prime untranslated region  (Genecopoeia)

Journal: BMC Evolutionary Biology

Article Title: Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae

doi: 10.1186/s12862-015-0491-1

Figure Lengend Snippet: Sample alignments showing the consensus initiation codon (cic) and subsequent translation products for MatK in orchids. (a) Nucleotide alignment of various orchid species and the non-orchid monocot species Asparagus aethiopicus , Hordeum vulgare , Saccharum officinarum and Oryza sativa . Asterisks next to species name indicate those noted in GenBank to contain matK as a pseudogene. Black arrow indicates cic used by other monocots and angiosperms for MatK expression. (b) Translated MatK amino acid sequence using the cic. Asterisk in translated amino acid sequence indicates stop codons in the MatK reading frame. Gray shadowing indicates highly conserved sequence among all taxa in the alignment, lighter gray indicates less conserved sequence, white background indicates a lack of conserved sequence. Note: gaps in nucleotide and amino acid alignment differ in relative position due to indel in Palmorchis trilobulata

Article Snippet: Five prime untranslated region of matK from Hordeum vulgare , Saccharum officinarum and Oryza sativa shown for contrast in sequence between non-orchid monocots and orchids in this region. (b) Translated MatK amino acid sequence using the aic for species previously containing premature stop codons when translated with the cic ( Phaius tancarvilleae , Govenia sp., Oreorchis sp., Cremastra appendiculata , Cryptostylis erecta , Caladenia catenata , Spiranthes sinensis , S. vernalis and S. cernua ).

Techniques: Expressing, Sequencing

Journal: BMC Evolutionary Biology

Article Title: Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae

doi: 10.1186/s12862-015-0491-1

Figure Lengend Snippet: Sample alignments showing the alternative initiation codon (aic) and subsequent MatK translation products. (a) Nucleotide alignment starting at the aic of the same sample orchid species and non-orchid monocot species ( Asparagus aethiopicus , Hordeum vulgare , Saccharum officinarum and Oryza sativa ) as in Figure . Asterisks indicate species noted in GenBank to contain matK as a pseudogene. Gray arrow shows hypothesized out-of-frame alternative initiation codon. Black arrow indicates consensus initiation codon (cic) used by other monocots and angiosperms for matK expression. The ‘-6’ indicates the position of the upstream initiation codon in-frame with the cic. Underlined sections are indels that realign the matK reading frame for translation using the consensus vs. the alternative initiation codon . Five prime untranslated region of matK from Hordeum vulgare , Saccharum officinarum and Oryza sativa shown for contrast in sequence between non-orchid monocots and orchids in this region. (b) Translated MatK amino acid sequence using the aic for species previously containing premature stop codons when translated with the cic ( Phaius tancarvilleae , Govenia sp. , Oreorchis sp. , Cremastra appendiculata , Cryptostylis erecta , Caladenia catenata , Spiranthes sinensis , S. vernalis and S. cernua ). Asterisks in translated amino acid sequence indicates stop codons in the MatK reading frame. Large gaps in N-terminus of MatK amino acid sequence are indicative of the 11 amino acids different between translations using the aic vs the cic, not true indels. The 11 amino acids that differ due to translation initiation codon are boxed for clarity. Gray shadowing indicates highly conserved sequence among all taxa in the alignment, lighter gray indicates less conserved sequence, white background indicates a lack of conserved sequence

Article Snippet: Five prime untranslated region of matK from Hordeum vulgare , Saccharum officinarum and Oryza sativa shown for contrast in sequence between non-orchid monocots and orchids in this region. (b) Translated MatK amino acid sequence using the aic for species previously containing premature stop codons when translated with the cic ( Phaius tancarvilleae , Govenia sp., Oreorchis sp., Cremastra appendiculata , Cryptostylis erecta , Caladenia catenata , Spiranthes sinensis , S. vernalis and S. cernua ).

Techniques: Expressing, Sequencing

Journal: BMC Evolutionary Biology

Article Title: Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae

doi: 10.1186/s12862-015-0491-1

Figure Lengend Snippet: Immunoblot detection of MatK from orchid species. Orchid protein was resolved by SDS-PAGE and transferred to nitrocellulose membrane. MatK protein was detected using anti-MatK antibody as described in Barthet and Hilu . Orchid species analysed represent two different subfamilies of Orchidaceae (Orchidoideae: Spiranthes vernalis, S. cernua , S. sinensis , Caladenia catenata and Cryptostylis erecta and Epidendroideae: Phaius tancarvilleae ) and are representative of orchids that require the alternative initiation codon for full-length MatK translation (Figure ). All immunoblots were repeated twice to verify results. (a) Immunoblot detection of MatK from 50 μg of total protein from Spiranthes vernalis, S. cernua and Phaius tancarvilleae . N = 3 biological replicates. Mass standard = PageRuler Prestained Protein Ladder (Thermo Scientific). Ponceau S stain of RbcS shown as loading control. (b) Immunoblot detection of MatK from 75 μg of total protein from Caladenia catenata , Cryptostylis erecta and Spiranthes sinensis . N = 1 biological replicate due to tissue limitations. Oryza sativa (rice) was used as a control for detection. Mass standard = 6–185 kDa Protein Ladder (NEB). Ponceau S stain of RbcS shown as loading control. All immunoblots were repeated twice to verify results. (c) Alignment of MatK peptide region used for antibody generation to orchid species examined in this study

Article Snippet: Five prime untranslated region of matK from Hordeum vulgare , Saccharum officinarum and Oryza sativa shown for contrast in sequence between non-orchid monocots and orchids in this region. (b) Translated MatK amino acid sequence using the aic for species previously containing premature stop codons when translated with the cic ( Phaius tancarvilleae , Govenia sp., Oreorchis sp., Cremastra appendiculata , Cryptostylis erecta , Caladenia catenata , Spiranthes sinensis , S. vernalis and S. cernua ).

Techniques: Western Blot, SDS Page, Membrane, Staining, Control

Journal: BMC Evolutionary Biology

Article Title: Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae

doi: 10.1186/s12862-015-0491-1

Figure Lengend Snippet: Accessions used for alignments in Figs. 1 and 2 . Designation of matK functionality in GenBank and species taxonomic affiliation are noted

Article Snippet: Five prime untranslated region of matK from Hordeum vulgare , Saccharum officinarum and Oryza sativa shown for contrast in sequence between non-orchid monocots and orchids in this region. (b) Translated MatK amino acid sequence using the aic for species previously containing premature stop codons when translated with the cic ( Phaius tancarvilleae , Govenia sp., Oreorchis sp., Cremastra appendiculata , Cryptostylis erecta , Caladenia catenata , Spiranthes sinensis , S. vernalis and S. cernua ).

Techniques: Functional Assay