Initiator tRNA Genes Template the 3’CCA End at High Frequencies in Bacteria

Ardell, David H.; Hou, Ya‐Ming

doi:10.1101/035220

Cited by 3 publications

(3 citation statements)

References 56 publications

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“…It has been reported that in bacteria, CCA tails were sometimes included in tRNA gene templates. It has been reported that the templated 3'CCA sequence in bacteria was very common in the initial tRNA (tRNA fMet ), and it was also common in tRNA Tyr [58]. Coincidentally, in our gymnosperm plant chloroplast tRNA gene, tRNA fMet and tRNA Tyr of each species all carried the encoded 3'CCA sequence.…”

Section: Distribution Of Anti-codonmentioning

confidence: 47%

Evolution and Structural Variations of Chloroplast tRNAs in Gymnosperms

Zhao¹,

Zhou²,

Zhang³

et al. 2020

Preprint

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Background: Transfer RNAs can participate in a variety of vital life activities. The gymnosperms with important ecological and economic values were the dominant and constructive species in the forest ecosystems in the North hemisphere. However, evolution and structural changes of chloroplast tRNA in gymnosperms remain largely unclear.Results: In this study, the nucleotide evolution, phylogenetic relationships and structural variations of 1,779 chloroplast tRNAs in gymnosperms were determined. The number and types of tRNA genes contained in the chloroplast genome of different gymnosperms were not much different, the average amount of tRNA contained was 33, and the occurrence frequency of various types of tRNA in gymnosperms was generally consistent. Nearly half of the anti-codons were absent. Molecular sequence variation analysis revealed the conservative secondary structure of tRNA. About a quarter of the tRNA genes were found to contain precoded 3’ CCA tails. A few tRNAs underwent novel structural changes that were closely related to their minimum free energy, these structural changes affected the stability of tRNA. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors and tRNALeu was the most primitive type of tRNA. The transition rate of chloroplast tRNAs was higher than the transversion rate in gymnosperms. The tRNAs continuously have experienced more loss than duplication events during the evolutionary process. Conclusions: These findings provided novel insights into the molecular evolution and biological characteristics of the chloroplast tRNA in gymnosperms.

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Section: Distribution Of Anti-codonmentioning

confidence: 47%

Evolution and Structural Variations of Chloroplast tRNAs in Gymnosperms

Zhao¹,

Zhou²,

Zhang³

et al. 2020

Preprint

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“…We annotated the functional types of tRNA genes either as elongator isotypes by anticodon alone or, for those containing the CAU anticodon, into initiator tRNA Met (”X”), elongator tRNA Met , or tRNA Ile CA U (”J”) using TFAM v1.4 [4] with the TFAM model used in [3, 5]. We aligned tRNA sequences using COVEA v2.4.4 [19] and the prokaryotic tRNA covariance model from tRNAscan-SE [34].…”

Section: Methodsmentioning

confidence: 99%

Robust Estimation of the Phylogenetic Origin of Plastids Using a tRNA-Based Phyloclassifier

Lawrence

Kch

et al. 2018

Preprint

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The trait of oxygenic photosynthesis was acquired by the last common ancestor of Archaeplastida through endosymbiosis of the cyanobacterial progenitor of modern-day plastids. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies report contradictory evidence that plastids branch either early or late within the cyanobacterial Tree of Life. Here we describe CYANO-MLP, a general-purpose phyloclassifier of cyanobacterial genomes implemented using a Multi-Layer Perceptron. CYANO-MLP exploits consistent phylogenetic signals in bioinformatically estimated structure-function maps of tRNAs. CYANO-MLP accurately classifies cyanobacterial genomes into one of eight well-supported cyanobacterial clades in a manner that is robust to missing data, unbalanced data and variation in model specification. CYANO-MLP supports a late-branching origin of plastids: we classify 99.32% of 440 plastid genomes into one of two late-branching cyanobacterial clades with strong statistical support, and confidently assign 98.41% of plastid genomes to one late-branching clade containing unicellular starch-producing marine/freshwater diazotrophic Cyanobacteria. CYANO-MLP correctly classifies the chromatophore of Paulinella chromatophora and rejects a sister relationship between plastids and the early-branching cyanobacterium Gloeomargarita lithophora. We show that recently applied phylogenetic models and character recoding strategies fit cyanobacterial/plastid phylogenomic datasets poorly, because of heterogeneity both in substitution processes over sites and compositions over lineages.

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“…21 For mycobacteria, the 3'-CCA of each tRNA is variably genomically encoded or added post-transcriptionally. 22 The resulting non-redundant reference library is then used to align forward and reverse sequencing reads, first separating uniquely aligned reads from reads matching multiple sequences in the library. Even with careful library curation, high sequence similarity or insufficient read length can result in multiply-mapped reads.…”

Section: Aqrna-seq Data Processing Workflowmentioning

confidence: 99%

Sequencing-based quantitative mapping of the cellular small RNA landscape

Yim

Huber

et al. 2019

Preprint

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Current next-generation RNA sequencing methods cannot provide accurate quantification of the population of small RNAs within a sample due to strong sequence-dependent biases in capture, ligation, and amplification during library preparation. We report the development of an RNA sequencing method -AQRNA-seq -that minimizes biases and enables absolute quantification of all small RNA species in a sample mixture. Validation of AQRNA-seq library preparation and data mining algorithms using a 963-member microRNA reference library, RNA oligonucleotide standards of varying lengths, and northern blots demonstrated a direct, linear correlation between sequencing read count and RNA abundance. Application of AQRNA-seq to bacterial tRNA pools, a traditionally hard-to-sequence class of RNAs, revealed 80-fold variation in tRNA isoacceptor copy numbers, patterns of site-specific tRNA fragmentation caused by stress, and quantitative maps of ribonucleoside modifications, all in a single AQRNA-seq experiment.AQRNA-seq thus provides a means to quantitatively map the small RNA landscape in cells and tissues.Next generation RNA sequencing platforms (RNA-seq) have advanced functional genomics by facilitating discoveries of new RNA species, gene annotations, and quantitative analysis of gene expression. 1, 2 RNA-seq has played a central role in unravelling the complexity of RNA function by facilitating quantitative profiling of the transcriptome as a function of cell state.Although a variety of RNA-seq methods provide precise and accurate analysis of changes in transcript abundance between samples or conditions, their major drawback is the inability to accurately quantify small RNA species within a sample. This is partly rooted in biased ligation of sequencing linkers to the 3'-and 5'-ends of RNAs, which varies by 10 3 -fold depending upon on the identity of the terminal nucleotides 3-7 and causes 10 6 -fold artifacts in sequencing read counts. 5,8,9 Highly structured and heavily modified RNA molecules, such as tRNAs, further challenge the quantitative accuracy of RNA-seq. 10, 11 These structural features cause polymerase fall-off during cDNA synthesis, which prevents detection of the transcripts.A variety of specialized RNA-seq methods, many limited specifically to either miRNA or tRNA only, 12-14 attempt to minimize ligation bias using linkers with randomized terminal nucleotides and molecular crowding agents to enhance ligation 4 and to reduce polymerase fall-off during reverse transcription (RT) with two-step ligation 8 and removal of some methyl modifications with AlkB. [15][16][17] Although polymerase fall-off effects are minimized, residual ligation biases persist and lead to "jackpot" sequences. 8 For example, the template-switching reverse transcriptase TGIRT used in DM-tRNA-seq 16 is biased by the identity of the overhanging nucleotide in the adapter strand. 18 The problem with existing RNA-seq techniques is that none have been systematically engineered to optimize ligation and amplification efficiencies or validated for quanti...

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Initiator tRNA Genes Template the 3’CCA End at High Frequencies in Bacteria

Cited by 3 publications

References 56 publications

Evolution and Structural Variations of Chloroplast tRNAs in Gymnosperms

Evolution and Structural Variations of Chloroplast tRNAs in Gymnosperms

Robust Estimation of the Phylogenetic Origin of Plastids Using a tRNA-Based Phyloclassifier

Sequencing-based quantitative mapping of the cellular small RNA landscape

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