Article
Biochemistry & Molecular Biology
Patricia P. Chan, Brian Y. Lin, Allysia J. Mak, Todd M. Lowe
Summary: tRNAscan-SE, a tool for predicting transfer RNA genes, has been widely used for over twenty years. Recent updates have greatly improved its ability to identify and classify tRNAs by creating nearly one hundred specialized isotype- and Glade-specific models.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Suresh Kumar Gupta, Abhaypratap Vishwakarma, Hawi Deressa Kenea, Ortal Galsurker, Hagai Cohen, Asaph Aharoni, Tzahi Arazi
Summary: The study found that the miR164 gene in tomato plays a crucial role in the development and ripening of fruits. Specifically, SlMIR164a and SlMIR164b have specialized roles in plant development, with SlMIR164b required for shoot and flower boundary specification, and SlMIR164a essential for fruit growth and the expansion of its outer epidermis.
Article
Genetics & Heredity
Gagandeep Singh, Dinesh Gupta
Summary: This study aims to characterize hypothetical proteins of the parasite to identify novel drug targets using a computational pipeline. The study reveals that out of the overall pool of hypothetical proteins, 266 proteins have conserved functional signatures, with 23 proteins playing essential roles in various biochemical, signalling and metabolic pathways.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Lilian Mbaisi Ang'ang'o, Jeremy Keith Herren, Ozlem Tastan Bishop
Summary: This research developed a robust bioinformatics annotation pipeline to annotate hypothetical proteins (HPs) from Vittaforma corneae. Various steps were used to retrieve sequences and homologs, perform physicochemical characterization, protein family classification, motif and domain identification, protein-protein interaction network analysis, and homology modeling. In total, 162 out of 2034 HPs were fully annotated, providing insights into the functions of microsporidian HPs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Jiaotong Yang, Pengfei Li, Yuping Li, Qiaoqiao Xiao
Summary: This article introduces an improved gene functional analysis platform (GelFAP v2.0) for G.elata, which integrates new genome data, transcriptome resources, and analysis tools. The platform helps researchers carry out gene functional research by constructing co-expression networks and annotating genes with functional information.
Article
Plant Sciences
Parminder Kaur Narang, Jyotirmayee Dey, Soumya Ranjan Mahapatra, Mrinmoy Ghosh, Namrata Misra, Mrutyunjay Suar, Vijay Kumar, Vishakha Raina
Summary: In this study, bioinformatics analysis was used to predict the function of a hypothetical protein from the model microalga Chlamydomonas reinhardtii, revealing its potential role in the carotenoid biosynthetic pathway. Homology modelling and docking analysis assisted in determining the protein's three-dimensional structure and active site region.
SOUTH AFRICAN JOURNAL OF BOTANY
(2021)
Article
Biology
Max Karlsson, Evelina Sjostedt, Per Oksvold, Asa Sivertsson, Jinrong Huang, Maria Bueno Alvez, Muhammad Arif, Xiangyu Li, Lin Lin, Jiaying Yu, Tao Ma, Fengping Xu, Peng Han, Hui Jiang, Adil Mardinoglu, Cheng Zhang, Kalle von Feilitzen, Xun Xu, Jian Wang, Huanming Yang, Lars Bolund, Wen Zhong, Linn Fagerberg, Cecilia Lindskog, Fredrik Ponten, Jan Mulder, Yonglun Luo, Mathias Uhlen
Summary: This study introduces a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering, and presents a whole-body map of protein-coding genes in the pig. The study provides insights into the expression patterns of these genes across different tissues and organs.
Article
Biochemistry & Molecular Biology
Harpreet Kaur, Vikram Singh, Manmohit Kalia, Balvinder Mohan, Neelam Taneja
Summary: Urinary tract infections are a serious health concern worldwide, especially in developing countries. The highly virulent Escherichia coli strain CFT073 contains 992 hypothetical proteins. Computational tools were used to analyze and classify these proteins, revealing their roles in various functional categories and metabolic pathways. Further analysis identified 35 non-homologous proteins as potential drug design targets, with 8 proteins showing virulence factors and 6 proteins successfully modelled for three-dimensional structures. The study provides valuable insights for understanding disease mechanisms and developing new drug targets against CFT073.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Cheng Ma, Caixia Gong
Summary: This study obtained for the first time a heterologously expressed ZIP homolog from Desulfovibrio vulgaris, named dvZip, and confirmed its zinc transport ability. It was revealed that dvZip may belong to the GufA subfamily and have 8 transmembrane segments.
