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Zhang Z, Diao R, Sun J, Liu Y, Zhao M, Wang Q, Xu Z, Zhong B. Diversified molecular adaptations of inorganic nitrogen assimilation and signaling machineries in plants. THE NEW PHYTOLOGIST 2024; 241:2108-2123. [PMID: 38155438 DOI: 10.1111/nph.19508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Plants evolved sophisticated machineries to monitor levels of external nitrogen supply, respond to nitrogen demand from different tissues and integrate this information for coordinating its assimilation. Although roles of inorganic nitrogen in orchestrating developments have been studied in model plants and crops, systematic understanding of the origin and evolution of its assimilation and signaling machineries remains largely unknown. We expanded taxon samplings of algae and early-diverging land plants, covering all main lineages of Archaeplastida, and reconstructed the evolutionary history of core components involved in inorganic nitrogen assimilation and signaling. Most components associated with inorganic nitrogen assimilation were derived from the ancestral Archaeplastida. Improvements of assimilation machineries by gene duplications and horizontal gene transfers were evident during plant terrestrialization. Clusterization of genes encoding nitrate assimilation proteins might be an adaptive strategy for algae to cope with changeable nitrate availability in different habitats. Green plants evolved complex nitrate signaling machinery that was stepwise improved by domains shuffling and regulation co-option. Our study highlights innovations in inorganic nitrogen assimilation and signaling machineries, ranging from molecular modifications of proteins to genomic rearrangements, which shaped developmental and metabolic adaptations of plants to changeable nutrient availability in environments.
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Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zilong Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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2
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Iasakov T. Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D). Int J Mol Sci 2023; 24:14370. [PMID: 37762674 PMCID: PMC10531765 DOI: 10.3390/ijms241814370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/11/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
The tfd (tfdI and tfdII) are gene clusters originally discovered in plasmid pJP4 which are involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusters tcb and clc. Although great effort has been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches has revealed that all tfd clusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed: tfdI, tfdII, tfdIII and tfdIV(A,B,C). Horizontal gene transfer between Burkholderiales and Sphingomonadales provides phenomenal linkage between tfdI, tfdII, tfdIII and tfdIV type clusters and their mosaic nature. It is hypothesized that the evolution of tfd gene clusters proceeded within first (tcb, clc and tfdI), second (tfdII and tfdIII) and third (tfdIV(A,B,C)) evolutionary lineages, in each of which, the genes were clustered in specific combinations. Their clustering is discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements are also proposed to explain the structural variations across members of clusters tfdII and tfdIII, respectively. Taking everything into account, these findings reconstruct the phylogeny of tfd clusters, have delineated their evolutionary trajectories, and allow the contribution of various evolutionary processes to be assessed.
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Affiliation(s)
- Timur Iasakov
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054 Ufa, Russia
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3
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Del Duca S, Semenzato G, Esposito A, Liò P, Fani R. The Operon as a Conundrum of Gene Dynamics and Biochemical Constraints: What We Have Learned from Histidine Biosynthesis. Genes (Basel) 2023; 14:genes14040949. [PMID: 37107707 PMCID: PMC10138114 DOI: 10.3390/genes14040949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Operons represent one of the leading strategies of gene organization in prokaryotes, having a crucial influence on the regulation of gene expression and on bacterial chromosome organization. However, there is no consensus yet on why, how, and when operons are formed and conserved, and many different theories have been proposed. Histidine biosynthesis is a highly studied metabolic pathway, and many of the models suggested to explain operons origin and evolution can be applied to the histidine pathway, making this route an attractive model for the study of operon evolution. Indeed, the organization of his genes in operons can be due to a progressive clustering of biosynthetic genes during evolution, coupled with a horizontal transfer of these gene clusters. The necessity of physical interactions among the His enzymes could also have had a role in favoring gene closeness, of particular importance in extreme environmental conditions. In addition, the presence in this pathway of paralogous genes, heterodimeric enzymes and complex regulatory networks also support other operon evolution hypotheses. It is possible that histidine biosynthesis, and in general all bacterial operons, may result from a mixture of several models, being shaped by different forces and mechanisms during evolution.
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Affiliation(s)
- Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment (CREA-AA), Via di Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Antonia Esposito
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment (CREA-AA), Via di Lanciola 12/A, Cascine del Riccio, 50125 Firenze, Italy
| | - Pietro Liò
- Department of Computer Science and Technology, University of Cambridge, Cambridge CB3 0FD, UK
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
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4
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Sloan DB, Warren JM, Williams AM, Kuster SA, Forsythe ES. Incompatibility and Interchangeability in Molecular Evolution. Genome Biol Evol 2023; 15:evac184. [PMID: 36583227 PMCID: PMC9839398 DOI: 10.1093/gbe/evac184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes-even single-nucleotide substitutions-create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: (1) function in multisubunit enzyme complexes and protein-protein interactions, (2) sensitivity to changes in gene dosage, (3) rapid rate of sequence evolution, and (4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Jessica M Warren
- Center for Mechanisms of Evolution, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Alissa M Williams
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Shady A Kuster
- Department of Biology, Colorado State University, Fort Collins, Colorado
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, Colorado
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5
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Annotation-free delineation of prokaryotic homology groups. PLoS Comput Biol 2022; 18:e1010216. [PMID: 35675326 PMCID: PMC9212150 DOI: 10.1371/journal.pcbi.1010216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/21/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
Phylogenomic studies of prokaryotic taxa often assume conserved marker genes are homologous across their length. However, processes such as horizontal gene transfer or gene duplication and loss may disrupt this homology by recombining only parts of genes, causing gene fission or fusion. We show using simulation that it is necessary to delineate homology groups in a set of bacterial genomes without relying on gene annotations to define the boundaries of homologous regions. To solve this problem, we have developed a graph-based algorithm to partition a set of bacterial genomes into Maximal Homologous Groups of sequences (MHGs) where each MHG is a maximal set of maximum-length sequences which are homologous across the entire sequence alignment. We applied our algorithm to a dataset of 19 Enterobacteriaceae species and found that MHGs cover much greater proportions of genomes than markers and, relatedly, are less biased in terms of the functions of the genes they cover. We zoomed in on the correlation between each individual marker and their overlapping MHGs, and show that few phylogenetic splits supported by the markers are supported by the MHGs while many marker-supported splits are contradicted by the MHGs. A comparison of the species tree inferred from marker genes with the species tree inferred from MHGs suggests that the increased bias and lack of genome coverage by markers causes incorrect inferences as to the overall relationship between bacterial taxa. Assuming genes to be the basic evolutionary unit has been commonplace in bacterial genomics. For example, when quantifying the extent of horizontal gene transfer it is common to infer gene trees and reconcile them against a species tree to account for recombination-based processes. We have developed a new method which challenges this assumption by identifying contiguous regions of true homology without regards to gene boundaries and applied it to Enterobacteriaceae, a family of bacteria containing several important human pathogens. Our results show that genes are composed of distinct homologous regions with conflicting phylogenetic histories. We further demonstrate that failing to take account of this conflict, together with the functional biases we show exist among single-copy marker genes, significantly changes the consensus evolutionary tree of Enterobacteriaceae.
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6
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Jadhav P, Khalid ZB, Zularisam AW, Krishnan S, Nasrullah M. The role of iron-based nanoparticles (Fe-NPs) on methanogenesis in anaerobic digestion (AD) performance. ENVIRONMENTAL RESEARCH 2022; 204:112043. [PMID: 34543635 DOI: 10.1016/j.envres.2021.112043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Several strategies have been proposed to improve the performance of the anaerobic digestion (AD) process. Among them, the use of various nanoparticles (NPs) (e.g. Fe, Ag, Cu, Mn, and metal oxides) is considered one of the most effective approaches to enhance the methanogenesis stage and biogas yield. Iron-based NPs (zero-valent iron with paramagnetic properties (Fe0) and iron oxides with ferromagnetic properties (Fe3O4/Fe2O3) enhance microbial activity and minimise the inhibition effect in methanogenesis. However, comprehensive and up-to-date knowledge on the function and impact of Fe-NPs on methanogens and methanogenesis stages in AD is frequently required. This review focuses on the applicative role of iron-based NPs (Fe-NPs) in the AD methanogenesis step to provide a comprehensive understanding application of Fe-NPs. In addition, insight into the interactions between methanogens and Fe-NPs (e.g. role of methanogens, microbe interaction and gene transfer with Fe-NPs) beneficial for CH4 production rate is provided. Microbial activity, inhibition effects and direct interspecies electron transfer through Fe-NPs have been extensively discussed. Finally, further studies towards detecting effective and optimised NPs based methods in the methanogenesis stage are reported.
