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An Event-Driven Approach for Studying Gene Block Evolution in Bacteria [article]

David C Ream, Asma R Bankapur, Iddo Friedberg
2015 arXiv   pre-print
To address this problem we introduce an event-based method for tracking gene block evolution in bacteria.  ...  An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed.  ...  For these 38 operons and related orthologous gene blocks, we show an implementation of the event-driven approach to operon evolution.  ... 
arXiv:1501.00302v2 fatcat:77ya53djzfcvbl3qclqeggwp2y

An event-driven approach for studying gene block evolution in bacteria

David C. Ream, Asma R. Bankapur, Iddo Friedberg
2015 Computer applications in the biosciences : CABIOS  
To address this problem, we introduce an eventbased method for tracking gene block evolution in bacteria.  ...  An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed.  ...  For these 38 operons and related orthologous gene blocks, we show an implementation of the event-driven approach to operon evolution.  ... 
doi:10.1093/bioinformatics/btv128 pmid:25717195 pmcid:PMC4481853 fatcat:ygphaizjvvepdkhpj2xuarq3ym

Targeting evolution of antibiotic resistance by SOS response inhibition

Yakimov Alexander, Bakhlanova Irina, Baitin Dmitry
2021 Computational and Structural Biotechnology Journal  
The regulators of homologous recombination involved in the processes of DNA repair should be considered as potential targets for blocking.  ...  Antibiotic resistance is acquired in response to antibiotic therapy by activating SOS-depended mutagenesis and horizontal gene transfer pathways.  ...  Julia Gorelik, and Michael Gorelik for critically reading the manuscript and valuable comments.  ... 
doi:10.1016/j.csbj.2021.01.003 pmid:33552448 pmcid:PMC7843400 fatcat:ceiij7o4cza6hcvqnn6o3c6f5e

Comparative Genomics Suggests That an Ancestral Polyploidy Event Leads to Enhanced Root Nodule Symbiosis in the Papilionoideae

Qi-Gang Li, Li Zhang, Chun Li, Jim M. Dunwell, Yuan-Ming Zhang
2013 Molecular biology and evolution  
In this study, we explored this role using an integrated comparative genomic approach and conducted gene expression comparisons and gene ontology enrichment analyses.  ...  Comparative genomics suggests that an ancestral polyploidy event leads to enhanced root nodule symbiosis in the Papilionoideae. Molecular Biology and Evolution, 30 (12). pp. 26022611.  ...  Acknowledgments and funding information We are grateful to the International Peach Genome Initiative for the assembled and annotated draft  ... 
doi:10.1093/molbev/mst152 pmid:24008584 fatcat:svgkasvdffezretdc335x5w3ci

Unraveling a tangled skein: Evolutionary analysis of the bacterial gibberellin biosynthetic operon [article]

Ryan S Nett, Nuy N Nguyen, Raimund Nagel, Ariana Marcassa, Trevor C Charles, Iddo Friedberg, Reuben J Peters
2019 biorxiv/medrxiv   pre-print
for microbes to gain an advantage in these interactions.  ...  Additionally, a maximum-parsimony ancestral gene block reconstruction algorithm was employed to characterize loss, gain, and horizontal gene transfer (HGT) of GA operon genes within alphaproteobacteria  ...  An event is a change in the gene block between any two species with homologous gene blocks.  ... 
doi:10.1101/868042 fatcat:st7lqmiy65dkhopxvey3qajfcm

Evolution ofbopAGene inBurkholderia: A Case of Convergent Evolution as a Mechanism for Bacterial Autophagy Evasion

Dong Yu, Zhiqiu Yin, Yuan Jin, Jing Zhou, Hongguang Ren, Mingda Hu, Beiping Li, Wei Zhou, Long Liang, Junjie Yue
2016 BioMed Research International  
The results of this study clearly demonstrated the role of convergent evolution in the evolution of how bacteria evade autophagy.  ...  Up to now, no information about the origin or evolution of the antiautophagic genes in bacteria is available.  ...  These results indicted the bopA gene was not acquired from the eukaryotes through a recent HGT event. BopA Gene in Bacteria.  ... 
doi:10.1155/2016/6745028 pmid:28018913 pmcid:PMC5149610 fatcat:hrexjqhnezak3j6bqrwgusnxhi

Replacing and Additive Horizontal Gene Transfer in Streptococcus

Sang Chul Choi, Matthew D. Rasmussen, Melissa J. Hubisz, Ilan Gronau, Michael J. Stanhope, Adam Siepel
2012 Molecular biology and evolution  
The prominent role of Horizontal Gene Transfer (HGT) in the evolution of bacteria is now well documented, but few studies have differentiated between evolutionary events that predominantly cause genes  ...  Putative virulence genes are correlated with transfer events, but this correlation is found to be driven by additive, not replacing, HGTs.  ...  Acknowledgments The authors thank Xavier Didelot for assistance with ClonalOrigin.  ... 
doi:10.1093/molbev/mss138 pmid:22617954 pmcid:PMC3472495 fatcat:bmdlt4uzcrf3jao7p5x2bngoty

Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon

Ryan S. Nett, Huy Nguyen, Raimund Nagel, Ariana Marcassa, Trevor C. Charles, Iddo Friedberg, Reuben J. Peters, Angela D. Kent
2020 mSphere  
for microbes to gain an advantage in these interactions.  ...  gene for the final biosynthetic step in most rhizobia, suggest varied functions for GA in these distinct plant-microbe interactions.  ...  An event is a change in the gene block between any two species with homologous gene blocks.  ... 
doi:10.1128/msphere.00292-20 pmid:32493722 pmcid:PMC7273348 fatcat:xxqypfz7pncwhaavbhlgwd26ay

Ecology drives a global network of gene exchange connecting the human microbiome

Chris S. Smillie, Mark B. Smith, Jonathan Friedman, Otto X. Cordero, Lawrence A. David, Eric J. Alm
2011 Nature  
Correspondence and requests for materials should be addressed to E.J.A. (ejalm@mit.edu). Author Contributions  ...  However, an alternative explanation for these observations is that closely related bacteria colonize similar environments, creating an apparent ecological effect that is actually driven by shared evolutionary  ...  An average pairwise distance of 7,000 km separates bacteria engaging in HGT.  ... 
doi:10.1038/nature10571 pmid:22037308 fatcat:ib3dy5vtgzatff7wq7ds3wlnwi

Tempo and mode of early gene loss in endosymbiotic bacteria from insects

F Delmotte, C Rispe, J Schaber, F J Silva, A Moya
2006 BMC Evolutionary Biology  
loss could be driven by the selective importance of genes.  ...  rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts.  ...  We are grateful to Jacqui Shykoff for her critical review of the manuscript and her help in revising the english.  ... 
doi:10.1186/1471-2148-6-56 pmid:16848891 pmcid:PMC1544356 fatcat:es2vknegbjbihcx5bwnqtpsskq

The Microbial Engines That Drive Earth's Biogeochemical Cycles

P. G. Falkowski, T. Fenchel, E. F. Delong
2008 Science  
Hence, although there is enormous genetic diversity in nature, there remains a relatively stable set of core genes coding for the major redox reactions essential for life and biogeochemical cycles.  ...  These genes created and coevolved with biogeochemical cycles and were passed from microbe to microbe primarily by horizontal gene transfer.  ...  The study of biogeography includes the study of patterns in space, in time, and along environmental gradients.  ... 
doi:10.1126/science.1153213 pmid:18497287 fatcat:xg62vppglrhujohl76rhsz52ce

Synthetic Biology of secondary metabolite biosynthesis in actinomycetes: Engineering precursor supply as a way to optimize antibiotic production

Wolfgang Wohlleben, Yvonne Mast, Günther Muth, Marlene Röttgen, Evi Stegmann, Tilmann Weber
2012 FEBS Letters  
The genes encoding the enzymes for their biosynthesis are normally organized in gene clusters, which include also the information for resistance (in the case of antibacterial compounds), regulation, and  ...  Here we report examples for the synthesis of building blocks and possibilities to modify and optimize antibiotic biosynthesis, exemplary for the synthesis of the manipulation of the synthesis of the glycopeptide  ...  These examples let us assume that primordial gene duplication events were the beginning of such enzyme evolutions.  ... 
doi:10.1016/j.febslet.2012.04.025 pmid:22710162 fatcat:vx7vqrpuuvhyndmfhp6plnh7cy

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer

Csaba Pál, Balázs Papp, Martin J Lercher
2005 Nature Genetics  
We used an analogous procedure for loss events, analyzing all branches starting from nodes in which both A and B were present.  ...  Although gene duplication may have been an important source for network changes during the early evolution of pathways 1 , the above analyses suggest that horizontal gene transfer was the dominant genetic  ... 
doi:10.1038/ng1686 pmid:16311593 fatcat:c5r2h57hcvawzjg557yosst7re

Soybean (Glycine max) NF-Y (Nuclear Factor of Y Box) gene family and its potential role under stress conditions and nodulation

Cabreira-Cagliari C, Bohn B, Dias NCF, Fagundes DGS, Margis-Pinheiro M, Bodanese-Zanettini MH, Cagliari A
2018 Journal of Plant Biology and Crop Research  
In this study, GmNF-Y genes were investigated through an extensive data mining using several bioinformatics approaches.  ...  Results showed that during evolution, GmNF-Y genes arose by block duplication and subfuctionalization processes could be occurring in this family.  ...  An unequal crossover mechanism should have driven the evolution in this subunit. Soybean experienced whole genome duplication during their evolution.  ... 
doi:10.33582/2637-7721/1009 fatcat:5jnoqobkxndntpx3a6fpq7g6me

Positive Selection in Bifidobacterium Genes Drives Species-Specific Host–Bacteria Communication

Marina S. Dyachkova, Evgeny V. Chekalin, Valery N. Danilenko
2019 Frontiers in Microbiology  
We used the maximum likelihood approach to detect positive selection in the PFNA genes.  ...  Our results provide evidence that episodic positive selection has played an important role in the divergence process and molecular evolution of sequences of the species-specific PFNA genes in most bifidobacterial  ...  The sites with PP > 0.95 are marked with an asterisk. The most reliable candidates for positive selection verified with an additional approach are highlighted in black.  ... 
doi:10.3389/fmicb.2019.02374 pmid:31681231 pmcid:PMC6803598 fatcat:pyk2j4easzgb3gqewnvhfolfyy
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