Article
Multidisciplinary Sciences
Dia A. Ghose, Kaitlyn E. Przydzial, Emily M. Mahoney, Amy E. Keating, Michael T. Laub
Summary: The evolution of novel functions in biology relies on gene duplication and divergence, creating large paralogous protein families. However, the specificity of these paralogs to their interaction partners can be sensitive to mutation. Through deep mutational scanning, it was demonstrated that a family of bacterial signaling proteins exhibits marginal specificity, with individual substitutions leading to substantial cross-talk between pathways. These findings suggest that the evolution of bacterial signaling proteins is constrained by sequence space crowding, and that evolution selects for good enough rather than optimized phenotypes in paralogs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Ikuko Morisaki, Hiroshi Shiraishi, Hiroyuki Fujinami, Nobuyuki Shimizu, Takatoshi Hikida, Yuji Arai, Takashi Kobayashi, Reiko Hanada, Josef M. Penninger, Minoru Fujiki, Toshikatsu Hanada
Summary: CLP1, an RNA kinase, plays crucial roles in mRNA and tRNA metabolism, while R140H mutation in CLP1 leads to PCH10 pathology. The knock-in mutant mice with this mutation showed motor neuron loss and accumulation of RNA fragments, suggesting their involvement in the disease pathogenesis and progression.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Jarrett Man, T. A. Harrington, Kyra Lally, Madelaine E. Bartlett
Summary: The coding sequences of developmental genes and defense genes show different characteristics in evolution. LRR-RLKs, a transmembrane receptor protein family, have faster evolution rates in the LRR domains than in the RLK domains in different subfamilies with diverse functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Elizabeth R. Ballou, Atlanta G. Cook, Edward W. J. Wallace
Summary: The RNase II family of 3'-5' exoribonucleases is found across all domains of life, with eukaryotic members Dis3 and Dis3L2 playing essential roles in RNA degradation. Some yeasts contain both active Dis3 and inactive pseudonucleases, which function as RNA-binding proteins affecting cell growth, cytokinesis, and fungal pathogenicity. The evolutionary origins of these pseudonucleases remain unknown, with their non-nuclease functions requiring specific structural domains across diverse fungal lineages.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Zhenfang Du, Benjamin P. Brown, Soyeon Kim, Donna Ferguson, Dean C. Pavlick, Gowtham Jayakumaran, Ryma Benayed, Jean-Nicolas Gallant, Yun-Kai Zhang, Yingjun Yan, Monica Red-Brewer, Siraj M. Ali, Alexa B. Schrock, Ahmet Zehir, Marc Ladanyi, Adam W. Smith, Jens Meiler, Christine M. Lovly
Summary: Understanding oncogenic variants at a mechanistic level helps in the development and optimization of treatment strategies. The study reveals the prevalence of ERBB family KDDs in multiple human cancers, and shows that EGFR-KDD functions through different dimerization modes, with its activity being maximally inhibited by blocking both intra- and inter-molecular dimerization. In conclusion, these findings define a new model of EGFR dimerization and provide important insights for the treatment of EGFR-KDD.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Danny Bergeron, Cedric Laforest, Stacey Carpentier, Annabelle Calve, Etienne Fafard-Couture, Gabrielle Deschamps-Francoeur, Michelle S. Scott
Summary: The study reveals that snoRNA copy regulation affects family sizes, genomic location of the members, and controls both member and total family abundance to meet the needs of individual tissues. Additionally, the expression variability of individual snoRNA family members is preferred over the total variability of the family, pointing towards differential regulation mechanisms exist to ensure uniformity of the total family abundance across tissues.
Article
Plant Sciences
Pengbo Xu, Xinyu Li, Junmiao Fan, Chong Wang, Anqi Lin, Hongli Lian
Summary: We characterized YTH genes in diploid forest strawberry and identified nine YTH genes belonging to two groups, YTHDC and YTHDF, with YTHDF further divided into three subfamilies. YTH3 and YTH4 are a gene pair generated by tandem repeat replication, sharing similarities in gene structure and motifs. Our study provides valuable information for studying YTH genes in strawberry.