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Affiliation(s)
- Pramod Jadhav
- Faculty of Civil Engineering Technology, Universiti Malaysia Pahang (UMP), Lebuhraya Tun Razak, Gambang, Kuantan, Pahang, 26300, Malaysia
| | - Zaied Bin Khalid
- Faculty of Civil Engineering Technology, Universiti Malaysia Pahang (UMP), Lebuhraya Tun Razak, Gambang, Kuantan, Pahang, 26300, Malaysia
| | - A W Zularisam
- Faculty of Civil Engineering Technology, Universiti Malaysia Pahang (UMP), Lebuhraya Tun Razak, Gambang, Kuantan, Pahang, 26300, Malaysia
| | - Santhana Krishnan
- Centre of Environmental Sustainability and Water Security (IPASA), Research Institute of Sustainable Environment (RISE), Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Johor Bahru, 81310, Malaysia; PSU Energy Systems Research Institute, Department of Civil Engineering, Faculty of Engineering, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Mohd Nasrullah
- Faculty of Civil Engineering Technology, Universiti Malaysia Pahang (UMP), Lebuhraya Tun Razak, Gambang, Kuantan, Pahang, 26300, Malaysia.
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7
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Abstract
Iron acquisition is essential for almost all living organisms. In certain environments, ferrous iron is the most prevalent form of this element. Feo is the most widespread system for ferrous iron uptake in bacteria and is critical for virulence in some species. The canonical architecture of Feo consists of a large transmembrane nucleoside triphosphatase (NTPase) protein, FeoB, and two accessory cytoplasmic proteins, FeoA and FeoC. The role of the latter components and the mechanism by which Feo orchestrates iron transport are unclear. In this study, we conducted a comparative analysis of Feo protein sequences to gain insight into the evolutionary history of this transporter. We identified instances of how horizontal gene transfer contributed to the evolution of Feo. Also, we found that FeoC, while absent in most lineages, is largely present in the Gammaproteobacteria group, although its sequence is poorly conserved. We propose that FeoC, which may couple FeoB NTPase activity with pore opening, was an ancestral element that has been dispensed with through mutations in FeoA and FeoB in some lineages. We provide experimental evidence supporting this hypothesis by isolating and characterizing FeoC-independent mutants of the Vibrio cholerae Feo system. Also, we confirmed that the closely related species Shewanella oneidensis does not require FeoC; thus, Vibrio FeoC sequences may resemble transitional forms on an evolutionary pathway toward FeoC-independent transporters. Finally, by combining data from our bioinformatic analyses with this experimental evidence, we propose an evolutionary model for the Feo system in bacteria. IMPORTANCE Feo, a ferrous iron transport system composed of three proteins (FeoA, -B, and -C), is the most prevalent bacterial iron transporter. It plays an important role in iron acquisition in low-oxygen environments and some host-pathogen interactions. The large transmembrane protein FeoB provides the channel for the transport of iron into the bacterial cell, but the functions of the two small, required accessory proteins FeoA and FeoC are not well understood. Analysis of the evolution of this transporter shows that FeoC is poorly conserved and has been lost from many bacterial lineages. Experimental evidence indicates that FeoC may have different functions in different species that retain this protein, and the loss of FeoC is promoted by mutations in FeoA or by the fusion of FeoA and FeoB.
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8
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Neukirchen S, Sousa FL. DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data. Microb Genom 2021; 7. [PMID: 34241589 PMCID: PMC8477390 DOI: 10.1099/mgen.0.000603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Current methods in comparative genomic analyses for metabolic potential prediction of proteins involved in, or associated with the Dsr (dissimilatory sulphite reductase)-dependent dissimilatory sulphur metabolism are both time-intensive and computationally challenging, especially when considering metagenomic data. We developed DiSCo, a Dsr-dependent dissimilatory sulphur metabolism classification tool, which automatically identifies and classifies the protein type from sequence data. It takes user-supplied protein sequences and lists the identified proteins and their classification in terms of protein family and predicted type. It can also extract the sequence data from user-input to serve as basis for additional downstream analyses. DiSCo provides the metabolic functional prediction of proteins involved in Dsr-dependent dissimilatory sulphur metabolism with high levels of accuracy in a fast manner. We ran DiSCo against a dataset composed of over 190 thousand (meta)genomic records and efficiently mapped Dsr-dependent dissimilatory sulphur proteins in 1798 lineages across both prokaryotic domains. This allowed the identification of new micro-organisms belonging to Thaumarchaeota and Spirochaetes lineages with the metabolic potential to use the Dsr-pathway for energy conservation. DiSCo is implemented in Perl 5 and freely available under the GNU GPLv3 at https://github.com/Genome-Evolution-and-Ecology-Group-GEEG/DiSCo.
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Affiliation(s)
- Sinje Neukirchen
- Department of Functional and Evolutionary Ecology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Filipa L Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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9
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Saha CK, Sanches Pires R, Brolin H, Delannoy M, Atkinson GC. FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation. Bioinformatics 2021; 37:1312-1314. [PMID: 32956448 PMCID: PMC8189683 DOI: 10.1093/bioinformatics/btaa788] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/12/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
SUMMARY Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin-antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run. AVAILABILITY AND IMPLEMENTATION FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chayan Kumar Saha
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå 901 87, Sweden
| | - Rodrigo Sanches Pires
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm 100 44, Sweden
| | - Harald Brolin
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Maxence Delannoy
- Département Génie Biologique, Campus SophiaTech, Université Nice Sophia Antipolis, Nice 06900, France
| | - Gemma Catherine Atkinson
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå 901 87, Sweden
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10
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Genomic islands and the evolution of livestock-associated Staphylococcus aureus genomes. Biosci Rep 2021; 40:226941. [PMID: 33185245 PMCID: PMC7689654 DOI: 10.1042/bsr20202287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/23/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genomic Islands (GIs) are commonly believed to be relics of horizontal transfer and associated with specific metabolic capacities, including virulence of the strain. Horizontal gene transfer (HGT) plays a vital role in the acquisition of GIs and the evolution and adaptation of bacterial genomes. OBJECTIVE The present study was designed to predict the GIs and role of HGT in evolution of livestock-associated Staphylococcus aureus (LA-SA). METHODS GIs were predicted with two methods namely, Ensemble algorithm for Genomic Island Detection (EGID) tool, and Seq word Sniffer script. Functional characterization of GI elements was performed with clustering of orthologs. The putative donor predictions of GIs was done with the aid of the pre_GI database. RESULTS The present study predicted a pan of 46 GIs across the LA-SA genomes. Functional characterization of GI sequences revealed few unique results like the presence of metabolic operons like leuABCD and folPK genes in GIs and showed the importance of GIs in the adaptation to the host niche. The developed framework for GI donor prediction results revealed Rickettsia and Mycoplasma as the major donors of GI elements. CONCLUSIONS The role of GIs during the evolutionary race of LA-SA could be concluded from the present study. Niche adaptation of LA-SA enhanced presumably due to these GIs. Future studies could focus on the evolutionary relationships between Rickettsia and Mycoplasma sp. with S. aureus and also the evolution of Leucine/Isoleucine mosaic operon (leuABCD).
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11
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Nguyen HN, Markin A, Friedberg I, Eulenstein O. Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it. Bioinformatics 2021; 36:i668-i674. [PMID: 33381825 PMCID: PMC7773486 DOI: 10.1093/bioinformatics/btaa794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2020] [Indexed: 11/25/2022] Open
Abstract
Motivation The evolution of complexity is one of the most fascinating and challenging problems in modern biology, and tracing the evolution of complex traits is an open problem. In bacteria, operons and gene blocks provide a model of tractable evolutionary complexity at the genomic level. Gene blocks are structures of co-located genes with related functions, and operons are gene blocks whose genes are co-transcribed on a single mRNA molecule. The genes in operons and gene blocks typically work together in the same system or molecular complex. Previously, we proposed a method that explains the evolution of orthologous gene blocks (orthoblocks) as a combination of a small set of events that take place in vertical evolution from common ancestors. A heuristic method was proposed to solve this problem. However, no study was done to identify the complexity of the problem. Results Here, we establish that finding the homologous gene block problem is NP-hard and APX-hard. We have developed a greedy algorithm that runs in polynomial time and guarantees an O(lnn) approximation. In addition, we formalize our problem as an integer linear program problem and solve it using the PuLP package and the standard CPLEX algorithm. Our exploration of several candidate operons reveals that our new method provides more optimal results than the results from the heuristic approach, and is significantly faster. Availability and implementation The software and data accompanying this paper are available under the GPLv3 and CC0 license respectively on: https://github.com/nguyenngochuy91/Relevant-Operon.
