Anticodon Domain Research Articles

Biallelic mutations in valyl-tRNA synthetase gene VARS are associated with a progressive neurodevelopmental epileptic encephalopathy

Aminoacyl-tRNA synthetases (ARSs) function to transfer amino acids to cognate tRNA molecules, which are required for protein translation. To date, biallelic mutations in 31 ARS genes are known to cause recessive, early-onset severe multi-organ diseases. VARS encodes the only known valine cytoplasmic-localized aminoacyl-tRNA synthetase. Here, we report seven patients from five unrelated families with five different biallelic missense variants in VARS. Subjects present with a range of global developmental delay, epileptic encephalopathy and primary or progressive microcephaly. Longitudinal assessment demonstrates progressive cortical atrophy and white matter volume loss. Variants map to the VARS tRNA binding domain and adjacent to the anticodon domain, and disrupt highly conserved residues. Patient primary cells show intact VARS protein but reduced enzymatic activity, suggesting partial loss of function. The implication of VARS in pediatric neurodegeneration broadens the spectrum of human diseases due to mutations in tRNA synthetase genes.

Cytoplasmic diversity, phylogenetic relationships and molecular evolution of Tunisian Citrus species as inferred from mutational events and pseudogene of chloroplast trnL-trnF spacer

The genus Citrus L. is among the most important fruit trees in the world. In this report, cytoplasmic polymorphism of twenty seven Tunisian Citrus cultivars was explored using the chloroplast trnL-trnF intergenic spacer. Chloroplast sequences showed variation in length and nucleotide content. Haplotype and nucleotide diversity showed low variations. Molecular phylogenetic tree identifies Citrus maternal origins and demonstrates two major groups distinguishing between mandarin and pummelo groups. The trnL-trnF intergenic spacer showed one copy of pseudogene of the original trnF gene in 27 Citrus species at position 275 bp with a size varying from 49 to 63 bp. The anticodon domain was identified as the most conserved element, but one transversion (T−>C) was found in the D-domain. Meanwhile, one transversion (T−>A) and one transition (T−>G) were found in the T-domain. Neutrality tests (Tajima, Fu & Li and Fu) which revealed positive and non-significant values and Pi and θW assume a neutral model of evolution and advocated a constant population size. The study demonstrates the resolving power of trnL-trnF sequence data to prove both pummelo and mandarin gene pool’s contribution in the development of Tunisian secondary species and inferring their genetic and phylogenetic relationships.

Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities.

We describe a family with QARS deficiency due to compound heterozygous QARS mutations, including c.1387G > A (p.R463*) in the catalytic core domain and c.2226C > G (p.Q742H) in the anticodon domain, both previously unreported and predicted damaging. The phenotype of the male index further confirms this specific aminoacyl-transfer RNA (tRNA) synthetase disorder as a novel genetic cause of progressive microcephaly with diffuse cerebral atrophy, severely deficient myelination, intractable seizures, and developmental arrest. However, in contrast to the two hitherto published families, the cerebellum and its myelination are not affected. An awareness that QARS mutations may cause isolated supratentorial changes is crucial for properly directing genetic analysis.

Plastid trnF pseudogenes are present in Jaltomata, the sister genus of Solanum (Solanaceae): Molecular evolution of tandemly repeated structural mutations

Extensive gene duplication arranged in a tandem array is rare in the plastome of embryophytes. Interestingly, we found pseudogene copies of the trnF gene in the genus Jaltomata, the sister genus of Solanum where such gene duplication has been previously reported. In each Jaltomata sequence available we found two pseudogene copies in close 5′-proximity to the original functional gene. The size of each pseudogene copy ranged between 17 and 48bp and the anticodon domain was identified as the most conserved element. A common ATT(G)n motif is particularly interesting and its modifications were found to border the 3′ of the duplicated regions. Other motifs were partial residues, or entire parts of the T- and D-domains, and both domains proved to be variable in length among the pseudogenes identified. The residues of the 3′ and 5′ acceptor stem were not found among the copies. We further compared the newly discovered copies of Jaltomata with those ones previously described from Solanum and inferred phylogenetic relationships of the copies aligned. The evolution of Solanum copies, in contrast to Jaltomata, is hard to explain as resulting only in parsimonious changes since reticulate evolutionary patterns were detected among the copies. The dynamic evolutionary patterns of Solanum might be explained by possible inter- or intrachromosomal recombination.

