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Shi M, Zhang Q, Li Y, Zhang W, Liao L, Cheng Y, Jiang Y, Huang X, Duan Y, Xia L, Ye W, Wang Y, Xia XQ. Global gene expression profile under low-temperature conditions in the brain of the grass carp (Ctenopharyngodon idellus). PLoS One 2020; 15:e0239730. [PMID: 32976524 PMCID: PMC7518592 DOI: 10.1371/journal.pone.0239730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 09/13/2020] [Indexed: 01/29/2023] Open
Abstract
Grass carp is an important commercial fish widely cultivated in China. A wide range of temperatures, particularly extremely low temperatures, have dramatic effects on the aquaculture of this teleost. However, relatively few studies have characterized the molecular responses of grass carp exposed to acute cooling in natural environment. Here, we investigated the transcriptome profiles of the grass carp brain in response to cooling. Through regulation pattern analyses, we identified 2,513 differentially expressed genes (DEGs) that responded to moderate cold stress (12°C), while 99 DEGs were induced by severe low temperature (4°C).The pathway analyses revealed that the DEGs sensitive to moderate cold were largely enriched in steroid biosynthesis, spliceosome, translation, protein metabolism, phagosome, gap junction and estrogen signaling pathways. Additionally, we discerned genes most likely involved in low temperature tolerance, of which the MAPK signaling pathway was dominantly enriched. Further examination and characterization of the candidate genes may help to elucidate the mechanisms underpinning extreme plasticity to severe cold stress in grass carp.
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Affiliation(s)
- Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Qiangxiang Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongming Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Lanjie Liao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yanxin Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Huang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - You Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weidong Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaping Wang
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- * E-mail: (XQX); (YW)
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (XQX); (YW)
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2
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The tubulin mutation database: A resource for the cytoskeleton community. Cytoskeleton (Hoboken) 2019; 76:186-191. [DOI: 10.1002/cm.21514] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/21/2018] [Accepted: 01/17/2019] [Indexed: 11/07/2022]
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Berthelot C, Clarke J, Desvignes T, William Detrich H, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine? Genome Biol Evol 2019; 11:220-231. [PMID: 30496401 PMCID: PMC6336007 DOI: 10.1093/gbe/evy262] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/25/2022] Open
Abstract
The evolution of antifreeze glycoproteins has enabled notothenioid fish to flourish in the freezing waters of the Southern Ocean. Whereas successful at the biodiversity level to life in the cold, paradoxically at the cellular level these stenothermal animals have problems producing, folding, and degrading proteins at their ambient temperatures of -1.86 °C. In this first multi-species transcriptome comparison of the amino acid composition of notothenioid proteins with temperate teleost proteins, we show that, unlike psychrophilic bacteria, Antarctic fish provide little evidence for the mass alteration of protein amino acid composition to enhance protein folding and reduce protein denaturation in the cold. The exception was the significant overrepresentation of positions where leucine in temperate fish proteins was replaced by methionine in the notothenioid orthologues. We hypothesize that these extra methionines have been preferentially assimilated into the genome to act as redox sensors in the highly oxygenated waters of the Southern Ocean. This redox hypothesis is supported by analyses of notothenioids showing enrichment of genes associated with responses to environmental stress, particularly reactive oxygen species. So overall, although notothenioid fish show cold-associated problems with protein homeostasis, they may have modified only a selected number of biochemical pathways to work efficiently below 0 °C. Even a slight warming of the Southern Ocean might disrupt the critical functions of this handful of key pathways with considerable impacts for the functioning of this ecosystem in the future.