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Affiliation(s)
- Huy N Nguyen
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.,Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Alexey Markin
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.,Interdepartmental Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Oliver Eulenstein
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA.,Interdepartmental Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
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12
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Nguyen HN, Jain A, Eulenstein O, Friedberg I. Tracing the ancestry of operons in bacteria. Bioinformatics 2020; 35:2998-3004. [PMID: 30689726 DOI: 10.1093/bioinformatics/btz053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/11/2019] [Accepted: 01/21/2019] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Complexity is a fundamental attribute of life. Complex systems are made of parts that together perform functions that a single component, or subsets of components, cannot. Examples of complex molecular systems include protein structures such as the F1Fo-ATPase, the ribosome, or the flagellar motor: each one of these structures requires most or all of its components to function properly. Given the ubiquity of complex systems in the biosphere, understanding the evolution of complexity is central to biology. At the molecular level, operons are classic examples of a complex system. An operon's genes are co-transcribed under the control of a single promoter to a polycistronic mRNA molecule, and the operon's gene products often form molecular complexes or metabolic pathways. With the large number of complete bacterial genomes available, we now have the opportunity to explore the evolution of these complex entities, by identifying possible intermediate states of operons. RESULTS In this work, we developed a maximum parsimony algorithm to reconstruct ancestral operon states, and show a simple vertical evolution model of how operons may evolve from the individual component genes. We describe several ancestral states that are plausible functional intermediate forms leading to the full operon. We also offer Reconstruction of Ancestral Gene blocks Using Events or ROAGUE as a software tool for those interested in exploring gene block and operon evolution. AVAILABILITY AND IMPLEMENTATION The software accompanying this paper is available under GPLv3 license on: https://github.com/nguyenngochuy91/Ancestral-Blocks-Reconstruction. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Huy N Nguyen
- Department of Veterinary Microbiology and Preventive Medicine, lowa State University, Ames, IA, USA.,Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Ashish Jain
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Oliver Eulenstein
- Department of Computer Science, Iowa State University, Ames, IA, USA.,Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, lowa State University, Ames, IA, USA.,Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
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13
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Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017. J Clin Microbiol 2020; 58:JCM.02070-19. [PMID: 32269101 PMCID: PMC7269400 DOI: 10.1128/jcm.02070-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/28/2020] [Indexed: 12/26/2022] Open
Abstract
Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant C. jejuni. Here, we aimed to elucidate the baseline diversity of the wider New Hampshire C. jejuni population during the outbreak. We used genome sequences of 52 clinical isolates sampled in New Hampshire in 2017, including 1 of the 2 isolates from the outbreak. Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant C. jejuni. Here, we aimed to elucidate the baseline diversity of the wider New Hampshire C. jejuni population during the outbreak. We used genome sequences of 52 clinical isolates sampled in New Hampshire in 2017, including 1 of the 2 isolates from the outbreak. Results revealed a remarkably diverse population composed of at least 28 sequence types, which are mostly represented by 1 or a few strains. A comparison of our isolates with 249 clinical C. jejuni from other states showed frequent phylogenetic intermingling, suggesting a lack of geographical structure and minimal local diversification within the state. Multiple independent acquisitions of resistance genes from 5 classes of antibiotics characterize the population, with 47/52 (90.4%) of the genomes carrying at least 1 horizontally acquired resistance gene. Frequently recombining genes include those associated with heptose biosynthesis, colonization, and stress resistance. We conclude that the diversity of clinical C. jejuni in New Hampshire in 2017 was driven mainly by the coexistence of phylogenetically diverse antibiotic-resistant lineages, widespread geographical mixing, and frequent recombination. This study provides an important baseline census of the standing pangenomic variation and drug resistance to aid the development of a statewide database for epidemiological studies and clinical decision making. Continued genomic surveillance will be necessary to accurately assess how the population of C. jejuni changes over the long term.
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Bundalovic-Torma C, Whitfield GB, Marmont LS, Howell PL, Parkinson J. A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries. PLoS Comput Biol 2020; 16:e1007721. [PMID: 32236097 PMCID: PMC7112194 DOI: 10.1371/journal.pcbi.1007721] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/11/2020] [Indexed: 12/20/2022] Open
Abstract
In bacteria functionally related genes comprising metabolic pathways and protein complexes are frequently encoded in operons and are widely conserved across phylogenetically diverse species. The evolution of these operon-encoded processes is affected by diverse mechanisms such as gene duplication, loss, rearrangement, and horizontal transfer. These mechanisms can result in functional diversification, increasing the potential evolution of novel biological pathways, and enabling pre-existing pathways to adapt to the requirements of particular environments. Despite the fundamental importance that these mechanisms play in bacterial environmental adaptation, a systematic approach for studying the evolution of operon organization is lacking. Herein, we present a novel method to study the evolution of operons based on phylogenetic clustering of operon-encoded protein families and genomic-proximity network visualizations of operon architectures. We applied this approach to study the evolution of the synthase dependent exopolysaccharide (EPS) biosynthetic systems: cellulose, acetylated cellulose, poly-β-1,6-N-acetyl-D-glucosamine (PNAG), Pel, and alginate. These polymers have important roles in biofilm formation, antibiotic tolerance, and as virulence factors in opportunistic pathogens. Our approach revealed the complex evolutionary landscape of EPS machineries, and enabled operons to be classified into evolutionarily distinct lineages. Cellulose operons show phyla-specific operon lineages resulting from gene loss, rearrangement, and the acquisition of accessory loci, and the occurrence of whole-operon duplications arising through horizonal gene transfer. Our evolution-based classification also distinguishes between PNAG production from Gram-negative and Gram-positive bacteria on the basis of structural and functional evolution of the acetylation modification domains shared by PgaB and IcaB loci, respectively. We also predict several pel-like operon lineages in Gram-positive bacteria and demonstrate in our companion paper (Whitfield et al PLoS Pathogens, in press) that Bacillus cereus produces a Pel-dependent biofilm that is regulated by cyclic-3',5'-dimeric guanosine monophosphate (c-di-GMP).
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Affiliation(s)
- Cedoljub Bundalovic-Torma
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Gregory B. Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Lindsey S. Marmont
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - P. Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - John Parkinson
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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15
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Abstract
S. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to S. enterica subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments. Salmonella is responsible for many nontyphoidal foodborne infections and enteric (typhoid) fever in humans. Of the two Salmonella species, Salmonella enterica is highly diverse and includes 10 known subspecies and approximately 2,600 serotypes. Understanding the evolutionary processes that generate the tremendous diversity in Salmonella is important in reducing and controlling the incidence of disease outbreaks and the emergence of virulent strains. In this study, we aim to elucidate the impact of homologous recombination in the diversification of S. enterica subspecies. Using a data set of previously published 926 Salmonella genomes representing the 10 S. enterica subspecies and Salmonella bongori, we calculated a genus-wide pan-genome composed of 84,041 genes and the S. enterica pan-genome of 81,371 genes. The size of the accessory genomes varies between 12,429 genes in S. enterica subsp. arizonae (subsp. IIIa) to 33,257 genes in S. enterica subsp. enterica (subsp. I). A total of 12,136 genes in the Salmonella pan-genome show evidence of recombination, representing 14.44% of the pan-genome. We identified genomic hot spots of recombination that include genes associated with flagellin and the synthesis of methionine and thiamine pyrophosphate, which are known to influence host adaptation and virulence. Last, we uncovered within-species heterogeneity in rates of recombination and preferential genetic exchange between certain donor and recipient strains. Frequent but biased recombination within a bacterial species may suggest that lineages vary in their response to environmental selection pressure. Certain lineages, such as the more uncommon non-enterica subspecies (non-S. enterica subsp. enterica), may also act as a major reservoir of genetic diversity for the wider population. IMPORTANCES. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to S. enterica subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments.
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16
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Shin B, Park C, Park W. OxyR-controlled surface polysaccharide production and biofilm formation in Acinetobacter oleivorans DR1. Appl Microbiol Biotechnol 2019; 104:1259-1271. [PMID: 31863146 DOI: 10.1007/s00253-019-10303-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/27/2019] [Accepted: 12/08/2019] [Indexed: 11/24/2022]
Abstract
The genomes of several Acinetobacter species possess three distinct polysaccharide-producing operons [two poly-N-acetyl glucosamine (PNAG) and one K-locus]. Using a microfluidic device, an increased amount of polysaccharides and enhanced biofilm formation were observed following continuous exposure to H2O2 and removal of the H2O2-sensing key regulator, OxyR, in Acinetobacter oleivorans DR1 cells. Gene expression analysis revealed that genes located in PNAG1, but not those in PNAG2, were induced and that genes in the K-locus were expressed in the presence of H2O2. Interestingly, the expression of the K-locus gene was enhanced in the PNAG1 mutant and vice versa. The absence of either OxyR or PNAG1 resulted in enhanced biofilm formation, higher surface hydrophobicity, and increased motility, implying that K-locus-driven polysaccharide production in both the oxyR and PNAG1 deletion mutants may be related to these phenotypes. Both the oxyR and K-locus deletion mutants were more sensitive to H2O2 compared with the wildtype and PNAG1 mutant strains. Purified OxyR binds to the promoter regions of both polysaccharide operons with a higher affinity toward the K-locus promoter. Although oxidized OxyR could bind to both promoter regions, the addition of dithiothreitol further enhanced the binding efficiency of OxyR, suggesting that OxyR might function as a repressor for controlling these polysaccharide operons.