Article
Multidisciplinary Sciences
Jacob M. Musser, Klaske J. Schippers, Michael Nickel, Giulia Mizzon, Andrea B. Kohn, Constantin Pape, Paolo Ronchi, Nikolaos Papadopoulos, Alexander J. Tarashansky, Jorg U. Hammel, Florian Wolf, Cong Liang, Ana Hernandez-Plaza, Carlos P. Cantalapiedra, Kaia Achim, Nicole L. Schieber, Leslie Pan, Fabian Ruperti, Warren R. Francis, Sergio Vargas, Svenja Kling, Maike Renkert, Maxim Polikarpov, Gleb Bourenkov, Roberto Feuda, Imre Gaspar, Pawel Burkhardt, Bo Wang, Peer Bork, Martin Beck, Thomas R. Schneider, Anna Kreshuk, Gert Worheide, Jaime Huerta-Cepas, Yannick Schwab, Leonid L. Moroz, Detlev Arendt
Summary: Through whole-body single-cell RNA sequencing in sponges, researchers identified 18 distinct cell types, including contractile pinacocytes, amoeboid phagocytes, and secretory neuroid cells. These cells interact closely with digestive choanocytes, which express scaffolding and receptor proteins, indicating a communication system organized around sponge digestive chambers. Visualizing neuroid cells revealed secretory vesicles and cellular projections enwrapping choanocyte microvilli and cilia, suggesting the presence of conserved modules that may have evolved into synaptic structures in other animals' nervous systems.
Article
Virology
Briallen Lobb, Anson Shapter, Andrew C. Doxey, Jozef I. Nissimov
Summary: A study found that 30% of the genes in the Coccolithovirus genome are shared by all 14 strains, and core genes are more likely to be similar to host proteins and involved in critical functions, providing a solid foundation for functional predictions of this genome.
Article
Plant Sciences
Giuseppe Andolfo, Juliane C. Dohm, Heinz Himmelbauer
Summary: The activation of plant immunity relies on R-gene receptors, but traditional methods of identifying these genes may be imprecise. A new method called HRP has been developed to better identify and annotate NB-LRR genes in plant genomes, showing increased efficiency and accuracy in comparison to previous approaches. This high-performance method has the potential to lead to the discovery of novel R-genes and the development of improved plant cultivars.
Article
Multidisciplinary Sciences
Yu Wang, He Zhang, Hyok Chol Ri, Zeyu An, Xin Wang, Jia-Nan Zhou, Dongran Zheng, Hao Wu, Pengchao Wang, Jianfei Yang, Ding-Kun Liu, Diyang Zhang, Wen-Chieh Tsai, Zheyong Xue, Zhichao Xu, Peng Zhang, Zhong-Jian Liu, Hailong Shen, Yuhua Li
Summary: Araliaceae species produce various triterpene and triterpenoid saponins. The lack of genome sequences of Panax relatives has hindered mechanistic insight into the divergence of triterpene saponins in Araliaceae. This study presents a chromosome-level genome of Aralia elata and reveals the loss of a key gene and tandem duplications of triterpene biosynthetic genes as driving factors for the structural divergences of saponins in Araliaceae.
NATURE COMMUNICATIONS
(2022)
Article
Entomology
Jia-Ying Zhu, Lu Li, Kai-Ran Xiao, Shu-Qi He, Fu-Rong Gui
Summary: The study identified 206 cuticular proteins (CPs) from the fall armyworm genome and found that 51 CP genes significantly changed after exposure to 17 insecticides, with 8 CP genes responding to 4 insecticides confirmed through RT-PCR analysis. These findings suggest a potential role of CPs in insecticide stress response in fall armyworms.
Article
Plant Sciences
Vanika Garg, Annapurna Chitikineni, Mamta Sharma, Raju Ghosh, Srinivasan Samineni, Rajeev K. Varshney, Himabindu Kudapa
Summary: Comparative transcriptome analysis was conducted to investigate the molecular mechanism of Fusarium wilt (FW) resistance in chickpea. Differentially expressed genes (DEGs) were identified between resistant and susceptible genotypes under control and stress conditions. A considerable number of transcription factor encoding genes showed differential expression patterns, and several previously reported FW resistance-related genes were co-localized with the identified DEGs.
