Article
Microbiology
Marie-Madlen Pust, Kenneth N. Timmis, Burkhard Tuemmler
Summary: The updated Wobble Hypothesis explains why a small number of tRNA species are sufficient to decode the Universal Genetic Code. However, it is still unknown why eubacteria lack certain tRNA isoacceptors and why eukaryotes universally lack specific anticodons. Direct tRNA sequencing could reveal nucleoside modification patterns, but AI-supported base-callers are needed for accurate recognition. Recent discoveries of antisense tRNAs and tRNA-derived fragments expand our knowledge of bacterial tRNA and their potential roles in gene expression, translation, bacterial physiology, or metabolism.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Maxime Fages-Lartaud, Martin Frank Hohmann-Marriott
Summary: The compact translation machinery of chloroplasts makes them a promising platform for biotechnological innovation. In this study, we synthesize all available information on tRNA modifications in chloroplasts and assess translation efficiency for each modified anticodon-codon pair. We also analyze the enzymes associated with tRNA modifications and aminoacylation in Chlamydomonas reinhardtii chloroplasts. This work provides a comprehensive analysis of codon and anticodon interactions in chloroplasts and their implications for translation efficiency.
Review
Biochemistry & Molecular Biology
Sujatha Thankeswaran Parvathy, Varatharajalu Udayasuriyan, Vijaipal Bhadana
Summary: Codon usage bias is a common phenomenon observed in bacteria, plants, and animals, with consistent and characteristic patterns across different species and genes. The formation of codon bias is influenced by factors such as genome composition, gene expression levels, and gene length. Understanding codon usage bias can provide insights into phylogenetic relationships and gene evolution among organisms.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Microbiology
Quinten Deparis, Jorge Duitama, Maria R. Foulquie-Moreno, Johan M. Thevelein
Summary: Mutations in tRNAs play a crucial role in evolution to overcome specific tRNA deficiencies, and stress conditions may have been a driving force for the selection of anticodon-switching mutations in tRNAs. The introduction of a low number of causative elements by whole-genome transformation may be advantageous for improving industrial yeast strains.
Article
Forestry
Yajun Zeng, Lianwen Shen, Shengqun Chen, Shuang Qu, Na Hou
Summary: This study analyzed the codon usage patterns of 26 Juglandaceae chloroplast genomes and found that chloroplast codons tend to exhibit conserved GC content and are primarily altered by natural selection.
Article
Plant Sciences
Maxime Fages-Lartaud, Kristoffer Hundvin, Martin Frank Hohmann-Marriott
Summary: This article provides a comprehensive perspective on the mechanisms driving codon selection in Chlamydomonas reinhardtii chloroplasts and the functional consequences for protein expression. It is found that highly expressed genes prefer translationally optimal codons, while genes with lower functional importance are affected by directional mutational bias. Codon optimality can be deduced from codon-anticodon pairing affinity and tRNA concentrations for certain amino acids. The impact of codon usage on protein yield, mRNA secondary structure, translation initiation and termination, amino acid composition, and cotranslational protein folding is also discussed.