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Affiliation(s)
- Bora Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Chulwoo Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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17
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Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts. Proc Natl Acad Sci U S A 2019; 116:22219-22228. [PMID: 31611373 DOI: 10.1073/pnas.1909844116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution of eukaryotic genomes. However, the mechanisms underlying expression and consequent selection and fixation of the prokaryotic genes in the new eukaryotic setting are largely unknown. Here we show that genes composing the pathway for the synthesis of the essential vitamin B1 (thiamine) were lost in an ancestor of a yeast lineage, the Wickerhamiella/Starmerella (W/S) clade, known to harbor an unusually large number of genes of alien origin. The thiamine pathway was subsequently reassembled, at least twice, by multiple HGT events from different bacterial donors involving both single genes and entire operons. In the W/S-clade species Starmerella bombicola we obtained direct genetic evidence that all bacterial genes of the thiamine pathway are functional. The reconstructed pathway is composed by yeast and bacterial genes operating coordinately to scavenge thiamine derivatives from the environment. The adaptation of the newly acquired operons to the eukaryotic setting involved a repertoire of mechanisms until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) gene fusions fostering coordinated expression, gene relocation, and possibly recombination generating mosaic genes. The results provide additional evidence that HGT occurred recurrently in this yeast lineage and was crucial for the reestablishment of lost functions and that similar mechanisms are used across a broad range of eukaryotic microbes to promote adaptation of prokaryotic genes to their new environment.
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18
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Douglas GM, Langille MGI. Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes. Genome Biol Evol 2019; 11:2750-2766. [PMID: 31504488 PMCID: PMC6777429 DOI: 10.1093/gbe/evz184] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.
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Affiliation(s)
- Gavin M Douglas
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
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19
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Johnson G, Wolfe AJ, Putonti C. Characterization of the ϕCTX-like Pseudomonas aeruginosa phage Dobby isolated from the kidney stone microbiota. Access Microbiol 2019; 1. [PMID: 32864566 PMCID: PMC7454045 DOI: 10.1099/acmi.0.000002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Bacteriophages (phages) are vital members of the human microbiota. They are abundant even within low biomass niches of the human body, including the lower urinary tract. While several prior studies have cultured bacteria from kidney stones, this is the first study to explore phages within the kidney stone microbiota. Here we report Dobby, a temperate phage isolated from a strain of Pseudomonas aeruginosa cultured from a kidney stone. Dobby is capable of lysing clinical P. aeruginosa strains within our collection from the urinary tract. Sequencing was performed producing a 37,152 bp genome that closely resembles the temperate P. aeruginosa phage ϕCTX, a member of the P2 phage group. Dobby does not, however, encode for the cytotoxin CTX. Dobby's genome was queried against publicly available bacterial sequences identifying 44 other ϕCTX-like prophages. These prophages are integrated within the genomes of P. aeruginosa strains from a variety of environments, including strains isolated from urine samples and other niches of the human body. Phylogenetic analysis suggests that the temperate ϕCTX phage species is widespread. With the isolation of Dobby, we now have evidence that phages are members of the kidney stone microbiota. Further investigation, however, is needed to determine their abundance and diversity within these communities.
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Affiliation(s)
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL USA.,Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL USA.,Department of Biology, Loyola University Chicago, Chicago, IL USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL USA
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20
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Kominek J, Doering DT, Opulente DA, Shen XX, Zhou X, DeVirgilio J, Hulfachor AB, Groenewald M, Mcgee MA, Karlen SD, Kurtzman CP, Rokas A, Hittinger CT. Eukaryotic Acquisition of a Bacterial Operon. Cell 2019; 176:1356-1366.e10. [PMID: 30799038 DOI: 10.1016/j.cell.2019.01.034] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/20/2018] [Accepted: 01/23/2019] [Indexed: 01/01/2023]
Abstract
Operons are a hallmark of bacterial genomes, where they allow concerted expression of functionally related genes as single polycistronic transcripts. They are rare in eukaryotes, where each gene usually drives expression of its own independent messenger RNAs. Here, we report the horizontal operon transfer of a siderophore biosynthesis pathway from relatives of Escherichia coli into a group of budding yeast taxa. We further show that the co-linearly arranged secondary metabolism genes are expressed, exhibit eukaryotic transcriptional features, and enable the sequestration and uptake of iron. After transfer, several genetic changes occurred during subsequent evolution, including the gain of new transcription start sites that were sometimes within protein-coding sequences, acquisition of polyadenylation sites, structural rearrangements, and integration of eukaryotic genes into the cluster. We conclude that the genes were likely acquired as a unit, modified for eukaryotic gene expression, and maintained by selection to adapt to the highly competitive, iron-limited environment.
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Affiliation(s)
- Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Drew T Doering
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dana A Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, 510642 Guangzhou, China
| | - Jeremy DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda B Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Mcsean A Mcgee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Steven D Karlen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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21
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Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U. Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax. Genes (Basel) 2018; 9:genes9030172. [PMID: 29558455 PMCID: PMC5867893 DOI: 10.3390/genes9030172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/01/2018] [Accepted: 03/09/2018] [Indexed: 11/16/2022] Open
Abstract
Within the Haloferax genus, both the surface (S)-layer protein, and the glycans that can decorate it, vary between species, which can potentially result in many different surface types, analogous to bacterial serotypes. This variation may mediate phenotypes, such as sensitivity to different viruses and mating preferences. Here, we describe S-layer glycoproteins found in multiple Haloferax strains and perform comparative genomics analyses of major and alternative glycosylation clusters of isolates from two coastal sites. We analyze the phylogeny of individual glycosylation genes and demonstrate that while the major glycosylation cluster tends to be conserved among closely related strains, the alternative cluster is highly variable. Thus, geographically- and genetically-related strains may exhibit diverse surface structures to such an extent that no two isolates present an identical surface profile.
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Affiliation(s)
- Yarden Shalev
- School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Shannon M Soucy
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
| | - J Peter Gogarten
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
| | - Jerry Eichler
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 8410501, Israel.
| | - Uri Gophna
- School of Molecular and Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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22
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Burgetz IJ, Shariff S, Pang A, Tillier* ERM. Positional Homology in Bacterial Genomes. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In comparative genomic studies, syntenic groups of homologous sequence in the same order have been used as supplementary information that can be used in helping to determine the orthology of the compared sequences. The assumption is that orthologous gene copies are more likely to share the same genome positions and share the same gene neighbors. In this study we have defined positional homologs as those that also have homologous neighboring genes and we investigated the usefulness of this distinction for bacterial comparative genomics. We considered the identification of positionaly homologous gene pairs in bacterial genomes using protein and DNA sequence level alignments and found that the positional homologs had on average relatively lower rates of substitution at the DNA level (synonymous substitutions) than duplicate homologs in different genomic locations, regardless of the level of protein sequence divergence (measured with non-synonymous substitution rate). Since gene order conservation can indicate accuracy of orthology assignments, we also considered the effect of imposing certain alignment quality requirements on the sensitivity and specificity of identification of protein pairs by BLAST and FASTA when neighboring information is not available and in comparisons where gene order is not conserved. We found that the addition of a stringency filter based on the second best hits was an efficient way to remove dubious ortholog identifications in BLAST and FASTA analyses. Gene order conservation and DNA sequence homology are useful to consider in comparative genomic studies as they may indicate different orthology assignments than protein sequence homology alone.
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Affiliation(s)
- Ingrid J. Burgetz
- Dept. of Medical Biophysics Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Salimah Shariff
- Dept. of Medical Biophysics Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Andy Pang
- Dept. of Medical Biophysics Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
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23
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Hosseini SR, Wagner A. Constraint and Contingency Pervade the Emergence of Novel Phenotypes in Complex Metabolic Systems. Biophys J 2017; 113:690-701. [PMID: 28793223 DOI: 10.1016/j.bpj.2017.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/25/2017] [Accepted: 06/19/2017] [Indexed: 01/23/2023] Open
Abstract
An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. We know examples of such constraints, but we have no systematic understanding about their extent and causes for any one biological system. We here study metabolisms, genomically encoded complex networks of enzyme-catalyzed biochemical reactions, and the constraints they experience in bringing forth novel phenotypes that allow survival on novel carbon sources. Our computational approach does not limit us to analyzing constrained variation in any one organism, but allows us to quantify constraints experienced by any metabolism. Specifically, we study metabolisms that are viable on one of 50 different carbon sources, and quantify how readily alterations of their chemical reactions create the ability to survive on a novel carbon source. We find that some metabolic phenotypes are much less likely to originate than others. For example, metabolisms viable on D-glucose are 1835 times more likely to give rise to metabolisms viable on D-fructose than on acetate. Likewise, we observe that some novel metabolic phenotypes are more contingent on parental phenotypes than others. Biochemical similarities among carbon sources can help explain the causes of these constraints. In addition, we study metabolisms that can be produced by recombination among 55 metabolisms of different bacterial strains or species, and show that their novel phenotypes are also contingent on and constrained by parental genotypes. To our knowledge, our analysis is the first to systematically quantify the incidence of constrained evolution in a broad class of biological system that is central to life and its evolution.