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Affiliation(s)
- Camille Berthelot
- Laboratoire Dynamique et Organisation des Génomes (Dyogen), Institut de Biologie de l'Ecole Normale Supérieure – UMR 8197, INSERM U1024, Paris Cedex 05, France
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, United Kingdom
| | | | - H William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Michael Peters
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | | | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
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Zhou T, Gui L, Liu M, Li W, Hu P, Duarte DFC, Niu H, Chen L. Transcriptomic responses to low temperature stress in the Nile tilapia, Oreochromis niloticus. FISH & SHELLFISH IMMUNOLOGY 2019; 84:1145-1156. [PMID: 30408600 DOI: 10.1016/j.fsi.2018.10.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/03/2018] [Accepted: 10/07/2018] [Indexed: 06/08/2023]
Abstract
The Nile tilapia, Oreochromis niloticus, is a species of high economic value and extensively cultured. The limited stress tolerance of this species to a low temperature usually leads to mass mortality and great loss. Nevertheless, there is limited information on the molecular mechanisms underlying the susceptibility to low temperature in the tilapia. In this study, tilapia was treated at 28 °C to a lethal temperature of 8 °C by a gradual decrement. Transcriptomic response of the immune organ, kidney, in tilapia was characterized using RNA-seq. In total, 2191 genes were annotated for significant expression, which were mainly associated with metabolism and immunity. Pathway analysis showed that immune-related pathways of phagosome and cell adhesion molecules (CAMs) pathway were significantly down-regulated under low temperature. Moreover, ferroptosis, a significantly changed pathway involved in tissue damage and acute renal failure, is reported here for the first time. The levels of serum parameters associated with kidney damage such as urea and uric acid (UA) increased significantly under low temperature. The immunofluorescence staining of the kidney showed that cell apoptosis occurred at low temperature. The results of the present study indicate that exposure to low temperature can cause kidney disfunction and down-regulate the immune-related pathway in the kidney of tilapia. This study provides new insight into the mechanism of kidney damage in fish under low temperature.
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Affiliation(s)
- Tao Zhou
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Lang Gui
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Mingli Liu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Wenhao Li
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Peng Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Daniel F C Duarte
- Faculty of Sciences and Technology, University of Algarve, Faro, Portugal
| | - Hongbo Niu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
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Characterization and putative post-translational regulation of α- and β-tubulin gene families in Salix arbutifolia. Sci Rep 2016; 6:19258. [PMID: 26753794 PMCID: PMC4709717 DOI: 10.1038/srep19258] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/10/2015] [Indexed: 11/08/2022] Open
Abstract
Microtubules, which are composed of heterodimers of α-tubulin (TUA) and β-tubulin (TUB) proteins, are closely associated with cellulose microfibril deposition and play pivotal roles in plant secondary cell wall development. In the present study, we identified eight TUA and twenty TUB genes in willow (Salix arbutifolia). Quantitative real-time PCR analysis showed that the small number of TUA gene family members relative to that of TUBs was complemented by a higher transcript copy number for each TUA gene, which is essential to the maintenance of the tubulin 1:1 heterodimer assembly. In Salix, five of eight TUAs were determined to be unusual because these contained a C-terminal methionine acid, leucine acid, glutamic acid, and glutamine acid, instead of the more typical tyrosine residue, which in turn generated the hypothesis of post-translational modifications (PTMs) that included deleucylation, demethiolation, deglutamynation, and deaspartylation. These PTMs are responsible for the removal of additional amino acid residues from TUAs prior to detyrosination, which is the first step of C-terminal PTMs. The additional PTMs of the TUA gene family might be responsible for the formation of different tubulin heterodimers that may have diverse functions for the adaptation of the woody perennial growth for Salix.