Structural insights into protein-only RNase P complexed with tRNA.

RNase P is the essential activity removing 5′-leader sequences from transfer RNA precursors. RNase P was always associated with ribonucleoprotein complexes before the discovery of protein-only RNase P enzymes called PRORPs (PROteinaceous RNase P) in eukaryotes. Here we provide biophysical and functional data to understand the mode of action of PRORP enzymes. Activity assays and footprinting experiments show that the anticodon domain of transfer RNA is dispensable, whereas individual residues in D and TψC loops are essential for PRORP function. PRORP proteins are characterized in solution and a molecular envelope is derived from small-angle X-ray scattering. Conserved residues are shown to be involved in the binding of one zinc atom to PRORP. These results facilitate the elaboration of a model of the PRORP/transfer RNA interaction. The comparison with the ribonucleoprotein RNase P/transfer RNA complex suggests that transfer RNA recognition by PRORP proteins is similar to that by ribonucleoprotein RNase P.

27 Structural analyses by NMR reveal insights into the enzymatic mechanism of tRNA t6A modification biosynthesis

Post-transcriptional modification is an inherent feature of RNA maturation and is particularly abundant in transfer RNA (tRNA) where over 90 distinct modifications are found across all phylogenetic groups. Of these, the universally conserved N6-threonylcarbamoyladenosine (t6A) modification 3′-adjacent to the anticodon is essential in translational fidelity for several tRNA species by ensuring accurate codon recognition. Recent studies of the t6A biosynthesis pathway in bacteria have identified four proteins that are necessary and sufficient for in vitro formation: YrdC, YgJD, YjeE and YeaZ. As this enzyme complex is comprised of essential proteins, two of which are unique to bacteria, YeaZ and YjeE, it is a potential target for anti-microbial development. Thus, a detailed understanding of the interactions within this pathway holds significant value but has yet to be accomplished; therefore, further structural characterisation and biochemical analyses are necessary. Of particular interest is YrdC, a universally conserved, monomeric 21 kDa protein that is believed to be the central component of this complex. Using quantitative methods, we have shown that YrdC binds to all components required for t6A biosynthesis: ATP, L-threonine and the unmodified target tRNA. Additionally, we have developed a novel application of saturation transfer difference NMR for detecting protein–RNA interactions and used it to observe the interaction of YrdC with a 17-nt tRNALys anticodon domain truncation. In order to map these binding interfaces under biological conditions, high-resolution structures are vital; therefore, the solution structure of E. coli YrdC was determined by NMR. Several key residues have been identified by 15N-HSQC titrations and molecular docking simulations were performed to map ligand-binding sites and protein–protein interaction interfaces.

MD simulations of HIV-1 RT primer–template complex: effect of modified nucleosides and antisense PNA oligomer

Human immunodeficiency virus type 1 (HIV-1) requires the human tRNA3 Lys as a reverse transcriptase (RT) primer. The annealing of 3’ terminal 18 nucleotides of tRNA3 Lys with the primer binding site (PBS) of viral RNA (vRNA) is crucial for reverse transcription. Additional contacts between the A rich (A-loop) region of vRNA and the anticodon domain of tRNA3 Lys are necessary, which show the specific requirement of tRNA3 Lys. The importance of modified nucleosides, present in tRNA3 Lys, in giving stability to the primer–template complex has been determined in earlier experiments. It has been observed that the PNA oligomer targeted to PBS of vRNA destabilized the crucial interactions between primer and template due to which the reverse transcription is inhibited. Molecular dynamics simulations have been carried out to study the effect of modified nucleosides on the vRNA–tRNA3 Lys complex stability and the destabilization effect of PNA oligomer on the vRNA–tRNA3 Lys–PNA complex. The root-mean-square deviation, hydrogen bonding, tertiary interactions, and free energy calculations of the simulation data support the experimental results. The analyses have revealed the structural changes in PBS region of vRNA which might be another strong reason for the inability of RT binding to 7F helix for its normal functioning of reverse transcription.

