tRNA Species Research Articles

Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma zedoaria (Zingiberaceae)

The first complete chloroplast genome of Curcuma zedoaria (Zingiberaceae) was reported in this study. The C. zedoaria chloroplast genome was 162,135 bp in length, and consisted of one large single-copy (LSC) region of 86,966 bp, one small single-copy (SSC) region of 15,737 bp, and a pair of inverted repeat (IR) regions 29,716 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and 8 rRNA genes (4 rRNA species). The phylogenetic analysis based on single nucleotide polymorphisms strongly supported that C. zedoaria, Curcuma roscoeana, Curcuma longa, and Stahlianthus involucratus clustered together in group Curcuma II within the family Zingiberaceae.

The complete chloroplast genome of Euonymus szechuanensis

The complete chloroplast genome from Euonymus szechuanensis, a rare deciduous shrub of the Celastraceae endemic to China, which is classified as vulnerable on the list of Threatened species in China because species diversity decreased sharply, is determined in this study. The whole chloroplast genome sequence of Euonymus szechuanensis has been characterized by Illumina pair-end sequencing. The circular genome is 157,465 bp long, containing a large single-copy region (LSC) of 86,401 bp and a small single-copy region (SSC) of 18,472 bp, which are separated by a pair of 26,296 bp inverted repeat regions (IRs). It encodes a total of 136 genes, including 84 protein-coding genes (76 PCG species), 44 tRNA genes (30 tRNA species), and 8 ribosomal RNA genes (4 rRNA species). Most of the gene species occur as a single copy, while 19 gene species occur in double copies. The overall A + T content of the circular genome is 62.8%, while the corresponding values of the LSC, SSC and IR regions are 65.0, 68.4 and 57.3%, respectively. Phylogenetic analysis suggested that E. szechuanensis was relatively close to Euonymus schensianus among the species analyzed. This complete chloroplast genome will provide valuable insight into conservation and restoration efforts for this rare and Threatened species.

The Sole Mycobacterium smegmatis MazF Toxin Targets tRNALys to Impart Highly Selective, Codon-Dependent Proteome Reprogramming.

Survival of mycobacteria, both free-living and host-dependent pathogenic species, is dependent on their ability to evade being killed by the stresses they routinely encounter. Toxin-antitoxin (TA) systems are unique to bacteria and archaea and are thought to function as stress survival proteins. Here, we study the activity of the endoribonuclease toxin derived from the MazEF TA system in Mycobacterium smegmatis, designated MazEF-ms. We first enlisted a specialized RNA-seq method, 5’ RNA-seq, to identify the primary RNA target(s) of the MazF-ms toxin. Just two tRNA species, tRNALys-UUU and tRNALys-CUU, were targeted for cleavage by MazF-ms at a single site within their anticodon sequence (UU↓U and CU↓U) to render these tRNAs nonfunctional for protein synthesis. The 5’ RNA-seq dataset also revealed hallmarks of ribosome stalling predominantly at Lys AAA codons even though both Lys tRNAs were cleaved by MazF-ms. Stalled ribosomes were then cleaved on their 5’ side by one or more RNases, resulting in very selective degradation of only those mRNAs harboring ribosomes stalled at Lys codons. This highly surgical, codon-dependent degradation of mRNA transcripts was validated using quantitative mass spectrometry of proteins that were newly synthesized during MazF-ms expression. The M. smegmatis proteome was altered as predicted, Lys AAA codon-rich proteins was downregulated while Lys AAA codon deficient proteins were upregulated. Analysis of specific subsets of proteins that were upregulated or downregulated was consistent with the growth-arrested phenotype of MazF-ms expressing cells. Curiously, the tRNA target and mechanism of action of MazF-ms paralleled that of one atypical MazF toxin in M. tuberculosis, suggesting manipulation of the levels of lysine tRNAs as the preferred conduit for reprogramming the proteomes via ribosome stalling at rare AAA codons in these GC-rich mycobacteria.

