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Abstract
A portal website that integrates a variety of information related to genomes of model and crop plants from databases (DBs) and the literature was generated. This website, named the Plant Genome DataBase Japan (PGDBj, http://pgdbj. jp/en/ ), is comprised of three component DBs and a cross-search engine which provides a seamless search over their contents. One of the three component DBs is the Ortholog DB, which provides gene cluster information based on the amino acid sequence similarity. Over 1,000,000 amino acid sequences of 40 Viridiplantae species were collected from the public DNA DBs, and plant genome DBs such as TAIR and RAP-DB were subjected to reciprocal BLAST searches for clustering. Another component DB is the Plant Resource DB for genomic- and bio-resources. This DB also integrates the SABRE DB, which provides cDNA and genome sequence resources maintained in the RIKEN BioResource Center and National BioResource Projects Japan. The third component DB of PGDBj is the DNA Marker DB, which manually or automatically collects curated information on DNA markers, quantitative trait loci (QTL), and related genetic linkage maps, from the literature and external DBs. By combining these component DBs and a cross-search engine, PGDBj serves as a useful platform to study genetic systems for both fundamental and applied researches for a wide range of plant species.
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Affiliation(s)
- Akihiro Nakaya
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, 1-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hisako Ichihara
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Erika Asamizu
- Department of Plant Life Sciences, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Sachiko Shirasawa
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yasukazu Nakamura
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Satoshi Tabata
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hideki Hirakawa
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan.
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23
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Abstract
Background Current genome sequencing projects reveal substantial numbers of taxonomically restricted, so called orphan genes that lack homology with genes from other evolutionary lineages. However, it is not clear to what extent orphan genes are real, genomic artifacts, or represent non-coding RNAs. Results Here, we use a simple set of assumptions to test the nature of orphan genes. First, a sequence that is transcribed is considered a real biological entity. Second, every sequence that is supported by proteome data or shows a depletion of non-synonymous substitutions is a protein-coding gene. Using genomic, transcriptomic and proteomic data for the nematode Pristionchus pacificus, we show that between 4129–7997 (42–81 %) of predicted orphan genes are expressed and 3818–7545 (39–76 %) of orphan genes are under negative selection. In three cases that exhibited strong evolutionary constraint but lacked expression evidence in 14 RNA-seq samples, we could experimentally validate the predicted gene structures. Comparing different data sets to infer selection on orphan gene clusters, we find that the presence of a closely related genome provides the most powerful resource to robustly identify evidence of negative selection. However, even in the absence of other genomic data, the availability of paralogous sequences was enough to show negative selection in 8–10 % of orphan genes. Conclusions Our study shows that the great majority of previously identified orphan genes in P. pacificus are indeed protein-coding genes. Even though this work represents a case study on a single species, our approach can be transferred to genomic data of other non-model organisms in order to ascertain the protein-coding nature of orphan genes.
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Affiliation(s)
- Neel Prabh
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany.
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24
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Abstract
Background Oenococcus oeni is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermentation that is often required for many types of wine. Expanding the understanding of strain-dependent genetic variations in its small and streamlined genome is important for realising its full potential in industrial fermentation processes. Results Whole genome comparison was performed on 191 strains of O. oeni; from this rich source of genomic information consensus pan-genome assemblies of the invariant (core) and variable (flexible) regions of this organism were established. Genetic variation in amino acid biosynthesis and sugar transport and utilisation was found to be common between strains. Furthermore, we characterised previously-unreported intra-specific genetic variations in the natural competence of this microbe. Conclusion By assembling a consensus pan-genome from a large number of strains, this study provides a tool for researchers to readily compare protein-coding genes across strains and infer functional relationships between genes in conserved syntenic regions. This establishes a foundation for further genetic, and thus phenotypic, research of this industrially-important species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2604-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter R Sternes
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, 5064, Australia
| | - Anthony R Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, South Australia, 5064, Australia.
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25
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Yamamoto N, Kudo T, Fujiwara S, Takatsuka Y, Hirokawa Y, Tsuzuki M, Takano T, Kobayashi M, Suda K, Asamizu E, Yokoyama K, Shibata D, Tabata S, Yano K. Pleurochrysome: A Web Database of Pleurochrysis Transcripts and Orthologs Among Heterogeneous Algae. Plant Cell Physiol 2016; 57:e6. [PMID: 26746174 PMCID: PMC4722176 DOI: 10.1093/pcp/pcv195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/27/2015] [Indexed: 05/04/2023]
Abstract
Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because of lack of comprehensive gene information. To provide such information to the research community, we built an open web database, the Pleurochrysome (http://bioinf.mind.meiji.ac.jp/phapt/), which currently stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions such as BLAST and keyword searches, this database also offers search functions to explore orthologous genes in the 12 organisms and to seek novel genes. The Pleurochrysome will promote molecular biological and phylogenetic research on coccolithophorids and other haptophytes by helping scientists mine data from the primary transcriptome of P. haptonemofera.