Article
Biochemistry & Molecular Biology
Meng-Han Huang, Gui-Xin Peng, Xue-Ling Mao, Jin-Tao Wang, Jing-Bo Zhou, Jian-Hui Zhang, Meirong Chen, En-Duo Wang, Xiao-Long Zhou
Summary: The study identified different isoforms of METTL8 that play various roles in different cell compartments. The isoforms have distinct localization and show different mechanisms in the modification of mitochondrial tRNA. The interaction between SARS2 and METTL8-Iso1 was found to enhance the modification activity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Xavier Hernandez-Alias, Christopher D. Katanski, Wen Zhang, Mahdi Assari, Christopher P. Watkins, Martin H. Schaefer, Luis Serrano, Tao Pan
Summary: Transfer RNA (tRNA) utilizes its abundance, modification, and aminoacylation properties for translational regulation. By developing a new tRNA analysis pipeline, we discovered correlations among various properties and identified the coordinating role of one common modification in tissue-specific gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Morghan C. Lucas, Leszek P. Pryszcz, Rebeca Medina, Ivan Milenkovic, Noelia Camacho, Virginie Marchand, Yuri Motorin, Lluis Ribas de Pouplana, Eva Maria Novoa
Summary: Nano-tRNAseq is a nanopore-based method that allows for simultaneous quantification of tRNA abundance and chemical modifications, providing a new tool for studying tRNA. Re-processing of raw nanopore current intensity signals leads to more accurate tRNA abundance information. Nano-tRNAseq can reveal changes in tRNA populations in response to oxidative stress.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Gyuhyeok Cho, Jangmin Lee, Jungwook Kim
Summary: The uridine at the 34th position of tRNA can be modified to affect decoding properties during translation. MnmC enzyme in bacteria like Escherichia coli converts cmnm(5)(s(2))U to mnm(5)(s(2))U, while MnmM enzyme in Bacillus subtilis converts nm(5)(s(2))U to mnm(5)(s(2))U.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Yoshitaka Murakami, Fan-Yan Wei, Yoshimi Kawamura, Haruki Horiguchi, Tsuyoshi Kadomatsu, Keishi Miyata, Kyoko Miura, Yuichi Oike, Yukio Ando, Mitsuharu Ueda, Kazuhito Tomizawa, Takeshi Chujo
Summary: A study found that a mitochondrial tRNA modification enzyme, NSUN3, is crucial for embryonic development in mice. Whole-body knockout leads to embryonic death, while heart-specific knockout causes heart aberration in older mice. The research highlights the importance of mitochondrial tRNA anticodon modification for mammalian embryonic development and demonstrates that the loss of a single mitochondrial tRNA modification can induce tissue aberration that worsens with age.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Michael Yarus
Summary: The study showed that minimally evolved codes retain qualities of the standard genetic code but constrain the possibility of evolution. The shape and size of wobble domains significantly affect the accuracy of codon assignments. Additionally, a plausible pathway to limited randomness is necessary to fit a highly ordered, degenerate code into a preset three-dimensional space.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Forestry
Yan-Feng Song, Qing-Hua Yang, Xian-Gui Yi, Zhao-Qing Zhu, Xian-Rong Wang, Meng Li
Summary: The study utilized SCUB analysis to investigate codon usage bias in subg. Cerasus, revealing natural selection as the main influencing factor, with gene expression level and GC content also impacting the usage pattern. The findings showed a consistent codon usage pattern across the 36 species, highlighting the importance of locus mutations and no-preference codons in phylogenetic reconstruction within the subgenus.
Article
Biochemistry & Molecular Biology
Kristoffer Skovbo Winther, Michael Askvad Sorensen, Sine Lo Svenningsen
Summary: Biogenic polyamines are essential for cell growth, as their deficiency can lead to reduced ribosome efficiency, overproduction of rRNA and multiple tRNA species, and impact on feedback regulation of stable RNA transcription. In addition, polyamine deficiency affects tRNA levels and modification patterns, particularly the lack of queuosine modification in specific tRNA species.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jiajing Sheng, Xuan She, Xiaoyu Liu, Jia Wang, Zhongli Hu
Summary: This study systematically analyzed the codon usage patterns of Miscanthus plants and related species, revealing a preference for A/T bases and A/T-ending codons in the chloroplast genomes. The results suggested that the codon usage patterns are mainly influenced by natural selection, and Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae could be considered as preferential exogenous expression receptors.