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6
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Desjardins M, Graham LA, Davies PL, Fletcher GL. Antifreeze protein gene amplification facilitated niche exploitation and speciation in wolffish. FEBS J 2012; 279:2215-30. [PMID: 22520964 DOI: 10.1111/j.1742-4658.2012.08605.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During winter, the coastal waters of Newfoundland can be considered a 'freeze risk ecozone' for teleost fishes, where the shallower habitats pose a high (and the deeper habitats a low) risk of freezing. Atlantic (Anarhichas lupus) and spotted (Anarhichas minor) wolffish, which inhabit these waters, reside at opposite ends of this ecozone, with the Atlantic wolffish being the species facing the greatest risk, because of its shallower niche. In order to resist freezing, this species secretes five times the level of antifreeze protein (AFP) activity into the plasma than does the spotted wolffish. The main basis for this interspecific difference in AFP levels is gene dosage, as the Atlantic wolffish has approximately three times as many AFP gene copies as the spotted wolffish. In addition, AFP transcript levels in liver (the primary source of circulating AFPs) are several times higher in the Atlantic wolffish. One explanation for the difference in gene dosage and transcript levels is the presence of tandemly arrayed repeats in the latter, which make up two-thirds of its AFP gene pool. Such repeats are not present in the spotted wolffish. The available evidence indicates that the two species diverged from a common ancestor at a time when the ebb and flow of northern glaciations would have resulted in the emergence of shallow water 'freeze risk ecozones'. The results of this study suggest that the duplication/amplification of AFP genes in a subpopulation of ancestral wolffish would have facilitated the exploitation of this high-risk habitat, resulting in the divergence and evolution of modern-day Atlantic and spotted wolffish species.
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Affiliation(s)
- Mariève Desjardins
- Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, Canada
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7
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DETRICH HWILLIAM, STUART ANDREW, SCHOENBORN MICHAEL, PARKER SANDRAK, METHÉ BARBARAA, AMEMIYA CHRIST. Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 representative taxa. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:369-81. [PMID: 20235119 PMCID: PMC3631310 DOI: 10.1002/jez.b.21341] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species flock in the cold Southern Ocean surrounding Antarctica. To enable genome-level studies of these psychrophilic fishes, we estimated the sizes of the genomes of 11 Antarctic species and generated high-quality BAC libraries for 2, the notothen Notothenia coriiceps and the icefish Chaenocephalus aceratus. Our results indicate that evolution of phylogenetically derived notothenioid families, [e.g., the icefishes (Channichthyidae)], was accompanied by genome expansion. Species (n=6) of the basal family Nototheniidae had C values that ranged between 0.98 and 1.20 pg, whereas those of the icefishes, the notothenioid crown group, were 1.66-1.83 pg (n=4 species). The BAC libraries VMRC-19 (N. coriiceps) and VMRC-21 (C. aceratus) comprised 12X and 10X coverage of the respective genomes and had average insert sizes of 138 and 168 kb. Greater than 60% of paired BAC ends sampled from each library ( approximately 0.1% of each genome) contained repetitive sequences, and the repetitive element landscapes of the 2 genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus) were similar. The representation and depth of coverage of the libraries were verified by identification of multiple Hox gene contigs: six discrete Hox clusters were found in N. coriiceps and at least five Hox clusters were found in C. aceratus. Given the unusual anatomical and physiological adaptations of the notothenioids, the availability of these BAC libraries sets the stage for expanded analysis of the psychrophilic mode of life.
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Affiliation(s)
| | - ANDREW STUART
- Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | | | - SANDRA K. PARKER
- Department of Biology, Northeastern University, Boston, Massachusetts
| | | | - CHRIS T. AMEMIYA
- Benaroya Research Institute at Virginia Mason, Seattle, Washington
- Department of Biology, University of Washington, Seattle, Washington
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8
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Pucciarelli S, La Terza A, Ballarini P, Barchetta S, Yu T, Marziale F, Passini V, Methé B, Detrich HW, Miceli C. Molecular cold-adaptation of protein function and gene regulation: The case for comparative genomic analyses in marine ciliated protozoa. Mar Genomics 2009; 2:57-66. [PMID: 21798173 DOI: 10.1016/j.margen.2009.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 03/16/2009] [Accepted: 03/25/2009] [Indexed: 12/01/2022]
Abstract
Euplotes focardii is a marine ciliated protozoan discovered in the Ross Sea near Terra Nova Bay, Antarctica. This organism is strictly psychrophilic, survives and reproduces optimally at 4-5 °C, and has a genome rich in A/T base pairs. Like other ciliated protozoans, Euplotes spp. are characterized by nuclear dimorphism: 1) the germline micronucleus contains the entire genome as large chromosomes; and 2) the somatic macronucleus (∼50 megabases, or 5% of the micronuclear genome) contains small linear DNA nanochromosomes [1-12 kilobases], each of which constitutes a single genetic unit. These characteristics make E. focardii an ideal model for genome-level analysis to understand the evolutionary mechanisms that determine the adaptation of organisms to cold environments. Here we describe two examples that are controlled by phylogenetically appropriate comparison with mesophilic and psychrotolerant Euplotes species: 1) the genes and encoded proteins of the E. focardii tubulin superfamily, including α-, β-, and γ-tubulins; and 2) the genes of the heat-shock protein (Hsp) 70 family. The tubulins provide particular insight into protein-level structural changes that are likely to facilitate microtubule nucleation and polymerization in an energy poor environment. By contrast, the hsp70 genes of E. focardii and of its psychrotolerant relative E. nobilii reveal adaptive alterations in the regulation of gene expression in the cold. The unique characteristics of the E. focardii genome and the results that we present here argue strongly for a concerted effort to characterize the relatively low complexity macronuclear genome of this psychrophilic organism.