How Nanopore Translocation Experiments Can Measure RNA Unfolding

Electrokinetic translocation of biomolecules through solid-state nanopores represents a label-free single-molecule technique that may be used to measure biomolecular structure and dynamics. Recent investigations have attempted to distinguish individual transfer RNA (tRNA) species based on the associated pore translocation times, ion-current noise, and blockage currents. By manufacturing sufficiently smaller pores, each tRNA is required to undergo a deformation to translocate. Accordingly, differences in nanopore translocation times and distributions may be used to infer the mechanical properties of individual tRNA molecules. To bridge our understanding of tRNA structural dynamics and nanopore measurements, we apply molecular dynamics simulations using a simplified “structure-based” energetic model. Calculating the free-energy landscape for distinct tRNA species implicates transient unfolding of the terminal RNA helix during nanopore translocation. This provides a structural and energetic framework for interpreting current experiments, which can aid the design of methods for identifying macromolecules using nanopores.

Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme.

BCDIN3 domain containing RNA methyltransferase, BCDIN3D, monomethylates the 5′-monophosphate of cytoplasmic tRNAHis with a G−1:A73 mispair at the top of an eight-nucleotide-long acceptor helix, using S-adenosyl-l-methionine (SAM) as a methyl group donor. In humans, BCDIN3D overexpression is associated with the tumorigenic phenotype and poor prognosis in breast cancer. Here, we present the crystal structure of human BCDIN3D complexed with S-adenosyl-l-homocysteine. BCDIN3D adopts a classical Rossmann-fold methyltransferase structure. A comparison of the structure with that of the closely related methylphosphate capping enzyme, MePCE, which monomethylates the 5′-γ-phosphate of 7SK RNA, revealed the important residues for monomethyl transfer from SAM onto the 5′-monophosphate of tRNAHis and for tRNAHis recognition by BCDIN3D. A structural model of tRNAHis docking onto BCDIN3D suggested the molecular mechanism underlying the different activities between BCDIN3D and MePCE. A loop in BCDIN3D is shorter, as compared to the corresponding region that forms an α-helix to recognize the 5′-end of RNA in MePCE, and the G−1:A73 mispair in tRNAHis allows the N-terminal α-helix of BCDIN3D to wedge the G−1:A73 mispair of tRNAHis. As a result, the 5′-monophosphate of G−1 of tRNAHis is deep in the catalytic pocket for 5′-phosphate methylation. Thus, BCDIN3D is a tRNAHis-specific 5′-monomethylphosphate capping enzyme that discriminates tRNAHis from other tRNA species, and the structural information presented in this study also provides the molecular basis for the development of drugs against breast cancers.

The complete chloroplast genome sequence of Populus koreana (Salicaceae)

The complete chloroplast genome sequence of Populus koreana was characterized using Illumina pair-end sequencing. The chloroplast genome of P. koreana was 156,868 bp in length, containing a large single-copy region (LSC) of 84,976 bp, a small single-copy region (SSC) of 16,606 bp, and two inverted repeat (IR) regions of 27,643 bp. The overall GC content is 30.70%, whereas the corresponding values of the LSC, SSC, and IR regions are 64.6%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species), and eight rRNA genes (four rRNA species). The neighbour-joining phylogenetic analysis showed that P. koreana and Populus fremontii clustered together as sisters to other Populus species.

The complete chloroplast genome sequence of Amomum villosum Lour.

Amomum villosum Lour. (Zingiberaceae) is an important edible and medicinal crop. The complete chloroplast (cp) genome of A. villosum was determined using Illumina sequencing platform. The size of whole cp genome was 164,069 bp, containing a small single copy (SSC) region of 15,353 bp and a large single copy (LSC) region of 88,798 bp, which were separated by a pair of inverted repeat (IRs) regions (29,959 bp). The A. villosum cp genome contained 133 genes, including eight ribosomal RNA genes (4 rRNA species), 38 transfer RNA genes (30 tRNA species) and 87 protein-coding genes (79 PCG species). The overall GC content of A. villosum cp genome is 36.05%. To investigate the evolution status of A. villosum, as well as Zingiberales, a phylogenetic tree with A. villosum and other 21 species was constructed based on their complete chloroplast genomes. Phylogenetic analysis revealed that A. villosum was closely related to Amomum krervanh.