News Item
Biochemistry & Molecular Biology
Robert W. Murphy, Andrew J. Crawford, Aaron M. Bauer, Jing Che, Stephen C. Donnellan, Uwe Fritz, Celio F. B. Haddad, Zoltan T. Nagy, Nikolay A. Poyarkov, Miguel Vences, Wen-Zhi Wang, Ya-Ping Zhang
MOLECULAR ECOLOGY RESOURCES
(2013)
Correction
Biochemistry & Molecular Biology
Mei-Jiao Zhou, Jin-Hua Xiao, Sheng-Nan Bian, Yan-Wei Li, Li-Ming Niu, Hao-Yuan Hu, Wen-Shan Wu, Robert W. Murphy, Da-Wei Huang
MOLECULAR ECOLOGY RESOURCES
(2013)
Article
Multidisciplinary Sciences
Yong-Yi Shen, Xiao Chen, Robert W. Murphy
Article
Multidisciplinary Sciences
Bo Wang, Jin-Hua Xiao, Sheng-Nan Bian, Li-Ming Niu, Robert W. Murphy, Da-Wei Huang
Article
Multidisciplinary Sciences
Shu-Yan Wang, Jing Luo, Robert W. Murphy, Shi-Fang Wu, Chun-Ling Zhu, Yun Gao, Ya-Ping Zhang
Article
Multidisciplinary Sciences
Christopher Blair, Victor H. Jimenez Arcos, Fausto R. Mendez de la Cruz, Robert W. Murphy
Article
Multidisciplinary Sciences
Bao-Fa Sun, Jin-Hua Xiao, Shunmin He, Li Liu, Robert W. Murphy, Da-Wei Huang
Article
Multidisciplinary Sciences
Shan-Jin Wu, Jing Luo, Qing-Qing Li, Yan-Qin Wang, Robert W. Murphy, Christopher Blair, Shi-Fang Wu, Bi-Song Yue, Ya-Ping Zhang
Article
Evolutionary Biology
Giovanna G. Montingelli, Felipe G. Grazziotin, Jaqueline Battilana, Robert W. Murphy, Ya-Ping Zhang, Hussam Zaher
JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH
(2019)
Letter
Multidisciplinary Sciences
Santiago J. Sanchez-Pacheco, Sungsik Kong, Paola Pulido-Santacruz, Robert W. Murphy, Laura Kubatko
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Zoology
Ngon Quang Lam, Tran Thi Anh Thu, Luan Thanh Nguyen, Robert W. Murphy, Sang Ngoc Nguyen
Summary: A new vine snake species, Ahaetulla rufusoculara sp. nov., from southern Vietnam's Soc Trang Province, is described based on morphological data and genetic sequences. It is distinguished by its bright red eyes, specific scale counts, and unique color patterns. The new species shows significant genetic divergence from its congeners in COI and Cytb sequences.
Article
Zoology
Vu Dang Hoang Nguyen, Luan Thanh Nguyen, Nikolai L. Orlov, Robert W. Murphy, Sang Ngoc Nguyen
Summary: A new species of the genus Gekko, Gekko phuyenensis sp. nov., from southern Vietnam's Phu Yen Province is described based on morphological and molecular evidence. This new species shows distinctive features such as moderate size and specific measurements that set it apart from its congeners. Phylogenetic analysis places G. phuyenensis sp. nov. as a sister lineage to G. cf. grossmanni from a different province in southern Vietnam, with significant genetic distances observed between them. This discovery brings the total number of known Gekko species in Vietnam to 14.
Article
Zoology
Manh Van Le, Vu Dang Hoang Nguyen, Hoa Thi Phan, Attapol Rujirawan, Anchalee Aowphol, Thi-Dieu-Hien Vo, Robert W. Murphy, Sang Ngoc Nguyen
Summary: The new species Subdoluseps vietnamensis sp. nov. from southern Vietnam is characterized by specific morphological features, such as medium size, tail length relative to snout-vent length, and four distinct black stripes on the dorsum. It genetically differs from its closest congeners, but clusters into the same matriline on the phylogenetic trees.
Article
Biology
Shaoying Liu, Chengran Zhou, Guanliang Meng, Tao Wan, Mingkun Tang, Chentao Yang, Robert W. W. Murphy, Zhenxin Fan, Yang Liu, Tao Zeng, Yun Zhao, Shanlin Liu
Summary: This study provides insights into the phylogeny and evolution of the Cricetid genus Neodon by sampling across its range in the Hengduan and Himalayan Mountains in China. The research reveals the presence of new species and identifies positively selected genes related to high-elevation adaptation.
COMMUNICATIONS BIOLOGY
(2022)
Article
Zoology
Sang Ngoc Nguyen, Vu Dang Hoang Nguyen, Luan Thanh Nguyen, Robert W. Murphy