• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4635019)   Today's Articles (6910)   Subscriber (50001)
For: Shulgina Y, Eddy SR. A computational screen for alternative genetic codes in over 250,000 genomes. eLife 2021;10:71402. [PMID: 34751130 PMCID: PMC8629427 DOI: 10.7554/elife.71402] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022]  Open
Number Cited by Other Article(s)
1
Qin W, Hu C, Gu S, Zhang J, Jiang C, Chai X, Liao Z, Yang M, Zhou F, Kang D, Pan T, Xiao Y, Chen K, Wang G, Ge F, Huang K, Zhang C, Warren A, Xiong J, Miao W. Dynamic shape-shifting of the single-celled eukaryotic predator Lacrymaria via unconventional cytoskeletal components. Curr Biol 2024:S0960-9822(24)01214-4. [PMID: 39353425 DOI: 10.1016/j.cub.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 07/07/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024]
2
Eren AM, Banfield JF. Modern microbiology: Embracing complexity through integration across scales. Cell 2024;187:5151-5170. [PMID: 39303684 PMCID: PMC11450119 DOI: 10.1016/j.cell.2024.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 09/22/2024]
3
Schuntermann DB, Jaskolowski M, Reynolds NM, Vargas-Rodriguez O. The central role of transfer RNAs in mistranslation. J Biol Chem 2024;300:107679. [PMID: 39154912 PMCID: PMC11415595 DOI: 10.1016/j.jbc.2024.107679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024]  Open
4
Ó Cinnéide E, Scaife C, Dillon ET, Wolfe KH. Evolution of the Genetic Code in the Ascoideales (CUG-Ser2) Yeast Clade: The Ancestral tRNA-Leu(CAG) Gene Is Retained in Most Saccharomycopsis Species but Is Nonessential and Not Used for Translation. Genome Biol Evol 2024;16:evae166. [PMID: 39081261 PMCID: PMC11342251 DOI: 10.1093/gbe/evae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2024] [Indexed: 08/24/2024]  Open
5
Salman A, Biziaev N, Shuvalova E, Alkalaeva E. mRNA context and translation factors determine decoding in alternative nuclear genetic codes. Bioessays 2024;46:e2400058. [PMID: 38724251 DOI: 10.1002/bies.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024]
6
Rozhoňová H, Martí-Gómez C, McCandlish DM, Payne JL. Robust genetic codes enhance protein evolvability. PLoS Biol 2024;22:e3002594. [PMID: 38754362 PMCID: PMC11098591 DOI: 10.1371/journal.pbio.3002594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/19/2024] [Indexed: 05/18/2024]  Open
7
Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 2024;384:eadj4503. [PMID: 38662846 PMCID: PMC11298794 DOI: 10.1126/science.adj4503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
8
Pan J, Wang Y, Li C, Zhang S, Ye Z, Ni J, Li H, Li Y, Yue H, Ruan C, Zhao D, Jiang Y, Wu X, Shen X, Zufall RA, Zhang Y, Li W, Lynch M, Long H. Molecular basis of phenotypic plasticity in a marine ciliate. THE ISME JOURNAL 2024;18:wrae136. [PMID: 39018220 PMCID: PMC11308186 DOI: 10.1093/ismejo/wrae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 07/19/2024]
9
Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial genome diversity across the subphylum Saccharomycotina. Front Microbiol 2023;14:1268944. [PMID: 38075892 PMCID: PMC10701893 DOI: 10.3389/fmicb.2023.1268944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/31/2023] [Indexed: 12/20/2023]  Open
10
Yarus M. The Genetic Code Assembles via Division and Fusion, Basic Cellular Events. Life (Basel) 2023;13:2069. [PMID: 37895450 PMCID: PMC10608286 DOI: 10.3390/life13102069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]  Open
11
McGowan J, Kilias ES, Alacid E, Lipscombe J, Jenkins BH, Gharbi K, Kaithakottil GG, Macaulay IC, McTaggart S, Warring SD, Richards TA, Hall N, Swarbreck D. Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids. PLoS Genet 2023;19:e1010913. [PMID: 37796765 PMCID: PMC10553269 DOI: 10.1371/journal.pgen.1010913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/10/2023] [Indexed: 10/07/2023]  Open
12
Opulente DA, Leavitt LaBella A, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Beth Hulfachor A, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic and ecological factors shaping specialism and generalism across an entire subphylum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.19.545611. [PMID: 37425695 PMCID: PMC10327049 DOI: 10.1101/2023.06.19.545611] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
13
Manzano-Marín A, Kvist S, Oceguera-Figueroa A. Evolution of an Alternative Genetic Code in the Providencia Symbiont of the Hematophagous Leech Haementeria acuecueyetzin. Genome Biol Evol 2023;15:evad164. [PMID: 37690114 PMCID: PMC10540940 DOI: 10.1093/gbe/evad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]  Open
14
Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial Genome Diversity across the Subphylum Saccharomycotina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551029. [PMID: 37577532 PMCID: PMC10418067 DOI: 10.1101/2023.07.28.551029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
15
Rosandić M, Paar V. The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code. Int J Mol Sci 2023;24:12029. [PMID: 37569405 PMCID: PMC10418607 DOI: 10.3390/ijms241512029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]  Open
16
Pfennig A, Lomsadze A, Borodovsky M. MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes. J Mol Biol 2023;435:168159. [PMID: 37244571 DOI: 10.1016/j.jmb.2023.168159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 05/29/2023]
17
Gaydukova SA, Moldovan MA, Vallesi A, Heaphy SM, Atkins JF, Gelfand MS, Baranov PV. Nontriplet feature of genetic code in Euplotes ciliates is a result of neutral evolution. Proc Natl Acad Sci U S A 2023;120:e2221683120. [PMID: 37216548 PMCID: PMC10235951 DOI: 10.1073/pnas.2221683120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/12/2023] [Indexed: 05/24/2023]  Open
18
Valášek LS, Lukeš J, Paris Z. Stops making sense - For the people? Clin Transl Med 2023;13:e1270. [PMID: 37203266 PMCID: PMC10196215 DOI: 10.1002/ctm2.1270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]  Open
19
Chen W, Geng Y, Zhang B, Yan Y, Zhao F, Miao M. Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates. Mol Biol Evol 2023;40:msad064. [PMID: 36952281 PMCID: PMC10089648 DOI: 10.1093/molbev/msad064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/13/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023]  Open
20
Zhang J, Qin W, Hu C, Gu S, Chai X, Yang M, Zhou F, Wang X, Chen K, Yan G, Wang G, Jiang C, Warren A, Xiong J, Miao W. Giant proteins in a giant cell: Molecular basis of ultrafast Ca2+-dependent cell contraction. SCIENCE ADVANCES 2023;9:eadd6550. [PMID: 36812318 PMCID: PMC9946354 DOI: 10.1126/sciadv.add6550] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
21
Shulgina Y, Eddy SR. Codetta: predicting the genetic code from nucleotide sequence. Bioinformatics 2023;39:6895099. [PMID: 36511586 PMCID: PMC9825746 DOI: 10.1093/bioinformatics/btac802] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/10/2022] [Indexed: 12/15/2022]  Open
22
Kachale A, Pavlíková Z, Nenarokova A, Roithová A, Durante IM, Miletínová P, Záhonová K, Nenarokov S, Votýpka J, Horáková E, Ross RL, Yurchenko V, Beznosková P, Paris Z, Valášek LS, Lukeš J. Short tRNA anticodon stem and mutant eRF1 allow stop codon reassignment. Nature 2023;613:751-758. [PMID: 36631608 DOI: 10.1038/s41586-022-05584-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 11/18/2022] [Indexed: 01/13/2023]
23
Zürcher JF, Robertson WE, Kappes T, Petris G, Elliott TS, Salmond GPC, Chin JW. Refactored genetic codes enable bidirectional genetic isolation. Science 2022;378:516-523. [PMID: 36264827 PMCID: PMC7614150 DOI: 10.1126/science.add8943] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
24
Viruses, immunity and evolution. Biosystems 2022;220:104761. [PMID: 35998747 DOI: 10.1016/j.biosystems.2022.104761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 12/25/2022]
25
Wang X, Dong Q, Chen G, Zhang J, Liu Y, Cai Y. Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance. BMC Genomics 2022;23:416. [PMID: 35655139 PMCID: PMC9164415 DOI: 10.1186/s12864-022-08435-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022]  Open
26
Borges AL, Lou YC, Sachdeva R, Al-Shayeb B, Penev PI, Jaffe AL, Lei S, Santini JM, Banfield JF. Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes. Nat Microbiol 2022;7:918-927. [PMID: 35618772 PMCID: PMC9197471 DOI: 10.1038/s41564-022-01128-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
27
Weinheimer AR, Aylward FO. Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages. THE ISME JOURNAL 2022;16:1657-1667. [PMID: 35260829 PMCID: PMC9123017 DOI: 10.1038/s41396-022-01214-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 11/08/2022]
28
Zhang B, Hou L, Qi H, Hou L, Zhang T, Zhao F, Miao M. An extremely streamlined macronuclear genome in the free-living protozoan Fabrea salina. Mol Biol Evol 2022;39:6553891. [PMID: 35325184 PMCID: PMC9004412 DOI: 10.1093/molbev/msac062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
29
DeBenedictis EA, Söll D, Esvelt KM. Measuring the tolerance of the genetic code to altered codon size. eLife 2022;11:76941. [PMID: 35293861 PMCID: PMC9094753 DOI: 10.7554/elife.76941] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022]  Open
30
Baranov PV, Atkins JF. Immune cells alter genetic decoding in cancer. Nature 2022;603:582-583. [PMID: 35264802 DOI: 10.1038/d41586-022-00637-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA