Article
Multidisciplinary Sciences
Jeffrey J. Power, Fernanda Pinheiro, Simone Pompei, Viera Kovacova, Melih Yueksel, Isabel Rathmann, Mona Foerster, Michael Laessig, Berenike Maier
Summary: Horizontal gene transfer is an important factor in bacterial evolution, allowing for rapid evolution and increased adaptation in recipient organisms. Adaptive evolution mainly occurs in populations with increased fitness, with HGT selection having a broad genetic basis and showing different types of selection in functional gene networks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
Summary: In this study, a computational toolbox called HGTphyloDetect was developed, which combines high-throughput analysis with phylogenetic inference to accurately identify horizontal gene transfer (HGT) events and illustrate the transmission pathway among evolutionarily distant or closely related species. The HGTphyloDetect toolbox is user-friendly, capable of detecting HGT events with high efficiency and low false discovery rate.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, Johann Peter Gogarten, Mukul S. Bansal
Summary: Horizontal gene transfer (HGT) is crucial for prokaryotic evolution, yet little is known about the scale of individual HGT events. A computational framework called HoMer is introduced to infer single-gene HGT events and potential multiple-gene transfers, aiding a better understanding of HGT and microbial evolution on a larger scale through systematic inference of HMGTs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
An N. T. Nguyen, Laura C. Woods, Rebecca Gorrell, Shamitraa Ramanan, Terry Kwok, Michael J. McDonald
Summary: Horizontal gene transfer is vital for microbial evolution, yet we have limited knowledge about the fitness effects and dynamics of these transferred genetic variants. Through evolutionary experiments on laboratory populations of Helicobacter pylori, which naturally take up DNA from their environment, we measured the fitness effects of thousands of transferred genetic variants. Our findings reveal that natural transformation increases the rate of adaptation but comes with a significant genetic load. However, recombination bypasses this cost by enhancing selection efficiency through separating harmful and beneficial genetic variants. Our results demonstrate that adaptation with horizontal gene transfer, which is pervasive in natural microbial populations, is influenced by a combination of selection, recombination, and genetic drift that existing evolutionary models fail to account for.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
M. Julhasur Rahman, Sherry L. Haller, Ana M. M. Stoian, Jie Li, Greg Brennan, Stefan Rothenburg
Summary: This study developed a model to understand the mechanisms of gene transfer in vaccinia virus. The findings indicate that gene capture events are mediated by LINE-1 retrotransposition and highlight the role of host retrotransposons as major drivers for virus evolution.
Article
Biotechnology & Applied Microbiology
Joshua G. Philips, Elena Martin-Avila, Andrea V. Robold
Summary: This review provides updated evidence on the likelihood, factors, and barriers for horizontal gene transfer in genetically modified plants, and presents the legislation and frameworks followed by the Australian Gene Technology Regulator in considering the risks posed by horizontal gene transfer.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biology
Yun Wang, Franz Baumdicker, Paul Schweiger, Sven Kuenzel, Fabian Staubach
Summary: The study reveals the significant impact of microbial genomic variation on host fitness, with the thiamine biosynthesis pathway playing a role in the variation of offspring production in Drosophila. Horizontal gene transfer can enhance microbiome flexibility and potentially contribute to host adaptation.
Article
Engineering, Environmental
Shuyao Zhu, Bingqing Yang, Yuqian Jia, Feiyu Yu, Zhiqiang Wang, Yuan Liu
Summary: This study aimed to explore the impact of different disinfectants on the horizontal transfer of antibiotic resistance genes (ARGs) and their underlying mechanisms. The results showed that quaternary ammonium salt, organic halogen, alcohol, and guanidine disinfectants significantly facilitated the conjugative transfer, while heavy metals, peroxides, and phenols displayed an inhibitory effect. Furthermore, guanidine disinfectants promoted conjugation through increased cell membrane permeability, over-production of reactive oxygen species (ROS), enhanced SOS response, and altered expression of conjugative transfer-related genes. Moreover, guanidine disinfectants also promoted bacterial energy metabolism and flagellum motility. These findings highlight the potential risks caused by the massive use of guanidine disinfectants, especially during the COVID-19 pandemic.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biology
Brendan Epstein, Peter Tiffin
Summary: This study reveals that symbiosis genes in rhizobial genomes undergo high rates of horizontal transfer, along with signatures of purifying selection. Particularly, genes involved in initiating symbiosis and in mediating benefits to the host show strong patterns of horizontal transfer and purifying selection.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Nuria Marti Gutierrez, Aleksei Mikhalchenko, Hong Ma, Amy Koski, Ying Li, Crystal Van Dyken, Rebecca Tippner-Hedges, David Yoon, Dan Liang, Tomonari Hayama, David Battaglia, Eunju Kang, Yeonmi Lee, Anthony Paul Barnes, Paula Amato, Shoukhrat Mitalipov
Summary: Cells can acquire mitochondrial DNA (mtDNA) from other cells without a parent-offspring relationship, and this acquisition can occur at high levels. The transfer of mtDNA may serve as a compensatory mechanism to restore compromised mitochondrial function. These findings have important implications for understanding mtDNA transfer and developing gene therapies.
Review
Biology
Matthieu Haudiquet, Jorge Moura de Sousa, Marie Touchon, Eduardo P. C. Rocha
Summary: Horizontal gene transfer (HGT) is a driving force in microbial adaptation, but it is controlled by mobile genetic elements (MGEs) whose interests may not align with those of their hosts. The interactions between cells and MGEs, as well as between MGEs themselves, result in complex evolutionary processes that affect gene flow and microbial adaptation.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Review
Microbiology
Logan C. C. Ott, Melha Mellata
Summary: This review discusses key studies on current models for bacterial conjugation in the gut, including in silico, in vitro, and in vivo models. The importance of studying plasmid transfer in the gut is emphasized, as it plays a significant role in the emergence and spread of antimicrobial resistance and virulence genes. The review highlights the need for alternate models that accurately represent the gut environment and provides directions for future research.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Max A. B. Haase, Jacek Kominek, Dana A. Opulente, Xing-Xing Shen, Abigail L. LaBella, Xiaofan Zhou, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Antonis Rokas, Chris Todd Hittinger
Summary: Dollo's law suggests that evolutionary losses are irreversible, but a study on yeast shows that traits lost millions of years ago can be reacquired through horizontal gene transfer, demonstrating that reversals to ancestral states are possible.
Article
Biochemical Research Methods
Borja Pitarch, Juan A. G. Ranea, Florencio Pazos
Summary: The methodology presented in the work combines sequence information with interactome information to predict residues controlling a protein's interaction specificity, showing to be a better predictor of interfacial residues than sequence conservation alone.
Article
Biochemistry & Molecular Biology
Yuichiro Hara, Reira Shibahara, Koyuki Kondo, Wataru Abe, Takekazu Kunieda
Summary: Trehalose, a versatile non-reducing sugar, is used as a potent protectant against environmental stresses and blood sugar in certain animal groups. Despite the unidentified trehalose biosynthesis genes in the large majority of metazoan phyla, bifunctional TPS-TPP genes have been identified across various taxa. Phylogenetic analyses revealed the acquisition of 'pan-metazoan' genes in early metazoan ancestors, indicating parallel evolution of trehalose synthesis through recurrent loss and horizontal gene transfer.
Article
Plant Sciences
Dovile Barcyte, Wenche Eikrem, Anette Engesmo, Sergio Seoane, Jens Wohlmann, Ales Horak, Tatiana Yurchenko, Marek Elias
Summary: Olisthodiscus represents a novel phylogenetically distinct ochrophyte lineage, with a plastid genome containing unique genes inherited from the rhodophyte ancestor and possessing a unique plastidial sulfate transporter SulT. Additionally, it is the only known ochrophyte with a cemA gene in its plastid genome, and phylogenetic analysis has ruled out the hypothesis of horizontal cemA transfer from a green algal plastid into Synurales.
JOURNAL OF PHYCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Vojtech Zarsky, Vladimir Klimes, Jan Paces, Cestmir Vlcek, Miluse Hradilova, Vladimir Benes, Eva Nyvltova, Ivan Hrdy, Jan Pyrih, Jan Mach, Lael Barlow, Courtney W. Stairs, Laura Eme, Neil Hall, Marek Elias, Joel B. Dacks, Andrew Roger, Jan Tachezy
Summary: The transition from free-living organisms to parasitic organisms involves massive gene losses and reductions in structural features, metabolic pathways, and metabolic complexity. Through genomic and transcriptomic analysis of amoebas, it was found that ancestral preconditions for the evolution of parasitism included the ability to form chitinous cysts, possess proteolytic enzyme machinery, compartmentalize metabolic pathways, and have components for anaerobic energy metabolism. Additionally, lateral gene transfer played an essential role in parasite evolution and adaptation to anaerobic environments.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Graham E. Larue, Marek Elias, Scott W. Roy
Summary: The research found a large number of U12-type introns in the slime mold Physarum polycephalum, which are associated with the spliceosome and have gained efficiently spliced U12-type introns. These results reveal an unappreciated dynamism of minor spliceosomal introns and spliceosomal introns in general.
Article
Biochemistry & Molecular Biology
Jan Pyrih, Tomas Panek, Ignacio Miguel Durante, Vendula Raskova, Kristyna Cimrhanzlova, Eva Kriegova, Anastasios D. Tsaousis, Marek Elias, Julius Lukes
Summary: This study reveals the presence of homologs of bacterial Ffh and FtsY proteins in various plastid-lacking unicellular eukaryotes, suggesting they constitute parts of an ancestral mitochondrial signal peptide-based protein-targeting system inherited from the last eukaryotic common ancestor. This system appears to have been lost from the majority of extant eukaryotes, with implications for protein targeting in different organisms.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Lenka Horvathova, Vojtech Zarsky, Tomas Panek, Romain Derelle, Jan Pyrih, Alzbeta Motyckova, Veronika Klapst'ova, Martina Vinopalova, Lenka Markova, Lubos Voleman, Vladimir Klimes, Marketa Petru, Zuzana Vaitova, Ivan Cepicka, Klara Hryzakova, Karel Harant, Michael W. Gray, Mohamed Chami, Ingrid Guilvout, Olivera Francetic, B. Franz Lang, Cestmir Vlcek, Anastasios D. Tsaousis, Marek Elias, Pavel Dolezal
Summary: The study reveals that certain primitive eukaryotes possess T2SS components similar to those found in Gram-negative bacteria, with some of them located in mitochondria. They are part of a broader functional pathway involving other proteins in eukaryotes.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Emily K. Herman, Alex Greninger, Mark van der Giezen, Michael L. Ginger, Inmaculada Ramirez-Macias, Haylea C. Miller, Matthew J. Morgan, Anastasios D. Tsaousis, Katrina Velle, Romana Vargova, Kristina Zahonova, Sebastian Rodrigo Najle, Georgina MacIntyre, Norbert Muller, Mattias Wittwer, Denise C. Zysset-Burri, Marek Elias, Claudio H. Slamovits, Matthew T. Weirauch, Lillian Fritz-Laylin, Francine Marciano-Cabral, Geoffrey J. Puzon, Tom Walsh, Charles Chiu, Joel B. Dacks
Summary: An -omics approach was used to investigate Naegleria fowleri biology and infection, revealing important cellular systems involved in its pathogenicity. Transcriptional analysis showed the upregulation of genes related to glutamate metabolism and ammonia transport in mouse-passaged N. fowleri, indicating adaptation to the host environment.
Editorial Material
Biochemistry & Molecular Biology
Marek Elias
Summary: In recent years, the diversity of eukaryotic microbes has been greatly expanded by recognizing or discovering new major branches of the algal tree of life. A new study defines the phylogenetic home for an elusive marine planktonic lineage previously known only by plastidial rRNA genes, placing it in a new class of the phylum Haptophyta.
Article
Microbiology
Dovile Barcyte, Martin Pusztai, Pavel Skaloud, Marek Elias
Summary: In this study, a new alga, Adglutina synurophila gen. et sp. nov., was described based on morphological and molecular phylogenetic analyses. It was isolated from colonies of the golden-brown alga Synura petersenii and belongs to the phylogroup Moewusinia. Adglutina is characterized by its unique morphology and its relationship with acidophilic Chlamydomonas species.
Article
Biology
Tomas Panek, Dovile Barcyte, Sebastian C. Treitli, Kristina Zahonova, Martin Sokol, Tereza Sevcikova, Eliska Zadrobilkova, Karin Jaske, Naoji Yubuki, Ivan Cepicka, Marek Elias
Summary: By studying the newly discovered non-photosynthetic lineage Leontynka, new insights into organellar genome evolution in Chlamydomonadales can be gained. Leontynka’s unique characteristics of plastid and mitochondrial genomes make it an interesting model for studying organellar genome evolution.
Article
Cell Biology
Skylar Dewees, Romana Vargova, Katherine R. Hardin, Rachel E. Turn, Saroja Devi, Joshua Linnert, Uwe Wolfrum, Tamara Caspary, Marek Elias, Richard A. Kahn
Summary: The ancient ARF family of regulatory GTPases includes ARL16, which may regulate the trafficking pathway from the Golgi to cilia.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Microbiology
Romana Vargova, Pavla Hanouskova, Jana Salamonova, David Zihala, Jeffrey D. Silberman, Marek Elias, Ivan Cepicka
Summary: In this study, detailed microscopic and transcriptome analyses were conducted on a poorly documented strain of an anaerobic free-living marine flagellate, PCS, in the CL3 fornicate lineage. The researchers discovered a new member of the Caviomonadidae family, Euthynema mutabile, which possesses an ultrastructurally discernible MRO. Transcriptome analyses also showed unique amino acid substitutions in I. spirale's eRF1 protein domain responsible for termination codon recognition. The study suggests that the CL3 clade has undergone a hydrogenosome-to-mitosome transition independent from that previously documented in the lineage leading to Giardia.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Dovile Barcyte, Martina Zatopkova, Yvonne Nemcova, Michal Richtar, Tatiana Yurchenko, Karin Jaske, Karen P. Fawley, Pavel Skaloud, Tereza Seveikova, Marvin W. Fawley, Marek Elias
Summary: This study investigates the diversity, phylogeny, and classification of the Eustigmataceae group within the Eustigmatophyceae. Through comprehensive analyses of hundreds of DNA sequences and plastid genomes, the researchers reveal the phylogenetic relationships within the Eustigmataceae group and confirm the presence of Chlorobotrys as a member of this group. Additionally, the study redefines the taxonomic name of this group and provides insights into the morphology and flagellar protein genes of Chlorobotryaceae members. Overall, this research provides a comprehensive understanding of one of the most diverse lineages of eustigmatophyte algae.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Emma E. George, Dovile Barcyte, Gordon Lax, Sam Livingston, Daria Tashyreva, Filip Husnik, Julius Lukes, Marek Elias, Patrick J. Keeling
Summary: Symbiosis between prokaryotes and microbial eukaryotes has had a significant impact on evolution and ecology. A highly complex community of endosymbionts and a bacteriophage were found within a single Cryptomonad cell. These findings provide insights into organelle evolution and the dynamics of endosymbiotic relationships.
Article
Biochemistry & Molecular Biology
Shaghayegh Sheikh, Tomas Panek, Ondrej Gahura, Jiri Tyc, Kristina Zahonova, Julius Lukes, Marek Elias, Hassan Hashimi
Summary: The study identifies a novel GTPase called MidX that is present in eukaryotes and giant viruses, and it is predicted to affect mitochondrial morphology by interacting with the inner membrane. MidX has a unique structure and mode of action compared to other proteins with similar functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Dovile Barcyte, Marek Elias
Summary: This study discovered a new genus in the order Chaetopeltidales, expanding our understanding of its diversity and providing insight into its virosphere.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.