Human tRNALys3UUU Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto–Enol Tautomerism

Human tRNALys3UUU (htRNALys3UUU) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency virus type 1) reverse transcription. The posttranscriptional modifications 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A37), and pseudouridine (Ψ39) in the tRNA's anticodon domain are critical for ribosomal binding and HIV-1 reverse transcription. To understand the importance of modified nucleoside contributions, we determined the structure and function of this tRNA's anticodon stem and loop (ASL) domain with these modifications at positions 34, 37, and 39, respectively (hASLLys3UUU-mcm5s2U34;ms2t6A37;Ψ39). Ribosome binding assays in vitro revealed that the hASLLys3UUU-mcm5s2U34;ms2t6A37;Ψ39 bound AAA and AAG codons, whereas binding of the unmodified ASLLys3UUU was barely detectable. The UV hyperchromicity, the circular dichroism, and the structural analyses indicated that Ψ39 enhanced the thermodynamic stability of the ASL through base stacking while ms2t6A37 restrained the anticodon to adopt an open loop conformation that is required for ribosomal binding. The NMR-restrained molecular-dynamics-derived solution structure revealed that the modifications provided an open, ordered loop for codon binding. The crystal structures of the hASLLys3UUU-mcm5s2U34;ms2t6A37;Ψ39 bound to the 30S ribosomal subunit with each codon in the A site showed that the modified nucleotides mcm5s2U34 and ms2t6A37 participate in the stability of the anticodon–codon interaction. Importantly, the mcm5s2U34·G3 wobble base pair is in the Watson–Crick geometry, requiring unusual hydrogen bonding to G in which mcm5s2U34 must shift from the keto to the enol form. The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons.

YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase

The post-transcriptional nucleoside modifications of tRNA's anticodon domain form the loop structure and dynamics required for effective and accurate recognition of synonymous codons. The N(6)-threonylcarbamoyladenosine modification at position 37 (t(6)A(37)), 3'-adjacent to the anticodon, of many tRNA species in all organisms ensures the accurate recognition of ANN codons by increasing codon affinity, enhancing ribosome binding, and maintaining the reading frame. However, biosynthesis of this complex modification is only partially understood. The synthesis requires ATP, free threonine, a single carbon source for the carbamoyl, and an enzyme yet to be identified. Recently, the universal protein family Sua5/YciO/YrdC was associated with t(6)A(37) biosynthesis. To further investigate the role of YrdC in t(6)A(37) biosynthesis, the interaction of the Escherichia coli YrdC with a heptadecamer anticodon stem and loop of lysine tRNA (ASL(Lys)(UUU)) was examined. YrdC bound the unmodified ASL(Lys)(UUU) with high affinity compared with the t(6)A(37)-modified ASL(Lys)(UUU) (K(d) = 0.27 ± 0.20 μM and 1.36 ± 0.39 μM, respectively). YrdC also demonstrated specificity toward the unmodified versus modified anticodon pentamer UUUUA and toward threonine and ATP. The protein did not significantly alter the ASL architecture, nor was it able to base flip A(37), as determined by NMR, circular dichroism, and fluorescence of 2-aminopuine at position 37. Thus, current data support the hypothesis that YrdC, with many of the properties of a putative threonylcarbamoyl transferase, most likely functions as a component of a heteromultimeric protein complex for t(6)A(37) biosynthesis.