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Affiliation(s)
- Naoki Yamamoto
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work. Present address: International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines.
| | - Toru Kudo
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan These authors contributed equally to this work.
| | - Shoko Fujiwara
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan These authors contributed equally to this work.
| | - Yukiko Takatsuka
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Yasutaka Hirokawa
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Mikio Tsuzuki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392 Japan, CREST, Japan
| | - Tomoyuki Takano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Masaaki Kobayashi
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Kunihiro Suda
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Erika Asamizu
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Koji Yokoyama
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
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26
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Cha MK, Bae YJ, Kim KJ, Park BJ, Kim IH. Characterization of two alkyl hydroperoxide reductase C homologs alkyl hydroperoxide reductase C_H1 and alkyl hydroperoxide reductase C_H2 in Bacillus subtilis. World J Biol Chem 2015; 6:249-264. [PMID: 26322180 PMCID: PMC4549766 DOI: 10.4331/wjbc.v6.i3.249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/06/2015] [Accepted: 06/11/2015] [Indexed: 02/05/2023] Open
Abstract
AIM: To identify alkyl hydroperoxide reductase subunit C (AhpC) homologs in Bacillus subtilis (B. subtilis) and to characterize their structural and biochemical properties. AhpC is responsible for the detoxification of reactive oxygen species in bacteria.
METHODS: Two AhpC homologs (AhpC_H1 and AhpC_H2) were identified by searching the B. subtilis database; these were then cloned and expressed in Escherichia coli. AhpC mutants carrying substitutions of catalytically important Cys residues (C37S, C47S, C166S, C37/47S, C37/166S, C47/166S, and C37/47/166S for AhpC_H1; C52S, C169S, and C52/169S for AhpC_H2) were obtained by site-directed mutagenesis and purified, and their structure-function relationship was analyzed. The B. subtilis ahpC genes were disrupted by the short flanking homology method, and the phenotypes of the resulting AhpC-deficient bacteria were examined.
RESULTS: Comparative characterization of AhpC homologs indicates that AhpC_H1 contains an extra C37, which forms a disulfide bond with the peroxidatic C47, and behaves like an atypical 2-Cys AhpC, while AhpC_H2 functions like a typical 2-Cys AhpC. Tryptic digestion analysis demonstrated the presence of intramolecular Cys37-Cys47 linkage, which could be reduced by thioredoxin, resulting in the association of the dimer into higher-molecular-mass complexes. Peroxidase activity analysis of Cys→Ser mutants indicated that three Cys residues were involved in the catalysis. AhpC_H1 was resistant to inactivation by peroxide substrates, but had lower activity at physiological H2O2 concentrations compared to AhpC_H2, suggesting that in B. subtilis, the enzymes may be physiologically functional at different substrate concentrations. The exposure to organic peroxides induced AhpC_H1 expression, while AhpC_H1-deficient mutants exhibited growth retardation in the stationary phase, suggesting the role of AhpC_H1 as an antioxidant scavenger of lipid hydroperoxides and a stress-response factor in B. subtilis.
CONCLUSION: AhpC_H1, a novel atypical 2-Cys AhpC, is functionally distinct from AhpC_H2, a typical 2-Cys AhpC.
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27
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Abstract
The genome of the nematode Caenorhabditis elegans was the first of any animal to be sequenced completely, and it remains the "gold standard" for completeness and annotations. Even before the C. elegans genome was completed, however, biologists began examining the generality of its features in the genomes of other Caenorhabditis species. With many such genomes now sequenced and available via WormBase, C. elegans researchers are often confronted with how to interpret comparative genomic data. In this article, we present practical approaches to addressing several common issues, including possible sources of error in homology annotations, the often complex relationships between sequence similarity, orthology, paralogy, and gene family evolution, the impact of sexual mode on genome assemblies and content, and the determination and use of synteny as a tool.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, 1210 Biology-Psychology Building, College Park, MD, 20742, USA.
| | - Cristel G Thomas
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada, M5S 3B2
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28
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Asamizu E, Ichihara H, Nakaya A, Nakamura Y, Hirakawa H, Ishii T, Tamura T, Fukami-Kobayashi K, Nakajima Y, Tabata S. Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. Plant Cell Physiol 2014; 55:e8. [PMID: 24363285 PMCID: PMC3894704 DOI: 10.1093/pcp/pct189] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows. (i) The Ortholog DB, providing gene cluster information based on the amino acid sequence similarity. Over 500,000 amino acid sequences of 20 Viridiplantae species were subjected to reciprocal BLAST searches and clustered. Sequences from plant genome DBs (e.g. TAIR10 and RAP-DB) were also included in the cluster with a direct link to the original DB. (ii) The Plant Resource DB, integrating the SABRE DB, which provides cDNA and genome sequence resources accumulated and maintained in the RIKEN BioResource Center and National BioResource Projects. (iii) The DNA Marker DB, providing manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps, from the literature and external DBs. As the PGDBj targets various plant species, including model plants, algae, and crops important as food, fodder and biofuel, researchers in the field of basic biology as well as a wide range of agronomic fields are encouraged to perform searches using DNA sequences, gene names, traits and phenotypes of interest. The PGDBj will return the search results from the component DBs and various types of linked external DBs.
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Affiliation(s)
- Erika Asamizu
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Hisako Ichihara
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Akihiro Nakaya
- Center for Transdisciplinary Research, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8585 Japan
| | - Yasukazu Nakamura
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Hideki Hirakawa
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Takahiro Ishii
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Takuro Tamura
- LINE Co., Ltd., 5-201 Kandamatsunaga-cho, Tokyo, 101-0023 Japan
| | | | - Yukari Nakajima
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
| | - Satoshi Tabata
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan
- *Corresponding author: Fax: +81-438-52-3918; E-mail,
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