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Affiliation(s)
- Sayed-Rzgar Hosseini
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland; The Swiss Institute of Bioinformatics, Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland; The Swiss Institute of Bioinformatics, Bioinformatics, Lausanne, Switzerland; The Santa Fe Institute, Santa Fe, New Mexico.
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24
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Grazziotin AL, Vidal NM, Venancio TM. Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. FEBS J 2015; 282:3395-3411. [PMID: 26084810 DOI: 10.1111/febs.13350] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 12/19/2022]
Abstract
Identification of essential genes is critical to understanding the physiology of a species, proposing novel drug targets and uncovering minimal gene sets required for life. Although essential gene sets of several organisms have been determined using large-scale mutagenesis techniques, systematic studies addressing their conservation, genomic context and functions remain scant. Here we integrate 17 essential gene sets from genome-wide in vitro screenings and three gene collections required for growth in vivo, encompassing 15 Bacteria and one Archaea. We refine and generalize important theories proposed using Escherichia coli. Essential genes are typically monogenic and more conserved than nonessential genes. Genes required in vivo are less conserved than those essential in vitro, suggesting that more divergent strategies are deployed when the organism is stressed by the host immune system and unstable nutrient availability. We identified essential analogous pathways that would probably be missed by orthology-based essentiality prediction strategies. For example, Streptococcus sanguinis carries horizontally transferred isoprenoid biosynthesis genes that are widespread in Archaea. Genes specifically essential in Mycobacterium tuberculosis and Burkholderia pseudomallei are reported as potential drug targets. Moreover, essential genes are not only preferentially located in operons, but also occupy the first position therein, supporting the influence of their regulatory regions in driving transcription of whole operons. Finally, these important genomic features are shared between Bacteria and at least one Archaea, suggesting that high order properties of gene essentiality and genome architecture were probably present in the last universal common ancestor or evolved independently in the prokaryotic domains.
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Affiliation(s)
- Ana Laura Grazziotin
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Newton Medeiros Vidal
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
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25
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Bay DC, Chan CS, Turner RJ. NarJ subfamily system specific chaperone diversity and evolution is directed by respiratory enzyme associations. BMC Evol Biol 2015; 15:110. [PMID: 26067063 PMCID: PMC4464133 DOI: 10.1186/s12862-015-0412-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/04/2015] [Indexed: 12/04/2022] Open
Abstract
Background Redox enzyme maturation proteins (REMPs) describe a diverse family of prokaryotic chaperones involved in the biogenesis of anaerobic complex iron sulfur molybdoenzyme (CISM) respiratory systems. Many REMP family studies have focused on NarJ subfamily members from Escherichia coli: NarJ, NarW, DmsD, TorD and YcdY. The aim of this bioinformatics study was to expand upon the evolution, distribution and genetic association of these 5 REMP members within 130 genome sequenced taxonomically diverse species representing 324 Prokaryotic sequences. NarJ subfamily member diversity was examined at the phylum-species level and at the amino acid/nucleotide level to determine how close their genetic associations were between their respective CISM systems within phyla. Results This study revealed that NarJ members possessed unique motifs that distinguished Gram-negative from Gram-positive/Archaeal species and identified a strict genetic association with its nitrate reductase complex (narGHI) operon compared to all other members. NarW appears to be found specifically in Gammaproteobacteria. DmsD also showed close associations with the dimethylsulfoxide reductase (dmsABC) operon compared to TorD. Phylogenetic analysis revealed that YcdY has recently evolved from DmsD and that YcdY has likely diverged into 2 subfamilies linked to Zn- dependent alkaline phosphatase (ycdX) operons and a newly identified operon containing part of Zn-metallopeptidase FtsH complex component (hflC) and NADH-quinone dehydrogenase (mdaB). TorD demonstrated the greatest diversity in operon association. TorD was identifed within operons from either trimethylamine-N-oxide reductase (torAC) or formate dehydrogenase (fdhGHI), where each type of TorD had a unique motif. Additionally a subgroup of dmsD and torD members were also linked to operons with biotin sulfoxide (bisC) and polysulfide reductase (nrfD) indicating a potential role in the maturation of diverse CISM. Conclusion Examination of diverse prokaryotic NarJ subfamily members demonstrates that the evolution and genetic association of each member is uniquely biased by its CISM operon association. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0412-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Denice C Bay
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
| | - Catherine S Chan
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Rm 156 Biological Science Bldg., 2500 University Dr. NW, Calgary, T2N 1 N4, AB, Canada.
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Garushyants SK, Kazanov MD, Gelfand MS. Horizontal gene transfer and genome evolution in Methanosarcina. BMC Evol Biol 2015; 15:102. [PMID: 26044078 PMCID: PMC4455057 DOI: 10.1186/s12862-015-0393-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/29/2015] [Indexed: 12/29/2022] Open
Abstract
Background Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae. Results About 5 % of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome. The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50 % of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46 % of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons. Conclusions While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0393-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia.
| | - Marat D Kazanov
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia.
| | - Mikhail S Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia. .,Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia.
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Ream DC, Bankapur AR, Friedberg I. An event-driven approach for studying gene block evolution in bacteria. ACTA ACUST UNITED AC 2015; 31:2075-83. [PMID: 25717195 PMCID: PMC4481853 DOI: 10.1093/bioinformatics/btv128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/20/2015] [Indexed: 11/24/2022]
Abstract
Motivation: Gene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. These models, however, are not generally applicable to all types of gene blocks, and consequently cannot be used to broadly compare and study gene block evolution. To address this problem, we introduce an event-based method for tracking gene block evolution in bacteria. Results: We show here that the evolution of gene blocks in proteobacteria can be described by a small set of events. Those include the insertion of genes into, or the splitting of genes out of a gene block, gene loss, and gene duplication. We show how the event-based method of gene block evolution allows us to determine the evolutionary rateand may be used to trace the ancestral states of their formation. We conclude that the event-based method can be used to help us understand the formation of these important bacterial genomic structures. Availability and implementation: The software is available under GPLv3 license on http://github.com/reamdc1/gene_block_evolution.git. Supplementary online material: http://iddo-friedberg.net/operon-evolution Contact:i.friedberg@miamioh.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David C Ream
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
| | - Asma R Bankapur
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
| | - Iddo Friedberg
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
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Bundalovic-Torma C, Parkinson J. Comparative Genomics and Evolutionary Modularity of Prokaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:77-96. [PMID: 26621462 DOI: 10.1007/978-3-319-23603-2_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The soaring number of high-quality genomic sequences has ushered in the era of post-genomic research where our understanding of organisms has dramatically shifted towards defining the function of genes within their larger biological contexts. As a result, novel high-throughput experimental technologies are being increasingly employed to uncover physical and functional associations of genes and proteins in complex biological processes. Through the construction and analysis of physical, genetic and metabolic networks generated for the model organisms, such as Escherichia coli, organizational principles of the genome have been deduced, such as modularity, which has important implications toward understanding prokaryotic evolution and adaptation to novel lifestyles.
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Affiliation(s)
- Cedoljub Bundalovic-Torma
- Department of Molecular Structure and Function, The Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay St. Rm 21-9830, Toronto, ON, Canada, M5G 0A4.
| | - John Parkinson
- Department of Molecular Structure and Function, The Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay St. Rm 20-9709, Toronto, ON, Canada, M5G 0A4.
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Abstract
Understanding the mechanisms that generate variation is a common pursuit unifying the life sciences. Bacteria represent an especially striking puzzle, because closely related strains possess radically different metabolic and ecological capabilities. Differences in protein repertoire arising from gene transfer are currently considered the primary mechanism underlying phenotypic plasticity in bacteria. Although bacterial coding plasticity has been extensively studied in previous decades, little is known about the role that regulatory plasticity plays in bacterial evolution. Here, we show that bacterial genes can rapidly shift between multiple regulatory modes by acquiring functionally divergent nonhomologous promoter regions. Through analysis of 270,000 regulatory regions across 247 genomes, we demonstrate that regulatory "switching" to nonhomologous alternatives is ubiquitous, occurring across the bacterial domain. Using comparative transcriptomics, we show that at least 16% of the expression divergence between Escherichia coli strains can be explained by this regulatory switching. Further, using an oligonucleotide regulatory library, we establish that switching affects bacterial promoter architecture. We provide evidence that regulatory switching can occur through horizontal regulatory transfer, which allows regulatory regions to move across strains, and even genera, independently from the genes they regulate. Finally, by experimentally characterizing the fitness effect of a regulatory transfer on a pathogenic E. coli strain, we demonstrate that regulatory switching elicits important phenotypic consequences. Taken together, our findings expose previously unappreciated regulatory plasticity in bacteria and provide a gateway for understanding bacterial phenotypic variation and adaptation.