Article
Biology
Giovanni Annona, Iori Sato, Juan Pascual-Anaya, David Osca, Ingo Braasch, Randal Voss, Jan Stundl, Vladimir Soukup, Allyse Ferrara, Quenton Fontenot, Shigeru Kuratani, John H. Postlethwait, Salvatore D'Aniello
Summary: Nitric oxide (NO) is a crucial signaling molecule in biological systems, playing important roles in cardiovascular, neurological, and immune functions. Understanding the evolution of NO synthases (Nos) genes, which produce NO in vivo, is still a puzzle, especially in fish compared to tetrapods. Recent studies have found the presence of nos3 gene, previously considered lost, in spotted gar, changing our perspective on the origin of nos genes. This study explored nos gene evolution in different vertebrate species and revealed lineage-specific gene duplications and losses, independent losses of nos3 in teleost lineages, and the expression of nos genes in the gills of certain gnathostome species. These findings provide insights into the roles and evolutionary history of nos genes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Plant Sciences
Yun-Hai Lu, Intikhab Alam, Yan-Qing Yang, Ya-Cen Yu, Wen-Chao Chi, Song-Biao Chen, Boulos Chalhoub, Li-Xi Jiang
Summary: The YABBY gene family, present in all seed plants, plays crucial roles in plant growth and development, including polarity establishment, leaf and flower formation, and response to hormonal signals and environmental stress. Through identification of 364 YABBY genes in 37 Brassicaceae genomes, it was found that these genes are largely conserved across species but exhibit considerable functional divergence.
Article
Oncology
Erica Kao, Navin Pinto, Angela Trobaugh-Lotrario, Gail H. Deutsch, Yu Wu, Wenjing Wang, Erin R. Rudzinski, Yajuan J. Liu
Summary: In this study, two cases of extra-renal pediatric spindle cell neoplasms with EGFR internal tandem duplications are reported. This is the first reported example of EGFR ITDs in extra-renal tumors. Broad testing for this group of tumors is necessary to identify potential therapeutic targets.
GENES CHROMOSOMES & CANCER
(2022)
Review
Endocrinology & Metabolism
David M. Irwin
Summary: Insulin has made significant contributions to clinical medicine and molecular biology, with genome sequencing revealing unexpected changes in insulin coding sequences in diverse vertebrates. The presence of multiple insulin genes potentially allows for specialized function, while changes in proteolytic processing suggest that the typical hormone structure may not be essential for all biological activities.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Baofang Xu, Dongyang Liu, Zerong Wang, Ruixia Tian, Yongchun Zuo
Summary: This study investigates the multi-substrate selectivity of the ALKBH demethylase family from the perspective of sequence and structural evolution. The construction of phylogenetic tree and comparison of key loops and non-homologous domains show that paralogs with close evolutionary relationships have similar domain compositions, indicating that variations in key loops lead to differences in substrate affinity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Developmental Biology
Adrian Garcia-Concejo, Dan Larhammar
Summary: PKC, one of the earliest identified kinases in human cells, forms a family of kinases that respond to various signaling molecules with diverse functions. Evolutionary analysis reveals a vertebrate predecessor with five PKC genes, leading to a total of 21 genes in jawed vertebrates due to genome doublings. The genome duplications account for the complexity of the PKC gene family in jawed vertebrates and greatly impact their evolution.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sean M. Cascarina, Eric D. Ross
Summary: This article investigates the role of SR-related proteins in the human body. By using an unbiased composition criteria, over 100 putative SR-related proteins were identified, and it was found that they are closely associated with functions such as RNA splicing and nuclear speckles. The newly discovered proteins have slightly different amino acid compositions but similar levels of post-translational modification, indicating their regulation and functional importance in vivo.
Article
Agronomy
Yingying Jin, Ruijuan Han, Wei Li, Lu Cai, Yiting Li, Dongfang Ma, Wang Chen
Summary: This study discovered and characterized the wheat CPP gene family, identifying 30 genes divided into two groups and three subgroups. The research found that most TaCPP genes were highly expressed in reproductive tissues and were significantly induced after drought, heat treatment, and infection, indicating their important role in stress tolerance.