Functional Recognition of the Modified Human tRNA Lys3UUU Anticodon Domain by HIV's Nucleocapsid Protein and a Peptide Mimic

The HIV-1 nucleocapsid protein, NCp7, facilitates the use of human tRNA Lys3 UUU as the primer for reverse transcription. NCp7 also remodels the htRNA's amino acid accepting stem and anticodon domains in preparation for their being annealed to the viral genome. To understand the possible influence of the htRNA's unique composition of post-transcriptional modifications on NCp7 recognition of htRNA Lys3 UUU, the protein's binding and functional remodeling of the human anticodon stem and loop domain (hASL Lys3) were studied. NCp7 bound the hASL Lys3 UUU modified with 5-methoxycarbonylmethyl-2-thiouridine at position-34 (mcm 5s 2U 34) and 2-methylthio- N 6 -threonylcarbamoyladenosine at position-37 (ms 2t 6A 37) with a considerably higher affinity than the unmodified hASL Lys3 UUU ( K d = 0.28 ± 0.03 and 2.30 ± 0.62 μM, respectively). NCp7 denatured the structure of the hASL Lys3 UUU-mcm 5s 2U 34;ms 2t 6A 37;Ψ 39 more effectively than that of the unmodified hASL Lys3 UUU. Two 15 amino acid peptides selected from phage display libraries demonstrated a high affinity (average K d = 0.55 ± 0.10 μM) and specificity for the ASL Lys3 UUU-mcm 5s 2U 34;ms 2t 6A 37 comparable to that of NCp7. The peptides recognized a t 6A 37-modified ASL with an affinity ( K d = 0.60 ± 0.09 μM) comparable to that for hASL Lys3 UUU-mcm 5s 2U 34;ms 2t 6A 37, indicating a preference for the t 6A 37 modification. Significantly, one of the peptides was capable of relaxing the hASL Lys3 UUU-mcm 5s 2U 34;ms 2t 6A 37;Ψ 39 structure in a manner similar to that of NCp7, and therefore could be used to further study protein recognition of RNA modifications. The post-transcriptional modifications of htRNA Lys3 UUU have been found to be important determinants of NCp7's recognition prior to the tRNA Lys3 UUU being annealed to the viral genome as the primer of reverse transcription.

The structure of the human tRNALys3 anticodon bound to the HIV genome Loop I is stabilized by modified nucleosides

Replication of HIV requires base pairing of the reverse transcriptase primer, human tRNALys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence and the tRNA's 3′‐terminus, an important discriminatory, secondary contact occurs between the viral A‐rich Loop I and the modified, U‐rich anticodon domain of tRNALys3. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral serosubtypes G and B were analyzed by UV and CD and the structure of one duplex was determined using NMR spectroscopy and restrained molecular dynamics. Thiouridine, s2U34, and pseudouridine, ?39, modifications appreciably stabilized the interaction of the anticodon region with the viral RNAs. The structure of the duplex composed of the HIV‐1 Loop I bound to a doubly modified tRNA's anticodon region resulted in two coaxially stacked A‐form RNA stems separated by two mismatched base pairs, U?? and G?A, that maintained a reasonable helix diameter. Thus, the important interaction of the primer's anticodon region with the viral RNA is strengthened by s2U34 and ?39 modifications that facilitate duplex interaction. This research was supported by a National Institutes of Health grant and National Science Foundation grants.

The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNALys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3′-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5′-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNALys3. The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s2U34, and pseudouridine, Ψ39, appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U162•Ψ39 and G163•A38, that maintained a reasonable A-form helix diameter. The tRNA's s2U34 stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Ψ39 stabilized the adjacent mismatched pairs.

Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNAMet

Human mitochondrial methionine transfer RNA (hmtRNAMetCAU) has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position-34 (f5C34). The role of this modification in (hmtRNAMetCAU) for the decoding of AUA, as well as AUG, in both the peptidyl- and aminoacyl-sites of the ribosome in either chain initiation or chain elongation is still unknown. We report the first synthesis and analyses of the tRNA's anticodon stem and loop domain containing the 5-formylcytidine modification. The modification contributes to the tRNA's anticodon domain structure, thermodynamic properties and its ability to bind codons AUA and AUG in translational initiation and elongation.