Article
Genetics & Heredity
Morgan Price, Adam O. Deutschbauer, Adam Arkin
Summary: To discover novel catabolic enzymes and transporters, the researchers combined high-throughput genetic data from 29 bacteria with an automated tool. They used GapMind to annotate the uptake and catabolism of compounds in bacterial and archaeal genomes, and systematically examined the gaps in predicted pathways. They identified new pathways or enzymes for the utilization of various compounds and annotated numerous enzymes and transporters.
Review
Plant Sciences
Xu Lu, Lijin Huang, Henrik Scheller, Jay D. Keasling
Summary: Terpenoid glycosides derived from medicinal plants have shown significant curative effects in the treatment of various diseases. UDP-dependent glycosyltransferases in plants play a crucial role in the biosynthesis of bioactive glycosides. In this review, the characteristics, evolution, and recent advances in terpenoid UDP-glycosyltransferases (UGTs) in medicinal plants over the past 20 years are summarized, providing a reference for the study of glycosylation and biosynthetic pathways of medicinal terpenoids in plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Multidisciplinary Sciences
Joao A. A. Ascensao, Kelly M. M. Wetmore, Benjamin H. H. Good, Adam P. P. Arkin, Oskar Hallatschek
Summary: Ascensao et al. engineered knockout libraries of a nascent bacterial community and found that ecological and epistatic patterns combine to shape adaptive landscapes, despite idiosyncratic behavior of individual knockouts. The study also revealed that fitness effects are correlated with evolutionary outcomes for certain conditions, indicating shifting patterns of adaptation.
NATURE COMMUNICATIONS
(2023)
Article
Computer Science, Interdisciplinary Applications
Sanya B. Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
Summary: The study constructed a knowledge graph (KG) for pharmacokinetic natural product-drug interactions (NPDIs), which can be used to discover plausible mechanistic explanations and guide scientific research.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Benjamin A. Adler, Karthik Chamakura, Heloise Carion, Jonathan Krog, Adam M. Deutschbauer, Ry Young, Vivek K. Mutalik, Adam P. Arkin
Summary: This study used a high-throughput genetic screen to identify genome-wide host suppressors of diverse single-gene lysis factors (Sgls). In addition to validating known mechanisms, the researchers discovered that the Sgl of PP7, a Pseudomonas aeruginosa ssRNA phage, targets MurJ, the flippase responsible for lipid II export, which was previously shown to be the target of the Sgl of coliphage M. These unrelated Sgls, which are predicted to have opposite membrane topology, represent a case of convergent evolution. Furthermore, the genetic screens revealed a common set of multicopy suppressors for uncharacterized Sgls, suggesting a shared or similar mechanism of action.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Microbiology
K. T. Ash, Y. Li, I. Alamilla, D. C. Joyner, D. E. Williams, P. J. McKay, B. M. Green, C. Iler, S. E. DeBlander, C. M. North, F. Kara-Murdoch, C. M. Swift, T. C. Hazen
Summary: The COVID-19 pandemic has created a need to monitor community infection rates and detect the presence of SARS-CoV-2. Wastewater-based epidemiology is an efficient, economical, fast, and non-invasive method to monitor a large community for a single pathogen or multiple pathogen targets.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
George A. Platt, Katherine J. Davis, Hannah D. Schweitzer, Heidi J. Smith, Matthew W. Fields, Elliott P. Barnhart, Robin Gerlach
Summary: The addition of small amounts of algal biomass to coal seams can enhance methane production and decrease the time required for maximum methane production. Different coals show varied results in methane production, and the microbial community in the coal is influenced by the addition of algal amendment, leading to a shift in coal-degrading bacteria and CO2-reducing methanogens.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Ye Li, K. T. Ash, Dominique C. Joyner, Daniel E. Williams, I. Alamilla, P. J. McKay, C. Iler, B. M. Green, F. Kara-Murdoch, C. M. Swift, Terry C. Hazen
Summary: In this study, a field trial was conducted in the University of Tennessee dormitories to investigate the decay of SARS-CoV-2 RNA in raw sewage. The results showed that temperature and concentration level of SARS-CoV-2 RNA were the most significant factors affecting its decay rate.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Kevin Yin, Pablo Cruz-Morales, Christopher M. Whitford, Jay D. Keasling
Summary: Polycyclopropanated (POP) compounds have the potential to be a more energy-dense alternative to current jet and rocket fuels, but further development is needed. This protocol outlines the production of polycyclopropanated fatty acids in Streptomyces, though the production of POP in other hosts has yet to be demonstrated. This method serves as a baseline for the future development of POP and other polyketide products. For more information, please refer to Cruz-Morales et al. (2022).
Article
Biochemistry & Molecular Biology
David B. Bernstein, Batu Akkas, Morgan N. Price, Adam P. Arkin
Summary: The accuracy of four consecutive E. coli GEMs was quantified using mutant fitness data, and the utility of the area under a precision-recall curve as an accuracy metric was demonstrated. Errors in the latest model were identified, including the availability of certain vitamins/cofactors to mutants and inaccurate predictions from isoenzyme gene-protein-reaction mapping. Machine learning identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Xiaoyue Chen, Graham A. Hudson, Charlotte Mineo, Bashar Amer, Edward E. K. Baidoo, Samantha A. Crowe, Yuzhong Liu, Jay D. Keasling, Henrik V. Scheller
Summary: Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. In this study, we leveraged MeJA-induced saponin biosynthesis in S. vaccaria and identified multiple enzymes that catalyze the oxidation and glycosylation of triterpenoids. We also discovered the biosynthetic pathway for the rare nucleotide sugar UDP-d-fucose. Our findings enable the production and optimization of high-value saponins in microorganisms and plants through synthetic biology approaches.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Lucas Waldburger, Mitchell G. Thompson, Alexandra J. Weisberg, Namil Lee, Jeff H. H. Chang, Jay D. Keasling, Patrick M. M. Shih
Summary: Transcription start sites (TSSs) play a fundamental role in understanding gene expression and regulation. Agrobacteria are prokaryotes widely used in plant biotechnology due to their ability to transfer DNA into host plant genomes. However, the genome-wide transcriptional regulation of agrobacteria, especially in less-studied lineages, remains poorly understood. A study using differential RNA-seq and an optimized algorithm has successfully identified thousands of TSSs with nucleotide resolution for representatives of each lineage, providing a framework for understanding the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The importance of parameter optimization in genome-wide TSS identification and genomics is also highlighted by the optimized algorithm.
Article
Food Science & Technology
Vayu Maini Rekdal, Nabila Rodriguez-Valeron, Mikel Olaizola Garcia, Diego Prado Vasquez, Pia M. Sorensen, Rasmus Munk, Jay D. Keasling
Summary: This study explores novel culinary applications of Neurospora intermedia, an edible fungus traditionally used in Java, Indonesia. The fungus can be used to produce oncom-like meat alternatives and enzymes for starch-to-sugar conversion. It also adds orange color and distinct volatile aroma to dishes. The novel foods produced in this study received favorable ratings in consumer trials.
INTERNATIONAL JOURNAL OF GASTRONOMY AND FOOD SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Aidan E. Cowan, Sarah H. Klass, Peter H. Winegar, Jay D. Keasling
Summary: Anthropogenic carbon emissions are causing rapid climate change and posing risks to ecosystems and human society. Innovations in microbial fermentation enable the production of fuels, chemicals, and materials without the use of fossil resources, thus reducing carbon emissions. Recent advances in microbial fermentation aim to increase product yield and efficiency, while also lowering production costs to compete economically with fossil-derived chemicals.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2023)
Article
Ecology
Hans K. Carlson, Denish Piya, Madeline L. Moore, Roniya T. Magar, Nathalie H. Elisabeth, Adam M. Deutschbauer, Adam P. Arkin, Vivek K. Mutalik
Summary: Lytic phages can have significant impacts on microbial ecosystem function, but the conditions under which phage predation modulates terrestrial systems are uncertain. Ionic strength and carbon composition play important roles in phage infection, but limited data exist on their thresholds and variability in environmental conditions. This study provides insights on the ion thresholds for phage infection and the influence of carbon source variability on phage predation on microbiome function.
ISME COMMUNICATIONS
(2023)