1
|
Sultana M, Tayyab M, Parveen S, Hussain M, Shafique L. Genetic characterization, structural analysis, and detection of positive selection in small heat shock proteins of Cypriniformes and Clupeiformes. FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:843-864. [PMID: 38587724 DOI: 10.1007/s10695-024-01337-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 03/22/2024] [Indexed: 04/09/2024]
Abstract
In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights.
Collapse
Affiliation(s)
- Mehwish Sultana
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Wildlife & Fisheries, University of Agriculture, Faisalabad, 38000, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
- Department of Zoology, Wildlife & Fisheries, University of Agriculture, Faisalabad, 38000, Punjab, Pakistan.
| | - Muhammad Hussain
- Department of Veterinary Science, University of Veterinary and Animal Sciences, Lahore, 54000, Punjab, Pakistan
| | - Laiba Shafique
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, 535011, People's Republic of China.
| |
Collapse
|
2
|
Daniel R, Simon M, Wemheuer B. Editorial: Molecular Ecology and Genetic Diversity of the Roseobacter Clade. Front Microbiol 2018; 9:1185. [PMID: 29910792 PMCID: PMC5992283 DOI: 10.3389/fmicb.2018.01185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/16/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Meinhard Simon
- Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.,Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia.,School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
3
|
Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
Collapse
Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| |
Collapse
|
4
|
Cheng WH, Huang KY, Huang PJ, Lee CC, Yeh YM, Ku FM, Lin R, Cheng ML, Chiu CH, Tang P. γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. Parasit Vectors 2017; 10:443. [PMID: 28950916 PMCID: PMC5615479 DOI: 10.1186/s13071-017-2381-4] [Citation(s) in RCA: 2] [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: 04/12/2017] [Accepted: 09/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND γ-Carboxymuconolactone decarboxylase (CMD) participates in the β-ketoadipate pathway, which catalyzes aromatic compounds to produce acetyl- or succinyl-CoA, in prokaryotes and yeast. Our previous study demonstrated that expression of a CMD homologue that contains two signatures (dualCMD) is negatively regulated by iron in Trichomonas vaginalis. However, we were not able to identify the components of the β-ketoadipate pathway in the parasite's genome. These observations prompted us to investigate the biological functions of this novel CMD homologue in T. vaginalis. METHODS The specific anti-TvCMD1 antibody was generated, and the expression of TvCMD1 in T. vaginalis cultured under iron-rich and iron-deficient were evaluated. Phylogenetic, metabolomic and substrate induction (protocatechuate and benzoate) analysis were conducted to clarify the function of dualCMD in trichomonad cells. Subcellular localization of TvCMD1 was observed by confocal microscopy. The cell cycle-related role of TvCMD1 was assessed by treating cells with G2/M inhibitor nocodazole. RESULTS We confirmed that T. vaginalis is not able to catabolize the aromatic compounds benzoate and protocatechuate, which are known substrates of the β-ketoadipate pathway. Using immunofluorescence microscopy, we found that TvCMD1 is spatially associated with the basal body, a part of the cytoskeletal organizing center in T. vaginalis. TvCMD1 accumulated upon treatment with the G2/M inhibitor nocodazole. Additionally, TvCMD1 was expressed and transported to/from the basal body during cytokinesis, suggesting that TvCMD1 plays a role in cell division. CONCLUSION We demonstrated that TvCMD1 is unlikely to participate in the β-ketoadipate pathway and demonstrated that it is a novel basal body-localizing (associated) protein. This model sheds light on the importance of genes that are acquired laterally in the coevolution of ancient protists, which surprisingly functions in cell cycle regulation of T. vaginalis.
Collapse
Affiliation(s)
- Wei-Hung Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan
| | - Po-Jung Huang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Fu-Man Ku
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Rose Lin
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Mei-Ling Cheng
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Petrus Tang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| |
Collapse
|
5
|
Huang L, Xu YB, Xu JX, Ling JY, Chen JL, Zhou JL, Zheng L, Du QP. Antibiotic resistance genes (ARGs) in duck and fish production ponds with integrated or non-integrated mode. CHEMOSPHERE 2017; 168:1107-1114. [PMID: 27816285 DOI: 10.1016/j.chemosphere.2016.10.096] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/19/2016] [Accepted: 10/24/2016] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance genes (ARGs) are emerging micropollutants with environmental persistence. Aquaculture environments are considered as potential reservoirs for ARGs pollution and horizontal gene transfer (HGT). This study analyzed water and sediment from eight culture ponds (integrated culture: duck-fish pond; monoculture: duck pond and fish pond) and a control pond (without any aquaculture activity) in Zhongshan, South China. Seventeen types of ARGs were detected in all ponds, which conferring resistance to four classes of antibiotics including tetracycline (tetA, tetB, tetC, tetE, tetG, tetL, tetA-P, tetM, tetO, tetS, tetW and tetX), AmpC beta-lactamase products (EBC and FOX), sulfonamide (sul1 and sul2) and erythromycin (ermA), with class 1 integron (intI1) as motility gene. The total concentrations of detected ARGs in culture pond water were much higher than control (about 1.6-4.0 times). Integrated culture showed lowest absolute abundance of ∑ARGs in water (3.686 × 107 copies mL-1) and the highest in sediment (4.574 × 108 copies g-1). Monoculture ponds showed higher relative abundance of ∑ARGs both in water (fish pond: 0.5149) and sediment (duck pond: 0.4919). As the main contributor to the ARGs abundance and significant correlations with ∑tet, ∑ARGs and intI1 (P < 0.01), tetA was suggested to be a potential indicator for the abundance of tetracycline resistance genes in these classes of aquaculture modes in the Pearl River Delta. This study provides a case for the ARGs abundance in aquaculture and as a reference for the upcoming health risk assessment in aquatic environment.
Collapse
Affiliation(s)
- Lu Huang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Yan-Bin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Jia-Xin Xu
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jia-Yin Ling
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jin-Liang Chen
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Jia-Le Zhou
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Li Zheng
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Qing-Ping Du
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| |
Collapse
|
6
|
Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
Collapse
Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
| |
Collapse
|
7
|
Chen DS, Wu YQ, Zhang W, Jiang SJ, Chen SZ. Horizontal gene transfer events reshape the global landscape of arm race between viruses and homo sapiens. Sci Rep 2016; 6:26934. [PMID: 27270140 PMCID: PMC4895215 DOI: 10.1038/srep26934] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/09/2016] [Indexed: 12/20/2022] Open
Abstract
Horizontal gene transfer (HGT) drives the evolution of recipient organism particularly if it provides a novel function which enhances the fitness or its adaption to the environment. Virus-host co-evolution is attractive for studying co-evolutionary processes, since viruses strictly replicate inside of the host cells and thus their evolution is inexorably tangled with host biology. HGT, as a mechanism of co-evolution between human and viruses, has been widely documented, however, the roles HGT play during the interaction between human and viruses are still in their infancy. In this study, we performed a comprehensive analysis on the genes horizontally transferred between viruses and their corresponding human hosts. Our study suggests that the HGT genes in human are predominantly enriched in immune related GO terms while viral HGT genes are tend to be encoded by viruses which promote the invasion of immune system of hosts. Based on our results, it gives us a hint about the evolution trajectory of HGT events. Overall, our study suggests that the HGT between human and viruses are highly relevant to immune interaction and probably reshaped the arm race between hosts and viruses.
Collapse
Affiliation(s)
- Dong-Sheng Chen
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Yi-Quan Wu
- Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University Munich, 80336 Munich, Germany
| | - Wei Zhang
- Research unit gene vector, Helmholtz Zentrum, 81377 Munich, Germany
| | - San-Jie Jiang
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Shan-Ze Chen
- Department of Pathophysiology, West China School of Preclinical Sciences and Forensic Medicine, Sichuan University, 610041 Chengdu, Sichuan Province, China
| |
Collapse
|
8
|
Conaco C, Tsoulfas P, Sakarya O, Dolan A, Werren J, Kosik KS. Detection of Prokaryotic Genes in the Amphimedon queenslandica Genome. PLoS One 2016; 11:e0151092. [PMID: 26959231 PMCID: PMC4784904 DOI: 10.1371/journal.pone.0151092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/22/2016] [Indexed: 12/20/2022] Open
Abstract
Horizontal gene transfer (HGT) is common between prokaryotes and phagotrophic eukaryotes. In metazoans, the scale and significance of HGT remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. Marine sponges (Porifera), which host many microorganisms in their tissues and lack an isolated germ line, are potential carriers of genes transferred from prokaryotes. In this study, we identified a number of potential horizontally transferred genes within the genome of the sponge, Amphimedon queenslandica. We further identified homologs of some of these genes in other sponges. The transferred genes, most of which possess catalytic activity for carbohydrate or protein metabolism, have assimilated host genome characteristics and are actively expressed. The diversity of functions contributed by the horizontally transferred genes is likely an important factor in the adaptation and evolution of A. queenslandica. These findings highlight the potential importance of HGT on the success of sponges in diverse ecological niches.
Collapse
Affiliation(s)
- Cecilia Conaco
- Marine Science Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Pantelis Tsoulfas
- University of Miami School of Medicine, Departments of Neurosurgery and Cell Biology, Miami, Florida, United States of America
| | - Onur Sakarya
- Natera, San Carlos, California, United States of America
| | - Amanda Dolan
- Biology Department, University of Rochester, New York, United States of America
| | - John Werren
- Biology Department, University of Rochester, New York, United States of America
| | - Kenneth S. Kosik
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, United States of America
| |
Collapse
|