Evolution of trnF(GAA) pseudogenes in cruciferous plants

In several studies we used the 5′-trnL(UAA)-trnF(GAA) region of the chloroplast DNA for phylogeographic reconstructions, gene diversity calculations and phylogenetic analyses among the genera Arabidopsis and Boechera. Despite the fact that extensive gene duplications are rare within the chloroplast genome of higher plants, within several genera of the Brassicaceae the anticodon domain of the trnF(GAA) gene exhibit extensive gene duplications with 1-12 tandemly repeated copies in close 5′-proximity of the functional gene. A recent re-examination and additional analysis of trnL(UAA)-trnF(GAA) regions from numerous cruciferous taxa not only reveal extensive trnF gene duplications, but also favour the hypothesis that in cruciferous taxa at least four independent phylogenetic lineages are characterized by these pseudogenes. Among these lineages there is one major clade of taxa carrying pseudogenes indicating an ancient split in crucifer evolution. In two case studies, Boechera and Arabidopsis, intra- and inter-molecular recombinations have been shown to be the reason for the reciprocal exchange of several similar motifs. However, functional constraints might favour two to three or five to six copies as shown for Arabidopsis and Boechera. Herein, we compare the occurrence and distribution of pseudogene copy number in the framework of a comprehensive survey of cpDNA haplotype variation in Boechera, the former genus Cardaminopsis and Arabidopsis thaliana and comment on the value of such kind of mutations in phylogenetic and evolutionary reconstructions.

Bringing order to translation: the contributions of transfer RNA anticodon‐domain modifications

The biosynthesis of RNA includes its post-transcriptional modifications, and the crucial functions of these modifications have supported their conservation within all three kingdoms. For example, the modifications located within or adjacent to the anticodon of the transfer RNA (tRNA) enhance the accuracy of codon binding, maintain the translational reading frame and enable translocation of the tRNA from the A-site to the P-site of the ribosome. Although composed of different chemistries, the more than 70 known modifications of tRNA have in common their ability to reduce conformational dynamics, and to bring order to the internal loops and hairpin structures of RNA. The modified nucleosides of the anticodon domain of tRNA restrict its dynamics and shape its architecture; therefore, the need of the ribosome to constrain or remodel each tRNA to fit the decoding site is diminished. This concept reduces an entropic penalty for translation and provides a physicochemical basis for the conservation of RNA modifications in general.

Anticodon Domain Modifications Contribute Order to tRNA for Ribosome-Mediated Codon Binding

The accuracy and efficiency with which tRNA decodes genomic information into proteins require posttranscriptional modifications in or adjacent to the anticodon. The modification uridine-5-oxyacetic acid (cmo (5)U 34) is found at wobble position 34 in a single isoaccepting tRNA species for six amino acids, alanine, leucine, proline, serine, threonine, and valine, each having 4-fold degenerate codons. cmo (5)U 34 makes possible the decoding of 24 codons by just six tRNAs. The contributions of this important modification to the structures and codon binding affinities of the unmodified and fully modified anticodon stem and loop domains of tRNA (Val3) UAC (ASL (Val3) UAC) were elucidated. The stems of the unmodified ASL (Val3) UAC and that with cmo (5)U 34 and N (6)-methyladenosine, m (6)A 37, adopted an A-form RNA conformation (rmsd approximately 0.6 A) as determined with NMR spectroscopy and torsion-angle molecular dynamics. However, the UV hyperchromicity, circular dichroism ellipticity, and structural analyses indicated that the anticodon modifications enhanced order in the loop. ASL (Val3) UAC-cmo (5)U 34;m (6)A 37 exhibited high affinities for its cognate and wobble codons GUA and GUG, and for GUU in the A-site of the programmed 30S ribosomal subunit, whereas the unmodified ASL (Val3) UAC bound less strongly to GUA and not at all to GUG and GUU. Together with recent crystal structures of ASL (Val3) UAC-cmo (5)U 34;m (6)A 37 bound to all four of the valine codons in the A-site of the ribosome's 30S subunit, these results clearly demonstrate that the xo (5)U 34-type modifications order the anticodon loop prior to A-site codon binding for an expanded codon reading, possibly reducing an entropic energy barrier to codon binding.