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Affiliation(s)
- Sandra Pucciarelli
- Dipartimento di Biologia Molecolare, Cellulare, Animale, University of Camerino, Camerino (MC), Italy
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Tartaglia LJ, Shain DH. Cold-adapted tubulins in the glacier ice worm, Mesenchytraeus solifugus. Gene 2008; 423:135-41. [DOI: 10.1016/j.gene.2008.07.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 07/04/2008] [Accepted: 07/18/2008] [Indexed: 01/02/2023]
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10
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Rogers AD. Evolution and biodiversity of Antarctic organisms: a molecular perspective. Philos Trans R Soc Lond B Biol Sci 2008; 362:2191-214. [PMID: 17553774 PMCID: PMC2443175 DOI: 10.1098/rstb.2006.1948] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Antarctic biota is highly endemic, and the diversity and abundance of taxonomic groups differ from elsewhere in the world. Such characteristics have resulted from evolution in isolation in an increasingly extreme environment over the last 100 Myr. Studies on Antarctic species represent some of the best examples of natural selection at the molecular, structural and physiological levels. Analyses of molecular genetics data are consistent with the diversity and distribution of marine and terrestrial taxa having been strongly influenced by geological and climatic cooling events over the last 70 Myr. Such events have resulted in vicariance driven by continental drift and thermal isolation of the Antarctic, and in pulses of species range contraction into refugia and subsequent expansion and secondary contact of genetically distinct populations or sister species during cycles of glaciation. Limited habitat availability has played a major role in structuring populations of species both in the past and in the present day. For these reasons, despite the apparent simplicity or homogeneity of Antarctic terrestrial and marine environments, populations of species are often geographically structured into genetically distinct lineages. In some cases, genetic studies have revealed that species defined by morphological characters are complexes of cryptic or sibling species. Climate change will cause changes in the distribution of many Antarctic and sub-Antarctic species through affecting population-level processes such as life history and dispersal.
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Merkulov S, Zhang WM, Komar AA, Schmaier AH, Barnes E, Zhou Y, Lu X, Iwaki T, Castellino FJ, Luo G, McCrae KR. Deletion of murine kininogen gene 1 (mKng1) causes loss of plasma kininogen and delays thrombosis. Blood 2008; 111:1274-81. [PMID: 18000168 PMCID: PMC2214772 DOI: 10.1182/blood-2007-06-092338] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 10/29/2007] [Indexed: 12/29/2022] Open
Abstract
High-molecular-weight kininogen (HK) plays an important role in the assembly of the plasma kallikrein-kinin system. While the human genome contains a single copy of the kininogen gene, 3 copies exist in the rat (1 encoding K-kininogen and 2 encoding T-kininogen). Here, we confirm that the mouse genome contains 2 homologous kininogen genes, mKng1 and mKng2, and demonstrate that these genes are expressed in a tissue-specific manner. To determine the roles of these genes in murine development and physiology, we disrupted mKng1, which is expressed primarily in the liver. mKng1(-/-) mice were viable, but lacked plasma HK and low-molecular-weight kininogen (LK), as well as DeltamHK-D5, a novel kininogen isoform that lacks kininogen domain 5. Moreover, despite normal tail vein bleeding times, mKng1(-/-) mice displayed a significantly prolonged time to carotid artery occlusion following Rose Bengal administration and laser-induced arterial injury. These results suggest that a single gene, mKng1, is responsible for production of plasma kininogen, and that plasma HK contributes to induced arterial thrombosis in mice.
