A precedented nuclear genetic code with all three termination codons reassigned as sense codons in the syndinean Amoebophrya sp. ex Karlodinium veneficum

PloS One
Tsvetan R Bachvaroff

Abstract

Amoebophrya is part of an enigmatic, diverse, and ubiquitous marine alveolate lineage known almost entirely from anonymous environmental sequencing. Two cultured Amoebophrya strains grown on core dinoflagellate hosts were used for transcriptome sequencing. BLASTx using different genetic codes suggests that Amoebophyra sp. ex Karlodinium veneficum uses the three typical stop codons (UAA, UAG, and UGA) to encode amino acids. When UAA and UAG are translated as glutamine about half of the alignments have better BLASTx scores, and when UGA is translated as tryptophan one fifth have better scores. However, the sole stop codon appears to be UGA based on conserved genes, suggesting contingent translation of UGA. Neither host sequences, nor sequences from the second strain, Amoebophrya sp. ex Akashiwo sanguinea had similar results in BLASTx searches. A genome survey of Amoebophyra sp. ex K. veneficum showed no evidence for transcript editing aside from mitochondrial transcripts. The dynein heavy chain (DHC) gene family was surveyed and of 14 transcripts only two did not use UAA, UAG, or UGA in a coding context. Overall the transcriptome displayed strong bias for A or U in third codon positions, while the tRNA genome survey showed bias a...Continue Reading

References

Nov 8, 1979·Nature·B G BarrellJ Drouin
Jul 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·F ZinoniA Böck
Jun 14, 1971·Journal of Molecular Biology·D Hirsh, L Gold
Aug 1, 1966·Journal of Molecular Biology·F H Crick
Jun 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·J E HeckmanU L RajBhandary
Jun 11, 1996·Proceedings of the National Academy of Sciences of the United States of America·V N GladyshevT C Stadtman
Nov 1, 1995·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·W P TateD N Wilson
Sep 1, 1997·Molecular Biology and Evolution·P J Keeling, W F Doolittle
Nov 11, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Mar 7, 2001·Current Biology : CB·C A LozuponeL F Landweber
Jul 4, 2002·Journal of Molecular Biology·Senjie LinMichael W Gray
Dec 14, 2002·Biochemical and Biophysical Research Communications·Takashi OsakaTakaharu Mizutani
Dec 31, 2002·The Journal of Eukaryotic Microbiology·John H GundersonD Wayne Coats
Feb 22, 2003·Journal of Molecular Biology·Patrick J Keeling, Brian S Leander
Jun 28, 2005·Nucleic Acids Research·Peter SchattnerTodd M Lowe
Feb 24, 2006·Journal of Molecular Biology·Nicola J PatronPatrick J Keeling
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Huan ZhangSenjie Lin
Jun 2, 2007·Journal of Molecular Evolution·Supratim SenguptaPaul G Higgs
Sep 6, 2008·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Mitsuko Hirosawa-TakamoriHerbert Jäckle
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Nov 4, 2009·The Journal of Eukaryotic Microbiology·Tsvetan R BachvaroffDonald Wayne Coats
Oct 28, 2010·BMC Evolutionary Biology·Ellen CocquytOlivier De Clerck
Apr 27, 2011·The Journal of Eukaryotic Microbiology·Tsvetan R BachvaroffCharles F Delwiche
May 5, 2011·PloS One·Tove M GabrielsenKjetill S Jakobsen
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
May 31, 2011·Journal of Bacteriology·Hyun Sook LeeSang-Jin Kim
Jun 10, 2011·Bioinformatics·Bas E DutilhMartijn A Huynen
Oct 14, 2011·Genome Research·Irwin JungreisManolis Kellis
Nov 15, 2011·Applied and Environmental Microbiology·Tsvetan R BachvaroffD Wayne Coats
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Oct 19, 2013·Molecular Phylogenetics and Evolution·Tsvetan R BachvaroffCharles F Delwiche
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Aug 26, 2016·Nature Protocols·Mihaela PerteaSteven L Salzberg

❮ Previous
Next ❯

Citations

Nov 27, 2019·PloS One·Ira Fleming, Andre R O Cavalcanti
Feb 19, 2021·Nature Communications·Hong ZhangJian Lu
Aug 5, 2021·Evolutionary Bioinformatics Online·Ernest P WilliamsAllen R Place

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
RNA-seq
RNAseq
deamination

Software Mentioned

BLAST
tRNA
blast2GO
tRNAscan
BLASTn
FileMaker Pro
BLASTx
FACIL
SE
Trinity

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.