The complete chloroplast genome sequence of Hippophae rhamnoides subsp. sinensis

The complete chloroplast genome sequence of Hippophae rahmnoides subsp. sinensis was characterized from Illumina pair-end sequencing. The chloroplast genome of H. rahmnoides subsp. sinensis was 156,355 bp in length, containing a large single-copy region (LSC) of 84,002 bp, a small single-copy region (SSC) of 19,055 bp, and two inverted repeat (IR) regions of 26,649 bp. The overall GC content is 36.6%, while the corresponding values of the LSC, SSC, and IR regions are 64.5%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 88 protein-coding genes, 38 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). The neighbour-joining phylogenetic analysis showed that H. rahmnoides subsp. sinensis and H. rahmnoides clustered together as sisters to other H. rahmnoides species.

The complete chloroplast genome of Amomum tsao-ko

Amomum tsao-ko (Zingiberaceae) is an important edible and medicinal crop. The complete chloroplast (cp) genome of A. tsao-ko was determined using Illumina sequencing platform. The size of whole cp genome was 163,648 bp, containing a small single copy (SSC) region of 15,355 bp and a large single copy (LSC) region of 88,741 bp, which were separated by a pair of inverted repeat (IRs) regions (29,776 bp). The A. tsao-ko cp genome contained 133 genes, including eight ribosomal RNA genes (4 rRNA species), 38 transfer RNA genes (30 tRNA species) and 87 protein-coding genes (79 PCG species). The overall GC content of A. tsao-ko cp genome is 36.02%. To investigate the evolution status of A. tsao-ko, as well as Zingiberales, a phylogenetic tree with A. tsao-ko and other 16 species was constructed based on their complete chloroplast genomes. Phylogenetic analysis revealed that A. tsao-ko was closely related to Alpinia zerumbet.

Characterization of the complete chloroplast genome of Festuca sinensis (Gramineae)

The complete chloroplast genome from Festuca sinensis, an important perennial bunchgrass of the Gramineae, is determined in this study. The whole chloroplast genome sequence of F. sinensis has been characterized by Illumina pair-end sequencing. The circular genome is 134,177 bp long, containing a large single-copy region (LSC) of 79,367 bp and a small single-copy region (SSC) of 12,510 bp, which are separated by a pair of 21,150 bp inverted repeat regions (IRs). It encodes a total of 150 genes, including 93 protein-coding genes (75 PCG species), 49 tRNA genes (30 tRNA species) and eight ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 30 gene species occur in double copies. The overall A + T content of is 61.6%, while the corresponding values of the LSC, SSC, and IR regions are 63.7, 67.4, and 56.0%, respectively. Phylogenetic analysis suggested that Festuca sinensis was relatively close to Festuca ovina compared with other species of Festuca genera in Gramineae among the species analyzed. This complete chloroplast genome will provide valuable insight into conservation and exploitation efforts for this species as well as useful resources for studying the Gramineae phylogeny.

The complete chloroplast genome sequence of Populus mexicana (Salicaceae)

The complete chloroplast genome sequence of Populus mexicana was characterized from Illumina pair-end sequencing. The chloroplast genome of P. mexicana was 156,188 bp in length, containing a large single-copy region (LSC) of 86,871 bp, a small single-copy region (SSC) of 16,559 bp, and 2 inverted repeat (IR) regions of 26,377 bp. The overall GC content is 36.74%, while the corresponding values of the LSC, SSC, and IR regions are 64.8, 69.3, and 60.3, respectively. The genome contains 111 complete genes, including 72 protein-coding genes (62 protein-coding gene species), 31 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). The neighbor-joining phylogenetic analysis showed that P. mexicana and Populus fremontii clustered together as sisters to other Populus species.

Mouse Trmt2B protein is a dual specific mitochondrial metyltransferase responsible for m5U formation in both tRNA and rRNA

ABSTRACTRNA molecules of all species contain modified nucleotides and particularly m5U residues. The vertebrate mitochondrial small subunit rRNA contains m5U nucleotide in a unique site. In this work we found an enzyme, TRMT2B, responsible for the formation of this nucleotide and m5U residues in a number of mitochondrial tRNA species. Inactivation of the Trmt2B gene leads to a reduction of the activity of respiratory chain complexes I, III and IV, containing the subunits synthesized by the mitochondrial protein synthesis apparatus. Comparative sequence analysis of m5U-specific RNA methyltransferases revealed an unusual evolutionary pathway of TRMT2B formation which includes consecutive substrate specificity switches from the large subunit rRNA to tRNA and then to the small subunit rRNA.

Niche origin of mesenchymal stem cells derived microvesicles determines opposing effects on NSCLC: Primary versus metastatic

Novel therapeutic approaches that address the malignant cells in their stroma microenvironment are urgently needed in lung cancer. The stroma resident mesenchymal stem cells (MSCs) interact with cancer cells in diverse ways including microvesicles (MVs) that transfer proteins and RNA species thereby modulating recipient cells' phenotype. Previously, we have demonstrated that MSCs' secretome from the primary non-small cell lung cancer (NSCLC) niche (lung) and metastatic niche (bone marrow (BM)) demonstrate opposite effects on NSCLC cells in a translation initiation (TI) dependent manner. Here, we examined the effect of MVs secreted from BM-MSCs' or lung-MSCs (healthy, NSCLC) to NSCLC phenotype. Briefly, NSCLC cell lines treated with Lung or BM-MSCs' MVs were assayed for viability (WST-1), cell count/death (trypan), migration (scratch), TI status and MAPKs activation (immunoblotting). Corresponding to previous published trends, Lung-MSCs' MVs promoted NSCLC cells' assayed traits whereas, BM-MSCs' MVs suppressed them. Activation of MAPKs and autophagy was registered in lung-MSCs MVs treated NSCLC cell lines only. Furthermore, lung-MSCs' MVs' treated NSCLC cells demonstrated an early (5min) activation of MAPKs and TI factors (peIF4E/peIF4GI) not evident in BM-MSCs MVs treated cells. These observations depict a role for MSCs'-MVs in NSCLC phenotype design and display distinct differences between the primary and metastatic niches that correspond to disease progression.In conclusion, the systemic nature of MVs marks them as attractive therapeutic markers/targets and we propose that identification of specific cargoes/signals that differentiate between MSCs MVs of primary and metastatic niches may introduce fresh therapeutic approaches.

Maternal circulating syncytiotrophoblast-derived extracellular vesicles contain biologically active 5’-tRNA halves

The placenta releases syncytiotrophoblast-derived extracellular vesicles (STB-EV) into the maternal circulation throughout gestation. STB-EV dependent signalling is believed to contribute to the widespread maternal adaptive physiological changes seen in pregnancy. Transfer RNA (tRNA) halves have been identified in vesicles released from other human and murine organ systems, which alter gene expression in target cells. Here, we characterise tRNA-half expression in STB-EV and demonstrate biological activity of a highly abundant tRNA-half. Short RNA from ex-vivo, dual-lobe placental perfusion STB-EV was sequenced, showing that most (>95%) comprised tRNA species. Whole placental tissue contained <50% tRNA species, suggesting selective packaging and export of tRNA into STB-EV. Most tRNA within STB-EV were 5′-tRNA halves cleaved at 30-32 nucleotides. The pattern of tRNA expression differed depending on the size/origin of the STB-EV; this was confirmed by qPCR. Protein synthesis was suppressed in human fibroblasts when they were cultured with a 5′-tRNA half identified from STB-EV sequencing. This study is the first to evaluate tRNA species in STB-EV. The presence of biologically active 5′-tRNA halves, specific to a vesicular origin, suggests a novel mechanism for maternal-fetal signalling in normal pregnancy.

Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS

RNA modifications are involved in numerous biological processes. These modifications are constitutive or modulated in response to adaptive processes and can impact RNA base-pairing formation, protein recognition, RNA structure and stability. tRNAs are the most abundantly modified RNA molecules. Analysis of the roles of their modifications in response to stress, environmental changes, and infections caused by pathogens, has fueled new research areas. Nevertheless, the detection of modified nucleotides in RNAs is still a challenging task. We present here a reliable method to identify and localize tRNA modifications, which was applied to the human pathogenic bacteria, Staphyloccocus aureus. The method is based on a separation of tRNA species on a two-dimensional polyacrylamide gel electrophoresis followed by nano liquid chromatography-mass spectrometry. We provided a list of modifications mapped on 25 out of the 40 tRNA species (one isoacceptor for each amino acid). This method can be easily used to monitor the dynamics of tRNA modifications in S. aureus in response to stress adaptation and during infection of the host, a relatively unexplored field.

Complete chloroplast genome of the plant Stahlianthus Involucratus (Zingiberaceae)

The first complete chloroplast genome of Stahlianthus involucratus (Zingiberaceae) was reported in this study. The S. involucratus chloroplast genome was 163,300 bp in length and consisted of one large single copy (LSC) region of 87,498 bp, one small single copy (SSC) region of 15,568 bp, and a pair of inverted repeat (IR) regions 30,117 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species) and 8 rRNA genes (4 rRNA species). The phylogenetic analysis based on single nucleotide polymorphisms strongly supported that S. involucratus, Curcuma roscoeana and Curcuma longa formed a cluster in group CurcumaII within family Zingiberaceae.

Complete chloroplast genome sequence of Amomum villosum

The first complete chloroplast genome of Amomum villosum (Zingiberaceae) was reported in this study. The A. villosum genome was 163,608 bp in length, and comprised a pair of inverted repeat (IR) regions of 29,820 bp each, a large single-copy (LSC) region of 88,680 bp, and a small single-copy (SSC) region of 15,288 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and 8 rRNA genes (4 rRNA species). The overall AT content was 63.92%. Phylogenetic analysis showed that A. villosum was closely related to two species Amomum kravanh and Amomum compactum within the genus Amomum in family Zingiberaceae.

The complete chloroplast genome sequence of Populus tremuloides (Salicaceae)

The complete chloroplast genome sequence of Populus tremuloides was characterized from Illumina pair-end sequencing. The chloroplast genome of P. tremuloides was 155,816 bp in length, containing a large single-copy region (LSC) of 85,804 bp, a small single-copy region (SSC) of 16,489 bp, and two inverted repeat (IR) regions of 26,962 bp. The overall GC content is 36.71%, while the correponding values of the LSC, SSC, and IR regions are 64.9%, 69.2%, and 60.3%, respectively. The genome contains 167 complete genes, including 86 protein-coding genes (77 protein-coding gene species), 73 tRNA genes (29 tRNA species) and 8 rRNA genes(4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. tremuloides and Populus tremula clustered together as sisters to other Populus species.

Characterisation of the complete chloroplast genome of an endemic herb plant species, Rheum palmatum (Polygonaceae) in China

Rheum palmatum has a long history in medicine, which is one of the main export medicinal herb in China. The complete chloroplast genome of R. palmatum was assembled and reported in this study. The R. palmatum chloroplast genome was 161,541 bp in length as the circular and consisted a large single-copy (LSC) region of 86,519 bp, a small single-copy (SSC) region of 13,112 bp and a pair of inverted-repeat (IR) regions of 30,955 bp. The nucleotide composition was asymmetric 31.2% A (Adenine), 31.5% T (Thymine), 19.0% C (Cytosine), and 18.3% G (Guanine) with an overall G + C content of 37.3%. It encoded 131 genes, including 86 protein-coding genes (76 PCG species), 37 transfer RNA genes (26 tRNAs species), and eight ribosomal RNA genes (four rRNAs species). The Phylogenetic relationships used neighbour-joining (NJ) method and the result showed that R. palmatum and Rheum officinale are phylogenetically related to each other in the family Polygonaceae. This study will be very important for Chinese medicinal herb research value and clinical drug development for future in China.

Characterization of the complete chloroplast genome of medicinal plant Rheum officinale (Polygonaceae)

The complete chloroplast (cp) genome of Rheum officinale Baill. was determined based on the Illumina Sequencing data. The cp genome is 161,563 bp in length. The overall G + C content of the cp genome was 37.31%. The R. officinale cp genome contains 129 genes, including 84 protein-coding genes, eight rRNA genes (four rRNA species), and 37 tRNA genes (20 tRNA species). A neighbour-joining phylogenetic tree clarified that the cp genome of R. officinale was closely related to that of R. palmatum in Polygonaceae.