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Affiliation(s)
- Sergei Merkulov
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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12
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Pucciarelli S, Marziale F, Di Giuseppe G, Barchetta S, Miceli C. Ribosomal cold-adaptation: characterization of the genes encoding the acidic ribosomal P0 and P2 proteins from the Antarctic ciliate Euplotes focardii. Gene 2005; 360:103-10. [PMID: 16143466 DOI: 10.1016/j.gene.2005.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Revised: 04/14/2005] [Accepted: 06/02/2005] [Indexed: 10/25/2022]
Abstract
Molecular adaptation at low temperature requires specificities represented mainly by modifications in the gene sequence and consequently in the protein primary structure. To characterize the molecular mechanisms responsible for ribosome cold-adaptation, we compared the ribosomal P0 and P2 genes from the Antarctic ciliate Euplotes focardii with homologous genes from mesophilic organisms, including the ciliates Tetrahymena thermophila and non cold-adapted Euplotes species. This analysis revealed the presence of non synonymous mutations unique to E. focardii. In the P0 protein the mutations produced amino acid substitutions that increased the molecular flexibility that may facilitate a conformational adjustment associated with the interaction with the GTPase center of the large subunit rRNA, and increased the hydrophobicity of the region involved in the interaction with P1/P2 heterodimer, probably to keep associated the ribosomal stalk in the cold. In the P2 protein the mutations produced amino acid substitutions that increased the N-terminus flexibility, which may facilitate interactions with P1 protein in the formation of the heterodimer, and reduced the mobility of the C-terminus, to stabilize the stalk during ribosomal activity. Finally, P proteins appeared to be valid markers for investigating the phylogenetic origin of early eukaryotes.
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Affiliation(s)
- Sandra Pucciarelli
- Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Via F Camerini 2, 62032 Camerino (MC), Italy
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Hughes AL, Friedman R. Expression patterns of duplicate genes in the developing root in Arabidopsis thaliana. J Mol Evol 2005; 60:247-56. [PMID: 15785853 DOI: 10.1007/s00239-004-0171-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Accepted: 10/01/2004] [Indexed: 11/29/2022]
Abstract
Data on gene expression in the development of the root in Arabidopsis thaliana were used to test for expression profile differences among multi-gene families and to examine the extent to which expression differences accompanied coding sequences divergence within families. Significant differences among families were observed on two principal axes, accounting for over 80% of the variance in the expression data. The number of synonymous nucleotide substitutions per synonymous site (d(S)) and the number of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)) were estimated between the members of two-member families (N = 428) and between phylogenetically independent sister pairs (N = 190) of sequences within larger families. Ribosomal proteins and a few other proteins were exceptional in showing highly divergent expression patterns in spite of very low levels of amino acid sequence divergence, as indicated by the low d(N) relative to d(S). However, the majority of gene duplicates showed relatively high levels of amino acid sequence divergence without appreciable change in expression pattern in the cell types analyzed.
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Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, SC 29208, USA.