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Nuñez PA, Romero H, Farber MD, Rocha EPC. Natural selection for operons depends on genome size. Genome Biol Evol 2014; 5:2242-54. [PMID: 24201372 PMCID: PMC3845653 DOI: 10.1093/gbe/evt174] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In prokaryotes, genome size is associated with metabolic versatility, regulatory complexity, effective population size, and horizontal transfer rates. We therefore analyzed the covariation of genome size and operon conservation to assess the evolutionary models of operon formation and maintenance. In agreement with previous results, intraoperonic pairs of essential and of highly expressed genes are more conserved. Interestingly, intraoperonic pairs of genes are also more conserved when they encode proteins at similar cell concentrations, suggesting a role of cotranscription in diminishing the cost of waste and shortfall in gene expression. Larger genomes have fewer and smaller operons that are also less conserved. Importantly, lower conservation in larger genomes was observed for all classes of operons in terms of gene expression, essentiality, and balanced protein concentration. We reached very similar conclusions in independent analyses of three major bacterial clades (α- and β-Proteobacteria and Firmicutes). Operon conservation is inversely correlated to the abundance of transcription factors in the genome when controlled for genome size. This suggests a negative association between the complexity of genetic networks and operon conservation. These results show that genome size and/or its proxies are key determinants of the intensity of natural selection for operon organization. Our data fit better the evolutionary models based on the advantage of coregulation than those based on genetic linkage or stochastic gene expression. We suggest that larger genomes with highly complex genetic networks and many transcription factors endure weaker selection for operons than smaller genomes with fewer alternative tools for genetic regulation.
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Affiliation(s)
- Pablo A Nuñez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (CICVyA-INTA), Buenos Aires, Argentina
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Chopra N, Saumitra, Pathak A, Bhatnagar R, Bhatnagar S. Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution. Genome Biol Evol 2014; 5:2268-84. [PMID: 24265503 PMCID: PMC3879964 DOI: 10.1093/gbe/evt175] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Prokaryotic MazF family toxins cooccur with cognate antitoxins having divergent
DNA-binding folds and can be of chromosomal or plasmid origin. Sequence similarity search
was carried out to identify the Toxin–Antitoxin (TA) operons of MazF family followed
by sequence analysis and phylogenetic studies. The genomic DNA upstream of the TA operons
was searched for the presence of regulatory motifs. The MazF family toxins showed a
conserved hydrophobic pocket in a multibinding site and are present in pathogenic
bacteria. The toxins of the MazF family are associated with four main types of cognate
antitoxin partners and cluster as a subfamily on the branches of the phylogenetic tree.
This indicates that transmission of the entire operon is the dominant mode of inheritance.
The plasmid borne TA modules were interspersed between the chromosomal TA modules of the
same subfamily, compatible with a frequent interchange of TA genes between the chromosome
and the plasmid akin to that observed for antibiotic resistance gens. The split network of
the MazF family toxins showed the AbrB-linked toxins as a hub of horizontal gene transfer.
Distinct motifs are present in the upstream region of each subfamily. The presence of MazF
family TA modules in pathogenic bacteria and identification of a conserved binding pocket
are significant for the development of novel antibacterials to disrupt the TA interaction.
However, the role of TAs in stress resistance needs to be established. Phylogenetic
studies provide insight into the evolution of MazF family TAs and effect on the bacterial
genome.
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Affiliation(s)
- Nikita Chopra
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
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32
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Zhou C, Ma Q, Li G. Elucidation of operon structures across closely related bacterial genomes. PLoS One 2014; 9:e100999. [PMID: 24959722 PMCID: PMC4069176 DOI: 10.1371/journal.pone.0100999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/01/2014] [Indexed: 11/30/2022] Open
Abstract
About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components.
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Affiliation(s)
- Chuan Zhou
- School of Mathematics, Shandong University, Jinan, China
| | - Qin Ma
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, China
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33
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Klinman JP, Bonnot F. Intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: PQQ, TTQ, CTQ, TPQ, and LTQ. Chem Rev 2014; 114:4343-65. [PMID: 24350630 PMCID: PMC3999297 DOI: 10.1021/cr400475g] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Judith P. Klinman
- Department of Chemistry University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
- Department of Molecular and Cell Biology University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
| | - Florence Bonnot
- Department of Chemistry University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, U.S.A. Supported by the National Institutes of Health (GM025765) to J.P.K
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34
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Barve A, Hosseini SR, Martin OC, Wagner A. Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms. BMC SYSTEMS BIOLOGY 2014; 8:48. [PMID: 24758311 PMCID: PMC4022055 DOI: 10.1186/1752-0509-8-48] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/15/2014] [Indexed: 11/13/2022]
Abstract
BACKGROUND A metabolism can evolve through changes in its biochemical reactions that are caused by processes such as horizontal gene transfer and gene deletion. While such changes need to preserve an organism's viability in its environment, they can modify other important properties, such as a metabolism's maximal biomass synthesis rate and its robustness to genetic and environmental change. Whether such properties can be modulated in evolution depends on whether all or most viable metabolisms - those that can synthesize all essential biomass precursors - are connected in a space of all possible metabolisms. Connectedness means that any two viable metabolisms can be converted into one another through a sequence of single reaction changes that leave viability intact. If the set of viable metabolisms is disconnected and highly fragmented, then historical contingency becomes important and restricts the alteration of metabolic properties, as well as the number of novel metabolic phenotypes accessible in evolution. RESULTS We here computationally explore two vast spaces of possible metabolisms to ask whether viable metabolisms are connected. We find that for all but the simplest metabolisms, most viable metabolisms can be transformed into one another by single viability-preserving reaction changes. Where this is not the case, alternative essential metabolic pathways consisting of multiple reactions are responsible, but such pathways are not common. CONCLUSIONS Metabolism is thus highly evolvable, in the sense that its properties could be fine-tuned by successively altering individual reactions. Historical contingency does not strongly restrict the origin of novel metabolic phenotypes.
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Affiliation(s)
- Aditya Barve
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Bldg. Y27, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Bioinformatics, Quartier Sorge, Batiment Genopode, 1015 Lausanne, Switzerland
| | - Sayed-Rzgar Hosseini
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Bldg. Y27, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Bioinformatics, Quartier Sorge, Batiment Genopode, 1015 Lausanne, Switzerland
- Computational Biology and Bioinformatics Master’s Program, Department of Computer Science, ETH Zurich, Universitätsstrasse. 6, CH-8092 Zurich, Switzerland
| | - Olivier C Martin
- INRA, UMR 0320/UMR 8120 Génétique Végétale, Univ Paris-Sud, F-91190 Gif-sur-Yvette, France
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Bldg. Y27, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Bioinformatics, Quartier Sorge, Batiment Genopode, 1015 Lausanne, Switzerland
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Genes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98. PLoS One 2013; 8:e84766. [PMID: 24376843 PMCID: PMC3871574 DOI: 10.1371/journal.pone.0084766] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 11/18/2013] [Indexed: 11/19/2022] Open
Abstract
Biodegradation of para-Nitrophenol (PNP) proceeds via two distinct pathways, having 1,2,3-benzenetriol (BT) and hydroquinone (HQ) as their respective terminal aromatic intermediates. Genes involved in these pathways have already been studied in different PNP degrading bacteria. Burkholderia sp. strain SJ98 degrades PNP via both the pathways. Earlier, we have sequenced and analyzed a ~41 kb fragment from the genomic library of strain SJ98. This DNA fragment was found to harbor all the lower pathway genes; however, genes responsible for the initial transformation of PNP could not be identified within this fragment. Now, we have sequenced and annotated the whole genome of strain SJ98 and found two ORFs (viz., pnpA and pnpB) showing maximum identity at amino acid level with p-nitrophenol 4-monooxygenase (PnpM) and p-benzoquinone reductase (BqR). Unlike the other PNP gene clusters reported earlier in different bacteria, these two ORFs in SJ98 genome are physically separated from the other genes of PNP degradation pathway. In order to ascertain the identity of ORFs pnpA and pnpB, we have performed in-vitro assays using recombinant proteins heterologously expressed and purified to homogeneity. Purified PnpA was found to be a functional PnpM and transformed PNP into benzoquinone (BQ), while PnpB was found to be a functional BqR which catalyzed the transformation of BQ into hydroquinone (HQ). Noticeably, PnpM from strain SJ98 could also transform a number of PNP analogues. Based on the above observations, we propose that the genes for PNP degradation in strain SJ98 are arranged differentially in form of non-contiguous gene clusters. This is the first report for such arrangement for gene clusters involved in PNP degradation. Therefore, we propose that PNP degradation in strain SJ98 could be an important model system for further studies on differential evolution of PNP degradation functions.