Functional guanine–arginine interaction between tRNA Pro and prolyl-tRNA synthetase that couples binding and catalysis

Aminoacyl-tRNA synthetases catalyze the attachment of specific amino acids to their cognate tRNAs. Specific aminoacylation is dictated by a set of recognition elements that mark tRNA molecules as substrates for particular synthetases. Escherichia coli prolyl-tRNA synthetase (ProRS) has previously been shown to recognize specific bases of tRNA Pro in both the anticodon domain, which mediate initial complex formation, and in the acceptor stem, which is proximal to the site of catalysis. In this work, we unambiguously define the molecular interaction between E. coli ProRS and the acceptor stem of cognate tRNA Pro. Oxidative cross-linking studies using 2'-deoxy-8-oxo-7,8-dihydroguanosine-containing proline tRNAs identify a direct interaction between a critical arginine residue (R144) in the active site of E. coli ProRS and the G72 residue in the acceptor stem of tRNA Pro. Assays conducted with motif 2 loop variants and tRNA mutants wherein specific atomic groups of G72 were deleted, are consistent with a functionally important hydrogen-bonding network between R144 and the major groove of G72. These results taken together with previous studies suggest that breaking this key contact uncouples the allosteric interaction between the anticodon domain and the aminoacylation active site, providing new insights into the communication network that governs the synthetase–tRNA interaction.

E. coli Glutamyl-tRNA Synthetase is Inhibited by Anticodon Stem-Loop Domains and a Minihelix

Portions of E. coli tRNAGlu having identity determinants for glutamyl-tRNA synthetase (ERS, EC 6.1.1.17) have been designed to be the first RNA inhibitors of a Class I synthetase. ERS recognizes the 2-thionyl group of 2-thio-5-methylaminomethyluridine (mnm5s2U34) in the first or wobble anticodon position of E. coli tRNAGlu. The interaction, as revealed by structural analysis, though specific, appears tenuous. Thus, it is surprising that RNAs designed from this tRNA's anticodon stem and loop domain with (ASLGlu-s2U34) and without s2U34 are bound by ERS and inhibit aminoacylation of the native tRNA. ASLGlu, ASLGlu-s2U34, and a minihelixGlu composed of identity determinants of the amino acid accepting stem were thermally stable under conditions of aminoacylation (Tms = 75 ± 1.5, 76 ± 0.9 and 83 ± 2.0 °C, respectively). In binding competition, the modified ASLGlu-s2U34 bound ERS with a higher affinity (half maximal inhibiting concentration, IC50, 5.1 ± 0.4 µM) than its unmodified counterpart, ASLGlu (IC50, 10.3 ± 0.6 µM). The minihelixGlu, ASLGlu-s2U34, and ASLGlu bound ERS with Kds of 9.9 ± 3.3, 6.5 ± 1.7 and 20.5 ± 3.8 µM. ERS aminoacylation of tRNAGlu was inhibited by the tRNA fragments. Unmodified ASLGlu, minihelixGlu, and ASLGlu-s2U34 exhibited a Kic of 1.9 ± 0.2 µM, 4.1 ± 0.2 µM, and 6.5 ± 0.1 µM, respectively. The modified ASLGlu-s2U34, though having a higher affinity for ERS, may be released more readily and thus, not be as good an inhibitor as the unmodified ASL. Thus, the RNA constructs are effective tools to study RNA-protein interaction.

Supernetwork Identifies Multiple Events of Plastid trnF(GAA) Pseudogene Evolution in the Brassicaceae

The occurrence of nonfunctional trnF pseudogenes has been rarely described in flowering plants. However, we describe the first large-scale supernetwork for the Brassiccaeae built from gene trees for 5 loci (adh, chs, matK, trnL-F, and ITS) and report multiple independent origins for trnF pseudogenes in crucifers. The duplicated regions of the original trnF gene are comprised of its anticodon domain and several other highly structured motifs not related to the original gene. Length variation of the trnL-F intergenic spacer region in different taxa ranges from 219 to 900 bp as a result of differences in pseudocopy number (1-14). It is speculated that functional constraints favor 2-3 or 5-6 copies, as found in Arabidopsis and Boechera. The phylogenetic distribution of microstructural changes for the trnL-F region supports ancient patterns of divergence in crucifer evolution for some but not all gene loci.

Introduction of Hypermodified Nucleotides in RNA

AbstractFor Abstract see ChemInform Abstract in Full Text.