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Lau DT, Saeed-Kothe A, Parker SK, William Detrich H. Adaptive Evolution of Gene Expression in Antarctic Fishes: Divergent Transcription of the 5′-to-5′ Linked Adult α1- and β-Globin Genes of the Antarctic TeleostNotothenia coriicepsis Controlled by Dual Promoters and Intergenic Enhancers1. ACTA ACUST UNITED AC 2001. [DOI: 10.1668/0003-1569(2001)041[0113:aeogei]2.0.co;2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Adaptive Evolution of Gene Expression in Antarctic Fishes: Divergent Transcription of the 5′-to-5′ Linked Adult α1- and β-Globin Genes of the Antarctic TeleostNotothenia coriicepsis Controlled by Dual Promoters and Intergenic Enhancers. ACTA ACUST UNITED AC 2001. [DOI: 10.1093/icb/41.1.113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Detrich HW, Parker SK, Williams RC, Nogales E, Downing KH. Cold adaptation of microtubule assembly and dynamics. Structural interpretation of primary sequence changes present in the alpha- and beta-tubulins of Antarctic fishes. J Biol Chem 2000; 275:37038-47. [PMID: 10956651 DOI: 10.1074/jbc.m005699200] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The microtubules of Antarctic fishes, unlike those of homeotherms, assemble at very low temperatures (-1.8 degrees C). The adaptations that enhance assembly of these microtubules are intrinsic to the tubulin dimer and reduce its critical concentration for polymerization at 0 degrees C to approximately 0.9 mg/ml (Williams, R. C., Jr., Correia, J. J., and DeVries, A. L. (1985) Biochemistry 24, 2790-2798). Here we demonstrate that microtubules formed by pure brain tubulins of Antarctic fishes exhibit slow dynamics at both low (5 degrees C) and high (25 degrees C) temperatures; the rates of polymer growth and shortening and the frequencies of interconversion between these states are small relative to those observed for mammalian microtubules (37 degrees C). To investigate the contribution of tubulin primary sequence variation to the functional properties of the microtubules of Antarctic fishes, we have sequenced brain cDNAs that encode 9 alpha-tubulins and 4 beta-tubulins from the yellowbelly rockcod Notothenia coriiceps and 4 alpha-tubulins and 2 beta-tubulins from the ocellated icefish Chionodraco rastrospinosus. The tubulins of these fishes were found to contain small sets of unique or rare residue substitutions that mapped to the lateral, interprotofilament surfaces or to the interiors of the alpha- and beta-polypeptides; longitudinal interaction surfaces are not altered in the fish tubulins. Four changes (A278T and S287T in alpha; S280G and A285S in beta) were present in the S7-H9 interprotofilament "M" loops of some monomers and would be expected to increase the flexibility of these regions. A fifth lateral substitution specific to the alpha-chain (M302L or M302F) may increase the hydrophobicity of the interprotofilament interaction. Two hydrophobic substitutions (alpha:S187A in helix H5 and beta:Y202F in sheet S6) may act to stabilize the monomers in conformations favorable to polymerization. We propose that cold adaptation of microtubule assembly in Antarctic fishes has occurred in part by evolutionary restructuring of the lateral surfaces and the cores of the tubulin monomers.
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Affiliation(s)
- H W Detrich
- Department of Biology, Northeastern University, Boston, Massachusetts 02115, USA
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Modig C, Wallin M, Olsson PE. Expression of cold-adapted beta-tubulins confer cold-tolerance to human cellular microtubules. Biochem Biophys Res Commun 2000; 269:787-91. [PMID: 10720493 DOI: 10.1006/bbrc.2000.2362] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isolated microtubule proteins from the cold-adapted fish, Atlantic cod (Gadus morhua), assemble at temperatures between 8 and 30 degrees C, while avian and mammalian microtubules normally do not assemble at temperatures below 20 degrees C. Tubulin, the main component in microtubules, is expressed as many isotypes. Microtubules with different isotype composition have been shown to have different dynamic properties in vitro. Our hypothesis was that cold-tolerance of microtubules is caused by tubulin isotypes that differ in the primary sequence compared to mammalian tubulins. Here we show that transfection of human HepG2 cells with cod beta-tubulin induced cold-adaptation of the endogenous microtubules. Incorporation of one single tubulin isotype can induce cold-tolerance to cold-intolerant microtubules. Three cod beta-tubulin isotypes were tested and two of these (beta1 and beta2) transferred cold-tolerance to HepG2 microtubules, thus not all cod beta-tubulins were able to confer cold-stability.
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Affiliation(s)
- C Modig
- Department of Zoology/Zoophysiology, Göteborg University, Göteborg, SE 405 30, Sweden.
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