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36
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Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics 2013; 14:485. [PMID: 23865623 PMCID: PMC3750248 DOI: 10.1186/1471-2164-14-485] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/15/2013] [Indexed: 11/10/2022] Open
Abstract
Background Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.
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Affiliation(s)
- Alexis P Yelton
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
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37
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Wolf YI, Koonin EV. A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes. Genome Biol Evol 2013; 4:1286-94. [PMID: 23160176 PMCID: PMC3542571 DOI: 10.1093/gbe/evs100] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Orthologous relationships between genes are routinely inferred from bidirectional best hits (BBH) in pairwise genome comparisons. However, to our knowledge, it has never been quantitatively demonstrated that orthologs form BBH. To test this “BBH-orthology conjecture,” we take advantage of the operon organization of bacterial and archaeal genomes and assume that, when two genes in compared genomes are flanked by two BBH show statistically significant sequence similarity to one another, these genes are bona fide orthologs. Under this assumption, we tested whether middle genes in “syntenic orthologous gene triplets” form BBH. We found that this was the case in more than 95% of the syntenic gene triplets in all genome comparisons. A detailed examination of the exceptions to this pattern, including maximum likelihood phylogenetic tree analysis, showed that some of these deviations involved artifacts of genome annotation, whereas very small fractions represented random assignment of the best hit to one of closely related in-paralogs, paralogous displacement in situ, or even less frequent genuine violations of the BBH–orthology conjecture caused by acceleration of evolution in one of the orthologs. We conclude that, at least in prokaryotes, genes for which independent evidence of orthology is available typically form BBH and, conversely, BBH can serve as a strong indication of gene orthology.
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38
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Williams D, Gogarten JP, Papke RT. Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol Evol 2013; 4:1223-44. [PMID: 23160063 PMCID: PMC3542582 DOI: 10.1093/gbe/evs098] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In vitro studies of the haloarchaeal genus Haloferax have demonstrated
their ability to frequently exchange DNA between species, whereas rates of homologous
recombination estimated from natural populations in the genus Halorubrum
are high enough to maintain random association of alleles between five loci. To quantify
the effects of gene transfer and recombination of commonly held (relaxed core) genes
during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history
of 21 genomes representing all major groups. Using a novel algorithm and a concatenated
ribosomal protein phylogeny as a reference, we created a directed horizontal genetic
transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed
that 90% of testable HGTs were by direct homologous replacement, rather than
nonhomologous integration followed by a loss. Network analysis revealed an inverse
log-linear relationship between HGT frequency and ribosomal protein evolutionary distance
that is maintained across the deepest divergences in Halobacteria. We use this
mathematical relationship to estimate the total transfers and amino acid substitutions
delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core
genes of each genome, we conservatively estimate that 11–20% of their
evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer
and homologous recombination of relaxed core genes between members of the class
Halobacteria disrupts the coevolution of genes; however, the generation of new
combinations of divergent but functionally related genes may lead to adaptive phenotypes
not available through cumulative mutations and recombination within a single
population.
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Affiliation(s)
- David Williams
- Department of Molecular and Cell Biology, University of Connecticut, CT, USA
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Norris V, Merieau A. Plasmids as scribbling pads for operon formation and propagation. Res Microbiol 2013; 164:779-87. [PMID: 23587635 DOI: 10.1016/j.resmic.2013.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/01/2013] [Indexed: 12/31/2022]
Abstract
Many bacterial genes are in operons and the process whereby operons are formed is therefore fundamental. To help elucidate this process, we propose in the Scribbling Pad hypothesis that bacteria have been constantly using plasmids for genetic experimentation and, in particular, for the construction of operons. This hypothesis simultaneously solves the problems of the creation of operons and the way operons are propagated. We cite results in the literature to support the hypothesis and make experimental predictions to test it.
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Affiliation(s)
- Vic Norris
- Theoretical Biology Unit, Department of Biology, University of Rouen, 76821 Mont Saint Aignan cedex, France.
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Geddes BA, Hausner G, Oresnik IJ. Phylogenetic analysis of erythritol catabolic loci within the Rhizobiales and proteobacteria. BMC Microbiol 2013; 13:46. [PMID: 23432981 PMCID: PMC3599248 DOI: 10.1186/1471-2180-13-46] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 02/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to use erythritol as a sole carbon source is not universal among the Rhizobiaceae. Based on the relatedness to the catabolic genes in Brucella it has been suggested that the eryABCD operon may have been horizontally transferred into Rhizobium. During work characterizing a locus necessary for the transport and catabolism of erythritol, adonitol and L-arabitol in Sinorhizobium meliloti, we became interested in the differences between the erythritol loci of S. meliloti and R. leguminosarum. Utilizing the Ortholog Neighborhood Viewer from the DOE Joint Genome Institute database it appeared that loci for erythritol and polyol utilization had distinct arrangements that suggested these loci may have undergone genetic rearrangements. RESULTS A data set was established of genetic loci containing erythritol/polyol orthologs for 19 different proteobacterial species. These loci were analyzed for genetic content and arrangement of genes associated with erythritol, adonitol and L-arabitol catabolism. Phylogenetic trees were constructed for core erythritol catabolic genes and contrasted with the species phylogeny. Additionally, phylogenetic trees were constructed for genes that showed differences in arrangement among the putative erythritol loci in these species. CONCLUSIONS Three distinct erythritol/polyol loci arrangements have been identified that reflect metabolic need or specialization. Comparison of the phylogenetic trees of core erythritol catabolic genes with species phylogeny provides evidence that is consistent with these loci having been horizontally transferred from the alpha-proteobacteria into both the beta and gamma-proteobacteria. ABC transporters within these loci adopt 2 unique genetic arrangements, and although biological data suggests they are functional erythritol transporters, phylogenetic analysis suggests they may not be orthologs and probably should be considered analogs. Finally, evidence for the presence of paralogs, and xenologs of erythritol catabolic genes in some of the genomes included in the analysis is provided.
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Affiliation(s)
- Barney A Geddes
- Department of Microbiology, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada
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Swanson MM, Reavy B, Makarova KS, Cock PJ, Hopkins DW, Torrance L, Koonin EV, Taliansky M. Novel bacteriophages containing a genome of another bacteriophage within their genomes. PLoS One 2012; 7:e40683. [PMID: 22815791 PMCID: PMC3398947 DOI: 10.1371/journal.pone.0040683] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
A novel bacteriophage infecting Staphylococus pasteuri was isolated during a screen for phages in Antarctic soils. The phage named SpaA1 is morphologically similar to phages of the family Siphoviridae. The 42,784 bp genome of SpaA1 is a linear, double-stranded DNA molecule with 3' protruding cohesive ends. The SpaA1 genome encompasses 63 predicted protein-coding genes which cluster within three regions of the genome, each of apparently different origin, in a mosaic pattern. In two of these regions, the gene sets resemble those in prophages of Bacillus thuringiensis kurstaki str. T03a001 (genes involved in DNA replication/transcription, cell entry and exit) and B. cereus AH676 (additional regulatory and recombination genes), respectively. The third region represents an almost complete genome (except for the short terminal segments) of a distinct bacteriophage, MZTP02. Nearly the same gene module was identified in prophages of B. thuringiensis serovar monterrey BGSC 4AJ1 and B. cereus Rock4-2. These findings suggest that MZTP02 can be shuttled between genomes of other bacteriophages and prophages, leading to the formation of chimeric genomes. The presence of a complete phage genome in the genome of other phages apparently has not been described previously and might represent a 'fast track' route of virus evolution and horizontal gene transfer. Another phage (BceA1) nearly identical in sequence to SpaA1, and also including the almost complete MZTP02 genome within its own genome, was isolated from a bacterium of the B. cereus/B. thuringiensis group. Remarkably, both SpaA1 and BceA1 phages can infect B. cereus and B. thuringiensis, but only one of them, SpaA1, can infect S. pasteuri. This finding is best compatible with a scenario in which MZTP02 was originally contained in BceA1 infecting Bacillus spp, the common hosts for these two phages, followed by emergence of SpaA1 infecting S. pasteuri.