Article
Evolutionary Biology
Motofumi Saito, Asako Sato, Shohei Nagata, Satoshi Tamaki, Masaru Tomita, Haruo Suzuki, Akio Kanai
GENOME BIOLOGY AND EVOLUTION
(2019)
Editorial Material
Genetics & Heredity
Akio Kanai, Tohru Yoshihisa
FRONTIERS IN GENETICS
(2019)
Article
Reproductive Biology
Yohei Hayashi, Masaru Mori, Kaori Igarashi, Keiko Tanaka, Asuka Takehara, Yumi Ito-Matsuoka, Akio Kanai, Nobuo Yaegashi, Tomoyoshi Soga, Yasuhisa Matsui
BIOLOGY OF REPRODUCTION
(2020)
Article
Genetics & Heredity
Trieu-Duc Vu, Yuki Lwasaki, Shuji Shigenobu, Akiko Maruko, Kenshiro Oshima, Erica Lioka, Chao-Li Huang, Takashi Abe, Satoshi Tamaki, Yi-Wen Lin, Chih-Kuan Chen, Mei-Yeh Lu, Masaru Hojo, Hao-Ven Wang, Shun-Fen Tzeng, Hao-Jen Huang, Akio Kanai, Takashi Gojobori, Tzen-Yuh Chiang, H. Sunny Sun, Wen-Hsiung Li, Norihiro Okada
Article
Microbiology
Masahiro C. Miura, Shohei Nagata, Satoshi Tamaki, Masaru Tomita, Akio Kanai
Summary: This study developed a bioinformatic pipeline to systematically collect and analyze Group II introns (G2Is) in prokaryotes. The results showed the presence of G2Is in both bacteria and archaea, with their numbers defined almost at the phylum level. Furthermore, a comprehensive sequence analysis led to the identification of three new categories of intron-encoded proteins (IEPs), and it was observed that about 30% of IEPs are non-canonical. The study also analyzed the relationship between genomic signatures and the mechanism of G2I increases.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Megumi Tsurumaki, Motofumi Saito, Masaru Tomita, Akio Kanai
Summary: The candidate phyla radiation (CPR) bacteria, consisting mainly of uncultured lineages, have smaller cells and genomes compared to non-CPR bacteria. They lack certain ribosomal proteins and exhibit unique protein lengths and sequences. The ribosomes of CPR bacteria appear to be smaller with simplified surface structures, which may contribute to their distinct characteristics.
Article
Microbiology
Teppei Morita, Nadim Majdalani, Masahiro C. Miura, Rerina Inose, Taku Oshima, Masaru Tomita, Akio Kanai, Susan Gottesman
Summary: The regulatory function of many bacterial small RNAs (sRNAs) is dependent on the RNA chaperone Hfq binding to the 3' portion of the sRNA intrinsic terminator. This study identified several genes, including an sRNA gene (cyaR) and three protein-coding genes (cspD, ygjH, and rof), that attenuate the termination of SgrS in Escherichia coli. Overexpression of the protein attenuators CspD and Rof resulted in increased readthrough at terminators of SgrS and other sRNAs, reducing their regulatory effects on target mRNAs. Further analysis revealed the unexpected role of Rho in sRNA termination and the stabilizing effect of CspD on both terminated and readthrough transcripts. This study provides evidence of the modulation of intrinsic termination as an additional layer of regulation in sRNA signaling.
Review
Geography, Physical
Naota Takeyama, Yuka Takahashi, Shohei Nagata, Yusuke Sawaki, Tomohiko Sato, Shigenori Maruyama, Akio Kanai
JOURNAL OF GEOGRAPHY-CHIGAKU ZASSHI
(2020)
Review
Geography, Physical
Megumi Tsurumaki, Motofumi Saito, Shigenori Maruyama, Akio Kanai
JOURNAL OF GEOGRAPHY-CHIGAKU ZASSHI
(2020)
Article
Microbiology
Motofumi Saito, Akane Nishigata, Josephine Galipon, Kazuharu Arakawa
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2019)