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Affiliation(s)
- Maud M. Swanson
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Brian Reavy
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter J. Cock
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | | | - Lesley Torrance
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Shen YQ, Bonnot F, Imsand EM, RoseFigura JM, Sjölander K, Klinman JP. Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone. Biochemistry 2012; 51:2265-75. [PMID: 22324760 DOI: 10.1021/bi201763d] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pyrroloquinoline quinone (PQQ) is a small, redox active molecule that serves as a cofactor for several bacterial dehydrogenases, introducing pathways for carbon utilization that confer a growth advantage. Early studies had implicated a ribosomally translated peptide as the substrate for PQQ production. This study presents a sequence- and structure-based analysis of the components of the pqq operon. We find the necessary components for PQQ production are present in 126 prokaryotes, most of which are Gram-negative and a number of which are pathogens. A total of five gene products, PqqA, PqqB, PqqC, PqqD, and PqqE, are identified as being obligatory for PQQ production. Three of the gene products in the pqq operon, PqqB, PqqC, and PqqE, are members of large protein superfamilies. By combining evolutionary conservation patterns with information from three-dimensional structures, we are able to differentiate the gene products involved in PQQ biosynthesis from those with divergent functions. The observed persistence of a conserved gene order within analyzed operons strongly suggests a role for protein-protein interactions in the course of cofactor biosynthesis. These studies propose previously unidentified roles for several of the gene products, as well as identifying possible new targets for antibiotic design and application.
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Affiliation(s)
- Yao-Qing Shen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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Abstract
Methods for identifying alien genes in genomes fall into two general classes. Phylogenetic methods examine the distribution of a gene's homologues among genomes to find those with relationships not consistent with vertical inheritance. These approaches include identifying orphan genes which lack homologues in closely related genomes and genes with unduly high levels of similarity to genes in otherwise unrelated genomes. Rigorous statistical tests are available to place confidence intervals for predicted alien genes. Parametric methods examine the compositional properties of genes within a genome to find those with atypical properties, likely indicating the directional mutational pressures of a donor genome. These methods may compare the properties of genes to genomic averages, properties of genes to each other, or properties of large, multigene regions of the chromosome. Here, we discuss the strengths and weaknesses of each approach.
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Affiliation(s)
- Rajeev K Azad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL, Adams MWW, Barnebey A, Yannone SM, Leigh JA, Baliga NS. Parallel evolution of transcriptome architecture during genome reorganization. Genome Res 2011; 21:1892-904. [PMID: 21750103 DOI: 10.1101/gr.122218.111] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Assembly of genes into operons is generally viewed as an important process during the continual adaptation of microbes to changing environmental challenges. However, the genome reorganization events that drive this process are also the roots of instability for existing operons. We have determined that there exists a statistically significant trend that correlates the proportion of genes encoded in operons in archaea to their phylogenetic lineage. We have further characterized how microbes deal with operon instability by mapping and comparing transcriptome architectures of four phylogenetically diverse extremophiles that span the range of operon stabilities observed across archaeal lineages: a photoheterotrophic halophile (Halobacterium salinarum NRC-1), a hydrogenotrophic methanogen (Methanococcus maripaludis S2), an acidophilic and aerobic thermophile (Sulfolobus solfataricus P2), and an anaerobic hyperthermophile (Pyrococcus furiosus DSM 3638). We demonstrate how the evolution of transcriptional elements (promoters and terminators) generates new operons, restores the coordinated regulation of translocated, inverted, and newly acquired genes, and introduces completely novel regulation for even some of the most conserved operonic genes such as those encoding subunits of the ribosome. The inverse correlation (r=-0.92) between the proportion of operons with such internally located transcriptional elements and the fraction of conserved operons in each of the four archaea reveals an unprecedented view into varying stages of operon evolution. Importantly, our integrated analysis has revealed that organisms adapted to higher growth temperatures have lower tolerance for genome reorganization events that disrupt operon structures.
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Affiliation(s)
- Sung Ho Yoon
- Institute for Systems Biology, Seattle, Washington 98109, USA
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Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. J Bacteriol 2011; 193:3964-77. [PMID: 21622749 DOI: 10.1128/jb.01524-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed in part to lateral genetic transfer (LGT), but little is known about the broader extent of LGT within this genus. Here we report the first systematic study of the modularity of genetic transfer among 13 Staphylococcus genomes covering four distinct named species. Using a topology-based phylogenetic approach, we found, among 1,354 sets of homologous genes examined, strong evidence of LGT in 368 (27.1%) gene sets, and weaker evidence in another 259 (19.1%). Within-gene and whole-gene transfer contribute almost equally to the topological discordance of these gene sets against a reference phylogeny. Comparing genetic transfer in single-copy and in multicopy gene sets, we observed a higher frequency of LGT in the latter, and a substantial functional bias in cases of whole-gene transfer (little such bias was observed in cases of fragmentary genetic transfer). We found evidence that lateral transfer, particularly of entire genes, impacts not only functions related to antibiotic, drug, and heavy-metal resistance, as well as membrane transport, but also core informational and metabolic functions not associated with mobile elements. Although patterns of sequence similarity support the cohesion of recognized species, LGT within S. aureus appears frequently to disrupt clonal complexes. Our results demonstrate that LGT and gene duplication play important parts in functional innovation in staphylococcal genomes.
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Atkinson GC, Baldauf SL. Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms. Mol Biol Evol 2010; 28:1281-92. [PMID: 21097998 DOI: 10.1093/molbev/msq316] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein synthesis elongation factor G (EF-G) is an essential protein with central roles in both the elongation and ribosome recycling phases of protein synthesis. Although EF-G evolution is predicted to be conservative, recent reports suggest otherwise. We have characterized EF-G in terms of its molecular phylogeny, genomic context, and patterns of amino acid substitution. We find that most bacteria carry a single "canonical" EF-G, which is phylogenetically conservative and encoded in an str operon. However, we also find a number of EF-G paralogs. These include a pair of EF-Gs that are mostly found together and in an eclectic subset of bacteria, specifically δ-proteobacteria, spirochaetes, and planctomycetes (the "spd" bacteria). These spdEFGs have also given rise to the mitochondrial factors mtEFG1 and mtEFG2, which probably arrived in eukaryotes before the eukaryotic last common ancestor. Meanwhile, chloroplasts apparently use an α-proteobacterial-derived EF-G rather than the expected cyanobacterial form. The long-term comaintenance of the spd/mtEFGs may be related to their subfunctionalization for translocation and ribosome recycling. Consistent with this, patterns of sequence conservation and site-specific evolutionary rate shifts suggest that the faster evolving spd/mtEFG2 has lost translocation function, but surprisingly, the protein also shows little conservation of sites related to recycling activity. On the other hand, spd/mtEFG1, although more slowly evolving, shows signs of substantial remodeling. This is particularly extensive in the GTPase domain, including a highly conserved three amino acid insertion in switch I. We suggest that subfunctionalization of the spd/mtEFGs is not a simple case of specialization for subsets of original activities. Rather, the duplication allows the release of one paralog from the selective constraints imposed by dual functionality, thus allowing it to become more highly specialized. Thus, the potential for fine tuning afforded by subfunctionalization may explain the maintenance of EF-G paralogs.
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Affiliation(s)
- Gemma C Atkinson
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
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Snir S, Trifonov E. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. J Comput Biol 2010; 17:1535-48. [DOI: 10.1089/cmb.2010.0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sagi Snir
- Department of Evolutionary Biology and the Institute of Evolution, Haifa University, Haifa, Israel
| | - Edward Trifonov
- Genome Diversity Center, Institute of Evolution, Haifa University, Haifa, Israel
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Inferring the Evolutionary History of Mo-Dependent Nitrogen Fixation from Phylogenetic Studies of nifK and nifDK. J Mol Evol 2010; 71:70-85. [DOI: 10.1007/s00239-010-9365-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
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Choi K, Gomez SM. Comparison of phylogenetic trees through alignment of embedded evolutionary distances. BMC Bioinformatics 2009; 10:423. [PMID: 20003527 PMCID: PMC3087345 DOI: 10.1186/1471-2105-10-423] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 12/15/2009] [Indexed: 11/12/2022] Open
Abstract
Background The understanding of evolutionary relationships is a fundamental aspect of modern biology, with the phylogenetic tree being a primary tool for describing these associations. However, comparison of trees for the purpose of assessing similarity and the quantification of various biological processes remains a significant challenge. Results We describe a novel approach for the comparison of phylogenetic distance information based on the alignment of representative high-dimensional embeddings (xCEED: Comparison of Embedded Evolutionary Distances). The xCEED methodology, which utilizes multidimensional scaling and Procrustes-related superimposition approaches, provides the ability to measure the global similarity between trees as well as incongruities between them. We demonstrate the application of this approach to the prediction of coevolving protein interactions and demonstrate its improved performance over the mirrortree, tol-mirrortree, phylogenetic vector projection, and partial correlation approaches. Furthermore, we show its applicability to both the detection of horizontal gene transfer events as well as its potential use in the prediction of interaction specificity between a pair of multigene families. Conclusions These approaches provide additional tools for the study of phylogenetic trees and associated evolutionary processes. Source code is available at http://gomezlab.bme.unc.edu/tools.
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Affiliation(s)
- Kwangbom Choi
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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